![[Jenkins]](/jenkins/static/36965a9f/images/svgs/logo.svg){kind=logo}
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 0fd3c9499be845c4494ef7554d10ac2361d5f4f8 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 0fd3c9499be845c4494ef7554d10ac2361d5f4f8 # timeout=10 Commit message: "Merge pull request #214 from Tehsurfer/syntax-hotfix" > git rev-list --no-walk 0fd3c9499be845c4494ef7554d10ac2361d5f4f8 # timeout=10 [SPARC-API] $ /bin/sh -xe /tmp/shiningpanda2920509105981953450.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/SPARC-API + export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python + pip install -r requirements.txt Requirement already satisfied: api==0.0.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (6.1.1) Requirement already satisfied: boto3==1.17.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.17.67) Requirement already satisfied: botocore==1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.20.67) Requirement already satisfied: certifi==2019.11.28 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2019.11.28) Requirement already satisfied: chardet==3.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (3.0.4) Collecting Click==7.1.2 (from -r requirements.txt (line 7)) 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (0.15.2) Requirement already satisfied: Flask==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (1.1.1) Requirement already satisfied: flask-marshmallow==0.10.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (0.10.1) Requirement already satisfied: flask-cors==3.0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 11)) (3.0.8) Requirement already satisfied: gunicorn==20.0.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 12)) (20.0.4) Requirement already satisfied: idna==2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 13)) (2.8) Requirement already satisfied: itsdangerous==1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 14)) (1.1.0) Requirement already satisfied: Jinja2==2.11.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 15)) (2.11.3) Requirement already satisfied: jmespath==0.9.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 16)) (0.9.4) Requirement already satisfied: MarkupSafe==1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 17)) (1.1.1) Requirement already satisfied: marshmallow==3.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 18)) (3.2.2) Requirement already satisfied: nose==1.3.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 19)) (1.3.7) Requirement already satisfied: osparc==0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 20)) (0.4.3) Requirement already satisfied: pillow in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 21)) (10.3.0) Requirement already satisfied: public==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 22)) (2019.4.13) Requirement already satisfied: pytest in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 23)) (5.4.3) Requirement already satisfied: pymongo==3.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 24)) (3.8.0) Requirement already satisfied: python-dateutil==2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 25)) (2.8.0) Requirement already satisfied: python-dotenv==0.10.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 26)) (0.10.3) Requirement already satisfied: query-string==2019.4.13 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 27)) (2019.4.13) Requirement already satisfied: requests==2.25.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 28)) (2.25.1) Requirement already satisfied: s3transfer==0.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 29)) (0.4.2) Requirement already satisfied: sendgrid==6.9.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 30)) (6.9.7) Requirement already satisfied: six==1.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 31)) (1.13.0) Requirement already satisfied: SQLAlchemy==1.3.20 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 32)) (1.3.20) Requirement already satisfied: urllib3==1.26.4 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 33)) (1.26.4) Requirement already satisfied: Werkzeug==0.16.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 34)) (0.16.0) Requirement already satisfied: psycopg2-binary==2.9.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 35)) (2.9.5) Requirement already satisfied: APScheduler==3.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 36)) (3.7.0) Requirement already satisfied: google-api-python-client==2.52.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 37)) (2.52.0) Requirement already satisfied: oauth2client==4.1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 38)) (4.1.3) Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 39)) (2.6.2) Requirement already satisfied: contentful==1.13.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 40)) (1.13.1) Requirement already satisfied: contentful_management==2.11.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 41)) (2.11.0) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (6.0.1) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (4.25.3) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (2024.1) Requirement already satisfied: rsa==4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (1.7.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements.txt (line 2)) (5.9.8) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.0.4->-r requirements.txt (line 12)) (69.2.0) Requirement already satisfied: python-http-client>=3.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (3.3.7) Requirement already satisfied: starkbank-ecdsa>=2.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sendgrid==6.9.7->-r requirements.txt (line 30)) (2.2.0) Requirement already satisfied: tzlocal~=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from APScheduler==3.7.0->-r requirements.txt (line 36)) (2.1) Requirement already satisfied: httplib2<1dev,>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (0.22.0) Requirement already satisfied: google-auth<3.0.0dev,>=1.19.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.29.0) Requirement already satisfied: google-auth-httplib2>=0.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (2.18.0) Requirement already satisfied: uritemplate<5,>=3.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from google-api-python-client==2.52.0->-r requirements.txt (line 37)) (4.1.1) Requirement already satisfied: pyasn1>=0.1.7 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.6.0) Requirement already satisfied: pyasn1-modules>=0.0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from oauth2client==4.1.3->-r requirements.txt (line 38)) (0.4.0) Requirement already satisfied: ecdsa<0.15 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (1.11.0) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (24.0) Requirement already satisfied: attrs>=17.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (23.2.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (10.2.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.13.1) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest->-r requirements.txt (line 23)) (0.2.13) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements.txt (line 2)) (1.16.0) Requirement already satisfied: googleapis-common-protos<2.0.dev0,>=1.56.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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 37)) (1.63.0) Requirement already satisfied: proto-plus<2.0.0dev,>=1.22.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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 37)) (1.23.0) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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 37)) (5.3.3) 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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httplib2<1dev,>=0.15.0->google-api-python-client==2.52.0->-r requirements.txt (line 37)) (3.1.2) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Installing collected packages: Click Attempting uninstall: Click Found existing installation: click 8.1.7 Uninstalling click-8.1.7: Successfully uninstalled click-8.1.7 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 24.3.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible. Successfully installed Click-7.1.2 + pip install -r requirements-dev.txt Requirement already satisfied: pytest==5.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (24.3.0) Requirement already satisfied: isort in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 6)) (24.0) Requirement already satisfied: py>=1.5.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (23.2.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==5.4.3->-r requirements-dev.txt (line 1)) (10.2.0) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.17.67) Requirement already satisfied: configparser>=3.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (6.0.1) Requirement already satisfied: deprecated>=1.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.2.14) Requirement already satisfied: future>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (4.25.3) Requirement already satisfied: python-jose==3.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2024.1) Requirement already satisfied: requests>=2.18 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.25.1) Requirement already satisfied: rsa==4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.7.0) Requirement already satisfied: docopt>=0.6 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (5.9.8) Requirement already satisfied: python-dateutil>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2.8.0) Requirement already satisfied: six<2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-jose==3.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.6.0) Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3)) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Requirement already satisfied: mypy-extensions>=0.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.2.0) Requirement already satisfied: tomli>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (2.0.1) Requirement already satisfied: typing-extensions>=4.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.11.0) Requirement already satisfied: wrapt<2,>=1.10 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from deprecated>=1.2.0->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.16.0) Requirement already satisfied: chardet<5,>=3.0.2 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (3.0.4) Requirement already satisfied: idna<3,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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<1.27,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests>=2.18->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (2019.11.28) Requirement already satisfied: botocore<1.21.0,>=1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (1.20.67) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from boto3->pennsieve==6.1.1->-r requirements-dev.txt (line 2)) (0.4.2) Using cached click-8.1.7-py3-none-any.whl (97 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-8.1.7 + pytest ============================= test session starts ============================== platform linux -- Python 3.9.19, pytest-5.4.3, py-1.11.0, pluggy-0.13.1 rootdir: /home/cmiss/Jenkins/workspace/SPARC-API collected 101 items tests/test_api.py ..............FF... [ 18%] tests/test_biolucida.py ............. [ 31%] tests/test_dataset_info.py .s.Fss..... [ 42%] tests/test_health.py . [ 43%] tests/test_monthly_stats.py ...... [ 49%] tests/test_osparc.py ............F. [ 63%] tests/test_pmr.py ..FF. [ 68%] tests/test_scicrunch.py FF...FFFFFFFFFFFFFFFFFFFFF [ 94%] tests/test_segmentation_info.py .. [ 96%] tests/test_thumbnails.py ... [ 99%] tests/test_update_contentful_entries.py . [100%] =================================== FAILURES =================================== ____________________________ test_onto_term_lookup _____________________________ client = <FlaskClient <Flask 'app.main'>> def test_onto_term_lookup(client): > r = client.get('/onto_term_lookup', query_string={'term': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'}) tests/test_api.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:1445: in find_by_onto_term results = response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError _____________________ test_non_existing_simulation_ui_file _____________________ client = <FlaskClient <Flask 'app.main'>> def test_non_existing_simulation_ui_file(client): > r = client.get('/simulation_ui_file/137') tests/test_api.py:200: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:1368: in simulation_ui_file results = process_results(dataset_search(create_pennsieve_identifier_query(identifier))) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ______________________ test_complex_title_dataset_search _______________________ client = <FlaskClient <Flask 'app.main'>> def test_complex_title_dataset_search(client): title = "Spatial distribution and morphometric characterization of vagal efferents associated with the myenteric plexus of the rat stomach" start = timer() > r = client.get('/dataset_info/using_title', query_string={'title': title}) tests/test_dataset_info.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:564: in get_dataset_info_title return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ______________________ test_osparc_successful_simulation _______________________ client = <FlaskClient <Flask 'app.main'>> def test_osparc_successful_simulation(client): data = { "opencor": { "model_url": "https://models.physiomeproject.org/e/611/HumanSAN_Fabbri_Fantini_Wilders_Severi_2017.cellml", "json_config": { "simulation": { "Ending point": 0.003, "Point interval": 0.001, }, "output": ["Membrane/V"] } }, "solver": { "name": "simcore/services/comp/opencor", "version": "1.0.3" } } res = { "status": "ok", "results": { "environment/time": [0.0, 0.001, 0.002, 0.003], "Membrane/V": [-47.787168, -47.74547155339473, -47.72515226841376, -47.71370033208329] } } r = client.post("/start_simulation", json=data) assert r.status_code == 200 json_data = json.loads(r.data) assert (status := json_data.get("status")) is not None assert status == "ok" assert (check_simulation_data := json_data.get("data")) is not None while True: r = client.post("/check_simulation", json=check_simulation_data) assert r.status_code == 200 json_data = json.loads(r.data) assert (status := json_data.get("status")) is not None > assert status == "ok" E AssertionError: assert 'nok' == 'ok' E - ok E + nok E ? + tests/test_osparc.py:144: AssertionError ___________ test_pmr_latest_exposure_workspace_with_latest_exposure ____________ client = <FlaskClient <Flask 'app.main'>> def test_pmr_latest_exposure_workspace_with_latest_exposure(client): r = client.post("/pmr_latest_exposure", json={"workspace_url": "https://models.physiomeproject.org/workspace/486"}) > assert r.status_code == 200 E assert 400 == 200 E + where 400 = <Response streamed [400 BAD REQUEST]>.status_code tests/test_pmr.py:24: AssertionError __________ test_pmr_latest_exposure_workspace_without_latest_exposure __________ client = <FlaskClient <Flask 'app.main'>> def test_pmr_latest_exposure_workspace_without_latest_exposure(client): r = client.post("/pmr_latest_exposure", json={"workspace_url": "https://models.physiomeproject.org/workspace/698"}) > assert r.status_code == 200 E assert 400 == 200 E + where 400 = <Response streamed [400 BAD REQUEST]>.status_code tests/test_pmr.py:31: AssertionError _____________________________ test_scicrunch_keys ______________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_keys(client): > r = client.get('/search/') tests/test_scicrunch.py:26: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:676: in kb_search return process_results(response.json()) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ____________________ test_scicrunch_versions_are_supported _____________________ def test_scicrunch_versions_are_supported(): # Lines below are to allow the test to be run from the root dir or sparc-api/tests current_directory = os.path.dirname(os.path.abspath(__file__)) app_directory = os.path.join(current_directory, '..', 'app') # List the contents of the 'app' directory, to find which versions we have files for available_versions = os.listdir(app_directory) r = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}&q=""') > results = r.json() tests/test_scicrunch.py:39: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ____________________________ test_scicrunch_search _____________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_search(client): > r = client.get('/search/heart') tests/test_scicrunch.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:676: in kb_search return process_results(response.json()) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ___________________________ test_scicrunch_all_data ____________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_all_data(client): r = client.get('/filter-search/') > assert json.loads(r.data)['numberOfHits'] > 40 E KeyError: 'numberOfHits' tests/test_scicrunch.py:120: KeyError ____________________________ test_scicrunch_filter _____________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_filter(client): r = client.get('/filter-search/', query_string={'term': 'organ', 'facet': 'heart'}) > assert json.loads(r.data)['numberOfHits'] > 4 E KeyError: 'numberOfHits' tests/test_scicrunch.py:125: KeyError _______________________ test_scicrunch_filter_scaffolds ________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_filter_scaffolds(client): r = client.get('/filter-search/?facet=scaffolds&term=datasets') > assert json.loads(r.data)['numberOfHits'] > 10 E KeyError: 'numberOfHits' tests/test_scicrunch.py:130: KeyError _________________________ test_scicrunch_basic_search __________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_basic_search(client): r = client.get('/filter-search/Heart/?facet=All+Species&term=species') > assert json.loads(r.data)['numberOfHits'] > 10 E KeyError: 'numberOfHits' tests/test_scicrunch.py:135: KeyError _________________________ test_scicrunch_boolean_logic _________________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_boolean_logic(client): r = client.get('/filter-search/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender') > assert json.loads(r.data)['numberOfHits'] > 20 E KeyError: 'numberOfHits' tests/test_scicrunch.py:140: KeyError ______________________ test_scicrunch_combined_facet_text ______________________ client = <FlaskClient <Flask 'app.main'>> def test_scicrunch_combined_facet_text(client): r = client.get('/filter-search/heart/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender') > assert json.loads(r.data)['numberOfHits'] > 1 E KeyError: 'numberOfHits' tests/test_scicrunch.py:145: KeyError _____________________________ test_getting_facets ______________________________ client = <FlaskClient <Flask 'app.main'>> def test_getting_facets(client): r = client.get('/get-facets/organ') facet_results = json.loads(r.data) > facets = [facet_result['key'] for facet_result in facet_results] tests/test_scicrunch.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ .0 = <dict_keyiterator object at 0x7fe419b684f0> > facets = [facet_result['key'] for facet_result in facet_results] E TypeError: string indices must be integers tests/test_scicrunch.py:151: TypeError _________________________ test_create_identifier_query _________________________ client = <FlaskClient <Flask 'app.main'>> def test_create_identifier_query(client): > r = client.get('/dataset_info/using_object_identifier?identifier=package:e6435710-dd9c-46b7-9dfd-932103469733') tests/test_scicrunch.py:156: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:572: in get_dataset_info_object_identifier return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError __________________________ test_create_anatomy_query ___________________________ client = <FlaskClient <Flask 'app.main'>> def test_create_anatomy_query(client): > r = client.get('/dataset_info/anatomy?identifier=90') tests/test_scicrunch.py:173: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:583: in get_dataset_info_anatomy return reform_anatomy_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ____________________________ test_response_version _____________________________ client = <FlaskClient <Flask 'app.main'>> def test_response_version(client): # Testing with dataset 44 identifier = "44" doi = "10.26275/duz8-mq3n" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:203: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:591: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ____________________________ test_response_abi_plot ____________________________ client = <FlaskClient <Flask 'app.main'>> def test_response_abi_plot(client): # Testing abi-plot with dataset 212 identifier = "212" doi = "10.26275/lok5-wje6" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:218: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:591: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError __________________________ test_response_abi_scaffold __________________________ client = <FlaskClient <Flask 'app.main'>> def test_response_abi_scaffold(client): # Testing abi-scaffold with dataset 76 identifier = "76" doi = "10.26275/jarb-s8jw" > run_doi_test = check_doi_status(client, identifier, doi) tests/test_scicrunch.py:252: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_scicrunch.py:53: in check_doi_status r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id}) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:591: in get_dataset_info_pennsieve_identifier return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ______________________ test_response_sample_subject_size _______________________ client = <FlaskClient <Flask 'app.main'>> def test_response_sample_subject_size(client): # Only filter search returns the sample and subjectSuze r = client.get('/filter-search/?facet=liver&term=organ') data = r.data.decode('utf-8') json_data = json.loads(data) print(json_data) > assert len(json_data['results']) == 1 E KeyError: 'results' tests/test_scicrunch.py:312: KeyError ----------------------------- Captured stdout call ----------------------------- {'error': 'JSONDecodeError', 'message': 'Could not parse SciCrunch output, please try again later'} _________________________ test_raw_response_structure __________________________ client = <FlaskClient <Flask 'app.main'>> def test_raw_response_structure(client): # 10.26275/zdxd-84xz # 10.26275/duz8-mq3n query = create_query_string("computational") > data = dataset_search(query) tests/test_scicrunch.py:425: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError _________________________ test_get_body_scaffold_info __________________________ client = <FlaskClient <Flask 'app.main'>> def test_get_body_scaffold_info(client): # Test if we get a shorter list of uberons with species specified > r = client.get('/get_body_scaffold_info/human') tests/test_scicrunch.py:455: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:916: in get_body_scaffold_info result = process_get_first_scaffold_info(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError _____________________________ test_getting_curies ______________________________ client = <FlaskClient <Flask 'app.main'>> def test_getting_curies(client): # Test if we get a shorter list of uberons with species specified r = client.get('/get-organ-curies/') uberons_results = json.loads(r.data) > total = len(uberons_results['uberon']['array']) E KeyError: 'uberon' tests/test_scicrunch.py:466: KeyError ____________________________ test_get_related_terms ____________________________ client = <FlaskClient <Flask 'app.main'>> def test_get_related_terms(client): # Test if we can get the uberon term of heart using the uberon term # of left ventricle r = client.get('/get-related-terms/UBERON:0002084') uberons_results = json.loads(r.data) print(uberons_results) > total = len(uberons_results['uberon']['array']) E KeyError: 'uberon' tests/test_scicrunch.py:484: KeyError ----------------------------- Captured stdout call ----------------------------- {'error': 'BaseException', 'message': 'Could not parse SciCrunch output, please try again later'} _____________________________ test_scaffold_files ______________________________ client = <FlaskClient <Flask 'app.main'>> def test_scaffold_files(client): r = client.get('/filter-search/?size=30') results = json.loads(r.data) > assert results['numberOfHits'] > 0 E KeyError: 'numberOfHits' tests/test_scicrunch.py:497: KeyError _____________________ test_finding_contextual_information ______________________ client = <FlaskClient <Flask 'app.main'>> def test_finding_contextual_information(client): > r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=76') tests/test_scicrunch.py:511: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:556: in get_dataset_info_discoverIds return process_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError ____________________ test_undefined_version_dataset_search _____________________ client = <FlaskClient <Flask 'app.main'>> def test_undefined_version_dataset_search(client): # Testing with dataset 17 which is not versioned identifier = "17" doi = "10.26275/mlua-o9oj" > r = client.get('/dataset_info/using_doi', query_string={'doi': doi}) tests/test_scicrunch.py:522: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get return self.open(*args, **kw) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open return Client.open( ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open response = self.run_wsgi_app(environ.copy(), buffered=buffered) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app app_rv = app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__ return self.wsgi_app(environ, start_response) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app response = self.handle_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app response = self.full_dispatch_request() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request rv = self.handle_user_exception(e) ../../shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception reraise(exc_type, exc_value, tb) ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise raise value ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request rv = self.dispatch_request() ../../shiningpanda/jobs/c6a9534b/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:538: in get_dataset_info_doi return reform_dataset_results(dataset_search(query)) app/main.py:655: in dataset_search return response.json() ../../shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:900: in json return complexjson.loads(self.text, **kwargs) /usr/lib/python3.9/json/__init__.py:346: in loads return _default_decoder.decode(s) /usr/lib/python3.9/json/decoder.py:337: in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <json.decoder.JSONDecoder object at 0x7fe42179aee0> s = '<html>\r\n<head><title>502 Bad Gateway</title></head>\r\n<body>\r\n<center><h1>502 Bad Gateway</h1></center>\r\n<hr><center>nginx/1.16.1</center>\r\n</body>\r\n</html>\r\n' idx = 0 def raw_decode(self, s, idx=0): """Decode a JSON document from ``s`` (a ``str`` beginning with a JSON document) and return a 2-tuple of the Python representation and the index in ``s`` where the document ended. This can be used to decode a JSON document from a string that may have extraneous data at the end. """ try: obj, end = self.scan_once(s, idx) except StopIteration as err: > raise JSONDecodeError("Expecting value", s, err.value) from None E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) /usr/lib/python3.9/json/decoder.py:355: JSONDecodeError =============================== warnings summary =============================== /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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( app/manifest_name_to_discover_name.py:5075 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5075: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-4\sam-3\sub-4_sam-3_ChAT_P4-3p1_20x.jp2': 'files/derivative/sub-4/sam-3/sub-4_sam-3_ChAT_P4-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5076 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5076: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-4\sam-3\sub-4_sam-3_TH_P4-3p1_20x.jp2': 'files/derivative/sub-4/sam-3/sub-4_sam-3_TH_P4-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5077 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5077: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-5\sam-1\sub-5_sam-1_ChAT_P5-1p1_20x.jp2': 'files/derivative/sub-5/sam-1/sub-5_sam-1_ChAT_P5-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5078 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5078: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-5\sam-1\sub-5_sam-1_TH_P5-1p4_20x.jp2': 'files/derivative/sub-5/sam-1/sub-5_sam-1_TH_P5-1p4_20x.jp2', app/manifest_name_to_discover_name.py:5079 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5079: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-5\sam-3\sub-5_sam-3_ChAT_P5-3p1_20x.jp2': 'files/derivative/sub-5/sam-3/sub-5_sam-3_ChAT_P5-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5080 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5080: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-5\sam-3\sub-5_sam-3_TH_P5-3p1_20x.jp2': 'files/derivative/sub-5/sam-3/sub-5_sam-3_TH_P5-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5081 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5081: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-6\sam-1\sub-6_sam-1_ChAT_NPcontrol_P6-1p1_20x.jp2': 'files/derivative/sub-6/sam-1/sub-6_sam-1_ChAT_NPcontrol_P6-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5082 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5082: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-6\sam-1\sub-6_sam-1_TH_NPcontrol_P6-1p1_20x.jp2': 'files/derivative/sub-6/sam-1/sub-6_sam-1_TH_NPcontrol_P6-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5083 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5083: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-6\sam-7\sub-6_sam-7_ChAT_P6-7p1_20x.jp2': 'files/derivative/sub-6/sam-7/sub-6_sam-7_ChAT_P6-7p1_20x.jp2', app/manifest_name_to_discover_name.py:5084 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5084: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-6\sam-7\sub-6_sam-7_TH_P6-7p1_20x.jp2': 'files/derivative/sub-6/sam-7/sub-6_sam-7_TH_P6-7p1_20x.jp2', app/manifest_name_to_discover_name.py:5085 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5085: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-7\sam-7\sub-7_sam-7_ChAT_NPcontrol_P7-7p4_20x.jp2': 'files/derivative/sub-7/sam-7/sub-7_sam-7_ChAT_NPcontrol_P7-7p4_20x.jp2', app/manifest_name_to_discover_name.py:5086 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5086: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-7\sam-7\sub-7_sam-7_TH_NPcontrol_P7-7p1_20x.jp2': 'files/derivative/sub-7/sam-7/sub-7_sam-7_TH_NPcontrol_P7-7p1_20x.jp2', app/manifest_name_to_discover_name.py:5087 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5087: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-8\sam-7\sub-8\sam-1\sub-8_sam-1_ChAT_P8-1p1_20x.jp2': 'files/derivative/sub-8/sam-1/sub-8_sam-1_ChAT_P8-1p1_20x (1).jp2', app/manifest_name_to_discover_name.py:5088 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5088: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-8\sam-7\sub-8\sam-1\sub-8_sam-1_TH_P8-1p1_20x.jp2': 'files/derivative/sub-8/sam-1/sub-8_sam-1_TH_P8-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5089 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5089: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-8\sam-7\sub-8\sam-7\sub-8_sam-7_ChAT_P8-7p1_20x.jp2': 'files/derivative/sub-8/sam-7/sub-8_sam-7_ChAT_P8-7p1_20x.jp2', app/manifest_name_to_discover_name.py:5090 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5090: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-8\sam-7\sub-8_sam-7_TH_P8-7p1_20x.jp2': 'files/derivative/sub-8/sam-7/sub-8_sam-7_TH_P8-7p1_20x.jp2', app/manifest_name_to_discover_name.py:5091 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5091: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-9\sam-3\sub-9_sam-3_ChAT_P9-3p1_20x.jp2': 'files/derivative/sub-9/sam-3/sub-9_sam-3_ChAT_P9-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5092 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5092: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-9\sam-3\sub-9_sam-3_TH_P9-3p3_20x.jp2': 'files/derivative/sub-9/sam-3/sub-9_sam-3_TH_P9-3p3_20x.jp2', app/manifest_name_to_discover_name.py:5093 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5093: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-10\sam-1\sub-10_sam-1_ChAT_P10-1p1_20x.jp2': 'files/derivative/sub-10/sam-1/sub-10_sam-1_ChAT_P10-1p1_20x (1).jp2', app/manifest_name_to_discover_name.py:5094 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5094: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-10\sam-1\sub-10_sam-1_TH_P10-1p1_20x.jp2': 'files/derivative/sub-10/sam-1/sub-10_sam-1_TH_P10-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5095 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5095: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-11\sam-1\sub-11_sam-1_ChAT_P11-1p2_20x.jp2': 'files/derivative/sub-11/sam-1/sub-11_sam-1_ChAT_P11-1p2_20x.jp2', app/manifest_name_to_discover_name.py:5096 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5096: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-11\sam-1\sub-11_sam-1_TH_P11-1p1_20x.jp2': 'files/derivative/sub-11/sam-1/sub-11_sam-1_TH_P11-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5097 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5097: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-11\sam-3\sub-11_sam-3_ChAT_P11-3p3_20x.jp2': 'files/derivative/sub-11/sam-3/sub-11_sam-3_ChAT_P11-3p3_20x.jp2', app/manifest_name_to_discover_name.py:5098 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5098: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-11\sam-3\sub-11_sam-3_TH_P11-3p1_20x.jp2': 'files/derivative/sub-11/sam-3/sub-11_sam-3_TH_P11-3p1_20x (1).jp2', app/manifest_name_to_discover_name.py:5099 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5099: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-12\sam-1\sub-12_sam-1_ChAT_P12-1p1_20x.jp2': 'files/derivative/sub-12/sam-1/sub-12_sam-1_ChAT_P12-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5100 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5100: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-12\sam-1\sub-12_sam-1_TH_P12-1p1_20x.jp2': 'files/derivative/sub-12/sam-1/sub-12_sam-1_TH_P12-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5101 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5101: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-12\sam-3\sub-12_sam-3_ChAT_P12-3p3_20x.jp2': 'files/derivative/sub-12/sam-3/sub-12_sam-3_ChAT_P12-3p3_20x.jp2', app/manifest_name_to_discover_name.py:5102 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5102: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-12\sam-3\sub-12_sam-3_TH_P12-3p1_20x.jp2': 'files/derivative/sub-12/sam-3/sub-12_sam-3_TH_P12-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5103 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5103: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-13\sam-1\sub-13_sam-1_ChAT_P13-1p1_20x.jp2': 'files/derivative/sub-13/sam-1/sub-13_sam-1_ChAT_P13-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5104 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5104: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-13\sam-1\sub-13_sam-1_TH_P13-1p1_20x.jp2': 'files/derivative/sub-13/sam-1/sub-13_sam-1_TH_P13-1p1_20x.jp2', app/manifest_name_to_discover_name.py:5105 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5105: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-13\sam-3\sub-13_sam-3_ChAT_P13-3p3_20x.jp2': 'files/derivative/sub-13/sam-3/sub-13_sam-3_ChAT_P13-3p3_20x.jp2', app/manifest_name_to_discover_name.py:5106 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5106: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-13\sam-3\sub-13_sam-3_TH_P13-3p1_20x.jp2': 'files/derivative/sub-13/sam-3/sub-13_sam-3_TH_P13-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5107 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5107: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-14\sam-2\sub-14_sam-2_ChAT_P14-2p1_20x.jp2': 'files/derivative/sub-14/sam-2/sub-14_sam-2_ChAT_P14-2p1_20x.jp2', app/manifest_name_to_discover_name.py:5108 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5108: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-14\sam-2\sub-14_sam-2_TH_P14-2p1_20x.jp2': 'files/derivative/sub-14/sam-2/sub-14_sam-2_TH_P14-2p1_20x.jp2', app/manifest_name_to_discover_name.py:5109 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5109: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-14\sam-3\sub-14_sam-3_ChAT_P14-3p3_20x.jp2': 'files/derivative/sub-14/sam-3/sub-14_sam-3_ChAT_P14-3p3_20x (1).jp2', app/manifest_name_to_discover_name.py:5110 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5110: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-14\sam-3\sub-14_sam-3_TH_P14-3p1_20x.jp2': 'files/derivative/sub-14/sam-3/sub-14_sam-3_TH_P14-3p1_20x.jp2', app/manifest_name_to_discover_name.py:5111 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5111: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-15\sam-2\sub-15_sam-2_ChAT_P15-2p2_20x.jp2': 'files/derivative/sub-15/sam-2/sub-15_sam-2_ChAT_P15-2p2_20x.jp2', app/manifest_name_to_discover_name.py:5112 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5112: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-15\sam-2\sub-15_sam-2_TH_P15-2p1_20x.jp2': 'files/derivative/sub-15/sam-2/sub-15_sam-2_TH_P15-2p1_20x.jp2', app/manifest_name_to_discover_name.py:5113 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5113: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-15\sam-3\sub-15_sam-3_ChAT_P15-3p3_20x.jp2': 'files/derivative/sub-15/sam-3/sub-15_sam-3_ChAT_P15-3p3_20x.jp2', app/manifest_name_to_discover_name.py:5114 /home/cmiss/Jenkins/workspace/SPARC-API/app/manifest_name_to_discover_name.py:5114: DeprecationWarning: invalid escape sequence \s 'files/derivative/sub-15\sam-3\sub-15_sam-3_TH_P15-3p1_20x.jp2': 'files/derivative/sub-15/sam-3/sub-15_sam-3_TH_P15-3p1_20x.jp2', /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12 /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/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/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_onto_term_lookup - json.decoder.JSONDecodeErro... FAILED tests/test_api.py::test_non_existing_simulation_ui_file - json.decoder... FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - json.d... FAILED tests/test_osparc.py::test_osparc_successful_simulation - AssertionErr... FAILED tests/test_pmr.py::test_pmr_latest_exposure_workspace_with_latest_exposure FAILED tests/test_pmr.py::test_pmr_latest_exposure_workspace_without_latest_exposure FAILED tests/test_scicrunch.py::test_scicrunch_keys - json.decoder.JSONDecode... FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - json.... FAILED tests/test_scicrunch.py::test_scicrunch_search - json.decoder.JSONDeco... FAILED tests/test_scicrunch.py::test_scicrunch_all_data - KeyError: 'numberOf... FAILED tests/test_scicrunch.py::test_scicrunch_filter - KeyError: 'numberOfHits' FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - KeyError: '... FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - KeyError: 'numb... FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - KeyError: 'num... FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - KeyError... FAILED tests/test_scicrunch.py::test_getting_facets - TypeError: string indic... FAILED tests/test_scicrunch.py::test_create_identifier_query - json.decoder.J... FAILED tests/test_scicrunch.py::test_create_anatomy_query - json.decoder.JSON... FAILED tests/test_scicrunch.py::test_response_version - json.decoder.JSONDeco... FAILED tests/test_scicrunch.py::test_response_abi_plot - json.decoder.JSONDec... FAILED tests/test_scicrunch.py::test_response_abi_scaffold - json.decoder.JSO... FAILED tests/test_scicrunch.py::test_response_sample_subject_size - KeyError:... FAILED tests/test_scicrunch.py::test_raw_response_structure - json.decoder.JS... FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - json.decoder.JS... FAILED tests/test_scicrunch.py::test_getting_curies - KeyError: 'uberon' FAILED tests/test_scicrunch.py::test_get_related_terms - KeyError: 'uberon' FAILED tests/test_scicrunch.py::test_scaffold_files - KeyError: 'numberOfHits' FAILED tests/test_scicrunch.py::test_finding_contextual_information - json.de... FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - json.... ====== 29 failed, 69 passed, 3 skipped, 50 warnings in 1184.39s (0:19:44) ====== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1087 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE