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 ec1f5fb9e9734b90e9e54899ad4176a7acf72013 (refs/remotes/origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f ec1f5fb9e9734b90e9e54899ad4176a7acf72013 # timeout=10
Commit message: "Merge pull request #193 from Tehsurfer/allow-scicrunch-patch-updates"
> git rev-list --no-walk ec1f5fb9e9734b90e9e54899ad4176a7acf72013 # timeout=10
[SPARC-API] $ /bin/sh -xe /tmp/shiningpanda10301555828702898965.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 (82 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)) (10.0.0)
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)) (6.0.0)
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)) (0.18.3)
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)) (4.24.2)
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)) (2023.3.post1)
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)) (3.0.1)
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)) (1.6.2)
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)) (5.9.5)
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)) (68.1.2)
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)) (2.22.0)
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)) (0.1.0)
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)) (2.11.1)
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)) (0.5.0)
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)) (0.3.0)
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)) (23.1)
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)) (23.1.0)
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)) (10.1.0)
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)) (0.2.6)
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)) (1.15.0)
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)) (1.60.0)
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)) (5.3.1)
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)) (3.1.1)
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 23.7.0 requires click>=8.0.0, but you have click 7.1.2 which is incompatible.
Successfully installed Click-7.1.2
[notice] A new release of pip is available: 23.2.1 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
+ 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)) (23.7.0)
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)) (5.12.0)
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)) (23.1)
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)) (23.1.0)
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)) (10.1.0)
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)) (0.2.6)
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)) (6.0.0)
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)) (0.18.3)
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)) (4.24.2)
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)) (2023.3.post1)
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)) (3.0.1)
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)) (1.6.2)
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)) (5.9.5)
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)) (0.5.0)
Collecting click>=8.0.0 (from black->-r requirements-dev.txt (line 3))
Obtaining dependency information for click>=8.0.0 from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata
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)) (0.11.2)
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)) (3.10.0)
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>=3.10.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from black->-r requirements-dev.txt (line 3)) (4.7.1)
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)) (1.15.0)
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
[notice] A new release of pip is available: 23.2.1 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.18, 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 ..............FFFF. [ 18%]
tests/test_biolucida.py ............. [ 31%]
tests/test_dataset_info.py FsFFssFFF.. [ 42%]
tests/test_health.py . [ 43%]
tests/test_monthly_stats.py ...... [ 49%]
tests/test_osparc.py .............. [ 63%]
tests/test_pmr.py ..... [ 68%]
tests/test_scicrunch.py FFFFFFFFFFFFFFFFFFFFFF.FFF [ 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.route("/onto_term_lookup")
def find_by_onto_term():
term = request.args.get('term')
headers = {
'Accept': 'application/json',
}
params = {
"api_key": Config.KNOWLEDGEBASE_KEY
}
query = create_onto_term_query(term)
response = requests.get(f'{Config.SCI_CRUNCH_INTERLEX_HOST}/_search', headers=headers, params=params, json=query)
results = response.json()
> hits = results['hits']['hits']
E KeyError: 'hits'
app/main.py:1418: KeyError
_____________________ 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:1340: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________ test_simulation_ui_file_old_s3_bucket _____________________
client = <FlaskClient <Flask 'app.main'>>
def test_simulation_ui_file_old_s3_bucket(client):
> r = client.get('/simulation_ui_file/135')
tests/test_api.py:205:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:1340: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________ test_simulation_ui_file_new_s3_bucket _____________________
client = <FlaskClient <Flask 'app.main'>>
def test_simulation_ui_file_new_s3_bucket(client):
> r = client.get('/simulation_ui_file/308')
tests/test_api.py:211:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:1340: in simulation_ui_file
results = process_results(dataset_search(create_pennsieve_identifier_query(identifier)))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________________ test_current_doi_list _____________________________
client = <FlaskClient <Flask 'app.main'>>
def test_current_doi_list(client):
doi_stem = "doi:"
start = timer()
> r = client.get('/current_doi_list')
tests/test_dataset_info.py:23:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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.route("/current_doi_list")
def get_all_doi():
query = create_doi_aggregate()
results = reform_aggregation_results(dataset_search(query))
doi_results = []
> for result in results['doi']['buckets']:
E TypeError: list indices must be integers or slices, not str
app/main.py:636: TypeError
___________________ test_generic_mouse_colon_dataset_search ____________________
client = <FlaskClient <Flask 'app.main'>>
def test_generic_mouse_colon_dataset_search(client):
title = "Generic mouse colon scaffold"
start = timer()
> r = client.get('/dataset_info/using_title', query_string={'title': title})
tests/test_dataset_info.py:132:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:561: in get_dataset_info_title
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
______________________ 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:561: in get_dataset_info_title
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
__________________ test_title_plot_annotation_dataset_search ___________________
client = <FlaskClient <Flask 'app.main'>>
def test_title_plot_annotation_dataset_search(client):
print()
title = "Sympathetic nerve stimulation of mouse and rabbit hearts"
start = timer()
> r = client.get('/dataset_info/using_title', query_string={'title': title})
tests/test_dataset_info.py:202:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:561: in get_dataset_info_title
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
----------------------------- Captured stdout call -----------------------------
____________________ test_object_identifier_dataset_search _____________________
client = <FlaskClient <Flask 'app.main'>>
def test_object_identifier_dataset_search(client):
#Dataset 212
print()
identifier = "package:b5f9e5d7-7e09-4855-a923-a966454967d7"
start = timer()
> r = client.get('/dataset_info/using_object_identifier', query_string={'identifier': identifier})
tests/test_dataset_info.py:231:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:569: in get_dataset_info_object_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
----------------------------- Captured stdout call -----------------------------
___________________ test_pennsieve_identifier_dataset_search ___________________
client = <FlaskClient <Flask 'app.main'>>
def test_pennsieve_identifier_dataset_search(client):
print()
identifier = "43"
start = timer()
> r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': identifier})
tests/test_dataset_info.py:259:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
----------------------------- Captured stdout call -----------------------------
_____________________________ 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:673: in kb_search
return process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________ 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()
> hits = results['hits']['hits']
E KeyError: 'hits'
tests/test_scicrunch.py:40: KeyError
__________________________ test_scicrunch_dataset_doi __________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_dataset_doi(client):
# Testing with dataset 55
identifier = "55"
> run_doi_test = check_doi_status(client, identifier, '10.26275/pzek-91wx')
tests/test_scicrunch.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
_____________________ test_scicrunch_multiple_dataset_doi ______________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_multiple_dataset_doi(client):
# Testing with dataset 55 and 68
> run_doi_test_1 = check_doi_status(client, "55", '10.26275/pzek-91wx')
tests/test_scicrunch.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
_____________________ test_scicrunch_multiple_dataset_ids ______________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_multiple_dataset_ids(client):
# Testing with dataset 55 and 68
> r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=55&discoverIds=68')
tests/test_scicrunch.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:553: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________________ 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:673: in kb_search
return process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
___________________________ test_scicrunch_all_data ____________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_all_data(client):
> r = client.get('/filter-search/')
tests/test_scicrunch.py:119:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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'})
tests/test_scicrunch.py:124:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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')
tests/test_scicrunch.py:129:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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')
tests/test_scicrunch.py:134:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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')
tests/test_scicrunch.py:139:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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')
tests/test_scicrunch.py:144:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
_____________________________ test_getting_facets ______________________________
client = <FlaskClient <Flask 'app.main'>>
def test_getting_facets(client):
> r = client.get('/get-facets/organ')
tests/test_scicrunch.py:149:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
type_ = 'organ'
@app.route("/get-facets/<type_>")
def get_facets(type_):
# Create facet query
type_map, data = create_facet_query(type_)
# Make a request for each sci-crunch parameter
results = []
for path in type_map[type_]:
data['aggregations'][f'{type_}']['terms']['field'] = path
response = requests.post(
f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
json=data)
try:
json_result = response.json()
results.append(json_result)
except json.JSONDecodeError:
return jsonify({'message': 'Could not parse SciCrunch output, please try again later',
'error': 'JSONDecodeError'}), 502
# Select terms from the results
terms = []
for result in results:
> terms += result['aggregations'][f'{type_}']['buckets']
E KeyError: 'aggregations'
app/main.py:729: KeyError
_________________________ 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:569: in get_dataset_info_object_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
__________________________ 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:580: in get_dataset_info_anatomy
return reform_anatomy_results(dataset_search(query))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def reform_anatomy_results(results):
processed_outputs = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:101: KeyError
____________________________ 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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
____________________________ 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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
__________________________ 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:588: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
______________________ 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')
tests/test_scicrunch.py:308:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
_________________________ 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)
# print(data['hits']['hits'][0]['_source']['objects'])
# print(data['hits']['hits'][0]['_source']['item'])
> assert _test_structure(data, raw_structure_base)
E AssertionError: assert False
E + where False = _test_structure({'errormsg': 'Could not complete request', 'success': False}, {'optional': [], 'required': [{'hits': {'optional': [], 'required': [{'hits': {...}}], 'type': <class 'dict'>}}], 'type': <class 'dict'>})
tests/test_scicrunch.py:428: AssertionError
----------------------------- Captured stdout call -----------------------------
key failed: hits
_________________________ 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:902: in get_body_scaffold_info
result = process_get_first_scaffold_info(dataset_search(query))
app/scicrunch_process_results.py:80: in process_get_first_scaffold_info
results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
_____________________________ 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_scaffold_files ______________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scaffold_files(client):
> r = client.get('/filter-search/?size=30')
tests/test_scicrunch.py:495:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../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:696: in filter_search
results = process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: 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:553: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def process_results(results):
> return jsonify({'numberOfHits': results['hits']['total'], 'results': _prepare_results(results)})
E KeyError: 'hits'
app/scicrunch_process_results.py:76: KeyError
____________________ 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:535: in get_dataset_info_doi
return reform_dataset_results(dataset_search(query))
app/scicrunch_process_results.py:110: in reform_dataset_results
kb_results = _prepare_results(results)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
results = {'errormsg': 'Could not complete request', 'success': False}
def _prepare_results(results):
output = []
> hits = results['hits']['hits']
E KeyError: 'hits'
app/scicrunch_process_results.py:15: KeyError
=============================== 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/pkg_resources/__init__.py:2871
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google.logging')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(pkg)
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('google')`.
Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
declare_namespace(parent)
/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/future/standard_library/__init__.py:65
/home/cmiss/Jenkins/shiningpanda/jobs/c6a9534b/virtualenvs/d41d8cd9/lib/python3.9/site-packages/future/standard_library/__init__.py:65: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
/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(
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 - KeyError: 'hits'
FAILED tests/test_api.py::test_non_existing_simulation_ui_file - KeyError: 'h...
FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - KeyError: '...
FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - KeyError: '...
FAILED tests/test_dataset_info.py::test_current_doi_list - TypeError: list in...
FAILED tests/test_dataset_info.py::test_generic_mouse_colon_dataset_search - ...
FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - KeyErr...
FAILED tests/test_dataset_info.py::test_title_plot_annotation_dataset_search
FAILED tests/test_dataset_info.py::test_object_identifier_dataset_search - Ke...
FAILED tests/test_dataset_info.py::test_pennsieve_identifier_dataset_search
FAILED tests/test_scicrunch.py::test_scicrunch_keys - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - KeyEr...
FAILED tests/test_scicrunch.py::test_scicrunch_dataset_doi - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_doi - KeyErro...
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_ids - KeyErro...
FAILED tests/test_scicrunch.py::test_scicrunch_search - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_all_data - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_filter - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - KeyError: '...
FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - KeyError...
FAILED tests/test_scicrunch.py::test_getting_facets - KeyError: 'aggregations'
FAILED tests/test_scicrunch.py::test_create_identifier_query - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_create_anatomy_query - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_response_version - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_response_abi_plot - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_response_abi_scaffold - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_response_sample_subject_size - KeyError:...
FAILED tests/test_scicrunch.py::test_raw_response_structure - AssertionError:...
FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_getting_curies - KeyError: 'uberon'
FAILED tests/test_scicrunch.py::test_scaffold_files - KeyError: 'hits'
FAILED tests/test_scicrunch.py::test_finding_contextual_information - KeyErro...
FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - KeyEr...
====== 35 failed, 63 passed, 3 skipped, 14 warnings in 143.86s (0:02:23) =======
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #938 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE