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 b3a6fd4c141bed3d0c2c23396d58aeb1a6d89102 (refs/remotes/origin/dev)
> git config core.sparsecheckout # timeout=10
> git checkout -f b3a6fd4c141bed3d0c2c23396d58aeb1a6d89102 # timeout=10
Commit message: "Merge pull request #13 from david-jianwei-yu/update-filter"
> git rev-list --no-walk b3a6fd4c141bed3d0c2c23396d58aeb1a6d89102 # timeout=10
[12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda3004534410724497946.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: gen3==4.15.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (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 4)) (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 5)) (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 6)) (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 7)) (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 8)) (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: 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)) (1.10.4)
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: 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 3)) (0.5.7)
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 3)) (2.8.2)
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 3)) (3.2.0)
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 3)) (1.1.1)
Requirement already satisfied: click in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.15.0->-r requirements.txt (line 3)) (7.1.2)
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 3)) (0.2.3)
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 3)) (0.5.21)
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 3)) (0.8.0)
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 3)) (2.28.2)
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 3)) (10.0)
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 3)) (4.64.1)
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 3)) (3.8.3)
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 3)) (1.11.1)
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 3)) (1.5.3)
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 3)) (2.1.0)
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 3)) (0.23.3)
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)) (66.1.1)
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 6)) (0.7.1)
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 6)) (3.6.0)
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 6)) (1.16.0)
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 7)) (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 8)) (0.14.0)
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)) (4.4.0)
Requirement already satisfied: anyio<5,>=3.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 2)) (3.6.2)
Requirement already satisfied: 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 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==4.15.0->-r requirements.txt (line 3)) (2022.12.7)
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 3)) (1.5.0)
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 3)) (0.16.3)
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 3)) (1.3.0)
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 3)) (1.24.1)
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 3)) (2022.7.1)
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 6)) (0.2.6)
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 3)) (0.1.11)
Requirement already satisfied: fastavro<=1.4.1 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 3)) (1.4.1)
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 3)) (1.2.0)
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 3)) (3.4.4)
Requirement already satisfied: importlib_metadata<2.0.0,>=1.3.0 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 3)) (1.7.0)
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 3)) (5.4.1)
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 3)) (1.8.2)
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 3)) (22.2.0)
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 3)) (1.3.3)
Requirement already satisfied: charset-normalizer<3.0,>=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 3)) (2.1.1)
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 3)) (6.0.4)
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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 3)) (4.0.2)
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 3)) (3.4)
Requirement already satisfied: urllib3<1.27,>=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 3)) (1.26.14)
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 3)) (0.8.0)
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 3)) (1.5.1)
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 3)) (3.19.0)
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 3)) (0.19.3)
Requirement already satisfied: zipp>=0.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from importlib_metadata<2.0.0,>=1.3.0->pypfb<1.0.0->gen3==4.15.0->-r requirements.txt (line 3)) (3.11.0)
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 3)) (23.0)
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 3)) (0.4.3)
+ 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: 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)) (23.0)
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: 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)) (22.2.0)
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)) (1.0.0)
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)
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.16, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API
plugins: anyio-3.6.2
collected 12 items
tests/test_api.py ......F..... [100%]
=================================== FAILURES ===================================
___________________________ test_graphql_pagination ____________________________
client = <starlette.testclient.TestClient object at 0x7fb40e128d60>
def test_graphql_pagination(client):
filter_pass_case = {
"node": "experiment",
"filter": {
"1": {
"node": "manifest_filter",
"filter": {
"additional_types": [
"text/vnd.abi.plot+tab-separated-values",
"text/vnd.abi.plot+csv"
]
}
},
"2": {
"node": "case_filter",
"filter": {
"species": [
"Rattus norvegicus"
]
}
},
"3": {
"node": "dataset_description_filter",
"filter": {
"study_organ_system": [
"stomach"
]
}
},
"4": {
"node": "case_filter",
"filter": {
"sex": [
"Male"
]
}
}
},
"relation": "and"
}
> response = client.post("/graphql/pagination/", json=filter_pass_case)
tests/test_api.py:195:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:635: in post
return self.request("POST", url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:476: in request
return super().request(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:587: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:701: in send
r = adapter.send(request, **kwargs)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:270: in send
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:267: in send
portal.call(self.app, scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:283: in call
return cast(T_Retval, self.start_task_soon(func, *args).result())
/usr/lib/python3.9/concurrent/futures/_base.py:446: in result
return self.__get_result()
/usr/lib/python3.9/concurrent/futures/_base.py:391: in __get_result
raise self._exception
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/anyio/from_thread.py:219: in _call_func
retval = await retval
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/applications.py:269: in __call__
await super().__call__(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/applications.py:124: in __call__
await self.middleware_stack(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:184: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/errors.py:162: in __call__
await self.app(scope, receive, _send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/middleware/cors.py:84: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:93: in __call__
raise exc
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/exceptions.py:82: in __call__
await self.app(scope, receive, sender)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:21: in __call__
raise e
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py:18: in __call__
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:670: in __call__
await route.handle(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:266: in handle
await self.app(scope, receive, send)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/routing.py:65: in app
response = await func(request)
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:227: in app
raw_response = await run_endpoint_function(
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/fastapi/routing.py:160: in run_endpoint_function
return await dependant.call(**values)
app/main.py:395: in graphql_pagination
update_pagination_item(item, search)
app/main.py:335: in update_pagination_item
filter_dict["submitter_id"].append(f.get_filtered_datasets(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <app.filter.Filter object at 0x7fb40e9e37c0>, filter = {'sex': ['Male']}
data = [{'age_category': 'prime adult stage', 'id': 'dacc34db-93c4-4d32-b2cf-8fa725e27152', 'sex': 'Male', 'species': 'Mus mu...'prime adult stage', 'id': '051b64de-cc4d-4a23-875b-d1a7b4e46935', 'sex': 'Male', 'species': 'Mus musculus', ...}, ...]
def get_filtered_datasets(self, filter, data):
field = list(filter.keys())[0]
if field in FIELDS:
data = self.generate_filtered_datasets(filter, field, data)
dataset_list = set()
for record in data:
> dataset_list.add(re.findall(
'dataset-[0-9]*-version-[0-9]*', record["submitter_id"])[0])
E IndexError: list index out of range
app/filter.py:33: IndexError
----------------------------- Captured stdout call -----------------------------
[2023-01-27 15:11:10,088][WARNING] Unable to write access token to cache file. Exceeded number of retries.
=============================== warnings summary ===============================
app/sgqlc.py:23
/home/cmiss/Jenkins/workspace/12-Labours-API/app/sgqlc.py:23: DeprecationWarning: invalid escape sequence \{
'\'([_a-z]+)\'', r'\1', re.sub('\{([^{].*[^}])\}', r'\1', f'{item.filter}'))
app/search.py:37
app/search.py:37
/home/cmiss/Jenkins/workspace/12-Labours-API/app/search.py:37: DeprecationWarning: invalid escape sequence \s
f'(\s{keyword}|{keyword}\s)', result[DataObjectMeta.value])
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_api.py::test_graphql_pagination - IndexError: list index ou...
=================== 1 failed, 11 passed, 3 warnings in 4.34s ===================
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #19 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE