Started by timer
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/SPARC-API
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] Done
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/nih-sparc/sparc-api.git
> git init /home/cmiss/Jenkins/workspace/SPARC-API # timeout=10
Fetching upstream changes from https://github.com/nih-sparc/sparc-api.git
> git --version # timeout=10
> git --version # 'git version 2.25.1'
> git fetch --tags --force --progress -- https://github.com/nih-sparc/sparc-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10
> git config remote.origin.url https://github.com/nih-sparc/sparc-api.git # timeout=10
> git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
> git rev-parse refs/remotes/origin/master^{commit} # timeout=10
Checking out Revision 7ed89235c4f25b6ed2a28de94d72f7b7ca3c6fec (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 7ed89235c4f25b6ed2a28de94d72f7b7ca3c6fec # timeout=10
Commit message: "Merge pull request #287 from ignapas/contact-us-gdocs"
> git rev-list --no-walk c8011bdb0572d796b8284b35c63a2f9373f8fe0d # timeout=10
[SPARC-API] $ /bin/bash /tmp/jenkins5054087969211602663.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)
Collecting gspread==6.2.1 (from -r requirements.txt (line 17))
Downloading gspread-6.2.1-py3-none-any.whl.metadata (11 kB)
Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 18)) (20.0.4)
Requirement already satisfied: httpx>=0.27.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 19)) (0.28.1)
Requirement already satisfied: hubspot-api-client==9.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 20)) (9.0.0)
Requirement already satisfied: idna==2.8 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 21)) (2.8)
Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 22)) (1.1.0)
Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 23)) (2.11.3)
Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 24)) (0.9.4)
Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 25)) (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 26)) (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 27)) (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 28)) (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 29)) (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 30)) (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 31)) (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 32)) (0.1.2)
Requirement already satisfied: Pillow in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 33)) (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 34)) (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 35)) (2019.4.13)
Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 36)) (8.4.1)
Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 37)) (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 38)) (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 39)) (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 40)) (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 41)) (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 42)) (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 43)) (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 44)) (1.13.0)
Requirement already satisfied: SQLAlchemy==2.0.40 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 45)) (2.0.40)
Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 46)) (1.26.4)
Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from -r requirements.txt (line 47)) (0.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from requests==2.31.0->-r requirements.txt (line 41)) (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)
Collecting google-auth-oauthlib>=0.4.1 (from gspread==6.2.1->-r requirements.txt (line 17))
Downloading google_auth_oauthlib-1.2.2-py3-none-any.whl.metadata (2.7 kB)
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 29)) (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 29)) (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 29)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 31)) (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 32)) (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 32)) (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 32)) (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 32)) (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 43)) (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 43)) (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 45)) (3.2.1)
Requirement already satisfied: typing-extensions>=4.6.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from SQLAlchemy==2.0.40->-r requirements.txt (line 45)) (4.13.2)
Requirement already satisfied: ecdsa<0.15 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from python-jose==3.2.0->Pennsieve==6.1.1->-r requirements.txt (line 31)) (0.14.1)
Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.70.0)
Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (1.26.1)
Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from google-auth<3.0.0dev,>=1.19.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (5.5.2)
Requirement already satisfied: pyparsing!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<4,>=2.4.2 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 16)) (3.2.3)
Requirement already satisfied: anyio in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 19)) (4.9.0)
Requirement already satisfied: httpcore==1.* in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpx>=0.27.0->-r requirements.txt (line 19)) (1.0.9)
Requirement already satisfied: h11>=0.16 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from httpcore==1.*->httpx>=0.27.0->-r requirements.txt (line 19)) (0.16.0)
Requirement already satisfied: exceptiongroup>=1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from pytest->-r requirements.txt (line 36)) (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 36)) (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 36)) (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 36)) (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 36)) (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 36)) (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 31)) (1.17.2)
Collecting requests-oauthlib>=0.7.0 (from google-auth-oauthlib>=0.4.1->gspread==6.2.1->-r requirements.txt (line 17))
Downloading requests_oauthlib-2.0.0-py2.py3-none-any.whl.metadata (11 kB)
Collecting oauthlib>=3.0.0 (from requests-oauthlib>=0.7.0->google-auth-oauthlib>=0.4.1->gspread==6.2.1->-r requirements.txt (line 17))
Downloading oauthlib-3.3.1-py3-none-any.whl.metadata (7.9 kB)
Requirement already satisfied: sniffio>=1.1 in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (from anyio->httpx>=0.27.0->-r requirements.txt (line 19)) (1.3.1)
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Downloading gspread-6.2.1-py3-none-any.whl (59 kB)
Downloading google_auth_oauthlib-1.2.2-py3-none-any.whl (19 kB)
Downloading requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB)
Downloading oauthlib-3.3.1-py3-none-any.whl (160 kB)
Installing collected packages: oauthlib, Click, requests-oauthlib, google-auth-oauthlib, gspread
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 google-auth-oauthlib-1.2.2 gspread-6.2.1 oauthlib-3.3.1 requests-oauthlib-2.0.0
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)
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Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3))
Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB)
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Using cached pytest-5.4.3-py3-none-any.whl (248 kB)
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Installing collected packages: pluggy, click, pytest
Attempting uninstall: pluggy
Found existing installation: pluggy 1.6.0
Uninstalling pluggy-1.6.0:
Successfully uninstalled pluggy-1.6.0
Attempting uninstall: click
Found existing installation: click 7.1.2
Uninstalling click-7.1.2:
Successfully uninstalled click-7.1.2
Attempting uninstall: pytest
Found existing installation: pytest 8.4.1
Uninstalling pytest-8.4.1:
Successfully uninstalled pytest-8.4.1
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Requirement already satisfied: pytest in /home/cmiss/python3.10.venv/lib/python3.10/site-packages (5.4.3)
Collecting pytest
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Installing collected packages: pluggy, pytest
Attempting uninstall: pluggy
Found existing installation: pluggy 0.13.1
Uninstalling pluggy-0.13.1:
Successfully uninstalled pluggy-0.13.1
Attempting uninstall: pytest
Found existing installation: pytest 5.4.3
Uninstalling pytest-5.4.3:
Successfully uninstalled pytest-5.4.3
Successfully installed pluggy-1.6.0 pytest-8.4.1
============================= test session starts ==============================
platform linux -- Python 3.10.18, pytest-8.4.1, pluggy-1.6.0
rootdir: /home/cmiss/Jenkins/workspace/SPARC-API
plugins: anyio-4.9.0
collected 122 items
tests/test_api.py ............E................. [ 24%]
tests/test_biolucida.py ............. [ 35%]
tests/test_dataset_info.py .s..ss..... [ 44%]
tests/test_health.py . [ 45%]
tests/test_monthly_stats.py ...FFF..F [ 52%]
tests/test_osparc.py .............. [ 63%]
tests/test_plot.py . [ 64%]
tests/test_pmr.py ......... [ 72%]
tests/test_scicrunch.py .................s.......... [ 95%]
tests/test_segmentation_info.py .. [ 96%]
tests/test_thumbnails.py ... [ 99%]
tests/test_update_contentful_entries.py . [100%]
==================================== ERRORS ====================================
_____________________ ERROR at setup of test_tasks_appends _____________________
@pytest.fixture
def sheets_service():
> creds = ServiceAccountCredentials.from_json_keyfile_name(
KEY_PATH,
SPREADS_SCOPE
)
tests/test_api.py:47:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'oauth2client.service_account.ServiceAccountCredentials'>
filename = None, scopes = 'https://www.googleapis.com/auth/spreadsheets'
token_uri = None, revoke_uri = None
@classmethod
def from_json_keyfile_name(cls, filename, scopes='',
token_uri=None, revoke_uri=None):
"""Factory constructor from JSON keyfile by name.
Args:
filename: string, The location of the keyfile.
scopes: List or string, (Optional) Scopes to use when acquiring an
access token.
token_uri: string, URI for OAuth 2.0 provider token endpoint.
If unset and not present in the key file, defaults
to Google's endpoints.
revoke_uri: string, URI for OAuth 2.0 provider revoke endpoint.
If unset and not present in the key file, defaults
to Google's endpoints.
Returns:
ServiceAccountCredentials, a credentials object created from
the keyfile.
Raises:
ValueError, if the credential type is not :data:`SERVICE_ACCOUNT`.
KeyError, if one of the expected keys is not present in
the keyfile.
"""
> with open(filename, 'r') as file_obj:
E TypeError: expected str, bytes or os.PathLike object, not NoneType
../../../python3.10.venv/lib/python3.10/site-packages/oauth2client/service_account.py:219: TypeError
=================================== FAILURES ===================================
__________________________________ test_email __________________________________
def test_email(): # Note that this will send an email to the test_"email_recipient" provided at the top of this doc
> responses = ms.send_stats(test_data)
tests/test_monthly_stats.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
scripts/monthly_stats.py:108: in send_stats
responses = [self.send_logging_email(email_body)] # send last email as log if in debug mode
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = '<h1 style="color: #1a1489;" data-darkreader-inline-color="">SPARC Download Statistics</h1> <p>This month, you have ha...</td> <td style="width: 10%;">SPARC</td> <td style="width: 14%;">1</td> </tr></tbody> </table>'
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
------------------------------ Captured log call -------------------------------
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
________________________________ test_full_run _________________________________
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
def run(self):
sendgrid_responses = []
try:
self.get_stats()
> sendgrid_responses = self.send_stats(self.user_stats)
scripts/monthly_stats.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
scripts/monthly_stats.py:108: in send_stats
responses = [self.send_logging_email(email_body)] # send last email as log if in debug mode
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = '<h1 style="color: #1a1489;" data-darkreader-inline-color="">SPARC Download Statistics</h1> <p>This month, you have ha...</td> <td style="width: 10%;">SPARC</td> <td style="width: 14%;">2</td> </tr></tbody> </table>'
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
During handling of the above exception, another exception occurred:
def test_full_run(): # For each recipient, this will send an email to the test_email for each email that would have been sent to a user
#Only check with the DB if it is set up
responses = []
if Config.DATABASE_URL is None:
responses = ms.run()
else:
#Test against a specified date, the entry in the database is set
#with the latest date being 2024, 7, 1
#do not provide a date, it will use the current date instead
> responses = ms.monthly_stats_required_check(None, False)
tests/test_monthly_stats.py:79:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
scripts/monthly_stats.py:50: in monthly_stats_required_check
sendgrid_responses = self.run()
scripts/monthly_stats.py:65: in run
self.send_logging_email(f'Hit error while running monthly stats. {error}')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = "Hit error while running monthly stats. local variable 'response' referenced before assignment"
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
------------------------------ Captured log call -------------------------------
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
ERROR root:monthly_stats.py:64 Hit error while running monthly stats. local variable 'response' referenced before assignment
Traceback (most recent call last):
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 62, in run
sendgrid_responses = self.send_stats(self.user_stats)
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 108, in send_stats
responses = [self.send_logging_email(email_body)] # send last email as log if in debug mode
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 228, in send_logging_email
return response
UnboundLocalError: local variable 'response' referenced before assignment
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
______________________________ test_next_year_run ______________________________
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
def run(self):
sendgrid_responses = []
try:
self.get_stats()
> sendgrid_responses = self.send_stats(self.user_stats)
scripts/monthly_stats.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
scripts/monthly_stats.py:108: in send_stats
responses = [self.send_logging_email(email_body)] # send last email as log if in debug mode
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = '<h1 style="color: #1a1489;" data-darkreader-inline-color="">SPARC Download Statistics</h1> <p>This month, you have ha...</td> <td style="width: 10%;">SPARC</td> <td style="width: 14%;">2</td> </tr></tbody> </table>'
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
During handling of the above exception, another exception occurred:
def test_next_year_run(): # For each recipient, this will send an email to the test_email for each email that would have been sent to a user
#Only check with the DB if it is set up
if Config.DATABASE_URL is None:
pytest.skip('DATABASE not set for this run')
else:
#Test against a specified date, the entry in the database is set
#with the latest date being 2024, 7, 1
timeNow = datetime.datetime(2025, 1, 1).date()
> responses = ms.monthly_stats_required_check(timeNow, False)
tests/test_monthly_stats.py:90:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
scripts/monthly_stats.py:50: in monthly_stats_required_check
sendgrid_responses = self.run()
scripts/monthly_stats.py:65: in run
self.send_logging_email(f'Hit error while running monthly stats. {error}')
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = "Hit error while running monthly stats. local variable 'response' referenced before assignment"
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
------------------------------ Captured log call -------------------------------
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
ERROR root:monthly_stats.py:64 Hit error while running monthly stats. local variable 'response' referenced before assignment
Traceback (most recent call last):
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 62, in run
sendgrid_responses = self.send_stats(self.user_stats)
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 108, in send_stats
responses = [self.send_logging_email(email_body)] # send last email as log if in debug mode
File "/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_stats.py", line 228, in send_logging_email
return response
UnboundLocalError: local variable 'response' referenced before assignment
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
________________________________ test_log_email ________________________________
def test_log_email():
> response = ms.send_logging_email('testing log email')
tests/test_monthly_stats.py:114:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <scripts.monthly_stats.MonthlyStats object at 0x7fc7ac21ffd0>
message = 'testing log email'
def send_logging_email(self, message):
try:
response = self.send_grid.sendgrid_email_with_unsubscribe_group(Config.METRICS_EMAIL_ADDRESS,
self.logging_address,
'SPARC monthly dataset download summary',
message)
if response.status_code == 202:
logging.info(f'Logging email sent successfully to {self.logging_address} (202)')
elif response.status_code == 403:
logging.error('Could not send sendgrid email because rate limit is hit (403)')
elif response.status_code == 401:
logging.error('Could not send sendgrid email. Sendgrid keys are likely incorrect (401)')
else:
logging.error(f'Unknown error. Status code: {response.status_code}')
except BaseException as err:
logging.error(err)
> return response
E UnboundLocalError: local variable 'response' referenced before assignment
scripts/monthly_stats.py:228: UnboundLocalError
------------------------------ Captured log call -------------------------------
ERROR root:monthly_stats.py:226 HTTP Error 401: Unauthorized
=============================== warnings summary ===============================
scripts/monthly_db.py:9
/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution, DistributionNotFound
../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
DESCRIPTOR = _descriptor.FileDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_CACHESEGMENT = _descriptor.Descriptor(
app/dbtable.py:12
/home/cmiss/Jenkins/workspace/SPARC-API/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 3 warnings
tests/test_api.py: 31 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 6 warnings
tests/test_monthly_stats.py: 15 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 34 warnings
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated
context = SSLContext(ssl_version or PROTOCOL_TLS)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 3 warnings
tests/test_api.py: 35 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 7 warnings
tests/test_monthly_stats.py: 19 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 35 warnings
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated
match_hostname(cert, asserted_hostname)
../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
tests/test_health.py::test_request_response
/home/cmiss/Jenkins/workspace/SPARC-API/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead.
assert_equals("healthy", json_response.get("status"))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_monthly_stats.py::test_email - UnboundLocalError: local variable 'response' referenced before assignment
FAILED tests/test_monthly_stats.py::test_full_run - UnboundLocalError: local variable 'response' referenced before assignment
FAILED tests/test_monthly_stats.py::test_next_year_run - UnboundLocalError: local variable 'response' referenced before assignment
FAILED tests/test_monthly_stats.py::test_log_email - UnboundLocalError: local variable 'response' referenced before assignment
ERROR tests/test_api.py::test_tasks_appends - TypeError: expected str, bytes or os.PathLike object, not NoneType
= 4 failed, 113 passed, 4 skipped, 274 warnings, 1 error in 296.39s (0:04:56) ==
Build step 'Execute shell' marked build as failure
[Slack Notifications] found #1554 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE