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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 [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 # 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 52b9dfe9de5a0d3ef25923d16e61846d4df261ca (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 52b9dfe9de5a0d3ef25923d16e61846d4df261ca # timeout=10 Commit message: "Merge pull request #191 from agarny/issue190" > git rev-list --no-walk 52b9dfe9de5a0d3ef25923d16e61846d4df261ca # timeout=10 [SPARC-API] $ /bin/sh -xe /tmp/shiningpanda13316899805192594347.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/SPARC-API + export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python + pip install -r requirements.txt Requirement already satisfied: api==0.0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.0.7) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (6.1.1) Requirement already satisfied: boto3==1.17.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.17.67) Requirement already satisfied: botocore==1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.20.67) Requirement already satisfied: certifi==2019.11.28 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2019.11.28) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 7)) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (1.1.1) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (0.10.1) Requirement already satisfied: flask-cors==3.0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (3.0.8) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (20.0.4) Requirement already satisfied: idna==2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (1.1.1) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (1.3.7) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (0.4.3) Requirement already satisfied: pillow in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (10.0.0) Requirement already satisfied: public==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (5.4.3) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (2.8.0) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (2019.4.13) Requirement already satisfied: requests==2.25.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (2.25.1) Requirement already satisfied: s3transfer==0.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (0.4.2) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (1.13.0) Requirement already satisfied: SQLAlchemy==1.3.20 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (1.3.20) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (0.16.0) Requirement already satisfied: psycopg2-binary==2.9.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (2.9.5) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (3.7.0) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2.52.0) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (4.1.3) Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (2.6.2) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (2.11.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (6.0.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (0.18.3) Requirement already satisfied: futures in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (4.24.2) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (2023.3.post1) Requirement already satisfied: rsa==4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (4.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (3.0.1) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.6.2) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (5.9.5) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.0.4->-r requirements.txt (line 12)) (68.1.2) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (2.2.0) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 36)) (2.1) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.22.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (0.1.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.11.1) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.5.0) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.3.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements.txt (line 2)) (0.14.1) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (1.11.0) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (23.1) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (23.1.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (10.1.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.2.6) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements.txt (line 2)) (1.15.0) Requirement already satisfied: googleapis-common-protos<2.0.dev0,>=1.56.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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 37)) (1.60.0) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (5.3.1) Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (3.1.1) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.1.7 Uninstalling click-8.1.7: Successfully uninstalled click-8.1.7 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 23.7.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 [notice] To update, run: pip install --upgrade pip + pip install -r requirements-dev.txt Requirement already satisfied: pytest==5.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 1)) (5.4.3) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1) Requirement already satisfied: black in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (23.7.0) Requirement already satisfied: isort in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 4)) (5.12.0) Requirement already satisfied: nose in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 6)) (23.1) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (23.1.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.1.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.6) Requirement already satisfied: boto3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.17.67) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (6.0.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.18.3) Requirement already satisfied: futures in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.24.2) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in 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(line 2)) (1.6.2) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (5.9.5) Requirement already satisfied: python-dateutil>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8.0) Requirement already satisfied: six<2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.5.0) Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3)) Obtaining dependency information for click>=8.0.0 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (1.0.0) Requirement already satisfied: pathspec>=0.9.0 in 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Requirement already satisfied: chardet<5,>=3.0.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.4) Requirement already satisfied: idna<3,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.4) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2019.11.28) Requirement already satisfied: botocore<1.21.0,>=1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.20.67) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.9.4) Requirement already satisfied: s3transfer<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.4.2) Using cached click-8.1.7-py3-none-any.whl (97 kB) Installing collected packages: click Attempting uninstall: click Found existing installation: click 7.1.2 Uninstalling click-7.1.2: Successfully uninstalled click-7.1.2 Successfully installed click-8.1.7 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 [notice] To update, run: pip install --upgrade pip + pytest ============================= test session starts ============================== platform linux -- Python 3.9.18, pytest-5.4.3, py-1.11.0, pluggy-0.13.1 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API collected 100 items tests/test_api.py F.................. [ 19%] tests/test_biolucida.py ............. [ 32%] tests/test_dataset_info.py .s..ss..... [ 43%] tests/test_health.py . [ 44%] tests/test_monthly_stats.py ...... [ 50%] tests/test_osparc.py .............. [ 64%] tests/test_pmr.py ..... [ 69%] tests/test_scicrunch.py ...............s......... [ 94%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== _____________________ test_direct_download_url_small_file ______________________ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> conn = <urllib3.connection.HTTPSConnection object at 0x7f5d1bf24310> method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' timeout = Timeout(connect=1, read=1, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connec... 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'}} timeout_obj = Timeout(connect=1, read=1, total=None), read_timeout = 1 def _make_request( self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw ): """ Perform a request on a given urllib connection object taken from our pool. :param conn: a connection from one of our connection pools :param timeout: Socket timeout in seconds for the request. This can be a float or integer, which will set the same timeout value for the socket connect and the socket read, or an instance of :class:`urllib3.util.Timeout`, which gives you more fine-grained control over your timeouts. """ self.num_requests += 1 timeout_obj = self._get_timeout(timeout) timeout_obj.start_connect() conn.timeout = timeout_obj.connect_timeout # Trigger any extra validation we need to do. try: self._validate_conn(conn) except (SocketTimeout, BaseSSLError) as e: # Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout. self._raise_timeout(err=e, url=url, timeout_value=conn.timeout) raise # conn.request() calls http.client.*.request, not the method in # urllib3.request. It also calls makefile (recv) on the socket. try: if chunked: conn.request_chunked(method, url, **httplib_request_kw) else: conn.request(method, url, **httplib_request_kw) # We are swallowing BrokenPipeError (errno.EPIPE) since the server is # legitimately able to close the connection after sending a valid response. # With this behaviour, the received response is still readable. except BrokenPipeError: # Python 3 pass except IOError as e: # Python 2 and macOS/Linux # EPIPE and ESHUTDOWN are BrokenPipeError on Python 2, and EPROTOTYPE is needed on macOS # https://erickt.github.io/blog/2014/11/19/adventures-in-debugging-a-potential-osx-kernel-bug/ if e.errno not in { errno.EPIPE, errno.ESHUTDOWN, errno.EPROTOTYPE, }: raise # Reset the timeout for the recv() on the socket read_timeout = timeout_obj.read_timeout # App Engine doesn't have a sock attr if getattr(conn, "sock", None): # In Python 3 socket.py will catch EAGAIN and return None when you # try and read into the file pointer created by http.client, which # instead raises a BadStatusLine exception. Instead of catching # the exception and assuming all BadStatusLine exceptions are read # timeouts, check for a zero timeout before making the request. if read_timeout == 0: raise ReadTimeoutError( self, url, "Read timed out. (read timeout=%s)" % read_timeout ) if read_timeout is Timeout.DEFAULT_TIMEOUT: conn.sock.settimeout(socket.getdefaulttimeout()) else: # None or a value conn.sock.settimeout(read_timeout) # Receive the response from the server try: try: # Python 2.7, use buffering of HTTP responses httplib_response = conn.getresponse(buffering=True) except TypeError: # Python 3 try: httplib_response = conn.getresponse() except BaseException as e: # Remove the TypeError from the exception chain in # Python 3 (including for exceptions like SystemExit). # Otherwise it looks like a bug in the code. > six.raise_from(e, None) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:445: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ value = None, from_value = None > ??? <string>:3: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> conn = <urllib3.connection.HTTPSConnection object at 0x7f5d1bf24310> method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' timeout = Timeout(connect=1, read=1, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connec... 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'}} timeout_obj = Timeout(connect=1, read=1, total=None), read_timeout = 1 def _make_request( self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw ): """ Perform a request on a given urllib connection object taken from our pool. :param conn: a connection from one of our connection pools :param timeout: Socket timeout in seconds for the request. This can be a float or integer, which will set the same timeout value for the socket connect and the socket read, or an instance of :class:`urllib3.util.Timeout`, which gives you more fine-grained control over your timeouts. """ self.num_requests += 1 timeout_obj = self._get_timeout(timeout) timeout_obj.start_connect() conn.timeout = timeout_obj.connect_timeout # Trigger any extra validation we need to do. try: self._validate_conn(conn) except (SocketTimeout, BaseSSLError) as e: # Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout. self._raise_timeout(err=e, url=url, timeout_value=conn.timeout) raise # conn.request() calls http.client.*.request, not the method in # urllib3.request. It also calls makefile (recv) on the socket. try: if chunked: conn.request_chunked(method, url, **httplib_request_kw) else: conn.request(method, url, **httplib_request_kw) # We are swallowing BrokenPipeError (errno.EPIPE) since the server is # legitimately able to close the connection after sending a valid response. # With this behaviour, the received response is still readable. except BrokenPipeError: # Python 3 pass except IOError as e: # Python 2 and macOS/Linux # EPIPE and ESHUTDOWN are BrokenPipeError on Python 2, and EPROTOTYPE is needed on macOS # https://erickt.github.io/blog/2014/11/19/adventures-in-debugging-a-potential-osx-kernel-bug/ if e.errno not in { errno.EPIPE, errno.ESHUTDOWN, errno.EPROTOTYPE, }: raise # Reset the timeout for the recv() on the socket read_timeout = timeout_obj.read_timeout # App Engine doesn't have a sock attr if getattr(conn, "sock", None): # In Python 3 socket.py will catch EAGAIN and return None when you # try and read into the file pointer created by http.client, which # instead raises a BadStatusLine exception. Instead of catching # the exception and assuming all BadStatusLine exceptions are read # timeouts, check for a zero timeout before making the request. if read_timeout == 0: raise ReadTimeoutError( self, url, "Read timed out. (read timeout=%s)" % read_timeout ) if read_timeout is Timeout.DEFAULT_TIMEOUT: conn.sock.settimeout(socket.getdefaulttimeout()) else: # None or a value conn.sock.settimeout(read_timeout) # Receive the response from the server try: try: # Python 2.7, use buffering of HTTP responses httplib_response = conn.getresponse(buffering=True) except TypeError: # Python 3 try: > httplib_response = conn.getresponse() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:440: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connection.HTTPSConnection object at 0x7f5d1bf24310> def getresponse(self): """Get the response from the server. If the HTTPConnection is in the correct state, returns an instance of HTTPResponse or of whatever object is returned by the response_class variable. If a request has not been sent or if a previous response has not be handled, ResponseNotReady is raised. If the HTTP response indicates that the connection should be closed, then it will be closed before the response is returned. When the connection is closed, the underlying socket is closed. """ # if a prior response has been completed, then forget about it. if self.__response and self.__response.isclosed(): self.__response = None # if a prior response exists, then it must be completed (otherwise, we # cannot read this response's header to determine the connection-close # behavior) # # note: if a prior response existed, but was connection-close, then the # socket and response were made independent of this HTTPConnection # object since a new request requires that we open a whole new # connection # # this means the prior response had one of two states: # 1) will_close: this connection was reset and the prior socket and # response operate independently # 2) persistent: the response was retained and we await its # isclosed() status to become true. # if self.__state != _CS_REQ_SENT or self.__response: raise ResponseNotReady(self.__state) if self.debuglevel > 0: response = self.response_class(self.sock, self.debuglevel, method=self._method) else: response = self.response_class(self.sock, method=self._method) try: try: > response.begin() /usr/lib/python3.9/http/client.py:1377: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <http.client.HTTPResponse object at 0x7f5d1bf243a0> def begin(self): if self.headers is not None: # we've already started reading the response return # read until we get a non-100 response while True: > version, status, reason = self._read_status() /usr/lib/python3.9/http/client.py:320: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <http.client.HTTPResponse object at 0x7f5d1bf243a0> def _read_status(self): > line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1") /usr/lib/python3.9/http/client.py:281: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <socket.SocketIO object at 0x7f5d1bf24430> b = <memory at 0x7f5d22f6be80> def readinto(self, b): """Read up to len(b) bytes into the writable buffer *b* and return the number of bytes read. If the socket is non-blocking and no bytes are available, None is returned. If *b* is non-empty, a 0 return value indicates that the connection was shutdown at the other end. """ self._checkClosed() self._checkReadable() if self._timeout_occurred: raise OSError("cannot read from timed out object") while True: try: > return self._sock.recv_into(b) /usr/lib/python3.9/socket.py:704: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> buffer = <memory at 0x7f5d22f6be80>, nbytes = 8192, flags = 0 def recv_into(self, buffer, nbytes=None, flags=0): self._checkClosed() if buffer and (nbytes is None): nbytes = len(buffer) elif nbytes is None: nbytes = 1024 if self._sslobj is not None: if flags != 0: raise ValueError( "non-zero flags not allowed in calls to recv_into() on %s" % self.__class__) > return self.read(nbytes, buffer) /usr/lib/python3.9/ssl.py:1275: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6> len = 8192, buffer = <memory at 0x7f5d22f6be80> def read(self, len=1024, buffer=None): """Read up to LEN bytes and return them. Return zero-length string on EOF.""" self._checkClosed() if self._sslobj is None: raise ValueError("Read on closed or unwrapped SSL socket.") try: if buffer is not None: > return self._sslobj.read(len, buffer) E socket.timeout: The read operation timed out /usr/lib/python3.9/ssl.py:1133: timeout During handling of the above exception, another exception occurred: self = <requests.adapters.HTTPAdapter object at 0x7f5d1bf2f460> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=1, read=1, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: > 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 ) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connection': 'keep-alive', 'X-Co...: 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=1, read=1, 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='/spaces/6bya4tyw8399/environments/master/entries', query='content_type=sparcAward', 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, ) # If we're going to release the connection in ``finally:``, then # the response doesn't need to know about the connection. Otherwise # it will also try to release it and we'll have a double-release # mess. response_conn = conn if not release_conn else None # Pass method to Response for length checking response_kw["request_method"] = method # Import httplib's response into our own wrapper object response = self.ResponseCls.from_httplib( httplib_response, pool=self, connection=response_conn, retries=retries, **response_kw ) # Everything went great! clean_exit = True except EmptyPoolError: # Didn't get a connection from the pool, no need to clean up clean_exit = True release_this_conn = False raise except ( TimeoutError, HTTPException, SocketError, ProtocolError, BaseSSLError, SSLError, CertificateError, ) as e: # Discard the connection for these exceptions. It will be # replaced during the next _get_conn() call. clean_exit = False if isinstance(e, (BaseSSLError, CertificateError)): e = SSLError(e) elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy: e = ProxyError("Cannot connect to proxy.", e) elif isinstance(e, (SocketError, HTTPException)): e = ProtocolError("Connection aborted.", e) > retries = retries.increment( method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] ) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = Retry(total=0, connect=None, read=False, redirect=None, status=None) method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' response = None error = ReadTimeoutError("HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1)") _pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> _stacktrace = <traceback object at 0x7f5d200e0700> 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) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py:532: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tp = <class 'urllib3.exceptions.ReadTimeoutError'>, value = None, tb = None def reraise(tp, value, tb=None): try: if value is None: value = tp() if value.__traceback__ is not tb: raise value.with_traceback(tb) > raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/packages/six.py:735: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' body = None headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connection': 'keep-alive', 'X-Co...: 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'} retries = Retry(total=0, connect=None, read=False, redirect=None, status=None) redirect = False, assert_same_host = False timeout = Timeout(connect=1, read=1, 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='/spaces/6bya4tyw8399/environments/master/entries', query='content_type=sparcAward', 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, ) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> conn = <urllib3.connection.HTTPSConnection object at 0x7f5d1bf24310> method = 'GET' url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' timeout = Timeout(connect=1, read=1, total=None), chunked = False httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connec... 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'}} timeout_obj = Timeout(connect=1, read=1, total=None), read_timeout = 1 def _make_request( self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw ): """ Perform a request on a given urllib connection object taken from our pool. :param conn: a connection from one of our connection pools :param timeout: Socket timeout in seconds for the request. This can be a float or integer, which will set the same timeout value for the socket connect and the socket read, or an instance of :class:`urllib3.util.Timeout`, which gives you more fine-grained control over your timeouts. """ self.num_requests += 1 timeout_obj = self._get_timeout(timeout) timeout_obj.start_connect() conn.timeout = timeout_obj.connect_timeout # Trigger any extra validation we need to do. try: self._validate_conn(conn) except (SocketTimeout, BaseSSLError) as e: # Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout. self._raise_timeout(err=e, url=url, timeout_value=conn.timeout) raise # conn.request() calls http.client.*.request, not the method in # urllib3.request. It also calls makefile (recv) on the socket. try: if chunked: conn.request_chunked(method, url, **httplib_request_kw) else: conn.request(method, url, **httplib_request_kw) # We are swallowing BrokenPipeError (errno.EPIPE) since the server is # legitimately able to close the connection after sending a valid response. # With this behaviour, the received response is still readable. except BrokenPipeError: # Python 3 pass except IOError as e: # Python 2 and macOS/Linux # EPIPE and ESHUTDOWN are BrokenPipeError on Python 2, and EPROTOTYPE is needed on macOS # https://erickt.github.io/blog/2014/11/19/adventures-in-debugging-a-potential-osx-kernel-bug/ if e.errno not in { errno.EPIPE, errno.ESHUTDOWN, errno.EPROTOTYPE, }: raise # Reset the timeout for the recv() on the socket read_timeout = timeout_obj.read_timeout # App Engine doesn't have a sock attr if getattr(conn, "sock", None): # In Python 3 socket.py will catch EAGAIN and return None when you # try and read into the file pointer created by http.client, which # instead raises a BadStatusLine exception. Instead of catching # the exception and assuming all BadStatusLine exceptions are read # timeouts, check for a zero timeout before making the request. if read_timeout == 0: raise ReadTimeoutError( self, url, "Read timed out. (read timeout=%s)" % read_timeout ) if read_timeout is Timeout.DEFAULT_TIMEOUT: conn.sock.settimeout(socket.getdefaulttimeout()) else: # None or a value conn.sock.settimeout(read_timeout) # Receive the response from the server try: try: # Python 2.7, use buffering of HTTP responses httplib_response = conn.getresponse(buffering=True) except TypeError: # Python 3 try: httplib_response = conn.getresponse() except BaseException as e: # Remove the TypeError from the exception chain in # Python 3 (including for exceptions like SystemExit). # Otherwise it looks like a bug in the code. six.raise_from(e, None) except (SocketTimeout, BaseSSLError, SocketError) as e: > self._raise_timeout(err=e, url=url, timeout_value=read_timeout) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:447: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f5d1bf2f4f0> err = timeout('The read operation timed out') url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward' timeout_value = 1 def _raise_timeout(self, err, url, timeout_value): """Is the error actually a timeout? Will raise a ReadTimeout or pass""" if isinstance(err, SocketTimeout): > raise ReadTimeoutError( self, url, "Read timed out. (read timeout=%s)" % timeout_value ) E urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:336: ReadTimeoutError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_direct_download_url_small_file(client): small_s3_file = '76%2F2%2Ffiles%2Fderivative%2FScaffold%2FmouseColon_metadata.json' > r = client.get(f"/s3-resource/{small_s3_file}") tests/test_api.py:20: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1944: in full_dispatch_request self.try_trigger_before_first_request_functions() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1992: in try_trigger_before_first_request_functions func() app/main.py:202: in get_metrics cf_response = get_funded_projects_count(contentful) app/metrics/contentful.py:45: in get_funded_projects_count response = client.entries({ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/contentful/client.py:262: in entries return self._get( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/contentful/client.py:567: in _get response = retry_request(self)(self._http_get)(url, query=query) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/contentful/utils.py:163: in wrapper return http_call(url, query) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/contentful/client.py:547: in _http_get response = requests.get( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:76: in get return request('get', url, params=params, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request return session.request(method=method, url=url, **kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request resp = self.send(prep, **send_kwargs) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send r = adapter.send(request, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <requests.adapters.HTTPAdapter object at 0x7f5d1bf2f460> request = <PreparedRequest [GET]>, stream = False timeout = Timeout(connect=1, read=1, 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 as e: # this may raise a string formatting error. err = ("Invalid timeout {}. Pass a (connect, read) " "timeout tuple, or a single float to set " "both timeouts to the same value".format(timeout)) raise ValueError(err) elif isinstance(timeout, TimeoutSauce): pass else: timeout = TimeoutSauce(connect=timeout, read=timeout) try: if not chunked: 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 ) # Send the request. else: if hasattr(conn, 'proxy_pool'): conn = conn.proxy_pool low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT) try: low_conn.putrequest(request.method, url, skip_accept_encoding=True) for header, value in request.headers.items(): low_conn.putheader(header, value) low_conn.endheaders() for i in request.body: low_conn.send(hex(len(i))[2:].encode('utf-8')) low_conn.send(b'\r\n') low_conn.send(i) low_conn.send(b'\r\n') low_conn.send(b'0\r\n\r\n') # Receive the response from the server try: # For Python 2.7, use buffering of HTTP responses r = low_conn.getresponse(buffering=True) except TypeError: # For compatibility with Python 3.3+ r = low_conn.getresponse() resp = HTTPResponse.from_httplib( r, pool=conn, connection=low_conn, preload_content=False, decode_content=False ) except: # If we hit any problems here, clean up the connection. # Then, reraise so that we can handle the actual exception. low_conn.close() raise except (ProtocolError, socket.error) 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) except ClosedPoolError as e: raise ConnectionError(e, request=request) except _ProxyError as e: raise ProxyError(e) except (_SSLError, _HTTPError) as e: if isinstance(e, _SSLError): # This branch is for urllib3 versions earlier than v1.22 raise SSLError(e, request=request) elif isinstance(e, ReadTimeoutError): > raise ReadTimeout(e, request=request) E requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:529: ReadTimeout ----------------------------- Captured stdout call ----------------------------- Error while setting featured dataset id: 'NoneType' object has no attribute 'init_index' ----------------------------- Captured stderr call ----------------------------- --- Logging error --- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 12, in init_algolia_client return SearchClient.create(APP_ID, API_KEY) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/search_client.py", line 53, in create config = SearchConfig(app_id, api_key) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/configs.py", line 63, in __init__ super(SearchConfig, self).__init__(app_id, api_key) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/configs.py", line 17, in __init__ app_id = os.environ["ALGOLIA_APP_ID"] if app_id is None else app_id File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/os.py", line 679, in __getitem__ raise KeyError(key) from None KeyError: 'ALGOLIA_APP_ID' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.9/logging/__init__.py", line 1083, in emit msg = self.format(record) File "/usr/lib/python3.9/logging/__init__.py", line 927, in format return fmt.format(record) File "/usr/lib/python3.9/logging/__init__.py", line 663, in format record.message = record.getMessage() File "/usr/lib/python3.9/logging/__init__.py", line 367, in getMessage msg = msg % self.args TypeError: not all arguments converted during string formatting Call stack: File "/usr/lib/python3.9/threading.py", line 937, in _bootstrap self._bootstrap_inner() File "/usr/lib/python3.9/threading.py", line 980, in _bootstrap_inner self.run() File "/usr/lib/python3.9/threading.py", line 917, in run self._target(*self._args, **self._kwargs) File "/usr/lib/python3.9/concurrent/futures/thread.py", line 83, in _worker work_item.run() File "/usr/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, **self.kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/executors/base.py", line 125, in run_job retval = job.func(*job.args, **job.kwargs) File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 237, in <lambda> featured_dataset_id_scheduler.add_job(lambda: set_featured_dataset_id(featuredDatasetIdSelectorTable), featured_dataset_id_trigger) File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/update_featured_dataset_id.py", line 74, in set_featured_dataset_id table_state["available_dataset_ids"] = get_all_dataset_ids() File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 25, in get_all_dataset_ids client = init_algolia_client() File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 15, in init_algolia_client logging.error('An error occured while instantiating the Algolia search client.', e) Message: 'An error occured while instantiating the Algolia search client.' Arguments: (KeyError('ALGOLIA_APP_ID'),) --- Logging error --- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 12, in init_algolia_client return SearchClient.create(APP_ID, API_KEY) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/search_client.py", line 53, in create config = SearchConfig(app_id, api_key) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/configs.py", line 63, in __init__ super(SearchConfig, self).__init__(app_id, api_key) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/algoliasearch/configs.py", line 17, in __init__ app_id = os.environ["ALGOLIA_APP_ID"] if app_id is None else app_id File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/os.py", line 679, in __getitem__ raise KeyError(key) from None KeyError: 'ALGOLIA_APP_ID' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.9/logging/__init__.py", line 1083, in emit msg = self.format(record) File "/usr/lib/python3.9/logging/__init__.py", line 927, in format return fmt.format(record) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/logging.py", line 74, in format return super().format(record) File "/usr/lib/python3.9/logging/__init__.py", line 663, in format record.message = record.getMessage() File "/usr/lib/python3.9/logging/__init__.py", line 367, in getMessage msg = msg % self.args TypeError: not all arguments converted during string formatting Call stack: File "/usr/lib/python3.9/threading.py", line 937, in _bootstrap self._bootstrap_inner() File "/usr/lib/python3.9/threading.py", line 980, in _bootstrap_inner self.run() File "/usr/lib/python3.9/threading.py", line 917, in run self._target(*self._args, **self._kwargs) File "/usr/lib/python3.9/concurrent/futures/thread.py", line 83, in _worker work_item.run() File "/usr/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, **self.kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/executors/base.py", line 125, in run_job retval = job.func(*job.args, **job.kwargs) File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 237, in <lambda> featured_dataset_id_scheduler.add_job(lambda: set_featured_dataset_id(featuredDatasetIdSelectorTable), featured_dataset_id_trigger) File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/update_featured_dataset_id.py", line 74, in set_featured_dataset_id table_state["available_dataset_ids"] = get_all_dataset_ids() File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 25, in get_all_dataset_ids client = init_algolia_client() File "/home/cmiss/Jenkins/workspace/SPARC-API/app/metrics/algolia.py", line 15, in init_algolia_client logging.error('An error occured while instantiating the Algolia search client.', e) File "/usr/lib/python3.9/logging/__init__.py", line 2064, in error root.error(msg, *args, **kwargs) File "/usr/lib/python3.9/logging/__init__.py", line 1475, in error self._log(ERROR, msg, args, **kwargs) File "/usr/lib/python3.9/logging/__init__.py", line 1589, in _log self.handle(record) File "/usr/lib/python3.9/logging/__init__.py", line 1599, in handle self.callHandlers(record) File "/usr/lib/python3.9/logging/__init__.py", line 1661, in callHandlers hdlr.handle(record) File "/usr/lib/python3.9/logging/__init__.py", line 952, in handle self.emit(record) File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/logging.py", line 310, in emit logging.StreamHandler.emit(self, record) Message: 'An error occured while instantiating the Algolia search client.' Arguments: (KeyError('ALGOLIA_APP_ID'),) =============================== warnings summary =============================== /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google.logging')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(parent) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/future/standard_library/__init__.py:65 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/future/standard_library/__init__.py:65: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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( /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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( tests/test_health.py::test_request_response /home/cmiss/Jenkins/workspace/SPARC-API/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead. assert_equals("healthy", json_response.get("status")) -- Docs: https://docs.pytest.org/en/latest/warnings.html =========================== short test summary info ============================ FAILED tests/test_api.py::test_direct_download_url_small_file - requests.exce... ======= 1 failed, 95 passed, 4 skipped, 14 warnings in 288.18s (0:04:48) ======= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #927 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE