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 c27726ce377e89f4921a338d901243190f7747b3 (refs/remotes/origin/dev)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f c27726ce377e89f4921a338d901243190f7747b3 # timeout=10
Commit message: "Merge pull request #25 from ddjnw1yu/error-handling"
 > git rev-list --no-walk c27726ce377e89f4921a338d901243190f7747b3 # timeout=10
[12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda5922663012322026290.sh
+ pwd
+ export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API
+ pip install -r requirements.txt
Requirement already satisfied: autopep8==1.6.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (1.6.0)
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==4.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (4.15.0)
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: python-dotenv==0.20.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.20.0)
Requirement already satisfied: python-irodsclient==1.1.4 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (1.1.4)
Requirement already satisfied: sgqlc==16.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (16.0)
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 9)) (0.18.2)
Requirement already satisfied: pycodestyle>=2.8.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==1.6.0->-r requirements.txt (line 1)) (2.10.0)
Requirement already satisfied: toml in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==1.6.0->-r requirements.txt (line 1)) (0.10.2)
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 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)) (1.10.11)
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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (3.8.4)
Requirement already satisfied: backoff in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (0.5.9)
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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (0.5.24)
Requirement already satisfied: python-dateutil in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.15.0->-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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (4.65.0)
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)) (68.0.0)
Requirement already satisfied: six>=1.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.4->-r requirements.txt (line 7)) (1.16.0)
Requirement already satisfied: PrettyTable>=0.7.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.4->-r requirements.txt (line 7)) (3.8.0)
Requirement already satisfied: defusedxml in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.4->-r requirements.txt (line 7)) (0.7.1)
Requirement already satisfied: graphql-core in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sgqlc==16.0->-r requirements.txt (line 8)) (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 9)) (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)) (3.7.1)
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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (2023.5.7)
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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (2023.3)
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==4.15.0->-r requirements.txt (line 4)) (1.25.1)
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==1.1.4->-r requirements.txt (line 7)) (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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (3.4.6)
Requirement already satisfied: fastavro<=1.5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4)) (1.5.4)
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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (4.0.2)
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==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (1.3.3)
Requirement already satisfied: aiosignal>=1.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests->gen3==4.15.0->-r requirements.txt (line 4)) (2.0.3)
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,>=3.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.15.0->-r requirements.txt (line 4)) (3.19.0)
Requirement already satisfied: marshmallow-enum<2.0.0,>=1.5.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.15.0->-r requirements.txt (line 4)) (1.5.1)
Requirement already satisfied: typing-inspect>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.15.0->-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==4.15.0->-r requirements.txt (line 4)) (0.19.3)
Requirement already satisfied: exceptiongroup 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)) (1.1.2)
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,>=3.3.0->dataclasses-json->gen3==4.15.0->-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>=0.4.0->dataclasses-json->gen3==4.15.0->-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: 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)) (1.2.0)
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)
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.17, pytest-7.1.2, pluggy-1.2.0
rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API
plugins: anyio-3.7.1, timeout-2.1.0
collected 16 items

tests/test_api.py ...........                                            [ 68%]
tests/test_data.py .....                                                 [100%]

============================== 16 passed in 7.21s ==============================
[Slack Notifications] found #869 as previous completed, non-aborted build
Finished: SUCCESS