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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 e518e5b6e2d5918d4b1720a12ee64df3169a123e (refs/remotes/origin/dev) > git config core.sparsecheckout # timeout=10 > git checkout -f e518e5b6e2d5918d4b1720a12ee64df3169a123e # timeout=10 Commit message: "Merge pull request #40 from ddjnw1yu/anyio-issue" > git rev-list --no-walk e518e5b6e2d5918d4b1720a12ee64df3169a123e # timeout=10 [12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda8687838522750903330.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API + pip install -r requirements.txt Requirement already satisfied: autopep8==2.0.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (2.0.2) 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 2)) (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 3)) (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 4)) (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 5)) (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 6)) (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 7)) (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 8)) (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 9)) (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 10)) (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 11)) (0.18.2) Requirement already satisfied: pycodestyle>=2.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==2.0.2->-r requirements.txt (line 1)) (2.11.0) Requirement already satisfied: tomli in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==2.0.2->-r requirements.txt (line 1)) (2.0.1) 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 2)) (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 2)) (1.10.12) 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 3)) (1.4.49) 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 4)) (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 4)) (3.8.5) 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 4)) (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 4)) (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 4)) (7.1.2) 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 4)) (0.6.0) 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 4)) (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 4)) (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 4)) (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 4)) (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 4)) (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 4)) (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 4)) (0.5.26) 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 4)) (2.8.2) 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 4)) (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 4)) (4.66.1) 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 4)) (1.26.16) 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 4)) (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 5)) (68.1.2) 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 7)) (2.4.3) 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 9)) (3.8.0) 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 9)) (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 9)) (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 10)) (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 11)) (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 2)) (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 2)) (4.7.1) 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 4)) (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 4)) (2023.7.22) 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 4)) (0.16.3) Requirement already satisfied: rfc3986[idna2008]<2,>=1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) (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 4)) (1.3.0) 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 4)) (2023.3.post1) 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 4)) (1.25.2) 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 9)) (0.2.6) Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 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 4)) (5.4.1) Requirement already satisfied: dictionaryutils<4.0.0,>=3.4.3 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 4)) (3.4.6) 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 4)) (1.8.2) Requirement already satisfied: gdcdictionary<2.0.0,>=1.2.0 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 4)) (1.2.0) 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 4)) (0.1.11) 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 4)) (23.1.0) Requirement already satisfied: charset-normalizer<4.0,>=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (3.2.0) 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 4)) (6.0.4) Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (4.0.3) 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 4)) (1.9.2) 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 4)) (1.4.0) 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 4)) (1.3.1) 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 4)) (3.4) 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 3)) (2.0.2) 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 4)) (3.20.1) 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 4)) (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 4)) (0.19.3) 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 4)) (23.1) 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 4)) (1.0.0) + 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)) (23.1.0) 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)) (23.1) 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)) (1.3.0) 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)) (3.4) 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)) (1.3.0) + pytest ============================= test session starts ============================== platform linux -- Python 3.9.18, pytest-7.1.2, pluggy-1.3.0 rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API plugins: anyio-3.6.2, timeout-2.1.0 collected 17 items tests/test_gen3_api.py FFFFFFFF [ 47%] tests/test_gen3_data.py FFFF [ 70%] tests/test_irods_api.py FF [ 82%] tests/test_irods_data.py F [ 88%] tests/test_orthanc_api.py FF [100%] =================================== FAILURES =================================== ___________________________ test_create_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7fca89378a60> def test_create_gen3_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_gen3_api.py:19: AssertionError ---------------------------- Captured stdout setup ----------------------------- Gen3 disconnected Reconnecting...1... iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ___________________________ test_revoke_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7fca894aef10> def test_revoke_gen3_access(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() response = client.delete( > "/access/revoke", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:39: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ___________________________ test_get_gen3_dictionary ___________________________ client = <starlette.testclient.TestClient object at 0x7fca893a5c70> def test_get_gen3_dictionary(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() response = client.post( > "/dictionary", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:53: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _____________________________ test_get_gen3_record _____________________________ client = <starlette.testclient.TestClient object at 0x7fca89378880> def test_get_gen3_record(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( > f"/record/{UUID}", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:66: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _________________________ test_get_gen3_graphql_query __________________________ client = <starlette.testclient.TestClient object at 0x7fca89378ca0> def test_get_gen3_graphql_query(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() DATASET_ID = "dataset-217-version-2" pass_case = { "node": "experiment_query", "filter": { "submitter_id": [DATASET_ID] }, "search": "" } response = client.post("/graphql/query", json=pass_case, > headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:96: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _______________________ test_get_gen3_graphql_pagination _______________________ client = <starlette.testclient.TestClient object at 0x7fca894739a0> def test_get_gen3_graphql_pagination(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() 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 {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:148: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _____________________________ test_get_gen3_filter _____________________________ client = <starlette.testclient.TestClient object at 0x7fca89378d90> def test_get_gen3_filter(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() response = client.get("/filter/?sidebar=true", > headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:209: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Default filter dictionary has been updated. All expired users have been deleted. Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. Default filter dictionary has been updated. All expired users have been deleted. iRODS disconnected Orthanc disconnected _________________________ test_get_gen3_metadata_file __________________________ client = <starlette.testclient.TestClient object at 0x7fca89373580> def test_get_gen3_metadata_file(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b" FORM = "json" response = client.get(f"/metadata/download/{UUID}/{FORM}", > headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_api.py:239: KeyError ---------------------------- Captured stdout setup ----------------------------- Default filter dictionary has been updated. All expired users have been deleted. iRODS disconnected Default filter dictionary has been updated.Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Default filter dictionary has been updated. All expired users have been deleted. All expired users have been deleted. All expired users have been deleted. iRODS disconnected Orthanc disconnected _____________________________ test_experiment_node _____________________________ client = <starlette.testclient.TestClient object at 0x7fca895d1be0> def test_experiment_node(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b" response = client.get( > f"/record/{UUID}", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_data.py:27: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected ________________________ test_dataset_description_node _________________________ client = <starlette.testclient.TestClient object at 0x7fca89501520> def test_dataset_description_node(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( > f"/record/{UUID}", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_data.py:72: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected ______________________________ test_manifest_node ______________________________ client = <starlette.testclient.TestClient object at 0x7fca894d59a0> def test_manifest_node(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "fd65a93f-ff62-45e4-b7b6-96419ef4f749" response = client.get( > f"/record/{UUID}", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_data.py:178: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected ________________________________ test_case_node ________________________________ client = <starlette.testclient.TestClient object at 0x7fca89472910> def test_case_node(client): dummy_data = { "identity": "dummy_email@gmail.com>dummy_machine_id>dummy_expiration_time" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() UUID = "c58ab983-6cf9-4174-a7a9-20cdf1d6bc33" response = client.get( > f"/record/{UUID}", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_gen3_data.py:230: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected __________________________ test_get_irods_collection ___________________________ client = <starlette.testclient.TestClient object at 0x7fca89472220> def test_get_irods_collection(client): pass_case_root = {} response = client.post("/collection", json=pass_case_root) result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_irods_api.py:16: AssertionError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected ___________________________ test_get_irods_data_file ___________________________ client = <starlette.testclient.TestClient object at 0x7fca894ae700> def test_get_irods_data_file(client): ACTION = "preview" FILEPATH = "dataset-217-version-2/derivative/scaffold_context_info.json" response = client.get(f"/data/{ACTION}/{FILEPATH}") result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_irods_api.py:49: AssertionError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected ____________________________ test_irods_collection _____________________________ client = <starlette.testclient.TestClient object at 0x7fca8936e4c0> def test_irods_collection(client): payload1 = { "path": "/dataset-217-version-2" } response = client.post("/collection", json=payload1) result = response.json() > assert result["folders"] == [ { "name": "derivative", "path": "/dataset-217-version-2/derivative" }, { "name": "primary", "path": "/dataset-217-version-2/primary" } ] E KeyError: 'folders' tests/test_irods_data.py:18: KeyError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected __________________________ test_get_orthanc_instance ___________________________ client = <starlette.testclient.TestClient object at 0x7fca89477f70> def test_get_orthanc_instance(client): pass_case = { "study": "1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538", "series": "1.3.6.1.4.1.14519.5.2.1.175414966301645518238419021688341658582" } response = client.post("/instance", json=pass_case) result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_orthanc_api.py:19: AssertionError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected _________________________ test_get_orthanc_dicom_file __________________________ client = <starlette.testclient.TestClient object at 0x7fca89539a60> def test_get_orthanc_dicom_file(client): IDENTIFIER = "5490c29e-b24b6cf6-8ad2e2af-5056e4b5-e67f118e" response = client.get(f"/dicom/export/{IDENTIFIER}") > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_orthanc_api.py:41: AssertionError ---------------------------- Captured stdout setup ----------------------------- iRODS disconnected Orthanc disconnected Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. iRODS disconnected Orthanc disconnected =========================== short test summary info ============================ FAILED tests/test_gen3_api.py::test_create_gen3_access - assert 500 == 400 FAILED tests/test_gen3_api.py::test_revoke_gen3_access - KeyError: 'access_to... FAILED tests/test_gen3_api.py::test_get_gen3_dictionary - KeyError: 'access_t... FAILED tests/test_gen3_api.py::test_get_gen3_record - KeyError: 'access_token' FAILED tests/test_gen3_api.py::test_get_gen3_graphql_query - KeyError: 'acces... FAILED tests/test_gen3_api.py::test_get_gen3_graphql_pagination - KeyError: '... FAILED tests/test_gen3_api.py::test_get_gen3_filter - KeyError: 'access_token' FAILED tests/test_gen3_api.py::test_get_gen3_metadata_file - KeyError: 'acces... FAILED tests/test_gen3_data.py::test_experiment_node - KeyError: 'access_token' FAILED tests/test_gen3_data.py::test_dataset_description_node - KeyError: 'ac... FAILED tests/test_gen3_data.py::test_manifest_node - KeyError: 'access_token' FAILED tests/test_gen3_data.py::test_case_node - KeyError: 'access_token' FAILED tests/test_irods_api.py::test_get_irods_collection - assert 500 == 200 FAILED tests/test_irods_api.py::test_get_irods_data_file - assert 500 == 200 FAILED tests/test_irods_data.py::test_irods_collection - KeyError: 'folders' FAILED tests/test_orthanc_api.py::test_get_orthanc_instance - assert 500 == 200 FAILED tests/test_orthanc_api.py::test_get_orthanc_dicom_file - assert 500 ==... ============================== 17 failed in 4.49s ============================== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1229 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE