Started by timer
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-API-DEV
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] Done
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/nih-sparc/sparc-api.git
> git init /home/cmiss/Jenkins/workspace/SPARC-API-DEV # timeout=10
Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git
> git --version # timeout=10
> git --version # 'git version 2.25.1'
> git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10
> git config remote.origin.url https://github.com/nih-sparc/sparc-api.git # timeout=10
> git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
> git rev-parse refs/remotes/origin/master^{commit} # timeout=10
Checking out Revision 5811603cf0fd89bceac76a035f181d268445a7bf (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 5811603cf0fd89bceac76a035f181d268445a7bf # timeout=10
Commit message: "Merge pull request #290 from nih-sparc/updating-to-mailersend"
> git rev-list --no-walk 5811603cf0fd89bceac76a035f181d268445a7bf # timeout=10
[SPARC-API-DEV] $ /bin/bash /tmp/jenkins4815904977858651867.sh
Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (2.6.2)
Requirement already satisfied: api==0.0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.7)
Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (3.7.0)
Requirement already satisfied: boto3==1.26 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.26.0)
Requirement already satisfied: botocore==1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 5)) (1.29.0)
Requirement already satisfied: certifi==2023.5.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 6)) (2023.5.7)
Requirement already satisfied: chardet==3.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 7)) (3.0.4)
Collecting Click==7.1.2 (from -r requirements.txt (line 8))
Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB)
Requirement already satisfied: contentful==1.13.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 9)) (1.13.1)
Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 10)) (2.11.0)
Requirement already satisfied: docutils==0.15.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 11)) (0.15.2)
Requirement already satisfied: Flask==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 12)) (1.1.1)
Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 13)) (2.3.0)
Requirement already satisfied: Flask-Cors==3.0.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 14)) (3.0.8)
Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 15)) (0.10.1)
Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 16)) (2.52.0)
Requirement already satisfied: gspread==6.2.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 17)) (6.2.1)
Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 18)) (20.0.4)
Requirement already satisfied: httpx>=0.27.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 19)) (0.28.1)
Requirement already satisfied: hubspot-api-client==9.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 20)) (9.0.0)
Requirement already satisfied: idna==2.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 21)) (2.8)
Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 22)) (1.1.0)
Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 23)) (2.11.3)
Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 24)) (0.9.4)
Requirement already satisfied: mailersend==0.5.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 25)) (0.5.8)
Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 26)) (1.1.1)
Requirement already satisfied: markdown==3.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 27)) (3.8)
Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 28)) (3.2.2)
Requirement already satisfied: nose==1.3.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 29)) (1.3.7)
Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 30)) (4.1.3)
Requirement already satisfied: osparc==0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 31)) (0.4.3)
Requirement already satisfied: Pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 32)) (6.1.1)
Requirement already satisfied: Pennsieve2==0.1.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 33)) (0.1.2)
Requirement already satisfied: Pillow in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 34)) (11.2.1)
Requirement already satisfied: psycopg2-binary==2.9.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 35)) (2.9.10)
Requirement already satisfied: public==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 36)) (2019.4.13)
Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 37)) (8.4.1)
Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 38)) (3.8.0)
Requirement already satisfied: python-dateutil==2.8.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 39)) (2.8.2)
Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 40)) (0.10.3)
Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 41)) (2019.4.13)
Requirement already satisfied: requests==2.31.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 42)) (2.31.0)
Requirement already satisfied: s3transfer==0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 43)) (0.6.0)
Requirement already satisfied: six==1.13.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 44)) (1.13.0)
Requirement already satisfied: SQLAlchemy==2.0.40 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 45)) (2.0.40)
Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 46)) (1.26.4)
Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 47)) (0.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests==2.31.0->-r requirements.txt (line 42)) (3.4.2)
Requirement already satisfied: setuptools>=0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (80.3.1)
Requirement already satisfied: pytz in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2025.2)
Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2.1)
Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Flask-Caching==2.3.0->-r requirements.txt (line 13)) (0.9.0)
Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.22.0)
Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.40.0)
Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.2.0)
Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.25.0rc0)
Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (4.1.1)
Requirement already satisfied: google-auth-oauthlib>=0.4.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from gspread==6.2.1->-r requirements.txt (line 17)) (1.2.2)
Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 30)) (0.6.1)
Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 30)) (0.4.2)
Requirement already satisfied: rsa>=3.1.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 30)) (4.0)
Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (7.2.0)
Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (1.2.18)
Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (1.0.0)
Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (3.0.5)
Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (4.25.7)
Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (3.2.0)
Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (3.0.4)
Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (1.8.0)
Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (0.6.2)
Requirement already satisfied: psutil>=5.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 32)) (7.0.0)
Requirement already satisfied: grpcio<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 33)) (1.71.0)
Requirement already satisfied: grpcio_tools<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 33)) (1.62.3)
Requirement already satisfied: pyjwt<3.0,>=2.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 33)) (2.10.1)
Requirement already satisfied: tqdm<5.0,>=4.64 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 33)) (4.67.1)
Requirement already satisfied: greenlet>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 45)) (3.2.1)
Requirement already satisfied: typing-extensions>=4.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 45)) (4.13.2)
Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->Pennsieve==6.1.1->-r requirements.txt (line 32)) (0.14.1)
Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.70.0)
Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.26.1)
Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (5.5.2)
Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (3.2.3)
Requirement already satisfied: anyio in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 19)) (4.9.0)
Requirement already satisfied: httpcore==1.* in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 19)) (1.0.9)
Requirement already satisfied: h11>=0.16 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpcore==1.*->httpx>=0.27.0->-r requirements.txt (line 19)) (0.16.0)
Requirement already satisfied: exceptiongroup>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (1.2.2)
Requirement already satisfied: iniconfig>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (2.1.0)
Requirement already satisfied: packaging>=20 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (25.0)
Requirement already satisfied: pluggy<2,>=1.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (1.6.0)
Requirement already satisfied: pygments>=2.7.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (2.19.1)
Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 37)) (2.2.1)
Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from deprecated>=1.2.0->Pennsieve==6.1.1->-r requirements.txt (line 32)) (1.17.2)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-auth-oauthlib>=0.4.1->gspread==6.2.1->-r requirements.txt (line 17)) (2.0.0)
Requirement already satisfied: oauthlib>=3.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib>=0.4.1->gspread==6.2.1->-r requirements.txt (line 17)) (3.3.1)
Requirement already satisfied: sniffio>=1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from anyio->httpx>=0.27.0->-r requirements.txt (line 19)) (1.3.1)
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Installing collected packages: Click
Attempting uninstall: Click
Found existing installation: click 8.2.1
Uninstalling click-8.2.1:
Successfully uninstalled click-8.2.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
black 25.1.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible.
Successfully installed Click-7.1.2
[notice] A new release of pip is available: 25.1.1 -> 25.2
[notice] To update, run: pip install --upgrade pip
Collecting pytest==5.4.3 (from -r requirements-dev.txt (line 1))
Using cached pytest-5.4.3-py3-none-any.whl.metadata (7.3 kB)
Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1)
Requirement already satisfied: black in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 3)) (25.1.0)
Requirement already satisfied: isort in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 4)) (6.0.1)
Requirement already satisfied: nose in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7)
Requirement already satisfied: packaging in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 6)) (25.0)
Requirement already satisfied: py>=1.5.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (1.11.0)
Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (25.3.0)
Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.7.0)
Collecting pluggy<1.0,>=0.12 (from pytest==5.4.3->-r requirements-dev.txt (line 1))
Using cached pluggy-0.13.1-py2.py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: wcwidth in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.13)
Requirement already satisfied: boto3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.0)
Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (7.2.0)
Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.18)
Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.0.0)
Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.5)
Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.25.7)
Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.2.0)
Requirement already satisfied: pytz>=2016 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2025.2)
Requirement already satisfied: requests>=2.18 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.31.0)
Requirement already satisfied: rsa==4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.0)
Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.4)
Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.8.0)
Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.2)
Requirement already satisfied: psutil>=5.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (7.0.0)
Requirement already satisfied: python-dateutil>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8.2)
Requirement already satisfied: six<2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.13.0)
Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.14.1)
Requirement already satisfied: pyasn1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.1)
Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3))
Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB)
Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (1.1.0)
Requirement already satisfied: pathspec>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (0.12.1)
Requirement already satisfied: platformdirs>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.3.7)
Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (2.2.1)
Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.13.2)
Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.17.2)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.4.2)
Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/python3.10.venv/lib/python3.10/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/python3.10.venv/lib/python3.10/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/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2023.5.7)
Requirement already satisfied: botocore<1.30.0,>=1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.29.0)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.9.4)
Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.0)
Using cached pytest-5.4.3-py3-none-any.whl (248 kB)
Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Using cached click-8.2.1-py3-none-any.whl (102 kB)
Installing collected packages: pluggy, click, pytest
Attempting uninstall: pluggy
Found existing installation: pluggy 1.6.0
Uninstalling pluggy-1.6.0:
Successfully uninstalled pluggy-1.6.0
Attempting uninstall: click
Found existing installation: click 7.1.2
Uninstalling click-7.1.2:
Successfully uninstalled click-7.1.2
Attempting uninstall: pytest
Found existing installation: pytest 8.4.1
Uninstalling pytest-8.4.1:
Successfully uninstalled pytest-8.4.1
Successfully installed click-8.2.1 pluggy-0.13.1 pytest-5.4.3
[notice] A new release of pip is available: 25.1.1 -> 25.2
[notice] To update, run: pip install --upgrade pip
Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (5.4.3)
Collecting pytest
Using cached pytest-8.4.1-py3-none-any.whl.metadata (7.7 kB)
Requirement already satisfied: exceptiongroup>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (1.2.2)
Requirement already satisfied: iniconfig>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.1.0)
Requirement already satisfied: packaging>=20 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (25.0)
Collecting pluggy<2,>=1.5 (from pytest)
Using cached pluggy-1.6.0-py3-none-any.whl.metadata (4.8 kB)
Requirement already satisfied: pygments>=2.7.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.19.1)
Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.2.1)
Using cached pytest-8.4.1-py3-none-any.whl (365 kB)
Using cached pluggy-1.6.0-py3-none-any.whl (20 kB)
Installing collected packages: pluggy, pytest
Attempting uninstall: pluggy
Found existing installation: pluggy 0.13.1
Uninstalling pluggy-0.13.1:
Successfully uninstalled pluggy-0.13.1
Attempting uninstall: pytest
Found existing installation: pytest 5.4.3
Uninstalling pytest-5.4.3:
Successfully uninstalled pytest-5.4.3
Successfully installed pluggy-1.6.0 pytest-8.4.1
[notice] A new release of pip is available: 25.1.1 -> 25.2
[notice] To update, run: pip install --upgrade pip
============================= test session starts ==============================
platform linux -- Python 3.10.18, pytest-8.4.1, pluggy-1.6.0
rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV
plugins: anyio-4.9.0
collected 113 items
tests/test_api.py F............................. [ 26%]
tests/test_biolucida.py ............. [ 38%]
tests/test_dataset_info.py Fs..ss..... [ 47%]
tests/test_health.py . [ 48%]
tests/test_osparc.py .............. [ 61%]
tests/test_plot.py . [ 61%]
tests/test_pmr.py ......... [ 69%]
tests/test_scicrunch.py .................s.......... [ 94%]
tests/test_segmentation_info.py .. [ 96%]
tests/test_thumbnails.py ... [ 99%]
tests/test_update_contentful_entries.py . [100%]
=================================== FAILURES ===================================
_____________________ test_direct_download_url_small_file ______________________
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f27baeca140>
conn = <urllib3.connection.HTTPSConnection object at 0x7f27baecaa40>
method = 'GET'
url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward'
timeout = Timeout(connect=1, read=1, total=None), chunked = False
httplib_request_kw = {'body': None, 'headers': {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip', 'Accept': '*/*', 'Connec... 'application/vnd.contentful.delivery.v1+json', 'Authorization': 'Bearer nsC2KAKBhQ3V4ztr3YciVqLEirmNoFuPDrulvW0eO6Q'}}
timeout_obj = Timeout(connect=1, read=1, total=None), read_timeout = 1
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = timeout_obj.connect_timeout
# Trigger any extra validation we need to do.
try:
self._validate_conn(conn)
except (SocketTimeout, BaseSSLError) as e:
# Py2 raises this as a BaseSSLError, Py3 raises it as socket timeout.
self._raise_timeout(err=e, url=url, timeout_value=conn.timeout)
raise
# conn.request() calls http.client.*.request, not the method in
# urllib3.request. It also calls makefile (recv) on the socket.
try:
if chunked:
conn.request_chunked(method, url, **httplib_request_kw)
else:
conn.request(method, url, **httplib_request_kw)
# We are swallowing BrokenPipeError (errno.EPIPE) since the server is
# legitimately able to close the connection after sending a valid response.
# With this behaviour, the received response is still readable.
except BrokenPipeError:
# Python 3
pass
except IOError as e:
# Python 2 and macOS/Linux
# EPIPE and ESHUTDOWN are BrokenPipeError on Python 2, and EPROTOTYPE is needed on macOS
# https://erickt.github.io/blog/2014/11/19/adventures-in-debugging-a-potential-osx-kernel-bug/
if e.errno not in {
errno.EPIPE,
errno.ESHUTDOWN,
errno.EPROTOTYPE,
}:
raise
# Reset the timeout for the recv() on the socket
read_timeout = timeout_obj.read_timeout
# App Engine doesn't have a sock attr
if getattr(conn, "sock", None):
# In Python 3 socket.py will catch EAGAIN and return None when you
# try and read into the file pointer created by http.client, which
# instead raises a BadStatusLine exception. Instead of catching
# the exception and assuming all BadStatusLine exceptions are read
# timeouts, check for a zero timeout before making the request.
if read_timeout == 0:
raise ReadTimeoutError(
self, url, "Read timed out. (read timeout=%s)" % read_timeout
)
if read_timeout is Timeout.DEFAULT_TIMEOUT:
conn.sock.settimeout(socket.getdefaulttimeout())
else: # None or a value
conn.sock.settimeout(read_timeout)
# Receive the response from the server
try:
try:
# Python 2.7, use buffering of HTTP responses
httplib_response = conn.getresponse(buffering=True)
except TypeError:
# Python 3
try:
httplib_response = conn.getresponse()
except BaseException as e:
# Remove the TypeError from the exception chain in
# Python 3 (including for exceptions like SystemExit).
# Otherwise it looks like a bug in the code.
> six.raise_from(e, None)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:445:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:440: in _make_request
httplib_response = conn.getresponse()
/usr/lib/python3.10/http/client.py:1375: in getresponse
response.begin()
/usr/lib/python3.10/http/client.py:318: in begin
version, status, reason = self._read_status()
/usr/lib/python3.10/http/client.py:279: in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
/usr/lib/python3.10/socket.py:717: in readinto
return self._sock.recv_into(b)
/usr/lib/python3.10/ssl.py:1307: in recv_into
return self.read(nbytes, buffer)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <ssl.SSLSocket [closed] fd=-1, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6>
len = 8192, buffer = <memory at 0x7f27c2c2fb80>
def read(self, len=1024, buffer=None):
"""Read up to LEN bytes and return them.
Return zero-length string on EOF."""
self._checkClosed()
if self._sslobj is None:
raise ValueError("Read on closed or unwrapped SSL socket.")
try:
if buffer is not None:
> return self._sslobj.read(len, buffer)
E TimeoutError: The read operation timed out
/usr/lib/python3.10/ssl.py:1163: TimeoutError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f27baec83a0>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=1, read=1, total=None), verify = True, cert = None
proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen
retries = retries.increment(
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:532: in increment
raise six.reraise(type(error), error, _stacktrace)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/packages/six.py:735: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699: in urlopen
httplib_response = self._make_request(
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:447: in _make_request
self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f27baeca140>
err = TimeoutError('The read operation timed out')
url = '/spaces/6bya4tyw8399/environments/master/entries?content_type=sparcAward'
timeout_value = 1
def _raise_timeout(self, err, url, timeout_value):
"""Is the error actually a timeout? Will raise a ReadTimeout or pass"""
if isinstance(err, SocketTimeout):
> raise ReadTimeoutError(
self, url, "Read timed out. (read timeout=%s)" % timeout_value
)
E urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:336: ReadTimeoutError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_direct_download_url_small_file(client):
small_s3_file = '217/files/derivative/brainstem_pig_metadata.json'
> r = client.get(f"/s3-resource/{small_s3_file}?s3BucketName=prd-sparc-discover50-use1")
tests/test_api.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1944: in full_dispatch_request
self.try_trigger_before_first_request_functions()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1992: in try_trigger_before_first_request_functions
func()
app/main.py:259: in get_metrics
cf_response = get_funded_projects_count(contentful)
app/metrics/contentful.py:45: in get_funded_projects_count
response = client.entries({
../../../python3.10.venv/lib/python3.10/site-packages/contentful/client.py:262: in entries
return self._get(
../../../python3.10.venv/lib/python3.10/site-packages/contentful/client.py:567: in _get
response = retry_request(self)(self._http_get)(url, query=query)
../../../python3.10.venv/lib/python3.10/site-packages/contentful/utils.py:163: in wrapper
return http_call(url, query)
../../../python3.10.venv/lib/python3.10/site-packages/contentful/client.py:547: in _http_get
response = requests.get(
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f27baec83a0>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=1, read=1, total=None), verify = True, cert = None
proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
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)
except ClosedPoolError as e:
raise ConnectionError(e, request=request)
except _ProxyError as e:
raise ProxyError(e)
except (_SSLError, _HTTPError) as e:
if isinstance(e, _SSLError):
# This branch is for urllib3 versions earlier than v1.22
raise SSLError(e, request=request)
elif isinstance(e, ReadTimeoutError):
> raise ReadTimeout(e, request=request)
E requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:532: ReadTimeout
----------------------------- Captured stdout call -----------------------------
Error while setting featured dataset id: Method not allowed with this API key
____________________________ test_current_doi_list _____________________________
self = <Response [504]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f27c82909d0>
s = '<html>\r\n<head><title>504 Gateway Time-out</title></head>\r\n<body>\r\n<center><h1>504 Gateway Time-out</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n'
idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_current_doi_list(client):
doi_stem = "doi:"
start = timer()
> r = client.get('/current_doi_list')
tests/test_dataset_info.py:23:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:730: in get_all_doi
results = reform_aggregation_results(dataset_search(query))
app/main.py:748: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [504]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
=============================== warnings summary ===============================
../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution, DistributionNotFound
../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
DESCRIPTOR = _descriptor.FileDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_CACHESEGMENT = _descriptor.Descriptor(
app/dbtable.py:12
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 3 warnings
tests/test_api.py: 36 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 6 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 34 warnings
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated
context = SSLContext(ssl_version or PROTOCOL_TLS)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 3 warnings
tests/test_api.py: 41 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 7 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 35 warnings
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated
match_hostname(cert, asserted_hostname)
../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
tests/test_health.py::test_request_response
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead.
assert_equals("healthy", json_response.get("status"))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_api.py::test_direct_download_url_small_file - requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='preview.contentful.com', port=443): Read timed out. (read timeout=1)
FAILED tests/test_dataset_info.py::test_current_doi_list - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
====== 2 failed, 107 passed, 4 skipped, 250 warnings in 927.99s (0:15:27) ======
Build step 'Execute shell' marked build as failure
[Slack Notifications] found #1356 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE