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Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/12-Labours-API [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] Done The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/ABI-Software/12-labours-api.git > git init /home/cmiss/Jenkins/workspace/12-Labours-API # timeout=10 Fetching upstream changes from https://github.com/ABI-Software/12-labours-api.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/ABI-Software/12-labours-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/ABI-Software/12-labours-api.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/dev^{commit} # timeout=10 Checking out Revision e6165556d4b552bf1d9f7b2e25b634c455836286 (refs/remotes/origin/dev) > git config core.sparsecheckout # timeout=10 > git checkout -f e6165556d4b552bf1d9f7b2e25b634c455836286 # timeout=10 Commit message: "Merge pull request #34 from ddjnw1yu/query-facet" > git rev-list --no-walk e6165556d4b552bf1d9f7b2e25b634c455836286 # timeout=10 [12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda6618933781433708387.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API + pip install -r requirements.txt Requirement already satisfied: autopep8==2.0.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (2.0.2) Requirement already satisfied: fastapi==0.80.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (0.80.0) Requirement already satisfied: fastapi-utils==0.2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (0.2.1) Requirement already satisfied: gen3==4.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (4.19.1) Requirement already satisfied: gunicorn==20.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (20.1.0) Requirement already satisfied: PyJWT==2.7.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (2.7.0) Requirement already satisfied: 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: pycodestyle>=2.10.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==2.0.2->-r requirements.txt (line 1)) (2.10.0) Requirement already satisfied: tomli in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from autopep8==2.0.2->-r requirements.txt (line 1)) (2.0.1) Requirement already satisfied: starlette==0.19.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 2)) (0.19.1) Requirement already satisfied: pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from fastapi==0.80.0->-r requirements.txt (line 2)) (1.10.11) 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==4.19.1->-r requirements.txt (line 4)) (0.8.0) Requirement already satisfied: aiohttp in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (3.8.4) Requirement already satisfied: backoff in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (1.11.1) Requirement already satisfied: cdislogging<2.0.0,>=1.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (1.1.1) Requirement already satisfied: click in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (7.1.2) Requirement already satisfied: dataclasses-json in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (0.5.9) 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==4.19.1->-r requirements.txt (line 4)) (0.2.3) Requirement already satisfied: httpx in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (0.23.3) Requirement already satisfied: humanfriendly in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (10.0) Requirement already satisfied: indexclient in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (2.2.1) Requirement already satisfied: jsonschema in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (3.2.0) Requirement already satisfied: pandas<2.0.0,>=1.4.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (1.5.3) Requirement already satisfied: pypfb<1.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (0.5.24) Requirement already satisfied: python-dateutil in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (2.8.2) Requirement already satisfied: requests in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (2.31.0) Requirement already satisfied: tqdm<5.0.0,>=4.61.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (4.65.0) Requirement already satisfied: urllib3<2.0.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (1.26.16) Requirement already satisfied: xmltodict<0.14.0,>=0.13.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gen3==4.19.1->-r requirements.txt (line 4)) (0.13.0) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.1.0->-r requirements.txt (line 5)) (68.0.0) Requirement already satisfied: PrettyTable>=0.7.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from python-irodsclient==1.1.8->-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 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==4.19.1->-r requirements.txt (line 4)) (3.4.3) Requirement already satisfied: certifi in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) (2023.5.7) 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==4.19.1->-r requirements.txt (line 4)) (0.16.3) Requirement already satisfied: rfc3986[idna2008]<2,>=1.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) (1.5.0) Requirement already satisfied: sniffio in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) (1.3.0) Requirement already satisfied: pytz>=2020.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 4)) (2023.3) Requirement already satisfied: numpy>=1.20.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 4)) (1.25.1) 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==1.1.8->-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 4)) (5.4.1) Requirement already satisfied: dictionaryutils<4.0.0,>=3.4.3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) (3.4.6) Requirement already satisfied: fastavro<=1.5.4 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) (1.5.4) 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==4.19.1->-r requirements.txt (line 4)) (1.2.0) Requirement already satisfied: python-json-logger<0.2.0,>=0.1.11 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) (0.1.11) Requirement already satisfied: attrs>=17.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (23.1.0) Requirement already satisfied: charset-normalizer<4.0,>=2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (3.2.0) Requirement already satisfied: multidict<7.0,>=4.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (6.0.4) Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (4.0.2) 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==4.19.1->-r requirements.txt (line 4)) (1.9.2) Requirement already satisfied: frozenlist>=1.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (1.3.3) Requirement already satisfied: aiosignal>=1.1.2 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) (1.3.1) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from requests->gen3==4.19.1->-r requirements.txt (line 4)) (3.4) Requirement already satisfied: greenlet!=0.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 3)) (2.0.2) Requirement already satisfied: marshmallow<4.0.0,>=3.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 4)) (3.19.0) 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==4.19.1->-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==4.19.1->-r requirements.txt (line 4)) (0.9.0) Requirement already satisfied: pyrsistent>=0.14.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from jsonschema->gen3==4.19.1->-r requirements.txt (line 4)) (0.19.3) Requirement already satisfied: exceptiongroup 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==4.19.1->-r requirements.txt (line 4)) (23.1) Requirement already satisfied: mypy-extensions>=0.3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from typing-inspect>=0.4.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 4)) (1.0.0) [notice] A new release of pip is available: 23.1.2 -> 23.2.1 [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: 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) [notice] A new release of pip is available: 23.1.2 -> 23.2.1 [notice] To update, run: pip install --upgrade pip + 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 FFFFDefault filter dictionary has been updated. Default filter dictionary has been updated. Default filter dictionary has been updated. All expired users have been deleted. Default filter dictionary has been updated. All expired users have been deleted. F.FAll expired users have been deleted. All expired users have been deleted. F.All expired users have been deleted. FF [ 68%] tests/test_data.py ....F [100%] =================================== FAILURES =================================== ___________________________ test_create_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7f61c75da940> def test_create_gen3_access(client): missing_data = {} response = client.post("/access/token", json=missing_data) result = response.json() assert response.status_code == 400 assert result["detail"] == "Missing field in the request body" dummy_data = { "identity": "dummyemail@gmail.com>machine_id" } response = client.post("/access/token", json=dummy_data) result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_api.py:27: AssertionError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. Encounter an error while creating or using the session connection. ___________________________ test_revoke_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7f61c7717550> def test_revoke_gen3_access(client): dummy_data = { "identity": "dummyemail@gmail.com>machine_id" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() response = client.delete( > "/access/revoke", headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_api.py:39: KeyError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. ___________________________ test_get_gen3_dictionary ___________________________ client = <starlette.testclient.TestClient object at 0x7f61c7717d90> def test_get_gen3_dictionary(client): pass_case = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS], } response = client.post("/dictionary", json=pass_case) > assert response.status_code == 200 E assert 404 == 200 E + where 404 = <Response [404]>.status_code tests/test_api.py:50: AssertionError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. __________________________ test_get_gen3_node_records __________________________ client = <starlette.testclient.TestClient object at 0x7f61c77173d0> def test_get_gen3_node_records(client): NODE_TYPE = "experiment" pass_case = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS], } > response = client.post(f"/records/{NODE_TYPE}", json=pass_case) tests/test_api.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:637: 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:589: in request resp = self.send(prep, **send_kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: 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:277: 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:217: 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:232: in get_gen3_node_records node_record = SUBMISSION.export_node(program, project, node, "json") ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:384: in export_node output = requests.get(api_url, auth=self._auth_provider).text ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request prep = self.prepare_request(req) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request p.prepare( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare self.prepare_auth(auth, url) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth r = auth(self) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__ request.headers["Authorization"] = self._get_auth_value() ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value return "bearer " + self.get_access_token() ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token return self.refresh_access_token( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token self._access_token = get_access_token_with_key(self._refresh_token) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:77: in get_access_token_with_key return _handle_access_token_response(resp, token_key) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ resp = <Response [500]>, token_key = 'access_token' def _handle_access_token_response(resp, token_key): """ Shared helper for both get_access_token_with_key and get_access_token_from_wts """ err_msg = "Failed to get an access token from {}:\n{}" if resp.status_code != 200: > raise Gen3AuthError(err_msg.format(resp.url, resp.text)) E gen3.auth.Gen3AuthError: Failed to get an access token from https://gen3.abi-ctt-ctp.cloud.edu.au/user/credentials/cdis/access_token: E Internal Server Error ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:58: Gen3AuthError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. _____________________________ test_get_gen3_record _____________________________ client = <starlette.testclient.TestClient object at 0x7f61c5753b80> def test_get_gen3_record(client): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" pass_case = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS], } > response = client.post(f"/record/{UUID}", json=pass_case) tests/test_api.py:99: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:637: 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:589: in request resp = self.send(prep, **send_kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:703: 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:277: 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:217: 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:253: in get_gen3_record record = SUBMISSION.export_record(program, project, uuid, "json") ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:348: in export_record output = requests.get(api_url, auth=self._auth_provider).text ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:73: in get return request("get", url, params=params, **kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:59: in request return session.request(method=method, url=url, **kwargs) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:575: in request prep = self.prepare_request(req) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:486: in prepare_request p.prepare( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:372: in prepare self.prepare_auth(auth, url) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/models.py:603: in prepare_auth r = auth(self) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:325: in __call__ request.headers["Authorization"] = self._get_auth_value() ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:446: in _get_auth_value return "bearer " + self.get_access_token() ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:433: in get_access_token return self.refresh_access_token( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:367: in refresh_access_token self._access_token = get_access_token_with_key(self._refresh_token) ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:77: in get_access_token_with_key return _handle_access_token_response(resp, token_key) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ resp = <Response [500]>, token_key = 'access_token' def _handle_access_token_response(resp, token_key): """ Shared helper for both get_access_token_with_key and get_access_token_from_wts """ err_msg = "Failed to get an access token from {}:\n{}" if resp.status_code != 200: > raise Gen3AuthError(err_msg.format(resp.url, resp.text)) E gen3.auth.Gen3AuthError: Failed to get an access token from https://gen3.abi-ctt-ctp.cloud.edu.au/user/credentials/cdis/access_token: E Internal Server Error ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/auth.py:58: Gen3AuthError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. ___________________________ test_graphql_pagination ____________________________ client = <starlette.testclient.TestClient object at 0x7f61c579e040> def test_graphql_pagination(client): dummy_data = { "identity": "dummyemail@gmail.com>machine_id" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() filter_pass_case = { "filter": { "manifest_filter>additional_types": [ "Plot" ], "case_filter>species": [ "Rat" ], "case_filter>sex": [ "Male" ] } } response = client.post("/graphql/pagination/", json=filter_pass_case, > headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_api.py:178: KeyError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. _______________________________ test_get_filter ________________________________ client = <starlette.testclient.TestClient object at 0x7f61c573eac0> def test_get_filter(client): dummy_data = { "identity": "dummyemail@gmail.com>machine_id" } response = client.post("/access/token", json=dummy_data) dummy_token = response.json() response = client.get("/filter/?sidebar=true", > headers={"Authorization": f"Bearer {dummy_token['access_token']}"}) E KeyError: 'access_token' tests/test_api.py:239: KeyError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. __________________________ test_get_irods_collection ___________________________ client = <starlette.testclient.TestClient object at 0x7f61c59a7fd0> def test_get_irods_collection(client): pass_case_root = {} response = client.post("/collection", json=pass_case_root) result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_api.py:276: AssertionError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. ___________________________ test_get_irods_data_file ___________________________ client = <starlette.testclient.TestClient object at 0x7f61c566b1f0> def test_get_irods_data_file(client): ACTION = "preview" FILEPATH = "dataset-217-version-2/derivative/scaffold_context_info.json" response = client.get(f"/data/{ACTION}/{FILEPATH}") result = response.json() > assert response.status_code == 200 E assert 500 == 200 E + where 500 = <Response [500]>.status_code tests/test_api.py:309: AssertionError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection. All expired users have been deleted. ____________________________ test_irods_collection _____________________________ client = <starlette.testclient.TestClient object at 0x7f61c77058b0> def test_irods_collection(client): payload1 = { "path": "/dataset-217-version-2" } response = client.post("/collection", json=payload1) result = response.json() > assert result["folders"] == [ { "name": "derivative", "path": "/dataset-217-version-2/derivative" }, { "name": "primary", "path": "/dataset-217-version-2/primary" } ] E KeyError: 'folders' tests/test_data.py:286: KeyError ---------------------------- Captured stdout setup ----------------------------- Encounter an error while creating or using the session connection. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- Encounter an error while creating or using the session connection.All expired users have been deleted. =========================== short test summary info ============================ FAILED tests/test_api.py::test_create_gen3_access - assert 500 == 200 FAILED tests/test_api.py::test_revoke_gen3_access - KeyError: 'access_token' FAILED tests/test_api.py::test_get_gen3_dictionary - assert 404 == 200 FAILED tests/test_api.py::test_get_gen3_node_records - gen3.auth.Gen3AuthErro... FAILED tests/test_api.py::test_get_gen3_record - gen3.auth.Gen3AuthError: Fai... FAILED tests/test_api.py::test_graphql_pagination - KeyError: 'access_token' FAILED tests/test_api.py::test_get_filter - KeyError: 'access_token' FAILED tests/test_api.py::test_get_irods_collection - assert 500 == 200 FAILED tests/test_api.py::test_get_irods_data_file - assert 500 == 200 FAILED tests/test_data.py::test_irods_collection - KeyError: 'folders' ========================= 10 failed, 6 passed in 4.40s ========================= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1111 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE