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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 097f8bea021ca6de0897fb7fcca5632ee9a5679b # timeout=10 [12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda4971994903059277731.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)) (4.0.0) 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: exceptiongroup>=1.0.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio<5,>=3.4.0->starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 2)) (1.1.3) 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) Collecting anyio==3.6.2 (from -r requirements-dev.txt (line 3)) Using cached anyio-3.6.2-py3-none-any.whl (80 kB) 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) Installing collected packages: anyio Attempting uninstall: anyio Found existing installation: anyio 4.0.0 Uninstalling anyio-4.0.0: Successfully uninstalled anyio-4.0.0 Successfully installed anyio-3.6.2 + 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 FDefault filter dictionary has been updated. Default filter dictionary has been updated. F [ 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 0x7f8d048db970> 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... Gen3 disconnected Reconnecting...2... Gen3 disconnected Reconnecting...3... iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ___________________________ test_revoke_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7f8d04a5ac10> 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 0x7f8d04ace0d0> 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 0x7f8d0480d970> 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 0x7f8d0480d790> 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 0x7f8d048c78b0> 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 0x7f8d048328b0> 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 Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _________________________ test_get_gen3_metadata_file __________________________ client = <starlette.testclient.TestClient object at 0x7f8d04b352b0> 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 ----------------------------- iRODS disconnected Orthanc disconnected ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected _____________________________ test_experiment_node _____________________________ client = <starlette.testclient.TestClient object at 0x7f8d049ddc40> 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 ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ________________________ test_dataset_description_node _________________________ client = <starlette.testclient.TestClient object at 0x7f8d048324c0> 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 ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ______________________________ test_manifest_node ______________________________ client = <starlette.testclient.TestClient object at 0x7f8d04832790> 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 ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ________________________________ test_case_node ________________________________ client = <starlette.testclient.TestClient object at 0x7f8d049fcb50> 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 ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected __________________________ test_get_irods_collection ___________________________ client = <starlette.testclient.TestClient object at 0x7f8d04ab5100> 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 ----------------------------- Captured stdout call ----------------------------- iRODS disconnected Orthanc disconnected ___________________________ test_get_irods_data_file ___________________________ client = <starlette.testclient.TestClient object at 0x7f8d0493e820> 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 ----------------------------- Captured stdout call ----------------------------- Default filter dictionary has been updated. All expired users have been deleted. Default filter dictionary has been updated. Default filter dictionary has been updated. iRODS disconnected All expired users have been deleted. All expired users have been deleted. Orthanc disconnected ____________________________ test_irods_collection _____________________________ client = <starlette.testclient.TestClient object at 0x7f8d048e5cd0> 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 ----------------------------- All expired users have been deleted. All expired users have been deleted. Default filter dictionary has been updated. Default filter dictionary has been updated. All expired users have been deleted. All expired users have been deleted. 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 ----------------------------- Default filter dictionary has been updated. 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 Default filter dictionary has been updated. Orthanc disconnectedDefault filter dictionary has been updated. All expired users have been deleted. __________________________ test_get_orthanc_instance ___________________________ client = <starlette.testclient.TestClient object at 0x7f8d04954490> 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 ----------------------------- All expired users have been deleted. Default filter dictionary has been updated. All expired users have been deleted. 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. iRODS disconnected Orthanc disconnected _________________________ test_get_orthanc_dicom_file __________________________ client = <starlette.testclient.TestClient object at 0x7f8d04a419a0> 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 9.76s ============================== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1218 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE