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Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/12-Labours-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/ABI-Software/12-labours-api.git > git init /home/cmiss/Jenkins/workspace/12-Labours-API # timeout=10 Fetching upstream changes from https://github.com/ABI-Software/12-labours-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/ABI-Software/12-labours-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/ABI-Software/12-labours-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/dev^{commit} # timeout=10 Checking out Revision fed7495860d0492a0d83f51077693f3de98e748d (refs/remotes/origin/dev) > git config core.sparsecheckout # timeout=10 > git checkout -f fed7495860d0492a0d83f51077693f3de98e748d # timeout=10 Commit message: "Merge pull request #43 from ddjnw1yu/access-control" > git rev-list --no-walk fed7495860d0492a0d83f51077693f3de98e748d # timeout=10 [12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda17924684921276847381.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API + pip install -r requirements.txt Requirement already satisfied: fastapi==0.80.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.80.0) Requirement already satisfied: fastapi-utils==0.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (0.2.1) Requirement already satisfied: gen3==4.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (4.19.1) Requirement already satisfied: gunicorn==20.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (20.1.0) Requirement already satisfied: PyJWT==2.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (2.7.0) Requirement already satisfied: pyorthanc==1.11.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (1.11.5) Requirement already satisfied: python-dotenv==0.20.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (0.20.0) Requirement already satisfied: python-irodsclient==1.1.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.8) Requirement already satisfied: sgqlc==16.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 9)) (16.3) Requirement already satisfied: uvicorn==0.18.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (0.18.2) Requirement already satisfied: starlette==0.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 1)) (0.19.1) Requirement already satisfied: pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 1)) (1.10.15) Requirement already satisfied: sqlalchemy<2.0.0,>=1.3.12 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi-utils==0.2.1->-r requirements.txt (line 2)) (1.4.52) Requirement already satisfied: aiofiles<0.9.0,>=0.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.8.0) Requirement already satisfied: aiohttp in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (3.9.5) Requirement already satisfied: backoff in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.11.1) Requirement already satisfied: cdislogging<2.0.0,>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.1.1) Requirement already satisfied: click in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (8.1.7) Requirement already satisfied: dataclasses-json in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.6.4) Requirement already satisfied: drsclient<0.3.0,>=0.2.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.2.3) Requirement already satisfied: httpx in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.23.3) Requirement already satisfied: humanfriendly in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (10.0) Requirement already satisfied: indexclient in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.2.1) Requirement already satisfied: jsonschema in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (3.2.0) Requirement already satisfied: pandas<2.0.0,>=1.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.5.3) Requirement already satisfied: pypfb<1.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.5.29) Requirement already satisfied: python-dateutil in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.9.0.post0) Requirement already satisfied: requests in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (2.31.0) Requirement already satisfied: tqdm<5.0.0,>=4.61.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (4.66.2) Requirement already satisfied: urllib3<2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (1.26.18) Requirement already satisfied: xmltodict<0.14.0,>=0.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 3)) (0.13.0) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.1.0->-r requirements.txt (line 4)) (69.5.1) Requirement already satisfied: pydicom<3.0.0,>=2.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pyorthanc==1.11.5->-r requirements.txt (line 6)) (2.4.4) Requirement already satisfied: PrettyTable>=0.7.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (3.10.0) Requirement already satisfied: defusedxml in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (0.7.1) Requirement already satisfied: six>=1.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) (1.16.0) Requirement already satisfied: graphql-core<4.0.0,>=3.1.7 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sgqlc==16.3->-r requirements.txt (line 9)) (3.2.3) Requirement already satisfied: h11>=0.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from uvicorn==0.18.2->-r requirements.txt (line 10)) (0.14.0) Requirement already satisfied: anyio<5,>=3.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) (3.6.2) Requirement already satisfied: typing-extensions>=3.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) (4.11.0) Requirement already satisfied: asyncio<4.0.0,>=3.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from drsclient<0.3.0,>=0.2.2->gen3==4.19.1->-r requirements.txt (line 3)) (3.4.3) Requirement already satisfied: certifi in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (2024.2.2) Requirement already satisfied: httpcore<0.17.0,>=0.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (0.16.3) Requirement already satisfied: rfc3986<2,>=1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from rfc3986[idna2008]<2,>=1.3->httpx->gen3==4.19.1->-r requirements.txt (line 3)) (1.5.0) Requirement already satisfied: sniffio in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) (1.3.1) Requirement already satisfied: pytz>=2020.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) (2024.1) Requirement already satisfied: numpy>=1.20.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) (1.26.4) Requirement already satisfied: wcwidth in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from PrettyTable>=0.7.2->python-irodsclient==1.1.8->-r requirements.txt (line 8)) (0.2.13) Requirement already satisfied: PyYAML<7.0.0,>=6.0.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (6.0.1) Requirement already satisfied: dictionaryutils<4.0.0,>=3.4.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (3.4.10) Requirement already satisfied: fastavro<1.9.0,>=1.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (1.8.4) Requirement already satisfied: gen3dictionary>=2.0.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (2.0.3) Requirement already satisfied: python-json-logger<0.2.0,>=0.1.11 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) (0.1.11) Requirement already satisfied: aiosignal>=1.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.3.1) Requirement already satisfied: attrs>=17.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (23.2.0) Requirement already satisfied: frozenlist>=1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.4.1) Requirement already satisfied: multidict<7.0,>=4.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (6.0.5) Requirement already satisfied: yarl<2.0,>=1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (1.9.4) Requirement already satisfied: async-timeout<5.0,>=4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) (4.0.3) Requirement already satisfied: charset-normalizer<4,>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests->gen3==4.19.1->-r requirements.txt (line 3)) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests->gen3==4.19.1->-r requirements.txt (line 3)) (3.7) Requirement already satisfied: greenlet!=0.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 2)) (3.0.3) Requirement already satisfied: marshmallow<4.0.0,>=3.18.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (3.21.1) Requirement already satisfied: typing-inspect<1,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (0.9.0) Requirement already satisfied: pyrsistent>=0.14.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) (0.20.0) Requirement already satisfied: packaging>=17.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from marshmallow<4.0.0,>=3.18.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (24.0) Requirement already satisfied: mypy-extensions>=0.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from typing-inspect<1,>=0.4.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) (1.0.0) [notice] A new release of pip is available: 24.0 -> 24.2 [notice] To update, run: pip install --upgrade pip + pip install -r requirements-dev.txt Requirement already satisfied: pytest==7.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 1)) (7.1.2) Requirement already satisfied: pytest-timeout==2.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 2)) (2.1.0) Requirement already satisfied: anyio==3.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements-dev.txt (line 3)) (3.6.2) Requirement already satisfied: attrs>=19.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (23.2.0) Requirement already satisfied: iniconfig in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (2.0.0) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (24.0) Requirement already satisfied: pluggy<2.0,>=0.12 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (1.5.0) Requirement already satisfied: py>=1.8.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (1.11.0) Requirement already satisfied: tomli>=1.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (2.0.1) Requirement already satisfied: idna>=2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (3.7) Requirement already satisfied: sniffio>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (1.3.1) [notice] A new release of pip is available: 24.0 -> 24.2 [notice] To update, run: pip install --upgrade pip + pytest ============================= test session starts ============================== platform linux -- Python 3.9.19, pytest-7.1.2, pluggy-1.5.0 rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API plugins: anyio-3.6.2, timeout-2.1.0 collected 39 items tests/test_api/test_access_api.py FFF [ 7%] tests/test_api/test_gen3_api.py FFFF [ 17%] tests/test_api/test_irods_api.py FE [ 23%] tests/test_api/test_orthanc_api.py .. [ 28%] tests/test_data/test_gen3_data.py FFFF [ 38%] tests/test_data/test_irods_data.py F [ 41%] tests/test_function/test_filter/test_filter_editor.py .. [ 46%] tests/test_function/test_filter/test_filter_formatter.py .... [ 56%] tests/test_function/test_filter/test_filter_generator.py ... [ 64%] tests/test_function/test_filter/test_filter_logic.py ... [ 71%] tests/test_function/test_pagination/test_pagination_formatter.py . [ 74%] tests/test_function/test_query/test_query_formatter.py ...... [ 89%] tests/test_function/test_search/test_search_logic.py .... [100%] ==================================== ERRORS ==================================== __________________ ERROR at setup of test_get_irods_data_file __________________ client = <starlette.testclient.TestClient object at 0x7f61424f4af0> token = {'detail': 'Please check the service (Gen3/iRODS) status'} @pytest.fixture def one_off_token(client, token): response = client.get( "/access/oneoff", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_irods_api.py:28: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} INFO app.main:main.py:183 Default filter has been updated. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 =================================== FAILURES =================================== ______________________________ test_create_access ______________________________ client = <starlette.testclient.TestClient object at 0x7f6142f7de80> def test_create_access(client): missing_data = {} response = client.post("/access/token", json=missing_data) result = response.json() > assert response.status_code == 400 E assert 500 == 400 E + where 500 = <Response [500]>.status_code tests/test_api/test_access_api.py:28: AssertionError ------------------------------ Captured log setup ------------------------------ WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...1... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...2... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...3... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...4... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...5... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...6... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...7... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...8... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...9... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...10... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...11... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. WARNING services.gen3.gen3_service:gen3_service.py:102 Reconnecting...12... WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. ERROR services.gen3.gen3_service:gen3_service.py:98 Hit the max retry limit. Unable to reconnect. ERROR services.gen3.gen3_service:gen3_service.py:99 Failed to get an access token from https://gen3.abi-ctt-ctp.cloud.edu.au/user/credentials/cdis/access_token: Internal Server Error WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ------------------------------ Captured log call ------------------------------- WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. ERROR services.gen3.gen3_service:gen3_service.py:98 Hit the max retry limit. Unable to reconnect. ERROR services.gen3.gen3_service:gen3_service.py:99 Failed to get an access token from https://gen3.abi-ctt-ctp.cloud.edu.au/user/credentials/cdis/access_token: Internal Server Error WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 __________________________ test_create_one_off_access __________________________ client = <starlette.testclient.TestClient object at 0x7f6142e79160> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_create_one_off_access(client, token): response = client.get( "/access/oneoff", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_access_api.py:45: KeyError ------------------------------ Captured log setup ------------------------------ WARNING services.gen3.gen3_service:gen3_service.py:94 Gen3 disconnected. ERROR services.gen3.gen3_service:gen3_service.py:98 Hit the max retry limit. Unable to reconnect. ERROR services.gen3.gen3_service:gen3_service.py:99 Failed to get an access token from https://gen3.abi-ctt-ctp.cloud.edu.au/user/credentials/cdis/access_token: Internal Server Error WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ______________________________ test_revoke_access ______________________________ client = <starlette.testclient.TestClient object at 0x7f6142ef4910> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_revoke_access(client, token): response = client.delete( "/access/revoke", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_access_api.py:55: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_get_gen3_record _____________________________ client = <starlette.testclient.TestClient object at 0x7f6142f0b370> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_record(client, token): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:28: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _________________________ test_get_gen3_graphql_query __________________________ client = <starlette.testclient.TestClient object at 0x7f6142f34d30> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_graphql_query(client, token): DATASET_ID = "dataset-217-version-2" pass_case = { "node": "experiment_query", "filter": {"submitter_id": [DATASET_ID]}, "search": "", } response = client.post( "/graphql/query?mode=data", json=pass_case, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:57: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _______________________ test_get_gen3_graphql_pagination _______________________ client = <starlette.testclient.TestClient object at 0x7f6142dc7e80> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_graphql_pagination(client, token): filter_pass_case = { "filter": { "dataset_description_filter>study_organ_system": ["Stomach", "Vagus nerve"], "manifest_filter>additional_types": ["Plot"], "case_filter>species": ["Rat"], "case_filter>sex": ["Male"], } } response = client.post( "/graphql/pagination", json=filter_pass_case, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:164: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_get_gen3_filter _____________________________ client = <starlette.testclient.TestClient object at 0x7f6142ded2e0> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_filter(client, token): response = client.get( "/filter?sidebar=true", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:230: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} INFO app.main:main.py:183 Default filter has been updated. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 __________________________ test_get_irods_collection ___________________________ client = <starlette.testclient.TestClient object at 0x7f6142dcfc40> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_irods_collection(client, token): pass_case_root = {} response = client.post( "/collection", json=pass_case_root, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_irods_api.py:38: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_experiment_node _____________________________ client = <starlette.testclient.TestClient object at 0x7f6140477820> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_experiment_node(client, token): UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:33: KeyError ------------------------------ Captured log setup ------------------------------ INFO app.main:main.py:183 Default filter has been updated. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ________________________ test_dataset_description_node _________________________ client = <starlette.testclient.TestClient object at 0x7f6142e3c940> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_dataset_description_node(client, token): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:74: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ______________________________ test_manifest_node ______________________________ client = <starlette.testclient.TestClient object at 0x7f6142e3c0a0> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_manifest_node(client, token): UUID = "fd65a93f-ff62-45e4-b7b6-96419ef4f749" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:175: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} INFO app.main:main.py:183 Default filter has been updated. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ________________________________ test_case_node ________________________________ client = <starlette.testclient.TestClient object at 0x7f6142f0ba30> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_case_node(client, token): UUID = "c58ab983-6cf9-4174-a7a9-20cdf1d6bc33" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:229: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ____________________________ test_irods_collection _____________________________ client = <starlette.testclient.TestClient object at 0x7f614042ac10> token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_irods_collection(client, token): payload1 = {"path": "/dataset-217-version-2"} response = client.post( "/collection", json=payload1, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_irods_data.py:29: KeyError ------------------------------ Captured log setup ------------------------------ WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': True, 'irods': False, 'orthanc': True} WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ---------------------------- Captured log teardown ----------------------------- INFO app.main:main.py:183 Default filter has been updated. =========================== short test summary info ============================ FAILED tests/test_api/test_access_api.py::test_create_access - assert 500 == 400 FAILED tests/test_api/test_access_api.py::test_create_one_off_access - KeyErr... FAILED tests/test_api/test_access_api.py::test_revoke_access - KeyError: 'acc... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_record - KeyError: 'acc... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_query - KeyErro... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_pagination - Ke... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_filter - KeyError: 'acc... FAILED tests/test_api/test_irods_api.py::test_get_irods_collection - KeyError... FAILED tests/test_data/test_gen3_data.py::test_experiment_node - KeyError: 'a... FAILED tests/test_data/test_gen3_data.py::test_dataset_description_node - Key... FAILED tests/test_data/test_gen3_data.py::test_manifest_node - KeyError: 'acc... FAILED tests/test_data/test_gen3_data.py::test_case_node - KeyError: 'access_... FAILED tests/test_data/test_irods_data.py::test_irods_collection - KeyError: ... ERROR tests/test_api/test_irods_api.py::test_get_irods_data_file - KeyError: ... ============== 13 failed, 25 passed, 1 error in 83.38s (0:01:23) =============== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #2636 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE