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 14da5c3fd3f1c838c19adb238063dd41cce6e6d3 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 14da5c3fd3f1c838c19adb238063dd41cce6e6d3 # timeout=10 Commit message: "Merge pull request #292 from nih-sparc/add-endpoint-to-retreive-list-of-all-sparc-datasets-uuids" > git rev-list --no-walk 14da5c3fd3f1c838c19adb238063dd41cce6e6d3 # timeout=10 [SPARC-API] $ /bin/bash /tmp/jenkins17475739331830818609.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 plugins: anyio-4.9.0 collected 113 items tests/test_api.py .........................FFF.. [ 26%] tests/test_biolucida.py ............. [ 38%] tests/test_dataset_info.py .s..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_get_reva_tracing_files __________________________ subject_id = 'sub-SR005' def getRevaTracingInSituFolderChildren(subject_id): try: coordinates_folder_name = 'CoordinatesData' in_situ_folder_name = 'InSitu' primary_folder = ps2.get(f'/packages/{Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}') if not primary_folder: msg = f"Primary folder not found: {Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}" logging.error(msg) return abort(404, description=msg) primary_children = primary_folder.get('children', []) subject_child = next((child for child in primary_children if child['content']['name'] == subject_id), None) if subject_child is None: msg = f"Subject folder not found for subject id: {subject_id}" logging.error(msg) return abort(404, description=msg) subject_folder = ps2.get(f"/packages/{subject_child['content']['id']}") if not subject_folder: msg = f"Subject folder could not be fetched for id: {subject_child['content']['id']}" logging.error(msg) return abort(404, description=msg) subject_children = subject_folder.get('children', []) coordinates_child = next((child for child in subject_children if child['content']['name'] == coordinates_folder_name), None) if coordinates_child is None: msg = f"CoordinatesData folder not found for subject: {subject_id}" logging.error(msg) return abort(404, description=msg) coordinates_folder = ps2.get(f"/packages/{coordinates_child['content']['id']}") if not coordinates_folder: msg = f"CoordinatesData folder could not be fetched for id: {coordinates_child['content']['id']}" logging.error(msg) > return abort(404, description=msg) app/main.py:1033: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:772: in abort return _aborter(status, *args, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <werkzeug.exceptions.Aborter object at 0x7fee42d91480>, code = 404 args = () kwargs = {'description': 'CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171'} def __call__(self, code, *args, **kwargs): if not args and not kwargs and not isinstance(code, integer_types): raise HTTPException(response=code) if code not in self.mapping: raise LookupError("no exception for %r" % code) > raise self.mapping[code](*args, **kwargs) E werkzeug.exceptions.NotFound: 404 Not Found: CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:753: NotFound During handling of the above exception, another exception occurred: subject_id = 'sub-SR005' @app.route("/reva/tracing-files/<subject_id>", methods=["GET"]) def getRevaTracingFiles(subject_id): try: vagus_nerve_folder_name = 'VagusNerve' > in_situ_children = getRevaTracingInSituFolderChildren(subject_id) app/main.py:1092: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ app/main.py:1054: in getRevaTracingInSituFolderChildren return abort(500, description=msg) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:772: in abort return _aborter(status, *args, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <werkzeug.exceptions.Aborter object at 0x7fee42d91480>, code = 500 args = () kwargs = {'description': 'Exception thrown when getting Reva InSitu Folder: 404 Not Found: CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171'} def __call__(self, code, *args, **kwargs): if not args and not kwargs and not isinstance(code, integer_types): raise HTTPException(response=code) if code not in self.mapping: raise LookupError("no exception for %r" % code) > raise self.mapping[code](*args, **kwargs) E werkzeug.exceptions.InternalServerError: 500 Internal Server Error: Exception thrown when getting Reva InSitu Folder: 404 Not Found: CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:753: InternalServerError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_reva_tracing_files(client): > r = client.get('/reva/tracing-files/sub-SR005') tests/test_api.py:435: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../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:1114: in getRevaTracingFiles return jsonify({"status": "Error while getting tracing files: ", "message": e}), 500 ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:370: in jsonify dumps(data, indent=indent, separators=separators) + "\n", ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:211: in dumps rv = _json.dumps(obj, **kwargs) /usr/lib/python3.10/json/__init__.py:238: in dumps **kw).encode(obj) /usr/lib/python3.10/json/encoder.py:199: in encode chunks = self.iterencode(o, _one_shot=True) /usr/lib/python3.10/json/encoder.py:257: in iterencode return _iterencode(o, 0) ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:100: in default return _json.JSONEncoder.default(self, o) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <flask.json.JSONEncoder object at 0x7fee3c2eaef0> o = <InternalServerError '500: Internal Server Error'> def default(self, o): """Implement this method in a subclass such that it returns a serializable object for ``o``, or calls the base implementation (to raise a ``TypeError``). For example, to support arbitrary iterators, you could implement default like this:: def default(self, o): try: iterable = iter(o) except TypeError: pass else: return list(iterable) # Let the base class default method raise the TypeError return JSONEncoder.default(self, o) """ > raise TypeError(f'Object of type {o.__class__.__name__} ' f'is not JSON serializable') E TypeError: Object of type InternalServerError is not JSON serializable /usr/lib/python3.10/json/encoder.py:179: TypeError ------------------------------ Captured log call ------------------------------- ERROR pennsieve2.direct.client:client.py:180 HTTP error occurred: 502 Server Error: Bad Gateway for url: https://api.pennsieve.io/packages/N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 ERROR root:main.py:1032 CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 ERROR root:main.py:1053 Exception thrown when getting Reva InSitu Folder: 404 Not Found: CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 ERROR root:main.py:1113 Error while getting REVA tracing files 500 Internal Server Error: Exception thrown when getting Reva InSitu Folder: 404 Not Found: CoordinatesData folder could not be fetched for id: N:collection:dd489aa4-036e-4da4-9f0c-d2fbe67f6171 _________________________ test_get_reva_micro_ct_files _________________________ subject_id = 'sub-SR005' @app.route("/reva/micro-ct-files/<subject_id>", methods=["GET"]) def getRevaMicroCtFiles(subject_id): micro_ct_visualization_folder_name = f'{subject_id}-MicroCTVisualization' try: primary_folder = ps2.get(f'/packages/{Config.REVA_MICRO_CT_PRIMARY_FOLDER_COLLECTION_ID}') > primary_children = primary_folder['children'] E TypeError: 'NoneType' object is not subscriptable app/main.py:1123: TypeError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_reva_micro_ct_files(client): > r = client.get('/reva/micro-ct-files/sub-SR005') tests/test_api.py:442: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../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:1151: in getRevaMicroCtFiles return jsonify({"status": "Error while getting microCT files: ", "message": e}), 500 ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:370: in jsonify dumps(data, indent=indent, separators=separators) + "\n", ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:211: in dumps rv = _json.dumps(obj, **kwargs) /usr/lib/python3.10/json/__init__.py:238: in dumps **kw).encode(obj) /usr/lib/python3.10/json/encoder.py:199: in encode chunks = self.iterencode(o, _one_shot=True) /usr/lib/python3.10/json/encoder.py:257: in iterencode return _iterencode(o, 0) ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:100: in default return _json.JSONEncoder.default(self, o) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <flask.json.JSONEncoder object at 0x7fee2c5a32b0> o = TypeError("'NoneType' object is not subscriptable") def default(self, o): """Implement this method in a subclass such that it returns a serializable object for ``o``, or calls the base implementation (to raise a ``TypeError``). For example, to support arbitrary iterators, you could implement default like this:: def default(self, o): try: iterable = iter(o) except TypeError: pass else: return list(iterable) # Let the base class default method raise the TypeError return JSONEncoder.default(self, o) """ > raise TypeError(f'Object of type {o.__class__.__name__} ' f'is not JSON serializable') E TypeError: Object of type TypeError is not JSON serializable /usr/lib/python3.10/json/encoder.py:179: TypeError ------------------------------ Captured log call ------------------------------- ERROR pennsieve2.direct.client:client.py:180 HTTP error occurred: 502 Server Error: Bad Gateway for url: https://api.pennsieve.io/packages/N:collection:e3717c9c-7f78-4b35-8a75-a5dc05f99ae0 ERROR root:main.py:1150 Error while getting REVA microCT files 'NoneType' object is not subscriptable ________________________ test_get_reva_landmarks_files _________________________ subject_id = 'sub-SR005' def getRevaTracingInSituFolderChildren(subject_id): try: coordinates_folder_name = 'CoordinatesData' in_situ_folder_name = 'InSitu' primary_folder = ps2.get(f'/packages/{Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}') if not primary_folder: msg = f"Primary folder not found: {Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}" logging.error(msg) return abort(404, description=msg) primary_children = primary_folder.get('children', []) subject_child = next((child for child in primary_children if child['content']['name'] == subject_id), None) if subject_child is None: msg = f"Subject folder not found for subject id: {subject_id}" logging.error(msg) return abort(404, description=msg) subject_folder = ps2.get(f"/packages/{subject_child['content']['id']}") if not subject_folder: msg = f"Subject folder could not be fetched for id: {subject_child['content']['id']}" logging.error(msg) > return abort(404, description=msg) app/main.py:1020: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:772: in abort return _aborter(status, *args, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <werkzeug.exceptions.Aborter object at 0x7fee42d91480>, code = 404 args = () kwargs = {'description': 'Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc'} def __call__(self, code, *args, **kwargs): if not args and not kwargs and not isinstance(code, integer_types): raise HTTPException(response=code) if code not in self.mapping: raise LookupError("no exception for %r" % code) > raise self.mapping[code](*args, **kwargs) E werkzeug.exceptions.NotFound: 404 Not Found: Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:753: NotFound During handling of the above exception, another exception occurred: subject_id = 'sub-SR005' @app.route("/reva/anatomical-landmarks-files/<subject_id>", methods=["GET"]) def getRevaAnatomicalLandmarksFiles(subject_id): try: anatomical_landmarks_folder_name = 'AnatomicalLandmarks' > in_situ_children = getRevaTracingInSituFolderChildren(subject_id) app/main.py:1061: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ app/main.py:1054: in getRevaTracingInSituFolderChildren return abort(500, description=msg) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:772: in abort return _aborter(status, *args, **kwargs) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <werkzeug.exceptions.Aborter object at 0x7fee42d91480>, code = 500 args = () kwargs = {'description': 'Exception thrown when getting Reva InSitu Folder: 404 Not Found: Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc'} def __call__(self, code, *args, **kwargs): if not args and not kwargs and not isinstance(code, integer_types): raise HTTPException(response=code) if code not in self.mapping: raise LookupError("no exception for %r" % code) > raise self.mapping[code](*args, **kwargs) E werkzeug.exceptions.InternalServerError: 500 Internal Server Error: Exception thrown when getting Reva InSitu Folder: 404 Not Found: Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/exceptions.py:753: InternalServerError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_reva_landmarks_files(client): > r = client.get('/reva/anatomical-landmarks-files/sub-SR005') tests/test_api.py:449: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../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:1085: in getRevaAnatomicalLandmarksFiles return jsonify({"status": "Error while getting anatomical landmarks files: ", "message": e}), 500 ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:370: in jsonify dumps(data, indent=indent, separators=separators) + "\n", ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:211: in dumps rv = _json.dumps(obj, **kwargs) /usr/lib/python3.10/json/__init__.py:238: in dumps **kw).encode(obj) /usr/lib/python3.10/json/encoder.py:199: in encode chunks = self.iterencode(o, _one_shot=True) /usr/lib/python3.10/json/encoder.py:257: in iterencode return _iterencode(o, 0) ../../../python3.10.venv/lib/python3.10/site-packages/flask/json/__init__.py:100: in default return _json.JSONEncoder.default(self, o) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <flask.json.JSONEncoder object at 0x7fee2d793b50> o = <InternalServerError '500: Internal Server Error'> def default(self, o): """Implement this method in a subclass such that it returns a serializable object for ``o``, or calls the base implementation (to raise a ``TypeError``). For example, to support arbitrary iterators, you could implement default like this:: def default(self, o): try: iterable = iter(o) except TypeError: pass else: return list(iterable) # Let the base class default method raise the TypeError return JSONEncoder.default(self, o) """ > raise TypeError(f'Object of type {o.__class__.__name__} ' f'is not JSON serializable') E TypeError: Object of type InternalServerError is not JSON serializable /usr/lib/python3.10/json/encoder.py:179: TypeError ------------------------------ Captured log call ------------------------------- ERROR pennsieve2.direct.client:client.py:180 HTTP error occurred: 502 Server Error: Bad Gateway for url: https://api.pennsieve.io/packages/N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc ERROR root:main.py:1019 Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc ERROR root:main.py:1053 Exception thrown when getting Reva InSitu Folder: 404 Not Found: Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc ERROR root:main.py:1084 Error while getting REVA anatomical landmarks files 500 Internal Server Error: Exception thrown when getting Reva InSitu Folder: 404 Not Found: Subject folder could not be fetched for id: N:collection:8bb5dac9-3bcd-488b-a5f8-3221564e18dc =============================== 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/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: 33 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: 37 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/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_get_reva_tracing_files - TypeError: Object of type InternalServerError is not JSON serializable FAILED tests/test_api.py::test_get_reva_micro_ct_files - TypeError: Object of type TypeError is not JSON serializable FAILED tests/test_api.py::test_get_reva_landmarks_files - TypeError: Object of type InternalServerError is not JSON serializable ====== 3 failed, 106 passed, 4 skipped, 243 warnings in 186.45s (0:03:06) ====== Build step 'Execute shell' marked build as failure [Slack Notifications] found #1588 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE