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] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9
/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
Using base prefix '/usr'
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python3.9
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda15997354082330586074.sh
+ pwd
+ export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API
+ pip install -r requirements.txt
Collecting autopep8==1.6.0 (from -r requirements.txt (line 1))
  Using cached autopep8-1.6.0-py2.py3-none-any.whl (45 kB)
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Collecting fastapi-utils==0.2.1 (from -r requirements.txt (line 3))
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Collecting pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 (from fastapi==0.80.0->-r requirements.txt (line 2))
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  Downloading SQLAlchemy-1.4.49-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
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  Downloading aiohttp-3.8.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB)
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Collecting cdislogging<2.0.0,>=1.1.0 (from gen3==4.15.0->-r requirements.txt (line 4))
  Using cached cdislogging-1.1.1.tar.gz (8.3 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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  Using cached drsclient-0.2.3.tar.gz (7.0 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting httpx (from gen3==4.15.0->-r requirements.txt (line 4))
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Collecting indexclient (from gen3==4.15.0->-r requirements.txt (line 4))
  Downloading indexclient-2.2.1.tar.gz (17 kB)
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Collecting jsonschema (from gen3==4.15.0->-r requirements.txt (line 4))
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Collecting pandas<2.0.0,>=1.4.2 (from gen3==4.15.0->-r requirements.txt (line 4))
  Using cached pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
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Collecting tqdm<5.0.0,>=4.61.2 (from gen3==4.15.0->-r requirements.txt (line 4))
  Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
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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)
Collecting six>=1.10.0 (from python-irodsclient==1.1.4->-r requirements.txt (line 7))
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Collecting PrettyTable>=0.7.2 (from python-irodsclient==1.1.4->-r requirements.txt (line 7))
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Collecting anyio<5,>=3.4.0 (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 2))
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Collecting httpcore<0.17.0,>=0.15.0 (from httpx->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting rfc3986[idna2008]<2,>=1.3 (from httpx->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting sniffio (from httpx->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting pytz>=2020.1 (from pandas<2.0.0,>=1.4.2->gen3==4.15.0->-r requirements.txt (line 4))
  Using cached pytz-2023.3-py2.py3-none-any.whl (502 kB)
Collecting numpy>=1.20.3 (from pandas<2.0.0,>=1.4.2->gen3==4.15.0->-r requirements.txt (line 4))
  Downloading numpy-1.25.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.7 MB)
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Collecting wcwidth (from PrettyTable>=0.7.2->python-irodsclient==1.1.4->-r requirements.txt (line 7))
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Collecting PyYAML<6.0.0,>=5.3.1 (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting click (from gen3==4.15.0->-r requirements.txt (line 4))
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Collecting dictionaryutils<4.0.0,>=3.4.3 (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4))
  Downloading dictionaryutils-3.4.6.tar.gz (14 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
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Collecting fastavro<=1.5.4 (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4))
  Downloading fastavro-1.5.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.6 MB)
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Collecting gdcdictionary<2.0.0,>=1.2.0 (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4))
  Using cached gdcdictionary-1.2.0.tar.gz (41 kB)
  Preparing metadata (setup.py): started
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Collecting python-json-logger<0.2.0,>=0.1.11 (from pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 4))
  Using cached python-json-logger-0.1.11.tar.gz (6.0 kB)
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Collecting attrs>=17.3.0 (from aiohttp->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting multidict<7.0,>=4.5 (from aiohttp->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting yarl<2.0,>=1.0 (from aiohttp->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting frozenlist>=1.1.1 (from aiohttp->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting aiosignal>=1.1.2 (from aiohttp->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting idna<4,>=2.5 (from requests->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting urllib3<3,>=1.21.1 (from requests->gen3==4.15.0->-r requirements.txt (line 4))
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Collecting greenlet!=0.4.17 (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 3))
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Collecting marshmallow<4.0.0,>=3.3.0 (from dataclasses-json->gen3==4.15.0->-r requirements.txt (line 4))
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Building wheels for collected packages: cdislogging, drsclient, indexclient, dictionaryutils, gdcdictionary, python-json-logger
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  Building wheel for gdcdictionary (setup.py): started
  Building wheel for gdcdictionary (setup.py): finished with status 'done'
  Created wheel for gdcdictionary: filename=gdcdictionary-1.2.0-py3-none-any.whl size=58325 sha256=8226183862026863524e8af64d747d19eef25242c1e9cb7393a9c904371cc92c
  Stored in directory: /home/cmiss/.cache/pip/wheels/bb/49/da/a08a40239a7e8d23f23e859f3522f2efaa59a82f8128968966
  Building wheel for python-json-logger (setup.py): started
  Building wheel for python-json-logger (setup.py): finished with status 'done'
  Created wheel for python-json-logger: filename=python_json_logger-0.1.11-py2.py3-none-any.whl size=5075 sha256=a112d28c00c5d725e2b5f0990ea7ccdc8a6229e632ae0a63e2e6a983767925cb
  Stored in directory: /home/cmiss/.cache/pip/wheels/cd/1a/89/a0c9b4fa33ccdd81cd3988a15e0dc055c1552da6db05fb3f91
Successfully built cdislogging drsclient indexclient dictionaryutils gdcdictionary python-json-logger
Installing collected packages: wcwidth, rfc3986, pytz, cdislogging, asyncio, urllib3, typing-extensions, tqdm, toml, sniffio, six, PyYAML, python-json-logger, python-dotenv, pyrsistent, pycodestyle, PrettyTable, packaging, numpy, mypy-extensions, multidict, idna, humanfriendly, h11, gunicorn, greenlet, graphql-core, frozenlist, fastavro, exceptiongroup, defusedxml, click, charset-normalizer, certifi, backoff, attrs, async-timeout, aiofiles, yarl, uvicorn, typing-inspect, sqlalchemy, sgqlc, requests, python-irodsclient, python-dateutil, pydantic, marshmallow, jsonschema, autopep8, anyio, aiosignal, starlette, pandas, marshmallow-enum, indexclient, httpcore, dictionaryutils, aiohttp, httpx, gdcdictionary, fastapi, dataclasses-json, fastapi-utils, drsclient, pypfb, gen3
Successfully installed PrettyTable-3.8.0 PyYAML-5.4.1 aiofiles-0.8.0 aiohttp-3.8.4 aiosignal-1.3.1 anyio-3.7.1 async-timeout-4.0.2 asyncio-3.4.3 attrs-23.1.0 autopep8-1.6.0 backoff-1.11.1 cdislogging-1.1.1 certifi-2023.5.7 charset-normalizer-3.2.0 click-7.1.2 dataclasses-json-0.5.9 defusedxml-0.7.1 dictionaryutils-3.4.6 drsclient-0.2.3 exceptiongroup-1.1.2 fastapi-0.80.0 fastapi-utils-0.2.1 fastavro-1.5.4 frozenlist-1.3.3 gdcdictionary-1.2.0 gen3-4.15.0 graphql-core-3.2.3 greenlet-2.0.2 gunicorn-20.1.0 h11-0.14.0 httpcore-0.16.3 httpx-0.23.3 humanfriendly-10.0 idna-3.4 indexclient-2.2.1 jsonschema-3.2.0 marshmallow-3.19.0 marshmallow-enum-1.5.1 multidict-6.0.4 mypy-extensions-1.0.0 numpy-1.25.1 packaging-23.1 pandas-1.5.3 pycodestyle-2.10.0 pydantic-1.10.11 pypfb-0.5.24 pyrsistent-0.19.3 python-dateutil-2.8.2 python-dotenv-0.20.0 python-irodsclient-1.1.4 python-json-logger-0.1.11 pytz-2023.3 requests-2.31.0 rfc3986-1.5.0 sgqlc-16.0 six-1.16.0 sniffio-1.3.0 sqlalchemy-1.4.49 starlette-0.19.1 toml-0.10.2 tqdm-4.65.0 typing-extensions-4.7.1 typing-inspect-0.9.0 urllib3-2.0.3 uvicorn-0.18.2 wcwidth-0.2.6 yarl-1.9.2
+ pip install -r requirements-dev.txt
Collecting pytest==7.1.2 (from -r requirements-dev.txt (line 1))
  Using cached pytest-7.1.2-py3-none-any.whl (297 kB)
Collecting pytest-timeout==2.1.0 (from -r requirements-dev.txt (line 2))
  Using cached pytest_timeout-2.1.0-py3-none-any.whl (12 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)
Collecting iniconfig (from pytest==7.1.2->-r requirements-dev.txt (line 1))
  Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
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)
Collecting pluggy<2.0,>=0.12 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
  Downloading pluggy-1.2.0-py3-none-any.whl (17 kB)
Collecting py>=1.8.2 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
  Using cached py-1.11.0-py2.py3-none-any.whl (98 kB)
Collecting tomli>=1.0.0 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
  Using cached tomli-2.0.1-py3-none-any.whl (12 kB)
Installing collected packages: tomli, py, pluggy, iniconfig, pytest, pytest-timeout
Successfully installed iniconfig-2.0.0 pluggy-1.2.0 py-1.11.0 pytest-7.1.2 pytest-timeout-2.1.0 tomli-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 6.93s ==============================
[Slack Notifications] found #838 as previous completed, non-aborted build
Finished: SUCCESS