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Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-API-DEV [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] Done The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/nih-sparc/sparc-api.git > git init /home/cmiss/Jenkins/workspace/SPARC-API-DEV # timeout=10 Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/nih-sparc/sparc-api.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision 43afb0e64dd397106585143c27752bd5584e96f5 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 43afb0e64dd397106585143c27752bd5584e96f5 # timeout=10 Commit message: "Merge pull request #271 from alan-wu/monthly-test" > git rev-list --no-walk 43afb0e64dd397106585143c27752bd5584e96f5 # timeout=10 [SPARC-API-DEV] $ /bin/bash /tmp/jenkins4464653528067784087.sh Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (2.6.2) Requirement already satisfied: api==0.0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.7) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (3.7.0) Requirement already satisfied: boto3==1.26 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.26.0) Requirement already satisfied: botocore==1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 5)) (1.29.0) Requirement already satisfied: certifi==2023.5.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 6)) (2023.5.7) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 7)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 8)) Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 9)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 10)) (2.11.0) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 11)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 12)) (1.1.1) Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 13)) (2.3.0) Requirement already satisfied: Flask-Cors==3.0.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 14)) (3.0.8) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 15)) (0.10.1) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 16)) (2.52.0) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 17)) (20.0.4) Requirement already satisfied: hubspot-api-client==9.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 18)) (9.0.0) Requirement already satisfied: idna==2.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 19)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 20)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 21)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 22)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 23)) (1.1.1) Requirement already satisfied: markdown==3.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 24)) (3.8) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 25)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 26)) (1.3.7) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 27)) (4.1.3) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 28)) (0.4.3) Requirement already satisfied: Pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 29)) (6.1.1) Requirement already satisfied: Pennsieve2==0.1.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 30)) (0.1.2) Requirement already satisfied: Pillow in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 31)) (11.2.1) Requirement already satisfied: psycopg2-binary==2.9.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 32)) (2.9.10) Requirement already satisfied: public==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 33)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 34)) (8.3.5) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 35)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 36)) (2.8.2) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 37)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 38)) (2019.4.13) Requirement already satisfied: requests==2.31.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 39)) (2.31.0) Requirement already satisfied: s3transfer==0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 40)) (0.6.0) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 41)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 42)) (1.13.0) Requirement already satisfied: SQLAlchemy==2.0.40 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 43)) (2.0.40) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 44)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 45)) (0.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests==2.31.0->-r requirements.txt (line 39)) (3.4.2) Requirement already satisfied: setuptools>=0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (80.3.1) Requirement already satisfied: pytz in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2025.2) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2.1) Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Flask-Caching==2.3.0->-r requirements.txt (line 13)) (0.9.0) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.40.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.2.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.25.0rc0) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 27)) (0.6.1) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 27)) (0.4.2) Requirement already satisfied: rsa>=3.1.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 27)) (4.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (7.2.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (1.2.18) Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (4.25.7) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (3.2.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (3.0.4) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 29)) (7.0.0) Requirement already satisfied: grpcio<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 30)) (1.71.0) Requirement already satisfied: grpcio_tools<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 30)) (1.62.3) Requirement already satisfied: pyjwt<3.0,>=2.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 30)) (2.10.1) Requirement already satisfied: tqdm<5.0,>=4.64 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 30)) (4.67.1) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 41)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 41)) (2.2.0) Requirement already satisfied: greenlet>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 43)) (3.2.1) Requirement already satisfied: typing-extensions>=4.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 43)) (4.13.2) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->Pennsieve==6.1.1->-r requirements.txt (line 29)) (0.14.1) Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.70.0) Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.26.1) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (5.5.2) Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (3.2.3) Requirement already satisfied: exceptiongroup>=1.0.0rc8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 34)) (1.2.2) Requirement already satisfied: iniconfig in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 34)) (2.1.0) Requirement already satisfied: packaging in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 34)) (25.0) Requirement already satisfied: pluggy<2,>=1.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 34)) (1.6.0) Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 34)) (2.2.1) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from deprecated>=1.2.0->Pennsieve==6.1.1->-r requirements.txt (line 29)) (1.17.2) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.2.1 Uninstalling click-8.2.1: Successfully uninstalled click-8.2.1 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. black 25.1.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 Collecting pytest==5.4.3 (from -r requirements-dev.txt (line 1)) Using cached pytest-5.4.3-py3-none-any.whl.metadata (7.3 kB) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1) Requirement already satisfied: black in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 3)) (25.1.0) Requirement already satisfied: isort in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 4)) (6.0.1) Requirement already satisfied: nose in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7) Requirement already satisfied: packaging in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 6)) (25.0) Requirement already satisfied: py>=1.5.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (1.11.0) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (25.3.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.7.0) Collecting pluggy<1.0,>=0.12 (from pytest==5.4.3->-r requirements-dev.txt (line 1)) Using cached pluggy-0.13.1-py2.py3-none-any.whl.metadata (15 kB) Requirement already satisfied: wcwidth in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.13) Requirement already satisfied: boto3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (7.2.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.18) Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.25.7) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2025.2) Requirement already satisfied: requests>=2.18 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.31.0) Requirement already satisfied: rsa==4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.4) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (7.0.0) Requirement already satisfied: python-dateutil>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8.2) Requirement already satisfied: six<2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.13.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.14.1) Requirement already satisfied: pyasn1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.1) Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3)) Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB) Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (1.1.0) Requirement already satisfied: pathspec>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (0.12.1) Requirement already satisfied: platformdirs>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.3.7) Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (2.2.1) Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.13.2) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from 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requirements-dev.txt (line 2)) (1.29.0) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.9.4) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.0) Using cached pytest-5.4.3-py3-none-any.whl (248 kB) Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Using cached click-8.2.1-py3-none-any.whl (102 kB) Installing collected packages: pluggy, click, pytest Attempting uninstall: pluggy Found existing installation: pluggy 1.6.0 Uninstalling pluggy-1.6.0: Successfully uninstalled pluggy-1.6.0 Attempting uninstall: click Found existing installation: click 7.1.2 Uninstalling click-7.1.2: Successfully uninstalled click-7.1.2 Attempting uninstall: pytest Found existing installation: pytest 8.3.5 Uninstalling pytest-8.3.5: Successfully uninstalled pytest-8.3.5 Successfully installed click-8.2.1 pluggy-0.13.1 pytest-5.4.3 Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (5.4.3) Collecting pytest Using cached pytest-8.3.5-py3-none-any.whl.metadata (7.6 kB) Requirement already satisfied: exceptiongroup>=1.0.0rc8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (1.2.2) Requirement already satisfied: iniconfig in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.1.0) Requirement already satisfied: packaging in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (25.0) Collecting pluggy<2,>=1.5 (from pytest) Using cached pluggy-1.6.0-py3-none-any.whl.metadata (4.8 kB) Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.2.1) Using cached pytest-8.3.5-py3-none-any.whl (343 kB) Using cached pluggy-1.6.0-py3-none-any.whl (20 kB) Installing collected packages: pluggy, pytest Attempting uninstall: pluggy Found existing installation: pluggy 0.13.1 Uninstalling pluggy-0.13.1: Successfully uninstalled pluggy-0.13.1 Attempting uninstall: pytest Found existing installation: pytest 5.4.3 Uninstalling pytest-5.4.3: Successfully uninstalled pytest-5.4.3 Successfully installed pluggy-1.6.0 pytest-8.3.5 ============================= test session starts ============================== platform linux -- Python 3.10.17, pytest-8.3.5, pluggy-1.6.0 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV collected 119 items tests/test_api.py .................FFFF...... [ 22%] tests/test_biolucida.py ............. [ 33%] tests/test_dataset_info.py FsFFssFFF.. [ 42%] tests/test_health.py . [ 43%] tests/test_monthly_stats.py ......... [ 51%] tests/test_osparc.py .............. [ 63%] tests/test_plot.py F [ 63%] tests/test_pmr.py ......... [ 71%] tests/test_scicrunch.py FFFFFFFFFFFFFFFFFFFFFFFFFFF. [ 94%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== ____________________________ test_onto_term_lookup _____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f691461ea70> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150c1450> method = 'GET' url = '/api/1/elastic/Interlex_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"bool": {"must": [{"match_phrase": {"existing_ids.iri": {"query": "http://purl.obolibrary.org/obo/NCBITaxon_9606"}}}]}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': 'application/json', 'Connection': 'keep-alive', 'Content-Length': '154', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/Interlex_pr/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f691461ea70> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f691461ea70>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69150c1360> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/api/1/elastic/Interlex_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f691461ea70>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150c1450> _stacktrace = <traceback object at 0x7f6914416b40> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/Interlex_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f691461ea70>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: @app.route("/onto_term_lookup") def find_by_onto_term(): term = request.args.get('term') headers = { 'Accept': 'application/json', } params = { "api_key": Config.KNOWLEDGEBASE_KEY } query = create_onto_term_query(term) try: > response = requests.get(f'{Config.SCI_CRUNCH_INTERLEX_HOST}/_search', headers=headers, params=params, json=query) app/main.py:2087: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69150c1360> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/Interlex_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f691461ea70>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_onto_term_lookup(client): > r = client.get('/onto_term_lookup', query_string={'term': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'}) tests/test_api.py:289: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:2100: in find_by_onto_term logging.error("An error occured while fetching from SciCrunch", ex) /usr/lib/python3.10/logging/__init__.py:2105: in error root.error(msg, *args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1506: in error self._log(ERROR, msg, args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1624: in _log self.handle(record) /usr/lib/python3.10/logging/__init__.py:1634: in handle self.callHandlers(record) /usr/lib/python3.10/logging/__init__.py:1696: in callHandlers hdlr.handle(record) /usr/lib/python3.10/logging/__init__.py:968: in handle self.emit(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit super().emit(record) /usr/lib/python3.10/logging/__init__.py:1108: in emit self.handleError(record) /usr/lib/python3.10/logging/__init__.py:1100: in emit msg = self.format(record) /usr/lib/python3.10/logging/__init__.py:943: in format return fmt.format(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format return super().format(record) /usr/lib/python3.10/logging/__init__.py:678: in format record.message = record.getMessage() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 2100, "An error occured while fetching from SciCrunch"> def getMessage(self): """ Return the message for this LogRecord. Return the message for this LogRecord after merging any user-supplied arguments with the message. """ msg = str(self.msg) if self.args: > msg = msg % self.args E TypeError: not all arguments converted during string formatting /usr/lib/python3.10/logging/__init__.py:368: TypeError ------------------------------ Captured log call ------------------------------- ERROR root:main.py:1834 Emailoctopus contact did not get added/updated for email: hubspot_webhook_test@test.com. Returned a response of 400: {"title":"An error occurred.","detail":"Bad request.","status":400,"errors":[{"detail":"This value is not a valid UUID.","parameter":"list_id"}],"type":"https://emailoctopus.com/api-documentation/v2#bad-request"} ERROR root:main.py:1931 Error processing event {'subscriptionType': 'contact.propertyChange', 'objectId': '83944215465'}: 'tags' _____________________ test_non_existing_simulation_ui_file _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905faf040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905faf400> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "137"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905faf040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905faf040>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905faf6d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905faf040>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905faf400> _stacktrace = <traceback object at 0x7f6905dab340> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905faf040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_non_existing_simulation_ui_file(client): > r = client.get('/simulation_ui_file/137') tests/test_api.py:296: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1995: in simulation_ui_file results = process_results(dataset_search(create_pennsieve_identifier_query(identifier))) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905faf6d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905faf040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________ test_simulation_ui_file_old_s3_bucket _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69063f24d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69063f2aa0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "135"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69063f24d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69063f24d0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69063f26e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69063f24d0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69063f2aa0> _stacktrace = <traceback object at 0x7f690616e080> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69063f24d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_simulation_ui_file_old_s3_bucket(client): > r = client.get('/simulation_ui_file/135') tests/test_api.py:301: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1995: in simulation_ui_file results = process_results(dataset_search(create_pennsieve_identifier_query(identifier))) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69063f26e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69063f24d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________ test_simulation_ui_file_new_s3_bucket _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905df30d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905df3820> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "308"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905df30d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905df30d0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905df3280> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905df30d0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905df3820> _stacktrace = <traceback object at 0x7f6905f94ec0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905df30d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_simulation_ui_file_new_s3_bucket(client): > r = client.get('/simulation_ui_file/308') tests/test_api.py:307: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1995: in simulation_ui_file results = process_results(dataset_search(create_pennsieve_identifier_query(identifier))) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905df3280> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905df30d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________________ test_current_doi_list _____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690615d0f0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690615c970> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"from": 0, "size": 0, "aggregations": {"doi": {"composite": {"size": 1000, "sources": [{"curie": {"terms": {"field": "item.curie.aggregate"}}}], "after": {"curie": ""}}}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '172', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690615d0f0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690615d0f0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690615ce50> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d0f0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690615c970> _stacktrace = <traceback object at 0x7f6905e8c680> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d0f0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_current_doi_list(client): doi_stem = "doi:" start = timer() > r = client.get('/current_doi_list') tests/test_dataset_info.py:23: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:720: in get_all_doi results = reform_aggregation_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690615ce50> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d0f0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ___________________ test_generic_mouse_colon_dataset_search ____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905d7ca00> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"fields": ["item.name"], "query": "(Generic) AND (mouse) AND (colon) AND (scaffold)"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '138', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905d7c100> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905d7ca00> _stacktrace = <traceback object at 0x7f690652df40> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_generic_mouse_colon_dataset_search(client): title = "Generic mouse colon scaffold" start = timer() > r = client.get('/dataset_info/using_title', query_string={'title': title}) tests/test_dataset_info.py:132: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:642: in get_dataset_info_title return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905d7c100> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ______________________ test_complex_title_dataset_search _______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690663abf0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690663baf0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"fields": ["item.name"], "query": "(Spatial) AND (distribution) A...nts) AND (associated) AND (with) AND (the) AND (myenteric) AND (plexus) AND (of) AND (the) AND (rat) AND (stomach)"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '317', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690663abf0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690663abf0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690663b9d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663abf0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690663baf0> _stacktrace = <traceback object at 0x7f6906577b00> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663abf0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_complex_title_dataset_search(client): title = "Spatial distribution and morphometric characterization of vagal efferents associated with the myenteric plexus of the rat stomach" start = timer() > r = client.get('/dataset_info/using_title', query_string={'title': title}) tests/test_dataset_info.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:642: in get_dataset_info_title return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690663b9d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663abf0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError __________________ test_title_plot_annotation_dataset_search ___________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905fb37f0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"fields": ["item.name"], "query": "(Sympathetic) AND (nerve) AND (stimulation) AND (of) AND (mouse) AND (and) AND (rabbit) AND (hearts)"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '190', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905fb01c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905fb37f0> _stacktrace = <traceback object at 0x7f6906599b80> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_title_plot_annotation_dataset_search(client): print() title = "Sympathetic nerve stimulation of mouse and rabbit hearts" start = timer() > r = client.get('/dataset_info/using_title', query_string={'title': title}) tests/test_dataset_info.py:202: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:642: in get_dataset_info_title return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905fb01c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ----------------------------- Captured stdout call ----------------------------- ____________________ test_object_identifier_dataset_search _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905f849a0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905f84fa0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"fields": ["*identifier"], "query": "*b5f9e5d7-7e09-4855-a923-a966454967d7"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '129', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905f849a0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905f849a0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905f85300> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f849a0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905f84fa0> _stacktrace = <traceback object at 0x7f6906549d00> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f849a0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_object_identifier_dataset_search(client): #Dataset 212 print() identifier = "package:b5f9e5d7-7e09-4855-a923-a966454967d7" start = timer() > r = client.get('/dataset_info/using_object_identifier', query_string={'identifier': identifier}) tests/test_dataset_info.py:231: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:650: in get_dataset_info_object_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905f85300> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f849a0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ----------------------------- Captured stdout call ----------------------------- ___________________ test_pennsieve_identifier_dataset_search ___________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690651fbe0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690651dcf0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "43"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690651fbe0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690651fbe0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690651dcc0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690651fbe0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690651dcf0> _stacktrace = <traceback object at 0x7f69066233c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690651fbe0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_pennsieve_identifier_dataset_search(client): print() identifier = "43" start = timer() > r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': identifier}) tests/test_dataset_info.py:259: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690651dcc0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690651fbe0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ----------------------------- Captured stdout call ----------------------------- ________________________________ test_abi_plot _________________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69065a3a30> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "26"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69065a2020> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69065a3a30> _stacktrace = <traceback object at 0x7f6914307240> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_abi_plot(client): # Testing abi-plot with dataset 26 dataset_id = "26" > r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) tests/test_plot.py:17: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69065a2020> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________________ test_scicrunch_keys ______________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69150bf910> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150bc220> method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = None headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69150bf910> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69150bf910>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69150be170> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150bf910>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150bc220> _stacktrace = <traceback object at 0x7f6906400580> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150bf910>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_keys(client): > r = client.get('/search/') tests/test_scicrunch.py:26: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:758: in kb_search response = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?q={query}&size={limit}&from={start}&api_key={Config.KNOWLEDGEBASE_KEY}') ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69150be170> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150bf910>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________ test_scicrunch_versions_are_supported _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906267b50> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906267f70> method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22' body = None headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906267b50> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906267b50>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906267280> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906267b50>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906267f70> _stacktrace = <traceback object at 0x7f6905c0f400> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906267b50>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: def test_scicrunch_versions_are_supported(): # Lines below are to allow the test to be run from the root dir or sparc-api/tests current_directory = os.path.dirname(os.path.abspath(__file__)) app_directory = os.path.join(current_directory, '..', 'app') # List the contents of the 'app' directory, to find which versions we have files for available_versions = os.listdir(app_directory) > r = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}&q=""') tests/test_scicrunch.py:38: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906267280> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906267b50>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError __________________________ test_scicrunch_dataset_doi __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6914094d90> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69140947f0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "55"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6914094d90> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6914094d90>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6914095ff0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6914094d90>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69140947f0> _stacktrace = <traceback object at 0x7f6914020440> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6914094d90>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_dataset_doi(client): # Testing with dataset 55 identifier = "55" > run_doi_test = check_doi_status(client, identifier, '10.26275/pzek-91wx') tests/test_scicrunch.py:68: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6914095ff0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6914094d90>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________ test_scicrunch_multiple_dataset_doi ______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906407040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906407340> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "55"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906407040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906407040>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69064078b0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906407040>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906407340> _stacktrace = <traceback object at 0x7f6905c2c2c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906407040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_multiple_dataset_doi(client): # Testing with dataset 55 and 68 > run_doi_test_1 = check_doi_status(client, "55", '10.26275/pzek-91wx') tests/test_scicrunch.py:84: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69064078b0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906407040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________ test_scicrunch_multiple_dataset_ids ______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906662b00> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906662bf0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["55", "68"]}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '73', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906662b00> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906662b00>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906662d70> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662b00>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906662bf0> _stacktrace = <traceback object at 0x7f6905c62000> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662b00>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_multiple_dataset_ids(client): # Testing with dataset 55 and 68 > r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=55&discoverIds=68') tests/test_scicrunch.py:102: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:634: in get_dataset_info_discoverIds return process_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906662d70> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662b00>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________________ test_scicrunch_search _____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690645c310> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690645da80> method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = None headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690645c310> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690645c310>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690645dea0> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690645c310>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690645da80> _stacktrace = <traceback object at 0x7f69064cc2c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690645c310>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_search(client): > r = client.get('/search/heart') tests/test_scicrunch.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:758: in kb_search response = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?q={query}&size={limit}&from={start}&api_key={Config.KNOWLEDGEBASE_KEY}') ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690645dea0> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690645c310>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ___________________________ test_scicrunch_all_data ____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69060fa230> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f99f0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '23', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69060fa230> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69060fa230>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69060fa320> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060fa230>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f99f0> _stacktrace = <traceback object at 0x7f6905c83440> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060fa230>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_all_data(client): > r = client.get('/filter-search/') tests/test_scicrunch.py:119: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69060fa320> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060fa230>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________________ test_scicrunch_filter _____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906f02020> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "(anatomy.organ.name.aggregate:((heart)))"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '105', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906f01780> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906f02020> _stacktrace = <traceback object at 0x7f6905c9e880> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_filter(client): > r = client.get('/filter-search/', query_string={'term': 'organ', 'facet': 'heart'}) tests/test_scicrunch.py:124: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906f01780> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _______________________ test_scicrunch_filter_scaffolds ________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905c27220> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "objects.additional_mimetype.name:(application%2fx.vnd.abi.scaffold.meta%2Bjson)"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '144', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905c27550> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905c27220> _stacktrace = <traceback object at 0x7f6905c868c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_filter_scaffolds(client): > r = client.get('/filter-search/?facet=scaffolds&term=datasets') tests/test_scicrunch.py:129: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905c27550> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _________________________ test_scicrunch_basic_search __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690662b550> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f691617fd30> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "(Heart)"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '72', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690662b550> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690662b550>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f691617ca60> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690662b550>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f691617fd30> _stacktrace = <traceback object at 0x7f6905c6ec80> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690662b550>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_basic_search(client): > r = client.get('/filter-search/Heart/?facet=All+Species&term=species') tests/test_scicrunch.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f691617ca60> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690662b550>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _________________________ test_scicrunch_image_search __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690663baf0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690663bca0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"query_string": {"fields": ["*mimetype.name"], "query": "\\"[\'\\"*jp2* OR *vnd.ome.xml* OR *jpx*\\"\']\\""}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '115', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690663baf0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690663baf0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690663b370> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663baf0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690663bca0> _stacktrace = <traceback object at 0x7f6905ff94c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663baf0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_image_search(client): > r = client.get('/multiple_dataset_info/using_multiple_mimetype/?q="*jp2*+OR+*vnd.ome.xml*+OR+*jpx*"') tests/test_scicrunch.py:138: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:625: in get_file_info_from_mimetype return process_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690663b370> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663baf0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _________________________ test_scicrunch_boolean_logic _________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905f23520> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905f204c0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "(attributes.subject.sex.value:((male) OR (female)))"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '116', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905f23520> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905f23520>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905f202e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f23520>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905f204c0> _stacktrace = <traceback object at 0x7f6906f73d80> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f23520>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_boolean_logic(client): > r = client.get('/filter-search/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender') tests/test_scicrunch.py:142: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905f202e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f23520>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ______________________ test_scicrunch_combined_facet_text ______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690608b010> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690608b100> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "(heart) AND (attributes.subject.sex.value:((male) OR (female)))"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '128', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690608b010> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690608b010>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690608b3d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690608b010>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690608b100> _stacktrace = <traceback object at 0x7f6906037f00> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690608b010>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_combined_facet_text(client): > r = client.get('/filter-search/heart/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender') tests/test_scicrunch.py:147: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690608b3d0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690608b010>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________________ test_getting_facets ______________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69060f9a50> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f9b40> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"from": 0, "size": 0, "aggregations": {"organ": {"terms": {"field": "anatomy.organ.name.aggregate", "size": 200, "order": [{"_count": "desc"}, {"_key": "asc"}]}}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '164', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69060f9a50> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69060f9a50>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69060fa8c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f9a50>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f9b40> _stacktrace = <traceback object at 0x7f6905b20340> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f9a50>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: type_ = 'organ' @app.route("/get-facets/<type_>") def get_facets(type_): # Create facet query type_map, data = create_facet_query(type_) # Make a request for each sci-crunch parameter results = [] for path in type_map[type_]: data['aggregations'][f'{type_}']['terms']['field'] = path try: > response = requests.post( f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}', json=data) app/main.py:803: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69060fa8c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f9a50>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_getting_facets(client): > r = client.get('/get-facets/organ') tests/test_scicrunch.py:152: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:812: in get_facets logging.error(f"Could not search SciCrunch for path {path}", ex) /usr/lib/python3.10/logging/__init__.py:2105: in error root.error(msg, *args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1506: in error self._log(ERROR, msg, args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1624: in _log self.handle(record) /usr/lib/python3.10/logging/__init__.py:1634: in handle self.callHandlers(record) /usr/lib/python3.10/logging/__init__.py:1696: in callHandlers hdlr.handle(record) /usr/lib/python3.10/logging/__init__.py:968: in handle self.emit(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit super().emit(record) /usr/lib/python3.10/logging/__init__.py:1108: in emit self.handleError(record) /usr/lib/python3.10/logging/__init__.py:1100: in emit msg = self.format(record) /usr/lib/python3.10/logging/__init__.py:943: in format return fmt.format(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format return super().format(record) /usr/lib/python3.10/logging/__init__.py:678: in format record.message = record.getMessage() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 812, "Could not search SciCrunch for path anatomy.organ.name.aggregate"> def getMessage(self): """ Return the message for this LogRecord. Return the message for this LogRecord after merging any user-supplied arguments with the message. """ msg = str(self.msg) if self.args: > msg = msg % self.args E TypeError: not all arguments converted during string formatting /usr/lib/python3.10/logging/__init__.py:368: TypeError _________________________ test_create_identifier_query _________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905a37df0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905a34520> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"fields": ["*identifier"], "query": "*e6435710-dd9c-46b7-9dfd-932103469733"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '129', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905a37df0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905a37df0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905a347c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905a37df0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905a34520> _stacktrace = <traceback object at 0x7f690581c100> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905a37df0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_create_identifier_query(client): > r = client.get('/dataset_info/using_object_identifier?identifier=package:e6435710-dd9c-46b7-9dfd-932103469733') tests/test_scicrunch.py:159: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:650: in get_dataset_info_object_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905a347c0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905a37df0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError __________________________ test_create_anatomy_query ___________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69060f1b70> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f1150> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 1, "from": 0, "query": {"match": {"pennsieve.identifier": {"query": "90"}}}, "_source": ["anatomy", "item.curie", "organisms"]}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '136', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69060f1b70> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69060f1b70>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69060f14e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f1b70>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69060f1150> _stacktrace = <traceback object at 0x7f6905ba7e40> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f1b70>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_create_anatomy_query(client): > r = client.get('/dataset_info/anatomy?identifier=90') tests/test_scicrunch.py:176: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:661: in get_dataset_info_anatomy return reform_anatomy_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69060f14e0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f1b70>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________________ test_response_version _____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905ea4550> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "44"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905ea4310> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905ea4550> _stacktrace = <traceback object at 0x7f6905b9b680> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_response_version(client): # Testing with dataset 44 identifier = "44" doi = "10.26275/duz8-mq3n" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905ea4310> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________________ test_response_abi_plot ____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906639ff0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906638e20> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "212"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906639ff0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906639ff0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906639d50> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906639ff0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906638e20> _stacktrace = <traceback object at 0x7f6905bceac0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906639ff0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_response_abi_plot(client): # Testing abi-plot with dataset 212 identifier = "212" doi = "10.26275/lok5-wje6" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:221: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906639d50> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906639ff0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError __________________________ test_response_abi_scaffold __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69060939d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906090fd0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": "76"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '61', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69060939d0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69060939d0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906093af0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060939d0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906090fd0> _stacktrace = <traceback object at 0x7f6906206640> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060939d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_response_abi_scaffold(client): # Testing abi-scaffold with dataset 76 identifier = "76" doi = "10.26275/jarb-s8jw" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:255: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:669: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906093af0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060939d0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ______________________ test_response_sample_subject_size _______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690601cb80> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690601efe0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 10, "from": 0, "query": {"query_string": {"query": "(anatomy.organ.name.aggregate:((liver)))"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '105', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690601cb80> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690601cb80>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690601edd0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690601cb80>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690601efe0> _stacktrace = <traceback object at 0x7f6906f2ed80> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690601cb80>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_response_sample_subject_size(client): # Only filter search returns the sample and subjectSuze > r = client.get('/filter-search/?facet=liver&term=organ') tests/test_scicrunch.py:311: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690601edd0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690601cb80>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _________________________ test_raw_response_structure __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69150c0880> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150c0a00> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"from": 0, "size": 20, "query": {"query_string": {"query": "computational"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '78', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69150c0880> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69150c0880>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69150c0340> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150c0880>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69150c0a00> _stacktrace = <traceback object at 0x7f6905b14f00> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150c0880>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_raw_response_structure(client): # 10.26275/zdxd-84xz # 10.26275/duz8-mq3n query = create_query_string("computational") > data = dataset_search(query) tests/test_scicrunch.py:428: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69150c0340> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150c0880>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _________________________ test_get_body_scaffold_info __________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f690615d030> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690615df00> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"pennsieve.identifier.aggregate": 307}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '60', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f690615d030> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f690615d030>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f690615d990> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d030>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f690615df00> _stacktrace = <traceback object at 0x7f6905d33840> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d030>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_body_scaffold_info(client): # Test if we get a shorter list of uberons with species specified > r = client.get('/get_body_scaffold_info/human') tests/test_scicrunch.py:458: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1165: in get_body_scaffold_info result = process_get_first_scaffold_info(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f690615d990> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d030>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________________ test_getting_curies ______________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f69065a1b40> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69065a2020> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"from": 0, "size": 0, "aggregations": {"names_and_curies": {"terms": {"script": {"lang": "painless", "inline": "def...'][\'anatomy\'][\'organ\'] != null ) { a = params[\'_source\'][\'anatomy\'][\'organ\'];}} return a;"}, "size": 200}}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '294', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f69065a1b40> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f69065a1b40>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69065a1c00> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a1b40>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69065a2020> _stacktrace = <traceback object at 0x7f6905be9680> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a1b40>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: @app.route("/get-organ-curies/") def get_available_uberonids(): species = request.args.getlist('species') requestBody = create_request_body_for_curies(species) result = {} try: > response = requests.post( f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}', json=requestBody) app/main.py:1952: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69065a1c00> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a1b40>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_getting_curies(client): # Test if we get a shorter list of uberons with species specified > r = client.get('/get-organ-curies/') tests/test_scicrunch.py:467: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1957: in get_available_uberonids logging.error("Failed getting Uberon IDs", ex) /usr/lib/python3.10/logging/__init__.py:2105: in error root.error(msg, *args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1506: in error self._log(ERROR, msg, args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1624: in _log self.handle(record) /usr/lib/python3.10/logging/__init__.py:1634: in handle self.callHandlers(record) /usr/lib/python3.10/logging/__init__.py:1696: in callHandlers hdlr.handle(record) /usr/lib/python3.10/logging/__init__.py:968: in handle self.emit(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit super().emit(record) /usr/lib/python3.10/logging/__init__.py:1108: in emit self.handleError(record) /usr/lib/python3.10/logging/__init__.py:1100: in emit msg = self.format(record) /usr/lib/python3.10/logging/__init__.py:943: in format return fmt.format(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format return super().format(record) /usr/lib/python3.10/logging/__init__.py:678: in format record.message = record.getMessage() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 1957, "Failed getting Uberon IDs"> def getMessage(self): """ Return the message for this LogRecord. Return the message for this LogRecord after merging any user-supplied arguments with the message. """ msg = str(self.msg) if self.args: > msg = msg % self.args E TypeError: not all arguments converted during string formatting /usr/lib/python3.10/logging/__init__.py:368: TypeError ____________________________ test_get_related_terms ____________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905e4e770> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905e4ee60> method = 'GET' url = '/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = None headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084', query='direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905e4e770> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905e4e770>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905e4d600> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905e4e770>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6905e4ee60> _stacktrace = <traceback object at 0x7f69058703c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905e4e770>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: query = 'UBERON:0002084' @app.route("/get-related-terms/<query>") def get_related_terms(query): payload = { 'direction': request.args.get('direction', default='OUTGOING'), 'relationshipType': request.args.get('relationshipType', default='BFO:0000050'), 'entail': request.args.get('entail', default='true'), 'api_key': Config.KNOWLEDGEBASE_KEY } result = {} try: > response = requests.get( f'{Config.SCI_CRUNCH_SCIGRAPH_HOST}/graph/neighbors/{query}', params=payload) app/main.py:1979: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905e4d600> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905e4e770>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_related_terms(client): # Test if we can get the uberon term of heart using the uberon term # of left ventricle > r = client.get('/get-related-terms/UBERON:0002084') tests/test_scicrunch.py:484: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1984: in get_related_terms logging.error(f"Failed getting related terms with payload {payload}", ex) /usr/lib/python3.10/logging/__init__.py:2105: in error root.error(msg, *args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1506: in error self._log(ERROR, msg, args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1624: in _log self.handle(record) /usr/lib/python3.10/logging/__init__.py:1634: in handle self.callHandlers(record) /usr/lib/python3.10/logging/__init__.py:1696: in callHandlers hdlr.handle(record) /usr/lib/python3.10/logging/__init__.py:968: in handle self.emit(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit super().emit(record) /usr/lib/python3.10/logging/__init__.py:1108: in emit self.handleError(record) /usr/lib/python3.10/logging/__init__.py:1100: in emit msg = self.format(record) /usr/lib/python3.10/logging/__init__.py:943: in format return fmt.format(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format return super().format(record) /usr/lib/python3.10/logging/__init__.py:678: in format record.message = record.getMessage() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 1984, "Failed getting related terms wit...ion': 'OUTGOING', 'relationshipType': 'BFO:0000050', 'entail': 'true', 'api_key': 'xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'}"> def getMessage(self): """ Return the message for this LogRecord. Return the message for this LogRecord after merging any user-supplied arguments with the message. """ msg = str(self.msg) if self.args: > msg = msg % self.args E TypeError: not all arguments converted during string formatting /usr/lib/python3.10/logging/__init__.py:368: TypeError _____________________________ test_scaffold_files ______________________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906662a10> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69066611e0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": "30", "from": 0}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '25', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906662a10> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906662a10>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f69066610f0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662a10>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69066611e0> _stacktrace = <traceback object at 0x7f6905af96c0> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662a10>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_scaffold_files(client): > r = client.get('/filter-search/?size=30') tests/test_scicrunch.py:498: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:779: in filter_search response = requests.post( ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f69066610f0> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662a10>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError _____________________ test_finding_contextual_information ______________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6905918040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69059183d0> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["76"]}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '67', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6905918040> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6905918040>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6905918190> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905918040>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f69059183d0> _stacktrace = <traceback object at 0x7f69060f7a80> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905918040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_finding_contextual_information(client): > r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=76') tests/test_scicrunch.py:514: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:634: in get_dataset_info_discoverIds return process_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6905918190> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905918040>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError ____________________ test_undefined_version_dataset_search _____________________ self = <urllib3.connection.HTTPSConnection object at 0x7f6906f222f0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: > conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection raise err _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ address = ('scicrunch.org', 443), timeout = None, source_address = None socket_options = [(6, 1, 1)] def create_connection( address, timeout=socket._GLOBAL_DEFAULT_TIMEOUT, source_address=None, socket_options=None, ): """Connect to *address* and return the socket object. Convenience function. Connect to *address* (a 2-tuple ``(host, port)``) and return the socket object. Passing the optional *timeout* parameter will set the timeout on the socket instance before attempting to connect. If no *timeout* is supplied, the global default timeout setting returned by :func:`socket.getdefaulttimeout` is used. If *source_address* is set it must be a tuple of (host, port) for the socket to bind as a source address before making the connection. An host of '' or port 0 tells the OS to use the default. """ host, port = address if host.startswith("["): host = host.strip("[]") err = None # Using the value from allowed_gai_family() in the context of getaddrinfo lets # us select whether to work with IPv4 DNS records, IPv6 records, or both. # The original create_connection function always returns all records. family = allowed_gai_family() try: host.encode("idna") except UnicodeError: return six.raise_from( LocationParseError(u"'%s', label empty or too long" % host), None ) for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): af, socktype, proto, canonname, sa = res sock = None try: sock = socket.socket(af, socktype, proto) # If provided, set socket level options before connecting. _set_socket_options(sock, socket_options) if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT: sock.settimeout(timeout) if source_address: sock.bind(source_address) > sock.connect(sa) E OSError: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError During handling of the above exception, another exception occurred: self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906f20250> method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' body = b'{"query": {"term": {"item.curie": "10.26275/mlua-o9oj"}}}' headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '57', 'Content-Type': 'application/json'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None release_conn = False, chunked = False, body_pos = None response_kw = {'decode_content': False, 'preload_content': False} parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_dev/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None) destination_scheme = None, conn = None, release_this_conn = True http_tunnel_required = False, err = None, clean_exit = False def urlopen( self, method, url, body=None, headers=None, retries=None, redirect=True, assert_same_host=True, timeout=_Default, pool_timeout=None, release_conn=None, chunked=False, body_pos=None, **response_kw ): """ Get a connection from the pool and perform an HTTP request. This is the lowest level call for making a request, so you'll need to specify all the raw details. .. note:: More commonly, it's appropriate to use a convenience method provided by :class:`.RequestMethods`, such as :meth:`request`. .. note:: `release_conn` will only behave as expected if `preload_content=False` because we want to make `preload_content=False` the default behaviour someday soon without breaking backwards compatibility. :param method: HTTP request method (such as GET, POST, PUT, etc.) :param url: The URL to perform the request on. :param body: Data to send in the request body, either :class:`str`, :class:`bytes`, an iterable of :class:`str`/:class:`bytes`, or a file-like object. :param headers: Dictionary of custom headers to send, such as User-Agent, If-None-Match, etc. If None, pool headers are used. If provided, these headers completely replace any pool-specific headers. :param retries: Configure the number of retries to allow before raising a :class:`~urllib3.exceptions.MaxRetryError` exception. Pass ``None`` to retry until you receive a response. Pass a :class:`~urllib3.util.retry.Retry` object for fine-grained control over different types of retries. Pass an integer number to retry connection errors that many times, but no other types of errors. Pass zero to never retry. If ``False``, then retries are disabled and any exception is raised immediately. Also, instead of raising a MaxRetryError on redirects, the redirect response will be returned. :type retries: :class:`~urllib3.util.retry.Retry`, False, or an int. :param redirect: If True, automatically handle redirects (status codes 301, 302, 303, 307, 308). Each redirect counts as a retry. Disabling retries will disable redirect, too. :param assert_same_host: If ``True``, will make sure that the host of the pool requests is consistent else will raise HostChangedError. When ``False``, you can use the pool on an HTTP proxy and request foreign hosts. :param timeout: If specified, overrides the default timeout for this one request. It may be a float (in seconds) or an instance of :class:`urllib3.util.Timeout`. :param pool_timeout: If set and the pool is set to block=True, then this method will block for ``pool_timeout`` seconds and raise EmptyPoolError if no connection is available within the time period. :param release_conn: If False, then the urlopen call will not release the connection back into the pool once a response is received (but will release if you read the entire contents of the response such as when `preload_content=True`). This is useful if you're not preloading the response's content immediately. You will need to call ``r.release_conn()`` on the response ``r`` to return the connection back into the pool. If None, it takes the value of ``response_kw.get('preload_content', True)``. :param chunked: If True, urllib3 will send the body using chunked transfer encoding. Otherwise, urllib3 will send the body using the standard content-length form. Defaults to False. :param int body_pos: Position to seek to in file-like body in the event of a retry or redirect. Typically this won't need to be set because urllib3 will auto-populate the value when needed. :param \\**response_kw: Additional parameters are passed to :meth:`urllib3.response.HTTPResponse.from_httplib` """ parsed_url = parse_url(url) destination_scheme = parsed_url.scheme if headers is None: headers = self.headers if not isinstance(retries, Retry): retries = Retry.from_int(retries, redirect=redirect, default=self.retries) if release_conn is None: release_conn = response_kw.get("preload_content", True) # Check host if assert_same_host and not self.is_same_host(url): raise HostChangedError(self, url, retries) # Ensure that the URL we're connecting to is properly encoded if url.startswith("/"): url = six.ensure_str(_encode_target(url)) else: url = six.ensure_str(parsed_url.url) conn = None # Track whether `conn` needs to be released before # returning/raising/recursing. Update this variable if necessary, and # leave `release_conn` constant throughout the function. That way, if # the function recurses, the original value of `release_conn` will be # passed down into the recursive call, and its value will be respected. # # See issue #651 [1] for details. # # [1] <https://github.com/urllib3/urllib3/issues/651> release_this_conn = release_conn http_tunnel_required = connection_requires_http_tunnel( self.proxy, self.proxy_config, destination_scheme ) # Merge the proxy headers. Only done when not using HTTP CONNECT. We # have to copy the headers dict so we can safely change it without those # changes being reflected in anyone else's copy. if not http_tunnel_required: headers = headers.copy() headers.update(self.proxy_headers) # Must keep the exception bound to a separate variable or else Python 3 # complains about UnboundLocalError. err = None # Keep track of whether we cleanly exited the except block. This # ensures we do proper cleanup in finally. clean_exit = False # Rewind body position, if needed. Record current position # for future rewinds in the event of a redirect/retry. body_pos = set_file_position(body, body_pos) try: # Request a connection from the queue. timeout_obj = self._get_timeout(timeout) conn = self._get_conn(timeout=pool_timeout) conn.timeout = timeout_obj.connect_timeout is_new_proxy_conn = self.proxy is not None and not getattr( conn, "sock", None ) if is_new_proxy_conn and http_tunnel_required: self._prepare_proxy(conn) # Make the request on the httplib connection object. > httplib_response = self._make_request( conn, method, url, timeout=timeout_obj, body=body, headers=headers, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request self._validate_conn(conn) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn conn.connect() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect conn = self._new_conn() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f6906f222f0> def _new_conn(self): """Establish a socket connection and set nodelay settings on it. :return: New socket connection. """ extra_kw = {} if self.source_address: extra_kw["source_address"] = self.source_address if self.socket_options: extra_kw["socket_options"] = self.socket_options try: conn = connection.create_connection( (self._dns_host, self.port), self.timeout, **extra_kw ) except SocketTimeout: raise ConnectTimeoutError( self, "Connection to %s timed out. (connect timeout=%s)" % (self.host, self.timeout), ) except SocketError as e: > raise NewConnectionError( self, "Failed to establish a new connection: %s" % e ) E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6906f222f0>: Failed to establish a new connection: [Errno 113] No route to host ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f6906f20160> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: > resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen retries = retries.increment( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'POST' url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf' response = None error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f222f0>: Failed to establish a new connection: [Errno 113] No route to host') _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6906f20250> _stacktrace = <traceback object at 0x7f6905c4ca40> def increment( self, method=None, url=None, response=None, error=None, _pool=None, _stacktrace=None, ): """Return a new Retry object with incremented retry counters. :param response: A response object, or None, if the server did not return a response. :type response: :class:`~urllib3.response.HTTPResponse` :param Exception error: An error encountered during the request, or None if the response was received successfully. :return: A new ``Retry`` object. """ if self.total is False and error: # Disabled, indicate to re-raise the error. raise six.reraise(type(error), error, _stacktrace) total = self.total if total is not None: total -= 1 connect = self.connect read = self.read redirect = self.redirect status_count = self.status other = self.other cause = "unknown" status = None redirect_location = None if error and self._is_connection_error(error): # Connect retry? if connect is False: raise six.reraise(type(error), error, _stacktrace) elif connect is not None: connect -= 1 elif error and self._is_read_error(error): # Read retry? if read is False or not self._is_method_retryable(method): raise six.reraise(type(error), error, _stacktrace) elif read is not None: read -= 1 elif error: # Other retry? if other is not None: other -= 1 elif response and response.get_redirect_location(): # Redirect retry? if redirect is not None: redirect -= 1 cause = "too many redirects" redirect_location = response.get_redirect_location() status = response.status else: # Incrementing because of a server error like a 500 in # status_forcelist and the given method is in the allowed_methods cause = ResponseError.GENERIC_ERROR if response and response.status: if status_count is not None: status_count -= 1 cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status) status = response.status history = self.history + ( RequestHistory(method, url, error, status, redirect_location), ) new_retry = self.new( total=total, connect=connect, read=read, redirect=redirect, status=status_count, other=other, history=history, ) if new_retry.is_exhausted(): > raise MaxRetryError(_pool, url, error or ResponseError(cause)) E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f222f0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_undefined_version_dataset_search(client): # Testing with dataset 17 which is not versioned identifier = "17" doi = "10.26275/mlua-o9oj" > r = client.get('/dataset_info/using_doi', query_string={'doi': doi}) tests/test_scicrunch.py:525: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:604: in get_dataset_info_doi return reform_dataset_results(dataset_search(query)) app/main.py:735: in dataset_search response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search', ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post return request("post", url, data=data, json=json, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request resp = self.send(prep, **send_kwargs) ../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f6906f20160> request = <PreparedRequest [POST]>, stream = False timeout = Timeout(connect=None, read=None, total=None), verify = True cert = None, proxies = OrderedDict() def send( self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None ): """Sends PreparedRequest object. Returns Response object. :param request: The :class:`PreparedRequest <PreparedRequest>` being sent. :param stream: (optional) Whether to stream the request content. :param timeout: (optional) How long to wait for the server to send data before giving up, as a float, or a :ref:`(connect timeout, read timeout) <timeouts>` tuple. :type timeout: float or tuple or urllib3 Timeout object :param verify: (optional) Either a boolean, in which case it controls whether we verify the server's TLS certificate, or a string, in which case it must be a path to a CA bundle to use :param cert: (optional) Any user-provided SSL certificate to be trusted. :param proxies: (optional) The proxies dictionary to apply to the request. :rtype: requests.Response """ try: conn = self.get_connection(request.url, proxies) except LocationValueError as e: raise InvalidURL(e, request=request) self.cert_verify(conn, request.url, verify, cert) url = self.request_url(request, proxies) self.add_headers( request, stream=stream, timeout=timeout, verify=verify, cert=cert, proxies=proxies, ) chunked = not (request.body is None or "Content-Length" in request.headers) if isinstance(timeout, tuple): try: connect, read = timeout timeout = TimeoutSauce(connect=connect, read=read) except ValueError: raise ValueError( f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, " f"or a single float to set both timeouts to the same value." ) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: resp = conn.urlopen( method=request.method, url=url, body=request.body, headers=request.headers, redirect=False, assert_same_host=False, preload_content=False, decode_content=False, retries=self.max_retries, timeout=timeout, chunked=chunked, ) except (ProtocolError, OSError) as err: raise ConnectionError(err, request=request) except MaxRetryError as e: if isinstance(e.reason, ConnectTimeoutError): # TODO: Remove this in 3.0.0: see #2811 if not isinstance(e.reason, NewConnectionError): raise ConnectTimeout(e, request=request) if isinstance(e.reason, ResponseError): raise RetryError(e, request=request) if isinstance(e.reason, _ProxyError): raise ProxyError(e, request=request) if isinstance(e.reason, _SSLError): # This branch is for urllib3 v1.22 and later. raise SSLError(e, request=request) > raise ConnectionError(e, request=request) E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f222f0>: Failed to establish a new connection: [Errno 113] No route to host')) ../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError =============================== warnings summary =============================== scripts/monthly_db.py:9 /home/cmiss/Jenkins/workspace/SPARC-API-DEV/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) base = declarative_base() ../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution, DistributionNotFound ../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. DESCRIPTOR = _descriptor.FileDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _CACHESEGMENT = _descriptor.Descriptor( app/dbtable.py:12 /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) base = declarative_base() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 3 warnings tests/test_api.py: 20 warnings tests/test_biolucida.py: 13 warnings tests/test_monthly_stats.py: 11 warnings tests/test_osparc.py: 17 warnings tests/test_pmr.py: 4 warnings tests/test_scicrunch.py: 1 warning tests/test_thumbnails.py: 2 warnings /home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated context = SSLContext(ssl_version or PROTOCOL_TLS) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 3 warnings tests/test_api.py: 23 warnings tests/test_biolucida.py: 13 warnings tests/test_dataset_info.py: 1 warning tests/test_monthly_stats.py: 14 warnings tests/test_osparc.py: 17 warnings tests/test_pmr.py: 4 warnings tests/test_scicrunch.py: 1 warning tests/test_segmentation_info.py: 1 warning tests/test_thumbnails.py: 2 warnings /home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated match_hostname(cert, asserted_hostname) ../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses from imp import find_module, load_module, acquire_lock, release_lock tests/test_health.py::test_request_response /home/cmiss/Jenkins/workspace/SPARC-API-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead. assert_equals("healthy", json_response.get("status")) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_api.py::test_onto_term_lookup - TypeError: not all arguments converted during string formatting FAILED tests/test_api.py::test_non_existing_simulation_ui_file - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905faf040>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69063f24d0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905df30d0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_current_doi_list - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d0f0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_generic_mouse_colon_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905d7fd00>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663abf0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_title_plot_annotation_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905fb2ec0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_object_identifier_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f849a0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_dataset_info.py::test_pennsieve_identifier_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690651fbe0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_plot.py::test_abi_plot - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69065a0bb0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_keys - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150bf910>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906267b50>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_dataset_doi - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6914094d90>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_doi - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906407040>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_ids - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662b00>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690645c310>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_all_data - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060fa230>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_filter - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f00bb0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905c26ef0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690662b550>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_image_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690663baf0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905f23520>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690608b010>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_getting_facets - TypeError: not all arguments converted during string formatting FAILED tests/test_scicrunch.py::test_create_identifier_query - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905a37df0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_create_anatomy_query - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060f1b70>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_response_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905ea75e0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_response_abi_plot - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906639ff0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_response_abi_scaffold - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69060939d0>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_response_sample_subject_size - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690601cb80>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_raw_response_structure - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f69150c0880>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f690615d030>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_getting_curies - TypeError: not all arguments converted during string formatting FAILED tests/test_scicrunch.py::test_get_related_terms - TypeError: not all arguments converted during string formatting FAILED tests/test_scicrunch.py::test_scaffold_files - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906662a10>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_finding_contextual_information - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6905918040>: Failed to establish a new connection: [Errno 113] No route to host')) FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6906f222f0>: Failed to establish a new connection: [Errno 113] No route to host')) ====== 38 failed, 78 passed, 3 skipped, 162 warnings in 263.55s (0:04:23) ====== Build step 'Execute shell' marked build as failure [Slack Notifications] found #1273 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE