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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 218583d2e88236d3b06186eaa2ab2795fc4d44ea (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 218583d2e88236d3b06186eaa2ab2795fc4d44ea # timeout=10 Commit message: "Merge pull request #272 from nih-sparc/add-endpoint-to-get-protocol-metrics" > git rev-list --no-walk 218583d2e88236d3b06186eaa2ab2795fc4d44ea # timeout=10 [SPARC-API-DEV] $ /bin/bash /tmp/jenkins12389508219806465446.sh Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 1)) (2.6.2) Requirement already satisfied: api==0.0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (0.0.7) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (3.7.0) Requirement already satisfied: boto3==1.26 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (1.26.0) Requirement already satisfied: botocore==1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 5)) (1.29.0) Requirement already satisfied: certifi==2023.5.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 6)) (2023.5.7) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 7)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 8)) Using cached click-7.1.2-py2.py3-none-any.whl.metadata (2.9 kB) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 9)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 10)) (2.11.0) Requirement already satisfied: docutils==0.15.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 11)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 12)) (1.1.1) Requirement already satisfied: Flask-Caching==2.3.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 13)) (2.3.0) Requirement already satisfied: Flask-Cors==3.0.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 14)) (3.0.8) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 15)) (0.10.1) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 16)) (2.52.0) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 17)) (20.0.4) Requirement already satisfied: httpx>=0.27.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 18)) (0.28.1) Requirement already satisfied: hubspot-api-client==9.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 19)) (9.0.0) Requirement already satisfied: idna==2.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 20)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 21)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 22)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 23)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 24)) (1.1.1) Requirement already satisfied: markdown==3.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 25)) (3.8) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 26)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 27)) (1.3.7) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 28)) (4.1.3) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 29)) (0.4.3) Requirement already satisfied: Pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 30)) (6.1.1) Requirement already satisfied: Pennsieve2==0.1.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 31)) (0.1.2) Requirement already satisfied: Pillow in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 32)) (11.2.1) Requirement already satisfied: psycopg2-binary==2.9.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 33)) (2.9.10) Requirement already satisfied: public==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 34)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 35)) (8.4.0) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 36)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 37)) (2.8.2) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 38)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 39)) (2019.4.13) Requirement already satisfied: requests==2.31.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 40)) (2.31.0) Requirement already satisfied: s3transfer==0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 41)) (0.6.0) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 42)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 43)) (1.13.0) Requirement already satisfied: SQLAlchemy==2.0.40 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 44)) (2.0.40) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 45)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 46)) (0.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests==2.31.0->-r requirements.txt (line 40)) (3.4.2) Requirement already satisfied: setuptools>=0.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (80.3.1) Requirement already satisfied: pytz in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2025.2) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 3)) (2.1) Requirement already satisfied: cachelib<0.10.0,>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Flask-Caching==2.3.0->-r requirements.txt (line 13)) (0.9.0) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.40.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (0.2.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (2.25.0rc0) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 16)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 28)) (0.6.1) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 28)) (0.4.2) Requirement already satisfied: rsa>=3.1.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 28)) (4.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (7.2.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (1.2.18) Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (4.25.7) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (3.2.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (3.0.4) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (0.6.2) Requirement already satisfied: psutil>=5.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve==6.1.1->-r requirements.txt (line 30)) (7.0.0) Requirement already satisfied: grpcio<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 31)) (1.71.0) Requirement already satisfied: grpcio_tools<2.0,>=1.51 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 31)) (1.62.3) Requirement already satisfied: pyjwt<3.0,>=2.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 31)) (2.10.1) Requirement already satisfied: tqdm<5.0,>=4.64 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from Pennsieve2==0.1.2->-r requirements.txt (line 31)) (4.67.1) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 42)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 42)) (2.2.0) Requirement already satisfied: greenlet>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 44)) (3.2.1) Requirement already satisfied: typing-extensions>=4.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 44)) (4.13.2) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->Pennsieve==6.1.1->-r requirements.txt (line 30)) (0.14.1) Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.70.0) Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.26.1) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (5.5.2) Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (3.2.3) Requirement already satisfied: anyio in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 18)) (4.9.0) Requirement already satisfied: httpcore==1.* in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 18)) (1.0.9) Requirement already satisfied: h11>=0.16 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpcore==1.*->httpx>=0.27.0->-r requirements.txt (line 18)) (0.16.0) Requirement already satisfied: exceptiongroup>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (1.2.2) Requirement already satisfied: iniconfig>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (2.1.0) Requirement already satisfied: packaging>=20 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (25.0) Requirement already satisfied: pluggy<2,>=1.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (1.6.0) Requirement already satisfied: pygments>=2.7.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (2.19.1) Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 35)) (2.2.1) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from deprecated>=1.2.0->Pennsieve==6.1.1->-r requirements.txt (line 30)) (1.17.2) Requirement already satisfied: sniffio>=1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from anyio->httpx>=0.27.0->-r requirements.txt (line 18)) (1.3.1) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.2.1 Uninstalling click-8.2.1: Successfully uninstalled click-8.2.1 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. black 25.1.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 Collecting pytest==5.4.3 (from -r requirements-dev.txt (line 1)) Using cached pytest-5.4.3-py3-none-any.whl.metadata (7.3 kB) Requirement already satisfied: pennsieve==6.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 2)) (6.1.1) Requirement already satisfied: black in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 3)) (25.1.0) Requirement already satisfied: isort in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 4)) (6.0.1) Requirement already satisfied: nose in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 5)) (1.3.7) Requirement already satisfied: packaging in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements-dev.txt (line 6)) (25.0) Requirement already satisfied: py>=1.5.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (1.11.0) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (25.3.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.7.0) Collecting pluggy<1.0,>=0.12 (from pytest==5.4.3->-r requirements-dev.txt (line 1)) Using cached pluggy-0.13.1-py2.py3-none-any.whl.metadata (15 kB) Requirement already satisfied: wcwidth in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (0.2.13) Requirement already satisfied: boto3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (7.2.0) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.18) Requirement already satisfied: future>=0.15.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.0.0) Requirement already satisfied: futures in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.5) Requirement already satisfied: protobuf>=3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.25.7) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.2.0) Requirement already satisfied: pytz>=2016 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2025.2) Requirement already satisfied: requests>=2.18 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.31.0) Requirement already satisfied: rsa==4.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.0) Requirement already satisfied: semver>=2.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.4) Requirement already satisfied: websocket-client>=0.57.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.8.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.2) Requirement 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click-8.2.1-py3-none-any.whl.metadata (2.5 kB) Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (1.1.0) Requirement already satisfied: pathspec>=0.9.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (0.12.1) Requirement already satisfied: platformdirs>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.3.7) Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (2.2.1) Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from black->-r requirements-dev.txt (line 3)) (4.13.2) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.17.2) Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.4.2) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.26.4) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2023.5.7) Requirement already satisfied: botocore<1.30.0,>=1.29.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.29.0) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.9.4) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.0) Using cached pytest-5.4.3-py3-none-any.whl (248 kB) Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Using cached click-8.2.1-py3-none-any.whl (102 kB) Installing collected packages: pluggy, click, pytest Attempting uninstall: pluggy Found existing installation: pluggy 1.6.0 Uninstalling pluggy-1.6.0: Successfully uninstalled pluggy-1.6.0 Attempting uninstall: click Found existing installation: click 7.1.2 Uninstalling click-7.1.2: Successfully uninstalled click-7.1.2 Attempting uninstall: pytest Found existing installation: pytest 8.4.0 Uninstalling pytest-8.4.0: Successfully uninstalled pytest-8.4.0 Successfully installed click-8.2.1 pluggy-0.13.1 pytest-5.4.3 Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (5.4.3) Collecting pytest Using cached pytest-8.4.0-py3-none-any.whl.metadata (7.7 kB) Requirement already satisfied: exceptiongroup>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (1.2.2) Requirement already satisfied: iniconfig>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.1.0) Requirement already satisfied: packaging>=20 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (25.0) Collecting pluggy<2,>=1.5 (from pytest) Using cached pluggy-1.6.0-py3-none-any.whl.metadata (4.8 kB) Requirement already satisfied: pygments>=2.7.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.19.1) Requirement already satisfied: tomli>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest) (2.2.1) Using cached pytest-8.4.0-py3-none-any.whl (363 kB) Using cached pluggy-1.6.0-py3-none-any.whl (20 kB) Installing collected packages: pluggy, pytest Attempting uninstall: pluggy Found existing installation: pluggy 0.13.1 Uninstalling pluggy-0.13.1: Successfully uninstalled pluggy-0.13.1 Attempting uninstall: pytest Found existing installation: pytest 5.4.3 Uninstalling pytest-5.4.3: Successfully uninstalled pytest-5.4.3 Successfully installed pluggy-1.6.0 pytest-8.4.0 ============================= test session starts ============================== platform linux -- Python 3.10.18, pytest-8.4.0, pluggy-1.6.0 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API-DEV plugins: anyio-4.9.0 collected 121 items tests/test_api.py ............................. [ 23%] tests/test_biolucida.py ............. [ 34%] tests/test_dataset_info.py .s..ss..... [ 43%] tests/test_health.py . [ 44%] tests/test_monthly_stats.py ......... [ 52%] tests/test_osparc.py .............F [ 63%] tests/test_plot.py . [ 64%] tests/test_pmr.py ......... [ 71%] tests/test_scicrunch.py .................s.......... [ 95%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== ________________________ test_osparc_failing_simulation ________________________ client = <FlaskClient <Flask 'app.main'>> def test_osparc_failing_simulation(client): data = { "opencor": { "model_url": "https://models.physiomeproject.org/e/611/HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml", "json_config": { "simulation": { "Ending point": 3.0, "Point interval": 1.0, }, "output": ["Membrane/V"] } }, "solver": { "name": "simcore/services/comp/opencor", "version": "1.0.3" } } res = { "status": "nok", "description": "the simulation failed" } > r = client.post("/start_simulation", json=data) tests/test_osparc.py:171: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1039: in post return self.open(*args, **kw) ../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open return Client.open( ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app rv = run_wsgi_app(self.application, environ, buffered=buffered) ../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function return cors_after_request(app.make_response(f(*args, **kwargs))) ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise raise value ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) app/main.py:2053: in start_simulation return json.dumps(do_start_simulation(data)) app/osparc/osparc.py:115: in start_simulation status = solvers_api.start_job(solver.id, solver.version, job.id) ../../../python3.10.venv/lib/python3.10/site-packages/osparc/api/solvers_api.py:1231: in start_job return self.start_job_with_http_info(solver_key, version, job_id, **kwargs) # noqa: E501 ../../../python3.10.venv/lib/python3.10/site-packages/osparc/api/solvers_api.py:1317: in start_job_with_http_info return self.api_client.call_api( ../../../python3.10.venv/lib/python3.10/site-packages/osparc/api_client.py:351: in call_api return self.__call_api(resource_path, method, ../../../python3.10.venv/lib/python3.10/site-packages/osparc/api_client.py:180: in __call_api response_data = self.request( ../../../python3.10.venv/lib/python3.10/site-packages/osparc/api_client.py:394: in request return self.rest_client.POST(url, ../../../python3.10.venv/lib/python3.10/site-packages/osparc/rest.py:271: in POST return self.request("POST", url, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <osparc.rest.RESTClientObject object at 0x7f0e0aeaead0>, method = 'POST' url = 'https://api.osparc.io/v0/solvers/simcore%2Fservices%2Fcomp%2Fopencor/releases/1.0.3/jobs/c15aed1b-2241-4c06-beb3-91c655decda2:start' query_params = [] headers = {'Accept': 'application/json', 'Authorization': 'Basic MDY3M2UzYjEtZjdjMC01YTdjLWI5ZjAtMDI1MTRiMWE0NzFmOmJjOTExYWZjLTViNmEtNTJhOC05NzFjLWM4NTJiYjBiZDg5Mw==', 'Content-Type': 'application/json', 'User-Agent': 'osparc-api/0.3.0/python'} body = None, post_params = {}, _preload_content = True, _request_timeout = None def request(self, method, url, query_params=None, headers=None, body=None, post_params=None, _preload_content=True, _request_timeout=None): """Perform requests. :param method: http request method :param url: http request url :param query_params: query parameters in the url :param headers: http request headers :param body: request json body, for `application/json` :param post_params: request post parameters, `application/x-www-form-urlencoded` and `multipart/form-data` :param _preload_content: if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. """ method = method.upper() assert method in ['GET', 'HEAD', 'DELETE', 'POST', 'PUT', 'PATCH', 'OPTIONS'] if post_params and body: raise ApiValueError( "body parameter cannot be used with post_params parameter." ) post_params = post_params or {} headers = headers or {} timeout = None if _request_timeout: if isinstance(_request_timeout, (int, ) if six.PY3 else (int, long)): # noqa: E501,F821 timeout = urllib3.Timeout(total=_request_timeout) elif (isinstance(_request_timeout, tuple) and len(_request_timeout) == 2): timeout = urllib3.Timeout( connect=_request_timeout[0], read=_request_timeout[1]) if 'Content-Type' not in headers: headers['Content-Type'] = 'application/json' try: # For `POST`, `PUT`, `PATCH`, `OPTIONS`, `DELETE` if method in ['POST', 'PUT', 'PATCH', 'OPTIONS', 'DELETE']: if query_params: url += '?' + urlencode(query_params) if re.search('json', headers['Content-Type'], re.IGNORECASE): request_body = None if body is not None: request_body = json.dumps(body) r = self.pool_manager.request( method, url, body=request_body, preload_content=_preload_content, timeout=timeout, headers=headers) elif headers['Content-Type'] == 'application/x-www-form-urlencoded': # noqa: E501 r = self.pool_manager.request( method, url, fields=post_params, encode_multipart=False, preload_content=_preload_content, timeout=timeout, headers=headers) elif headers['Content-Type'] == 'multipart/form-data': # must del headers['Content-Type'], or the correct # Content-Type which generated by urllib3 will be # overwritten. del headers['Content-Type'] r = self.pool_manager.request( method, url, fields=post_params, encode_multipart=True, preload_content=_preload_content, timeout=timeout, headers=headers) # Pass a `string` parameter directly in the body to support # other content types than Json when `body` argument is # provided in serialized form elif isinstance(body, str) or isinstance(body, bytes): request_body = body r = self.pool_manager.request( method, url, body=request_body, preload_content=_preload_content, timeout=timeout, headers=headers) else: # Cannot generate the request from given parameters msg = """Cannot prepare a request message for provided arguments. Please check that your arguments match declared content type.""" raise ApiException(status=0, reason=msg) # For `GET`, `HEAD` else: r = self.pool_manager.request(method, url, fields=query_params, preload_content=_preload_content, timeout=timeout, headers=headers) except urllib3.exceptions.SSLError as e: msg = "{0}\n{1}".format(type(e).__name__, str(e)) raise ApiException(status=0, reason=msg) if _preload_content: r = RESTResponse(r) # In the python 3, the response.data is bytes. # we need to decode it to string. if six.PY3: try: r.data = r.data.decode('utf8') except UnicodeDecodeError: # NOTE: hdf5 files cannot be decoded pass if not 200 <= r.status <= 299: > raise ApiException(http_resp=r) E osparc.exceptions.ApiException: (502) E Reason: Bad Gateway E HTTP response headers: HTTPHeaderDict({'Content-Length': '65', 'Content-Type': 'application/json', 'Date': 'Sat, 14 Jun 2025 13:09:07 GMT', 'Server': 'uvicorn'}) E HTTP response body: {"errors":["Production_director-v2 service unexpectedly failed"]} ../../../python3.10.venv/lib/python3.10/site-packages/osparc/rest.py:230: ApiException =============================== warnings summary =============================== scripts/monthly_db.py:9 /home/cmiss/Jenkins/workspace/SPARC-API-DEV/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) base = declarative_base() ../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution, DistributionNotFound ../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. __version_info__ = tuple(LooseVersion(__version__).version) ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. DESCRIPTOR = _descriptor.FileDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _descriptor.FieldDescriptor( ../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool. _CACHESEGMENT = _descriptor.Descriptor( app/dbtable.py:12 /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) base = declarative_base() ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 2 warnings tests/test_api.py: 26 warnings tests/test_biolucida.py: 13 warnings tests/test_dataset_info.py: 6 warnings tests/test_monthly_stats.py: 11 warnings tests/test_osparc.py: 9 warnings tests/test_plot.py: 1 warning tests/test_pmr.py: 4 warnings tests/test_scicrunch.py: 34 warnings tests/test_thumbnails.py: 2 warnings /home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated context = SSLContext(ssl_version or PROTOCOL_TLS) ../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 2 warnings tests/test_api.py: 30 warnings tests/test_biolucida.py: 13 warnings tests/test_dataset_info.py: 7 warnings tests/test_monthly_stats.py: 14 warnings tests/test_osparc.py: 9 warnings tests/test_plot.py: 1 warning tests/test_pmr.py: 4 warnings tests/test_scicrunch.py: 35 warnings tests/test_thumbnails.py: 2 warnings /home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated match_hostname(cert, asserted_hostname) ../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12 /home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses from imp import find_module, load_module, acquire_lock, release_lock tests/test_health.py::test_request_response /home/cmiss/Jenkins/workspace/SPARC-API-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead. assert_equals("healthy", json_response.get("status")) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_osparc.py::test_osparc_failing_simulation - osparc.exceptions.ApiException: (502) Reason: Bad Gateway HTTP response headers: HTTPHeaderDict({'Content-Length': '65', 'Content-Type': 'application/json', 'Date': 'Sat, 14 Jun 2025 13:09:07 GMT', 'Server': 'uvicorn'}) HTTP response body: {"errors":["Production_director-v2 service unexpectedly failed"]} ====== 1 failed, 116 passed, 4 skipped, 237 warnings in 407.26s (0:06:47) ====== Build step 'Execute shell' marked build as failure [Slack Notifications] found #1286 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE