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 d7c1450ee9db5cf5db27fd60a8acf398ec53f233 (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f d7c1450ee9db5cf5db27fd60a8acf398ec53f233 # timeout=10
Commit message: "Merge pull request #248 from nih-sparc/fix-webhook-email-list-creation-error"
> git rev-list --no-walk d7c1450ee9db5cf5db27fd60a8acf398ec53f233 # timeout=10
[SPARC-API] $ /bin/sh -xe /tmp/shiningpanda8101482207776983619.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==2023.5.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2023.5.7)
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.metadata (2.9 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: hubspot-api-client==9.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (9.0.0)
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 14)) (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 15)) (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 16)) (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 17)) (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 18)) (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 19)) (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 20)) (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 21)) (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 22)) (11.0.0)
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 23)) (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 24)) (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 25)) (3.8.0)
Requirement already satisfied: python-dateutil==2.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (2.8.2)
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 27)) (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 28)) (2019.4.13)
Requirement already satisfied: requests==2.31.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (2.31.0)
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 30)) (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 31)) (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 32)) (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 33)) (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 34)) (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 35)) (0.16.0)
Requirement already satisfied: psycopg2-binary==2.9.9 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (2.9.9)
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 37)) (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 38)) (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 39)) (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 40)) (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 41)) (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 42)) (2.11.0)
Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 43)) (2.3.0)
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)) (7.1.0)
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)) (1.2.15)
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)) (1.0.0)
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)) (5.29.1)
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)) (2024.2)
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)) (3.0.2)
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)) (1.8.0)
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)) (6.1.0)
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)) (75.6.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests==2.31.0->-r requirements.txt (line 29)) (3.4.0)
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 31)) (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 31)) (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 37)) (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 38)) (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 38)) (2.36.0)
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 38)) (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/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 38)) (2.23.0)
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 38)) (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 39)) (0.6.1)
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 39)) (0.4.1)
Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Flask-Caching==2.3.0->-r requirements.txt (line 43)) (0.9.0)
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 24)) (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 24)) (24.2)
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 24)) (24.2.0)
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 24)) (10.5.0)
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 24)) (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 24)) (0.2.13)
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)) (1.17.0)
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 38)) (1.66.0)
Requirement already satisfied: proto-plus<2.0.0dev,>=1.22.3 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 38)) (1.25.0)
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 38)) (5.5.0)
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 38)) (3.2.0)
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Installing collected packages: Click
Attempting uninstall: Click
Found existing installation: click 8.1.7
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 24.10.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible.
Successfully installed Click-7.1.2
+ 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)) (24.10.0)
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)) (5.13.2)
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)) (24.2)
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)) (24.2.0)
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)) (10.5.0)
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)) (0.2.13)
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)) (7.1.0)
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)) (1.2.15)
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)) (1.0.0)
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)) (5.29.1)
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 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2024.2)
Requirement already satisfied: requests>=2.18 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)) (2.31.0)
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-dev.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-dev.txt (line 2)) (3.0.2)
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-dev.txt (line 2)) (1.8.0)
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)) (6.1.0)
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)) (2.8.2)
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)) (0.6.1)
Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3))
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 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (0.12.1)
Requirement already satisfied: platformdirs>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.3.6)
Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (2.2.1)
Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.12.2)
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-dev.txt (line 2)) (1.17.0)
Requirement already satisfied: charset-normalizer<4,>=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)) (3.4.0)
Requirement already satisfied: idna<4,>=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<3,>=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)) (2023.5.7)
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
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.21, pytest-5.4.3, py-1.11.0, pluggy-0.13.1
rootdir: /home/cmiss/Jenkins/workspace/SPARC-API
collected 110 items
tests/test_api.py ...............FFFF. [ 18%]
tests/test_biolucida.py ............. [ 30%]
tests/test_dataset_info.py .s..ss..... [ 40%]
tests/test_health.py . [ 40%]
tests/test_monthly_stats.py ......... [ 49%]
tests/test_osparc.py .............. [ 61%]
tests/test_pmr.py ......... [ 70%]
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_onto_term_lookup _____________________________
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'})
> assert r.status_code == 200
E assert 500 == 200
E + where 500 = <Response streamed [500 INTERNAL SERVER ERROR]>.status_code
tests/test_api.py:232: AssertionError
----------------------------- Captured stderr call -----------------------------
--- Logging error ---
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 169, in _new_conn
conn = connection.create_connection(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py", line 73, in create_connection
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
File "/usr/lib/python3.9/socket.py", line 966, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 353, in connect
conn = self._new_conn()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 181, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 1759, in find_by_onto_term
response = requests.get(f'{Config.SCI_CRUNCH_INTERLEX_HOST}/_search', headers=headers, params=params, json=query)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))
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 "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/bin/pytest", line 8, in <module>
sys.exit(main())
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/config/__init__.py", line 124, in main
ret = config.hook.pytest_cmdline_main(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 240, in pytest_cmdline_main
return wrap_session(config, _main)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 191, in wrap_session
session.exitstatus = doit(config, session) or 0
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 247, in _main
config.hook.pytest_runtestloop(session=session)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 272, in pytest_runtestloop
item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 85, in pytest_runtest_protocol
runtestprotocol(item, nextitem=nextitem)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 100, in runtestprotocol
reports.append(call_and_report(item, "call", log))
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 186, in call_and_report
call = call_runtest_hook(item, when, **kwds)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 216, in call_runtest_hook
return CallInfo.from_call(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 244, in from_call
result = func()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 217, in <lambda>
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 135, in pytest_runtest_call
item.runtest()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/python.py", line 1477, in runtest
self.ihook.pytest_pyfunc_call(pyfuncitem=self)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/python.py", line 182, in pytest_pyfunc_call
result = testfunction(**testargs)
File "/home/cmiss/Jenkins/workspace/SPARC-API/tests/test_api.py", line 231, in test_onto_term_lookup
r = client.get('/onto_term_lookup', query_string={'term': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'})
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 1029, in get
return self.open(*args, **kw)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py", line 222, in open
return Client.open(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 993, in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 884, in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 1119, in run_wsgi_app
app_rv = app(environ, start_response)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 2463, in __call__
return self.wsgi_app(environ, start_response)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 2446, in wsgi_app
response = self.full_dispatch_request()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 1949, in full_dispatch_request
rv = self.dispatch_request()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 1935, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 1772, in find_by_onto_term
logging.error("An error occured while fetching from SciCrunch", ex)
Message: 'An error occured while fetching from SciCrunch'
Arguments: (ConnectionError(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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))")),)
--- Logging error ---
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 169, in _new_conn
conn = connection.create_connection(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py", line 73, in create_connection
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
File "/usr/lib/python3.9/socket.py", line 966, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 353, in connect
conn = self._new_conn()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 181, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 1759, in find_by_onto_term
response = requests.get(f'{Config.SCI_CRUNCH_INTERLEX_HOST}/_search', headers=headers, params=params, json=query)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))
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 "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/bin/pytest", line 8, in <module>
sys.exit(main())
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/config/__init__.py", line 124, in main
ret = config.hook.pytest_cmdline_main(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 240, in pytest_cmdline_main
return wrap_session(config, _main)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 191, in wrap_session
session.exitstatus = doit(config, session) or 0
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 247, in _main
config.hook.pytest_runtestloop(session=session)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/main.py", line 272, in pytest_runtestloop
item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 85, in pytest_runtest_protocol
runtestprotocol(item, nextitem=nextitem)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 100, in runtestprotocol
reports.append(call_and_report(item, "call", log))
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 186, in call_and_report
call = call_runtest_hook(item, when, **kwds)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 216, in call_runtest_hook
return CallInfo.from_call(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 244, in from_call
result = func()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 217, in <lambda>
lambda: ihook(item=item, **kwds), when=when, reraise=reraise
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/runner.py", line 135, in pytest_runtest_call
item.runtest()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/python.py", line 1477, in runtest
self.ihook.pytest_pyfunc_call(pyfuncitem=self)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/hooks.py", line 286, in __call__
return self._hookexec(self, self.get_hookimpls(), kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
return self._inner_hookexec(hook, methods, kwargs)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pluggy/callers.py", line 187, in _multicall
res = hook_impl.function(*args)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/_pytest/python.py", line 182, in pytest_pyfunc_call
result = testfunction(**testargs)
File "/home/cmiss/Jenkins/workspace/SPARC-API/tests/test_api.py", line 231, in test_onto_term_lookup
r = client.get('/onto_term_lookup', query_string={'term': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'})
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 1029, in get
return self.open(*args, **kw)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py", line 222, in open
return Client.open(
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 993, in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 884, in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py", line 1119, in run_wsgi_app
app_rv = app(environ, start_response)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 2463, in __call__
return self.wsgi_app(environ, start_response)
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 2446, in wsgi_app
response = self.full_dispatch_request()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 1949, in full_dispatch_request
rv = self.dispatch_request()
File "/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py", line 1935, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/home/cmiss/Jenkins/workspace/SPARC-API/app/main.py", line 1772, in find_by_onto_term
logging.error("An error occured while fetching from SciCrunch", ex)
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 fetching from SciCrunch'
Arguments: (ConnectionError(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 0x7f6a695ab040>: Failed to establish a new connection: [Errno -2] Name or service not known'))")),)
_____________________ test_non_existing_simulation_ui_file _____________________
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>
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
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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):
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
host = 'scicrunch.org', port = 443, family = <AddressFamily.AF_INET: 2>
type = <SocketKind.SOCK_STREAM: 1>, proto = 0, flags = 0
def getaddrinfo(host, port, family=0, type=0, proto=0, flags=0):
"""Resolve host and port into list of address info entries.
Translate the host/port argument into a sequence of 5-tuples that contain
all the necessary arguments for creating a socket connected to that service.
host is a domain name, a string representation of an IPv4/v6 address or
None. port is a string service name such as 'http', a numeric port number or
None. By passing None as the value of host and port, you can pass NULL to
the underlying C API.
The family, type and proto arguments can be optionally specified in order to
narrow the list of addresses returned. Passing zero as a value for each of
these arguments selects the full range of results.
"""
# We override this function since we want to translate the numeric family
# and socket type values to enum constants.
addrlist = []
> for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
E socket.gaierror: [Errno -2] Name or service not known
/usr/lib/python3.9/socket.py:966: gaierror
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6942f700>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6942f700>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"query": {"term": {"pennsieve.identifier.aggregate": "137"}}}', 'headers': {'User-Agent': 'python-requests...ip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
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)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6942f700>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>
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 0x7f6a6942f2e0>: Failed to establish a new connection: [Errno -2] Name or service not known
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f6a6942f910>
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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6942f700>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
# 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 = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>: Failed to establish a new connection: [Errno -2] Name or service not known')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6942f700>
_stacktrace = <traceback object at 0x7f6a69350840>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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:238:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:1951: in full_dispatch_request
rv = self.handle_user_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:1820: in handle_user_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:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1667: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
app/main.py:701: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f6a6942f910>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6942f2e0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:519: ConnectionError
____________________ test_simulation_ui_file_old_s3_bucket _____________________
self = <urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>
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
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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):
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
host = 'scicrunch.org', port = 443, family = <AddressFamily.AF_INET: 2>
type = <SocketKind.SOCK_STREAM: 1>, proto = 0, flags = 0
def getaddrinfo(host, port, family=0, type=0, proto=0, flags=0):
"""Resolve host and port into list of address info entries.
Translate the host/port argument into a sequence of 5-tuples that contain
all the necessary arguments for creating a socket connected to that service.
host is a domain name, a string representation of an IPv4/v6 address or
None. port is a string service name such as 'http', a numeric port number or
None. By passing None as the value of host and port, you can pass NULL to
the underlying C API.
The family, type and proto arguments can be optionally specified in order to
narrow the list of addresses returned. Passing zero as a value for each of
these arguments selects the full range of results.
"""
# We override this function since we want to translate the numeric family
# and socket type values to enum constants.
addrlist = []
> for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
E socket.gaierror: [Errno -2] Name or service not known
/usr/lib/python3.9/socket.py:966: gaierror
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a53d5a070>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a53d5a070>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"query": {"term": {"pennsieve.identifier.aggregate": "135"}}}', 'headers': {'User-Agent': 'python-requests...ip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
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)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a53d5a070>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>
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 0x7f6a53f004c0>: Failed to establish a new connection: [Errno -2] Name or service not known
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f6a53d5a340>
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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a53d5a070>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
# 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 = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>: Failed to establish a new connection: [Errno -2] Name or service not known')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a53d5a070>
_stacktrace = <traceback object at 0x7f6a53c16700>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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:243:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:1951: in full_dispatch_request
rv = self.handle_user_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:1820: in handle_user_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:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1667: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
app/main.py:701: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f6a53d5a340>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a53f004c0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:519: ConnectionError
____________________ test_simulation_ui_file_new_s3_bucket _____________________
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>
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
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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):
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
host = 'scicrunch.org', port = 443, family = <AddressFamily.AF_INET: 2>
type = <SocketKind.SOCK_STREAM: 1>, proto = 0, flags = 0
def getaddrinfo(host, port, family=0, type=0, proto=0, flags=0):
"""Resolve host and port into list of address info entries.
Translate the host/port argument into a sequence of 5-tuples that contain
all the necessary arguments for creating a socket connected to that service.
host is a domain name, a string representation of an IPv4/v6 address or
None. port is a string service name such as 'http', a numeric port number or
None. By passing None as the value of host and port, you can pass NULL to
the underlying C API.
The family, type and proto arguments can be optionally specified in order to
narrow the list of addresses returned. Passing zero as a value for each of
these arguments selects the full range of results.
"""
# We override this function since we want to translate the numeric family
# and socket type values to enum constants.
addrlist = []
> for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
E socket.gaierror: [Errno -2] Name or service not known
/usr/lib/python3.9/socket.py:966: gaierror
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6896fbe0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6896fbe0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"query": {"term": {"pennsieve.identifier.aggregate": "308"}}}', 'headers': {'User-Agent': 'python-requests...ip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '62', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
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)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6896fbe0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>
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 0x7f6a6896f7f0>: Failed to establish a new connection: [Errno -2] Name or service not known
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f6a68963d90>
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,
)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6896fbe0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_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_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,
)
# 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 = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>: Failed to establish a new connection: [Errno -2] Name or service not known')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f6a6896fbe0>
_stacktrace = <traceback object at 0x7f6a53e34180>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/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:249:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:1951: in full_dispatch_request
rv = self.handle_user_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:1820: in handle_user_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:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1667: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
app/main.py:701: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f6a68963d90>
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_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6a6896f7f0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:519: ConnectionError
=============================== 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/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/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(
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; 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/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_onto_term_lookup - assert 500 == 200
FAILED tests/test_api.py::test_non_existing_simulation_ui_file - requests.exc...
FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - requests.ex...
FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - requests.ex...
====== 4 failed, 102 passed, 4 skipped, 10 warnings in 1381.48s (0:23:01) ======
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #1321 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE