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Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-API [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] Done The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/nih-sparc/sparc-api.git > git init /home/cmiss/Jenkins/workspace/SPARC-API # timeout=10 Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/nih-sparc/sparc-api.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision 92353e82a7f0ea7ee583bd7bbb90e552612a9f12 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 92353e82a7f0ea7ee583bd7bbb90e552612a9f12 # timeout=10 Commit message: "Merge pull request #284 from nih-sparc/fix-failing-api-test" > git rev-list --no-walk 359c0e2db1c863a4e386be3d6364520334321ae5 # timeout=10 [SPARC-API] $ /bin/bash /tmp/jenkins18016979298115878776.sh Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (2.6.2) Requirement already satisfied: api==0.0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.7) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (3.7.0) Requirement already satisfied: boto3==1.26 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.26.0) Requirement already satisfied: botocore==1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 5)) (1.29.0) Requirement already satisfied: certifi==2023.5.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 6)) (2023.5.7) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 7)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 8)) Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 9)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 10)) (2.11.0) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 11)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 12)) (1.1.1) Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 13)) (2.3.0) Requirement already satisfied: Flask-Cors==3.0.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 14)) (3.0.8) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 15)) (0.10.1) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 16)) (2.52.0) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 17)) (20.0.4) Requirement already satisfied: httpx>=0.27.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 18)) (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 19)) (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 20)) (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 21)) (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 22)) (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 23)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 24)) (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 25)) (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 26)) (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 27)) (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 28)) (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 29)) (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 30)) (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 31)) (0.1.2) Requirement already satisfied: Pillow in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 32)) (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 33)) (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 34)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 35)) (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 36)) (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 37)) (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 38)) (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 39)) (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 40)) (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 41)) (0.6.0) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 42)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 43)) (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 44)) (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 45)) (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 46)) (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 40)) (3.4.2) Requirement already satisfied: setuptools>=0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (80.3.1) Requirement already satisfied: pytz in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2025.2) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2.1) Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Flask-Caching==2.3.0->-r requirements.txt (line 13)) (0.9.0) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.40.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.2.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.25.0rc0) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 28)) (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 28)) (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 28)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 30)) (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 31)) (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 31)) (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 31)) (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 31)) (4.67.1) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 42)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 42)) (2.2.0) Requirement already satisfied: greenlet>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 44)) (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 44)) (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 30)) (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 18)) (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 18)) (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 18)) (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 35)) (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 35)) (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 35)) (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 35)) (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 35)) (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 35)) (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 30)) (1.17.2) 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 18)) (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 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 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 ============================= test session starts ============================== platform linux -- Python 3.10.18, pytest-8.4.1, pluggy-1.6.0 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API plugins: anyio-4.9.0 collected 122 items tests/test_api.py .............................. [ 24%] tests/test_biolucida.py ............. [ 35%] tests/test_dataset_info.py .s..ss..... [ 44%] tests/test_health.py . [ 45%] tests/test_monthly_stats.py ......... [ 52%] tests/test_osparc.py .............. [ 63%] tests/test_plot.py . [ 64%] tests/test_pmr.py ......... [ 72%] tests/test_scicrunch.py .................s.....F.... [ 95%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== ____________________________ test_get_related_terms ____________________________ self = <Response [502]>, 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 0x7f0147675cf0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</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: query = 'UBERON:0002084' @app.route("/get-related-terms/<query>") def get_related_terms(query): payload = { 'direction': request.args.get('direction', default='OUTGOING'), 'relationshipType': request.args.get('relationshipType', default='BFO:0000050'), 'entail': request.args.get('entail', default='true'), 'api_key': Config.KNOWLEDGEBASE_KEY } result = {} try: response = requests.get( f'{Config.SCI_CRUNCH_SCIGRAPH_HOST}/graph/neighbors/{query}', params=payload) > result = reform_related_terms(response.json()) app/main.py:2209: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Response [502]>, 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 During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_related_terms(client): # Test if we can get the uberon term of heart using the uberon term # of left ventricle > r = client.get('/get-related-terms/UBERON:0002084') tests/test_scicrunch.py:484: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:2211: in get_related_terms logging.error(f"Failed getting related terms with payload {payload}", ex) /usr/lib/python3.10/logging/__init__.py:2105: in error root.error(msg, *args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1506: in error self._log(ERROR, msg, args, **kwargs) /usr/lib/python3.10/logging/__init__.py:1624: in _log self.handle(record) /usr/lib/python3.10/logging/__init__.py:1634: in handle self.callHandlers(record) /usr/lib/python3.10/logging/__init__.py:1696: in callHandlers hdlr.handle(record) /usr/lib/python3.10/logging/__init__.py:968: in handle self.emit(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:384: in emit super().emit(record) /usr/lib/python3.10/logging/__init__.py:1108: in emit self.handleError(record) /usr/lib/python3.10/logging/__init__.py:1100: in emit msg = self.format(record) /usr/lib/python3.10/logging/__init__.py:943: in format return fmt.format(record) ../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:137: in format return super().format(record) /usr/lib/python3.10/logging/__init__.py:678: in format record.message = record.getMessage() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API/app/main.py, 2211, "Failed getting related terms with pa...ion': 'OUTGOING', 'relationshipType': 'BFO:0000050', 'entail': 'true', 'api_key': 'xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'}"> def getMessage(self): """ Return the message for this LogRecord. Return the message for this LogRecord after merging any user-supplied arguments with the message. """ msg = str(self.msg) if self.args: > msg = msg % self.args E TypeError: not all arguments converted during string formatting /usr/lib/python3.10/logging/__init__.py:368: TypeError =============================== warnings summary =============================== scripts/monthly_db.py:9 /home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) base = declarative_base() ../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution, DistributionNotFound ../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. DESCRIPTOR = _descriptor.FileDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _CACHESEGMENT = _descriptor.Descriptor( app/dbtable.py:12 /home/cmiss/Jenkins/workspace/SPARC-API/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: 2 warnings tests/test_api.py: 34 warnings tests/test_biolucida.py: 13 warnings tests/test_dataset_info.py: 6 warnings tests/test_monthly_stats.py: 11 warnings tests/test_osparc.py: 15 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: 2 warnings tests/test_api.py: 38 warnings tests/test_biolucida.py: 13 warnings tests/test_dataset_info.py: 7 warnings tests/test_monthly_stats.py: 14 warnings tests/test_osparc.py: 15 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/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_scicrunch.py::test_get_related_terms - TypeError: not all arguments converted during string formatting ====== 1 failed, 117 passed, 4 skipped, 265 warnings in 325.13s (0:05:25) ====== Build step 'Execute shell' marked build as failure [Slack Notifications] found #1523 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE