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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-DEV [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] Done The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/nih-sparc/sparc-api.git > git init /home/cmiss/Jenkins/workspace/SPARC-API-DEV # timeout=10 Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/nih-sparc/sparc-api.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision 35fdd332328cde19d9e7555c4f3ee1f71109327f (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 35fdd332328cde19d9e7555c4f3ee1f71109327f # timeout=10 Commit message: "Merge pull request #258 from nih-sparc/fix-failing-test" > git rev-list --no-walk 35fdd332328cde19d9e7555c4f3ee1f71109327f # timeout=10 [SPARC-API-DEV] $ /bin/sh -xe /tmp/shiningpanda15714463838346761214.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/SPARC-API-DEV + export SCICRUNCH_HOST=https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_dev + export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python + pip install -r requirements.txt Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (2.6.2) Requirement already satisfied: api==0.0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (0.0.7) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (3.7.0) Requirement already satisfied: boto3==1.26 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.26.0) Requirement already satisfied: botocore==1.29.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.29.0) Requirement already satisfied: certifi==2023.5.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (2023.5.7) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.11.0) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (1.1.1) Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (2.3.0) Requirement already satisfied: Flask-Cors==3.0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (3.0.8) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (0.10.1) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (2.52.0) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (20.0.4) Requirement already satisfied: hubspot-api-client==9.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (9.0.0) Requirement already satisfied: idna==2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (1.1.1) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (1.3.7) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (4.1.3) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (0.4.3) Requirement already satisfied: Pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (6.1.1) Requirement already satisfied: Pennsieve2==0.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (0.1.2) Requirement already satisfied: Pillow in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (11.1.0) Requirement already satisfied: psycopg2-binary==2.9.9 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (2.9.9) Requirement already satisfied: public==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (5.4.3) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (2.8.2) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2019.4.13) Requirement already satisfied: requests==2.31.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (2.31.0) Requirement already satisfied: s3transfer==0.6.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (0.6.0) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (1.13.0) Requirement already satisfied: SQLAlchemy==1.3.20 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 42)) (1.3.20) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 43)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 44)) (0.16.0) Requirement already satisfied: setuptools>=0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (78.1.0) Requirement already satisfied: pytz in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2025.2) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.38.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.24.2) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 26)) (0.6.1) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 26)) (0.4.2) Requirement already satisfied: rsa>=3.1.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 26)) (4.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (7.2.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (1.2.18) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (4.25.6) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (3.2.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (3.0.4) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 28)) (7.0.0) Requirement already satisfied: grpcio<2.0,>=1.51 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 29)) (1.71.0) Requirement already satisfied: grpcio_tools<2.0,>=1.51 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 29)) (1.62.3) Requirement already satisfied: pyjwt<3.0,>=2.6 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 29)) (2.10.1) Requirement already satisfied: tqdm<5.0,>=4.64 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 29)) (4.67.1) Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests==2.31.0->-r requirements.txt (line 38)) (3.4.1) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 40)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 40)) (2.2.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->Pennsieve==6.1.1->-r requirements.txt (line 28)) (0.14.1) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (1.11.0) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (24.2) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (25.3.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (10.6.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 33)) (0.2.13) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from deprecated>=1.2.0->Pennsieve==6.1.1->-r requirements.txt (line 28)) (1.17.2) Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.69.2) Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.26.1) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (3.2.3) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.1.8 Uninstalling click-8.1.8: Successfully uninstalled click-8.1.8 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 + pip install -r requirements-dev.txt Requirement already satisfied: pytest==5.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 1)) (5.4.3) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1) Requirement already satisfied: black in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (25.1.0) Requirement already satisfied: isort in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 4)) (6.0.1) Requirement already satisfied: nose in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 6)) (24.2) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (1.11.0) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.6.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.13) Requirement already satisfied: boto3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.25.6) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2025.2) Requirement already satisfied: requests>=2.18 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.31.0) Requirement already satisfied: rsa==4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8.2) Requirement already satisfied: six<2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.13.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.14.1) Requirement already satisfied: pyasn1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.1) Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3)) Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB) Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (1.0.0) Requirement already satisfied: pathspec>=0.9.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (0.12.1) Requirement already satisfied: platformdirs>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.3.7) Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (2.2.1) Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.13.2) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.4.1) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.4) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2023.5.7) Requirement already satisfied: botocore<1.30.0,>=1.29.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.9.4) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.0) Using cached click-8.1.8-py3-none-any.whl (98 kB) Installing collected packages: click Attempting uninstall: click Found existing installation: click 7.1.2 Uninstalling click-7.1.2: Successfully uninstalled click-7.1.2 Successfully installed click-8.1.8 + pytest ============================= test session starts ============================== platform linux -- Python 3.9.22, pytest-5.4.3, py-1.11.0, pluggy-0.13.1 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV collected 116 items tests/test_api.py .......................FF [ 21%] tests/test_biolucida.py ............. [ 32%] tests/test_dataset_info.py .s..ss..... [ 42%] tests/test_health.py . [ 43%] tests/test_monthly_stats.py F........ [ 50%] tests/test_osparc.py .............. [ 62%] tests/test_plot.py . [ 63%] tests/test_pmr.py ......... [ 71%] 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_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'] subject_child = next((child for child in primary_children if child['content']['name'] == subject_id), None) if subject_child is None: logging.error(f'REVA microCT folder not found with subject id: {subject_id}') return jsonify({"status": "ERROR", "message": f"MicroCT folder not found with subject id: {subject_id}"}), 404 subject_folder = ps2.get(f"/packages/{subject_child['content']['id']}") subject_children = subject_folder['children'] micro_ct_child = next((child for child in subject_children if child['content']['name'] == micro_ct_visualization_folder_name), None) if micro_ct_child is None: logging.error(f'REVA microCT {micro_ct_visualization_folder_name} folder not found for subject: {subject_id}') return jsonify({"status": "ERROR", "message": f"{micro_ct_visualization_folder_name} folder not found for subject: {subject_id}"}), 404 micro_ct_visualization_folder = ps2.get(f"/packages/{micro_ct_child['content']['id']}") micro_ct_children = micro_ct_visualization_folder['children'] micro_ct_files = [] for micro_child in micro_ct_children: file_package_id = micro_child['content']['id'] micro_child_file = ps2.get(f"/packages/{file_package_id}/view") > micro_child_file_id = micro_child_file[0]['content']['id'] E TypeError: 'NoneType' object is not subscriptable app/main.py:1112: 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:272: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1123: in getRevaMicroCtFiles return jsonify({"status": "Error while getting microCT files: ", "message": e}), 500 ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:370: in jsonify dumps(data, indent=indent, separators=separators) + "\n", ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:211: in dumps rv = _json.dumps(obj, **kwargs) /usr/lib/python3.9/json/__init__.py:234: in dumps return cls( /usr/lib/python3.9/json/encoder.py:199: in encode chunks = self.iterencode(o, _one_shot=True) /usr/lib/python3.9/json/encoder.py:257: in iterencode return _iterencode(o, 0) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:100: in default return _json.JSONEncoder.default(self, o) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <flask.json.JSONEncoder object at 0x7f874ac86880> 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/python3.9/json/encoder.py:179: TypeError ----------------------------- Captured stderr call ----------------------------- ERROR:pennsieve2.direct.client:HTTP error occurred: 502 Server Error: Bad Gateway for url: https://api.pennsieve.io/packages/N:package:e006b969-ab65-44ef-91fa-1a9ee2185d92/view ERROR:root:Error while getting REVA microCT files 'NoneType' object is not subscriptable ------------------------------ 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:package:e006b969-ab65-44ef-91fa-1a9ee2185d92/view ERROR root:main.py:1122 Error while getting REVA microCT files 'NoneType' object is not subscriptable ________________________ test_get_reva_landmarks_files _________________________ 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) anatomical_landmarks_child = next((child for child in in_situ_children if child['content']['name'] == anatomical_landmarks_folder_name), None) if anatomical_landmarks_child is None: logging.error(f"REVA tracing folder {anatomical_landmarks_folder_name} not found for subject: {subject_id}") return jsonify({"status": "ERROR", "message": f"{anatomical_landmarks_folder_name} folder not found for subject: {subject_id}"}), 404 anatomical_landmarks_folder = ps2.get(f"/packages/{anatomical_landmarks_child['content']['id']}") anatomical_landmarks_children = anatomical_landmarks_folder['children'] anatomical_landmarks_folders = [] for anatomical_landmark_child in anatomical_landmarks_children: landmark_folder_name = anatomical_landmark_child['content']['name'] landmark_folder_id = anatomical_landmark_child['content']['id'] anatomical_landmark_folder = ps2.get(f"/packages/{landmark_folder_id}") landmark_children = anatomical_landmark_folder['children'] landmark_files = [] for landmark_child in landmark_children: landmark_file_package_id = landmark_child['content']['id'] landmark_file = ps2.get(f"/packages/{landmark_file_package_id}/view") > landmark_file_id = landmark_file[0]['content']['id'] E TypeError: 'NoneType' object is not subscriptable app/main.py:1050: TypeError 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:279: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:1057: in getRevaAnatomicalLandmarksFiles return jsonify({"status": "Error while getting anatomical landmarks files: ", "message": e}), 500 ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:370: in jsonify dumps(data, indent=indent, separators=separators) + "\n", ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:211: in dumps rv = _json.dumps(obj, **kwargs) /usr/lib/python3.9/json/__init__.py:234: in dumps return cls( /usr/lib/python3.9/json/encoder.py:199: in encode chunks = self.iterencode(o, _one_shot=True) /usr/lib/python3.9/json/encoder.py:257: in iterencode return _iterencode(o, 0) ../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/json/__init__.py:100: in default return _json.JSONEncoder.default(self, o) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <flask.json.JSONEncoder object at 0x7f8761244dc0> 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/python3.9/json/encoder.py:179: TypeError ----------------------------- Captured stderr call ----------------------------- ERROR:pennsieve2.direct.client:HTTP error occurred: 502 Server Error: Bad Gateway for url: https://api.pennsieve.io/packages/N:package:fd8962d1-130a-4f42-b7cf-2a4fd09fdaba/view ERROR:root:Error while getting REVA anatomical landmarks files 'NoneType' object is not subscriptable ------------------------------ 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:package:fd8962d1-130a-4f42-b7cf-2a4fd09fdaba/view ERROR root:main.py:1056 Error while getting REVA anatomical landmarks files 'NoneType' object is not subscriptable _____________________________ test_pennsieve_login _____________________________ def test_pennsieve_login(): key = ms.pennsieve_login() r = requests.get(f"{Config.PENNSIEVE_API_HOST}/datasets", headers={"Authorization": f"Bearer {key}"}) > assert_true(r.status_code == 200) tests/test_monthly_stats.py:49: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nose.tools.trivial.Dummy testMethod=nop>, expr = False msg = 'False is not true' def assertTrue(self, expr, msg=None): """Check that the expression is true.""" if not expr: msg = self._formatMessage(msg, "%s is not true" % safe_repr(expr)) > raise self.failureException(msg) E AssertionError: False is not true /usr/lib/python3.9/unittest/case.py:688: AssertionError =============================== warnings summary =============================== /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution, DistributionNotFound /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. DESCRIPTOR = _descriptor.FileDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _CACHESEGMENT = _descriptor.Descriptor( /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12 /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses from imp import find_module, load_module, acquire_lock, release_lock tests/test_health.py::test_request_response /home/cmiss/Jenkins/workspace/SPARC-API-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead. assert_equals("healthy", json_response.get("status")) -- Docs: https://docs.pytest.org/en/latest/warnings.html =========================== short test summary info ============================ FAILED tests/test_api.py::test_get_reva_micro_ct_files - TypeError: Object of... FAILED tests/test_api.py::test_get_reva_landmarks_files - TypeError: Object o... FAILED tests/test_monthly_stats.py::test_pennsieve_login - AssertionError: Fa... ====== 3 failed, 109 passed, 4 skipped, 10 warnings in 573.32s (0:09:33) ======= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1215 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE