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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/shiningpanda11108180674744372443.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. F.All expired users have been deleted. FF.FF [ 68%] tests/test_data.py FFF.F [100%] =================================== FAILURES =================================== ___________________________ test_create_gen3_access ____________________________ client = <starlette.testclient.TestClient object at 0x7ff23b746970> 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 0x7ff23b87df40> 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 0x7ff23b87d370> 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 0x7ff23b6d5220> 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 0x7ff23a0b0bb0> 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 0x7ff23a468850> 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 0x7ff23a3f6340> 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. All expired users have been deleted. __________________________ test_get_irods_collection ___________________________ client = <starlette.testclient.TestClient object at 0x7ff23b836220> 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. All expired users have been deleted. --------------------------- Captured stdout teardown --------------------------- ___________________________ test_get_irods_data_file ___________________________ client = <starlette.testclient.TestClient object at 0x7ff23a401af0> 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_experiment_node _____________________________ client = <starlette.testclient.TestClient object at 0x7ff23a006490> def test_experiment_node(client): UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b" payload = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS] } > response = client.post( f"/record/{UUID}", json=payload) tests/test_data.py:23: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. ________________________ test_dataset_description_node _________________________ client = <starlette.testclient.TestClient object at 0x7ff23a616f40> def test_dataset_description_node(client): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" payload = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS] } > response = client.post( f"/record/{UUID}", json=payload) tests/test_data.py:65: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. ______________________________ test_manifest_node ______________________________ client = <starlette.testclient.TestClient object at 0x7ff23a0701c0> def test_manifest_node(client): UUID = "fd65a93f-ff62-45e4-b7b6-96419ef4f749" payload = { "access": [Gen3Config.GEN3_PUBLIC_ACCESS] } > response = client.post( f"/record/{UUID}", json=payload) tests/test_data.py:168: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../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. Default filter dictionary has been updated. ----------------------------- Captured stdout call ----------------------------- All expired users have been deleted. ____________________________ test_irods_collection _____________________________ client = <starlette.testclient.TestClient object at 0x7ff23a48a610> 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_experiment_node - gen3.auth.Gen3AuthError: Fa... FAILED tests/test_data.py::test_dataset_description_node - gen3.auth.Gen3Auth... FAILED tests/test_data.py::test_manifest_node - gen3.auth.Gen3AuthError: Fail... FAILED tests/test_data.py::test_irods_collection - KeyError: 'folders' ========================= 13 failed, 3 passed in 3.92s ========================= Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1113 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE