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/shiningpanda6800353875855181380.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)) (1.10.12)
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 2)) (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 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)) (3.8.5)
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 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)) (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 3)) (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 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)) (0.5.26)
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 3)) (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 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)) (4.66.1)
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 3)) (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 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)) (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 6)) (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 8)) (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 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)) (4.7.1)
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 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)) (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 3)) (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 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)) (1.3.0)
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 3)) (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 3)) (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 8)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 3)) (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 2)) (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 3)) (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 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)) (0.19.3)
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 3)) (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 3)) (1.0.0)
[notice] A new release of pip is available: 23.2.1 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
+ pip install -r requirements-dev.txt
Requirement already satisfied: pytest==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)
[notice] A new release of pip is available: 23.2.1 -> 23.3.1
[notice] To update, run: pip install --upgrade pip
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.18, pytest-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 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 0x7f8e955a9c40>
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}
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 0x7f8e9568de20>
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 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}
------------------------------ Captured log call -------------------------------
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 0x7f8e955fc4c0>
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 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_revoke_access ______________________________
client = <starlette.testclient.TestClient object at 0x7f8e956e8580>
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 0x7f8e94465b80>
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 0x7f8e94419a60>
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 ------------------------------
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_get_gen3_graphql_pagination _______________________
client = <starlette.testclient.TestClient object at 0x7f8e9442f580>
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}
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_gen3_filter _____________________________
client = <starlette.testclient.TestClient object at 0x7f8e9446caf0>
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}
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 0x7f8e9446c370>
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 0x7f8e956d4b80>
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 ------------------------------
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_dataset_description_node _________________________
client = <starlette.testclient.TestClient object at 0x7f8e9442fdc0>
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
INFO app.main:main.py:183 Default filter has been updated.
______________________________ test_manifest_node ______________________________
client = <starlette.testclient.TestClient object at 0x7f8e94355040>
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}
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 0x7f8e94419580>
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 0x7f8e944193a0>
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}
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
=========================== 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 15.35s ====================
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #1379 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE