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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 9962cb941eb83fdc13d883094a21f10edff226e0 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 9962cb941eb83fdc13d883094a21f10edff226e0 # timeout=10 Commit message: "Merge pull request #250 from nih-sparc/add-reva-files-endpoints" > git rev-list --no-walk f4a43096b63de70f027f55b2037b2f0ceb226743 # timeout=10 [SPARC-API-DEV] $ /bin/sh -xe /tmp/shiningpanda8651385715201937913.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: api==0.0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.0.7) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (6.1.1) Collecting pennsieve2==0.1.2 (from -r requirements.txt (line 3)) Downloading pennsieve2-0.1.2-py3-none-any.whl.metadata (4.2 kB) Collecting boto3==1.26 (from -r requirements.txt (line 4)) Downloading boto3-1.26.0-py3-none-any.whl.metadata (7.0 kB) Collecting botocore==1.29.0 (from -r requirements.txt (line 5)) Downloading botocore-1.29.0-py3-none-any.whl.metadata (5.9 kB) 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: docutils==0.15.2 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (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 10)) (1.1.1) 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 11)) (0.10.1) 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 12)) (3.0.8) 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 13)) (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 14)) (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 15)) (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 16)) (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 17)) (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 18)) (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 19)) (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 20)) (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 21)) (1.3.7) 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 22)) (0.4.3) Requirement already satisfied: pillow in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (11.0.0) 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 24)) (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 25)) (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 26)) (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 27)) (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 28)) (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 29)) (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 30)) (2.31.0) Collecting s3transfer==0.6.0 (from -r requirements.txt (line 31)) Downloading s3transfer-0.6.0-py3-none-any.whl.metadata (1.6 kB) 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 32)) (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 33)) (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 34)) (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 35)) (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 36)) (0.16.0) 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 37)) (2.9.9) 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 38)) (3.7.0) 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 39)) (2.52.0) 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 40)) (4.1.3) 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 41)) (2.6.2) 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 42)) (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 43)) (2.11.0) 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 44)) (2.3.0) 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 2)) (7.1.0) 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 2)) (1.2.15) 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 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.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.txt (line 2)) (5.29.1) 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 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.txt (line 2)) (2024.2) 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.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.txt (line 2)) (3.0.2) 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 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.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.txt (line 2)) (6.1.0) Collecting grpcio<2.0,>=1.51 (from pennsieve2==0.1.2->-r requirements.txt (line 3)) Downloading grpcio-1.69.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB) Collecting grpcio_tools<2.0,>=1.51 (from pennsieve2==0.1.2->-r requirements.txt (line 3)) Downloading grpcio_tools-1.69.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Collecting protobuf>=3.2.0 (from pennsieve==6.1.1->-r requirements.txt (line 2)) Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes) Collecting pyjwt<3.0,>=2.6 (from pennsieve2==0.1.2->-r requirements.txt (line 3)) Downloading PyJWT-2.10.1-py3-none-any.whl.metadata (4.0 kB) Collecting tqdm<5.0,>=4.64 (from pennsieve2==0.1.2->-r requirements.txt (line 3)) Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.0.4->-r requirements.txt (line 13)) (75.6.0) 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 30)) (3.4.0) 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 32)) (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 32)) (2.2.0) 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 38)) (2.1) 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 39)) (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 39)) (2.36.0) 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 39)) (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 39)) (2.23.0) 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 39)) (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 40)) (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 40)) (0.4.1) 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 44)) (0.9.0) 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 2)) (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 25)) (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 25)) (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 25)) (24.2.0) 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 25)) (10.5.0) 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 25)) (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 25)) (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 2)) (1.17.0) Requirement already satisfied: googleapis-common-protos<2.0.dev0,>=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 39)) (1.66.0) Requirement already satisfied: proto-plus<2.0.0dev,>=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 39)) (1.25.0) 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 39)) (5.5.0) INFO: pip is looking at multiple versions of grpcio-tools to determine which version is compatible with other requirements. This could take a while. Collecting grpcio_tools<2.0,>=1.51 (from pennsieve2==0.1.2->-r requirements.txt (line 3)) Downloading grpcio_tools-1.68.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.68.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.67.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.67.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.66.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.66.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.66.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) INFO: pip is still looking at multiple versions of grpcio-tools to determine which version is compatible with other requirements. This could take a while. Downloading grpcio_tools-1.65.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.65.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.65.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.65.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.64.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C. Downloading grpcio_tools-1.64.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.64.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.63.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.63.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB) Downloading grpcio_tools-1.62.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.2 kB) 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 39)) (3.2.0) Downloading pennsieve2-0.1.2-py3-none-any.whl (27 kB) Downloading boto3-1.26.0-py3-none-any.whl (132 kB) Downloading botocore-1.29.0-py3-none-any.whl (9.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.8/9.8 MB 5.0 MB/s eta 0:00:00 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Downloading s3transfer-0.6.0-py3-none-any.whl (79 kB) Downloading grpcio-1.69.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.0/6.0 MB 114.3 MB/s eta 0:00:00 Downloading grpcio_tools-1.62.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 2.4 MB/s eta 0:00:00 Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_x86_64.whl (294 kB) Downloading PyJWT-2.10.1-py3-none-any.whl (22 kB) Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) Installing collected packages: tqdm, pyjwt, protobuf, grpcio, Click, grpcio_tools, botocore, s3transfer, boto3, pennsieve2 Attempting uninstall: protobuf Found existing installation: protobuf 5.29.1 Uninstalling protobuf-5.29.1: Successfully uninstalled protobuf-5.29.1 Attempting uninstall: Click Found existing installation: click 8.1.8 Uninstalling click-8.1.8: Successfully uninstalled click-8.1.8 Attempting uninstall: botocore Found existing installation: botocore 1.20.67 Uninstalling botocore-1.20.67: Successfully uninstalled botocore-1.20.67 Attempting uninstall: s3transfer Found existing installation: s3transfer 0.4.2 Uninstalling s3transfer-0.4.2: Successfully uninstalled s3transfer-0.4.2 Attempting uninstall: boto3 Found existing installation: boto3 1.17.67 Uninstalling boto3-1.17.67: Successfully uninstalled boto3-1.17.67 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. black 24.10.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 boto3-1.26.0 botocore-1.29.0 grpcio-1.69.0 grpcio_tools-1.62.3 pennsieve2-0.1.2 protobuf-4.25.5 pyjwt-2.10.1 s3transfer-0.6.0 tqdm-4.67.1 + 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)) (24.10.0) 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)) (5.13.2) 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)) (24.2.0) 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)) (10.5.0) 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)) (7.1.0) 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)) (1.2.15) 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)) (4.25.5) 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)) (2024.2) 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)) (3.0.2) 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)) (6.1.0) 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)) (4.3.6) 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)) (4.12.2) 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)) (1.17.0) 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)) (3.4.0) 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 3.9.21, pytest-5.4.3, py-1.11.0, pluggy-0.13.1 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV collected 113 items tests/test_api.py ....................FFF [ 20%] tests/test_biolucida.py ............. [ 31%] tests/test_dataset_info.py .s..ss..... [ 41%] tests/test_health.py . [ 42%] tests/test_monthly_stats.py ......... [ 50%] tests/test_osparc.py .............. [ 62%] tests/test_pmr.py ......... [ 70%] tests/test_scicrunch.py .................s......... [ 94%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== __________________________ test_get_reva_subject_ids ___________________________ @app.route("/reva/subject-ids", methods=["GET"]) def getRevaSubjectIds(): try: primary_folder = ps2.get(f'/packages/{Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}') > primary_children = primary_folder['children'] E TypeError: 'NoneType' object is not subscriptable app/main.py:951: TypeError During handling of the above exception, another exception occurred: client = <FlaskClient <Flask 'app.main'>> def test_get_reva_subject_ids(client): > r = client.get('/reva/subject-ids') tests/test_api.py:262: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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:959: in getRevaSubjectIds return jsonify({"status": "Error while getting REVA subject id 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 0x7ff8ad3fbf40> 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: 404 Client Error: for url: https://api.pennsieve.io/packages/None ERROR:root:Error while getting REVA subject id files: 'NoneType' object is not subscriptable ------------------------------ Captured log call ------------------------------- ERROR pennsieve2.direct.client:client.py:180 HTTP error occurred: 404 Client Error: for url: https://api.pennsieve.io/packages/None ERROR root:main.py:958 Error while getting REVA subject id files: 'NoneType' object is not subscriptable _________________________ test_get_reva_tracing_files __________________________ subject_id = 'sub-SR005' @app.route("/reva/tracing-files/<subject_id>", methods=["GET"]) def getRevaTracingFiles(subject_id): coordinates_folder_name = 'Coordinates-Data' in_situ_folder_name = 'InSitu' vagus_nerve_folder_name = 'Vagus-nerve' try: primary_folder = ps2.get(f'/packages/{Config.REVA_3D_TRACING_PRIMARY_FOLDER_COLLECTION_ID}') > primary_children = primary_folder['children'] E TypeError: 'NoneType' object is not subscriptable app/main.py:969: TypeError 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:269: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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:1008: in getRevaTracingFiles return jsonify({"status": "Error while getting tracing 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 0x7ff8bc140310> 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: 404 Client Error: for url: https://api.pennsieve.io/packages/None ERROR:root:Error while getting REVA tracing files 'NoneType' object is not subscriptable ------------------------------ Captured log call ------------------------------- ERROR pennsieve2.direct.client:client.py:180 HTTP error occurred: 404 Client Error: for url: https://api.pennsieve.io/packages/None ERROR root:main.py:1007 Error while getting REVA tracing files 'NoneType' object is not subscriptable _________________________ 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:1016: 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:276: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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:1043: 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 0x7ff8aeff6a00> 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: 404 Client Error: for url: https://api.pennsieve.io/packages/None 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: 404 Client Error: for url: https://api.pennsieve.io/packages/None ERROR root:main.py:1042 Error while getting REVA microCT files 'NoneType' object is not subscriptable =============================== 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_subject_ids - TypeError: Object of ty... FAILED tests/test_api.py::test_get_reva_tracing_files - TypeError: Object of ... FAILED tests/test_api.py::test_get_reva_micro_ct_files - TypeError: Object of... ====== 3 failed, 106 passed, 4 skipped, 10 warnings in 401.38s (0:06:41) ======= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1115 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE