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 fed7495860d0492a0d83f51077693f3de98e748d (refs/remotes/origin/dev) > git config core.sparsecheckout # timeout=10 > git checkout -f fed7495860d0492a0d83f51077693f3de98e748d # timeout=10 Commit message: "Merge pull request #43 from ddjnw1yu/access-control" > git rev-list --no-walk fed7495860d0492a0d83f51077693f3de98e748d # timeout=10 [12-Labours-API] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9 /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp Using base prefix '/usr' New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python3.9 Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python Installing setuptools, pip, wheel...done. [12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda3356911864359777699.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API + pip install -r requirements.txt Collecting fastapi==0.80.0 (from -r requirements.txt (line 1)) Downloading fastapi-0.80.0-py3-none-any.whl.metadata (25 kB) Collecting fastapi-utils==0.2.1 (from -r requirements.txt (line 2)) Downloading fastapi_utils-0.2.1-py3-none-any.whl.metadata (4.8 kB) Collecting gen3==4.19.1 (from -r requirements.txt (line 3)) Downloading gen3-4.19.1-py3-none-any.whl.metadata (1.3 kB) Collecting gunicorn==20.1.0 (from -r requirements.txt (line 4)) Downloading gunicorn-20.1.0-py3-none-any.whl.metadata (3.8 kB) Collecting PyJWT==2.7.0 (from -r requirements.txt (line 5)) Downloading PyJWT-2.7.0-py3-none-any.whl.metadata (4.1 kB) Collecting pyorthanc==1.11.5 (from -r requirements.txt (line 6)) Downloading pyorthanc-1.11.5-py3-none-any.whl.metadata (7.6 kB) Collecting python-dotenv==0.20.0 (from -r requirements.txt (line 7)) Downloading python_dotenv-0.20.0-py3-none-any.whl.metadata (19 kB) Collecting python-irodsclient==1.1.8 (from -r requirements.txt (line 8)) Downloading python_irodsclient-1.1.8-py2.py3-none-any.whl.metadata (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 3.2 MB/s eta 0:00:00 Collecting sgqlc==16.3 (from -r requirements.txt (line 9)) Downloading sgqlc-16.3-py3-none-any.whl.metadata (18 kB) Collecting uvicorn==0.18.2 (from -r requirements.txt (line 10)) Downloading uvicorn-0.18.2-py3-none-any.whl.metadata (6.2 kB) Collecting starlette==0.19.1 (from fastapi==0.80.0->-r requirements.txt (line 1)) Downloading starlette-0.19.1-py3-none-any.whl.metadata (5.6 kB) Collecting pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 (from fastapi==0.80.0->-r requirements.txt (line 1)) Downloading pydantic-1.10.15-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (150 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 150.6/150.6 kB 10.4 MB/s eta 0:00:00 Collecting sqlalchemy<2.0.0,>=1.3.12 (from fastapi-utils==0.2.1->-r requirements.txt (line 2)) Downloading SQLAlchemy-1.4.52-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB) Collecting aiofiles<0.9.0,>=0.8.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading aiofiles-0.8.0-py3-none-any.whl.metadata (7.0 kB) Collecting aiohttp (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading aiohttp-3.9.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.5 kB) Collecting backoff (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading backoff-2.2.1-py3-none-any.whl.metadata (14 kB) Collecting cdislogging<2.0.0,>=1.1.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached cdislogging-1.1.1-py3-none-any.whl Collecting click (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting dataclasses-json (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading dataclasses_json-0.6.4-py3-none-any.whl.metadata (25 kB) Collecting drsclient<0.3.0,>=0.2.2 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached drsclient-0.2.3-py3-none-any.whl Collecting httpx (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB) Collecting humanfriendly (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) Collecting indexclient (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached indexclient-2.2.1-py3-none-any.whl Collecting jsonschema (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB) Collecting pandas<2.0.0,>=1.4.2 (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting pypfb<1.0.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading pypfb-0.5.29-py3-none-any.whl.metadata (912 bytes) Collecting python-dateutil (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting requests (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting tqdm<5.0.0,>=4.61.2 (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 3.9 MB/s eta 0:00:00 Collecting urllib3<2.0.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB) Collecting xmltodict<0.14.0,>=0.13.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading xmltodict-0.13.0-py2.py3-none-any.whl.metadata (7.7 kB) Requirement already satisfied: setuptools>=3.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from gunicorn==20.1.0->-r requirements.txt (line 4)) (69.5.1) Collecting httpx (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading httpx-0.23.3-py3-none-any.whl.metadata (7.1 kB) Collecting pydicom<3.0.0,>=2.3.0 (from pyorthanc==1.11.5->-r requirements.txt (line 6)) Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB) Collecting PrettyTable>=0.7.2 (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) Downloading prettytable-3.10.0-py3-none-any.whl.metadata (30 kB) Collecting defusedxml (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB) Collecting six>=1.10.0 (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting graphql-core<4.0.0,>=3.1.7 (from sgqlc==16.3->-r requirements.txt (line 9)) Downloading graphql_core-3.2.3-py3-none-any.whl.metadata (10 kB) Collecting h11>=0.8 (from uvicorn==0.18.2->-r requirements.txt (line 10)) Downloading h11-0.14.0-py3-none-any.whl.metadata (8.2 kB) Collecting anyio<5,>=3.4.0 (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) Downloading anyio-4.3.0-py3-none-any.whl.metadata (4.6 kB) Collecting typing-extensions>=3.10.0 (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) Using cached typing_extensions-4.11.0-py3-none-any.whl.metadata (3.0 kB) Collecting asyncio<4.0.0,>=3.4.3 (from drsclient<0.3.0,>=0.2.2->gen3==4.19.1->-r requirements.txt (line 3)) Downloading asyncio-3.4.3-py3-none-any.whl.metadata (1.7 kB) Collecting backoff (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading backoff-1.11.1-py2.py3-none-any.whl.metadata (12 kB) Collecting certifi (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Collecting httpcore<0.17.0,>=0.15.0 (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) Downloading httpcore-0.16.3-py3-none-any.whl.metadata (16 kB) Collecting rfc3986<2,>=1.3 (from rfc3986[idna2008]<2,>=1.3->httpx->gen3==4.19.1->-r requirements.txt (line 3)) Downloading rfc3986-1.5.0-py2.py3-none-any.whl.metadata (6.5 kB) Collecting sniffio (from httpx->gen3==4.19.1->-r requirements.txt (line 3)) Downloading sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB) Collecting pytz>=2020.1 (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB) Collecting numpy>=1.20.3 (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 3)) Downloading numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 3.5 MB/s eta 0:00:00 Collecting wcwidth (from PrettyTable>=0.7.2->python-irodsclient==1.1.8->-r requirements.txt (line 8)) Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) Collecting PyYAML<7.0.0,>=6.0.1 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Downloading PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting dictionaryutils<4.0.0,>=3.4.8 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Downloading dictionaryutils-3.4.10.tar.gz (14 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting fastavro<1.9.0,>=1.8.2 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Downloading fastavro-1.8.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB) Collecting gen3dictionary>=2.0.3 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Downloading gen3dictionary-2.0.3.tar.gz (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.9/47.9 kB 3.3 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting python-json-logger<0.2.0,>=0.1.11 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Using cached python_json_logger-0.1.11-py2.py3-none-any.whl Collecting aiosignal>=1.1.2 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading aiosignal-1.3.1-py3-none-any.whl.metadata (4.0 kB) Collecting attrs>=17.3.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Using cached attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB) Collecting frozenlist>=1.1.1 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading frozenlist-1.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB) Collecting multidict<7.0,>=4.5 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading multidict-6.0.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB) Collecting yarl<2.0,>=1.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading yarl-1.9.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB) Collecting async-timeout<5.0,>=4.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading async_timeout-4.0.3-py3-none-any.whl.metadata (4.2 kB) Collecting charset-normalizer<4,>=2 (from requests->gen3==4.19.1->-r requirements.txt (line 3)) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB) Collecting idna<4,>=2.5 (from requests->gen3==4.19.1->-r requirements.txt (line 3)) Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB) Collecting greenlet!=0.4.17 (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 2)) Downloading greenlet-3.0.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB) Collecting marshmallow<4.0.0,>=3.18.0 (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) Downloading marshmallow-3.21.1-py3-none-any.whl.metadata (7.2 kB) Collecting typing-inspect<1,>=0.4.0 (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) Downloading typing_inspect-0.9.0-py3-none-any.whl.metadata (1.5 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB) Collecting referencing>=0.28.4 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) Downloading referencing-0.34.0-py3-none-any.whl.metadata (2.8 kB) Collecting rpds-py>=0.7.1 (from 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typing_inspect-0.9.0-py3-none-any.whl (8.8 kB) Downloading yarl-1.9.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (304 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 304.3/304.3 kB 20.3 MB/s eta 0:00:00 Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading exceptiongroup-1.2.1-py3-none-any.whl (16 kB) Using cached mypy_extensions-1.0.0-py3-none-any.whl (4.7 kB) Using cached packaging-24.0-py3-none-any.whl (53 kB) Building wheels for collected packages: dictionaryutils, gen3dictionary Building wheel for dictionaryutils (pyproject.toml): started Building wheel for dictionaryutils (pyproject.toml): finished with status 'done' Created wheel for dictionaryutils: filename=dictionaryutils-3.4.10-py3-none-any.whl size=15783 sha256=b92db6e384d6289adf4f307756c1b78abefa70a0d599da949ec94277a2ef4385 Stored in directory: /home/cmiss/.cache/pip/wheels/53/ec/a4/a406da1729fabc06a2958c390216e7afc4dceea890f861dc86 Building wheel for gen3dictionary (pyproject.toml): started Building wheel for gen3dictionary (pyproject.toml): finished with status 'done' Created wheel for gen3dictionary: filename=gen3dictionary-2.0.3-py3-none-any.whl size=73344 sha256=b8392788e11369edd7ea3a81ab9365deddbad5c08c677edfcf15cf667308fc0d Stored in directory: /home/cmiss/.cache/pip/wheels/e6/5d/87/89d7db1d183d2a6045eea55f727953d4ff6ffab35a6200e2aa Successfully built dictionaryutils gen3dictionary Installing collected packages: wcwidth, rfc3986, pytz, cdislogging, asyncio, xmltodict, urllib3, typing-extensions, tqdm, sniffio, six, PyYAML, python-json-logger, python-dotenv, pyrsistent, PyJWT, pydicom, PrettyTable, packaging, numpy, mypy-extensions, multidict, idna, humanfriendly, h11, gunicorn, greenlet, graphql-core, frozenlist, fastavro, exceptiongroup, defusedxml, click, charset-normalizer, certifi, backoff, attrs, async-timeout, aiofiles, yarl, uvicorn, typing-inspect, sqlalchemy, sgqlc, requests, python-irodsclient, python-dateutil, pydantic, marshmallow, jsonschema, anyio, aiosignal, starlette, pandas, indexclient, httpcore, dictionaryutils, dataclasses-json, aiohttp, httpx, gen3dictionary, fastapi, pyorthanc, fastapi-utils, drsclient, pypfb, gen3 Successfully installed PrettyTable-3.10.0 PyJWT-2.7.0 PyYAML-6.0.1 aiofiles-0.8.0 aiohttp-3.9.5 aiosignal-1.3.1 anyio-4.3.0 async-timeout-4.0.3 asyncio-3.4.3 attrs-23.2.0 backoff-1.11.1 cdislogging-1.1.1 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 dataclasses-json-0.6.4 defusedxml-0.7.1 dictionaryutils-3.4.10 drsclient-0.2.3 exceptiongroup-1.2.1 fastapi-0.80.0 fastapi-utils-0.2.1 fastavro-1.8.4 frozenlist-1.4.1 gen3-4.19.1 gen3dictionary-2.0.3 graphql-core-3.2.3 greenlet-3.0.3 gunicorn-20.1.0 h11-0.14.0 httpcore-0.16.3 httpx-0.23.3 humanfriendly-10.0 idna-3.7 indexclient-2.2.1 jsonschema-3.2.0 marshmallow-3.21.1 multidict-6.0.5 mypy-extensions-1.0.0 numpy-1.26.4 packaging-24.0 pandas-1.5.3 pydantic-1.10.15 pydicom-2.4.4 pyorthanc-1.11.5 pypfb-0.5.29 pyrsistent-0.20.0 python-dateutil-2.9.0.post0 python-dotenv-0.20.0 python-irodsclient-1.1.8 python-json-logger-0.1.11 pytz-2024.1 requests-2.31.0 rfc3986-1.5.0 sgqlc-16.3 six-1.16.0 sniffio-1.3.1 sqlalchemy-1.4.52 starlette-0.19.1 tqdm-4.66.2 typing-extensions-4.11.0 typing-inspect-0.9.0 urllib3-1.26.18 uvicorn-0.18.2 wcwidth-0.2.13 xmltodict-0.13.0 yarl-1.9.4 + pip install -r requirements-dev.txt Collecting pytest==7.1.2 (from -r requirements-dev.txt (line 1)) Downloading pytest-7.1.2-py3-none-any.whl.metadata (7.8 kB) Collecting pytest-timeout==2.1.0 (from -r requirements-dev.txt (line 2)) Downloading pytest_timeout-2.1.0-py3-none-any.whl.metadata (16 kB) Collecting anyio==3.6.2 (from -r requirements-dev.txt (line 3)) Downloading anyio-3.6.2-py3-none-any.whl.metadata (4.7 kB) Requirement already satisfied: attrs>=19.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (23.2.0) Collecting iniconfig (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Using cached iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB) Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (24.0) Collecting pluggy<2.0,>=0.12 (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Downloading pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB) Collecting py>=1.8.2 (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Using cached py-1.11.0-py2.py3-none-any.whl.metadata (2.8 kB) Collecting tomli>=1.0.0 (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB) Requirement already satisfied: idna>=2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (3.7) Requirement already satisfied: sniffio>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (1.3.1) Downloading pytest-7.1.2-py3-none-any.whl (297 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 297.0/297.0 kB 15.2 MB/s eta 0:00:00 Downloading pytest_timeout-2.1.0-py3-none-any.whl (12 kB) Downloading anyio-3.6.2-py3-none-any.whl (80 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.6/80.6 kB 5.4 MB/s eta 0:00:00 Downloading pluggy-1.5.0-py3-none-any.whl (20 kB) Using cached py-1.11.0-py2.py3-none-any.whl (98 kB) Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB) Installing collected packages: tomli, py, pluggy, iniconfig, anyio, pytest, pytest-timeout Attempting uninstall: anyio Found existing installation: anyio 4.3.0 Uninstalling anyio-4.3.0: Successfully uninstalled anyio-4.3.0 Successfully installed anyio-3.6.2 iniconfig-2.0.0 pluggy-1.5.0 py-1.11.0 pytest-7.1.2 pytest-timeout-2.1.0 tomli-2.0.1 + pytest ============================= test session starts ============================== platform linux -- Python 3.9.19, pytest-7.1.2, pluggy-1.5.0 rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API plugins: anyio-3.6.2, timeout-2.1.0 collected 39 items tests/test_api/test_access_api.py FFF [ 7%] tests/test_api/test_gen3_api.py FFFF [ 17%] tests/test_api/test_irods_api.py FE [ 23%] tests/test_api/test_orthanc_api.py .. [ 28%] tests/test_data/test_gen3_data.py FFFF [ 38%] tests/test_data/test_irods_data.py F [ 41%] tests/test_function/test_filter/test_filter_editor.py .. [ 46%] tests/test_function/test_filter/test_filter_formatter.py .... [ 56%] tests/test_function/test_filter/test_filter_generator.py ... [ 64%] tests/test_function/test_filter/test_filter_logic.py ... [ 71%] tests/test_function/test_pagination/test_pagination_formatter.py . [ 74%] tests/test_function/test_query/test_query_formatter.py ...... [ 89%] tests/test_function/test_search/test_search_logic.py .... [100%] ==================================== ERRORS ==================================== __________________ ERROR at setup of test_get_irods_data_file __________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} @pytest.fixture def one_off_token(client, token): response = client.get( "/access/oneoff", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_irods_api.py:28: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 =================================== FAILURES =================================== ______________________________ test_create_access ______________________________ client = def test_create_access(client): missing_data = {} response = client.post("/access/token", json=missing_data) result = response.json() > assert response.status_code == 400 E assert 500 == 400 E + where 500 = .status_code tests/test_api/test_access_api.py:28: AssertionError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ------------------------------ Captured log call ------------------------------- ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 __________________________ test_create_one_off_access __________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_create_one_off_access(client, token): response = client.get( "/access/oneoff", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_access_api.py:45: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ______________________________ test_revoke_access ______________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_revoke_access(client, token): response = client.delete( "/access/revoke", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_access_api.py:55: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_get_gen3_record _____________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_record(client, token): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:28: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _________________________ test_get_gen3_graphql_query __________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_graphql_query(client, token): DATASET_ID = "dataset-217-version-2" pass_case = { "node": "experiment_query", "filter": {"submitter_id": [DATASET_ID]}, "search": "", } response = client.post( "/graphql/query?mode=data", json=pass_case, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:57: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _______________________ test_get_gen3_graphql_pagination _______________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_graphql_pagination(client, token): filter_pass_case = { "filter": { "dataset_description_filter>study_organ_system": ["Stomach", "Vagus nerve"], "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 {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:164: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_get_gen3_filter _____________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_gen3_filter(client, token): response = client.get( "/filter?sidebar=true", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_gen3_api.py:230: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 __________________________ test_get_irods_collection ___________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_get_irods_collection(client, token): pass_case_root = {} response = client.post( "/collection", json=pass_case_root, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_api/test_irods_api.py:38: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 _____________________________ test_experiment_node _____________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_experiment_node(client, token): UUID = "22c4459b-5f4f-4e62-abd2-2aa205fe838b" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:33: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ________________________ test_dataset_description_node _________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_dataset_description_node(client, token): UUID = "5b9ae1bd-e780-4869-a458-b3422084c480" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:74: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ______________________________ test_manifest_node ______________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_manifest_node(client, token): UUID = "fd65a93f-ff62-45e4-b7b6-96419ef4f749" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:175: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ________________________________ test_case_node ________________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_case_node(client, token): UUID = "c58ab983-6cf9-4174-a7a9-20cdf1d6bc33" response = client.get( f"/record/{UUID}", > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_gen3_data.py:229: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 ____________________________ test_irods_collection _____________________________ client = token = {'detail': 'Please check the service (Gen3/iRODS) status'} def test_irods_collection(client, token): payload1 = {"path": "/dataset-217-version-2"} response = client.post( "/collection", json=payload1, > headers={"Authorization": f"Bearer {token['access_token']}"}, ) E KeyError: 'access_token' tests/test_data/test_irods_data.py:29: KeyError ------------------------------ Captured log setup ------------------------------ ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 INFO app.main:main.py:166 {'gen3': False, 'irods': False, 'orthanc': True} WARNING app.main:main.py:185 Failed to update default filter. ERROR services.gen3.gen3_service:gen3_service.py:128 Failed to create the Gen3 submission. WARNING root:irods_service.py:95 iRODS disconnected. ERROR services.irods.irods_service:irods_service.py:96 Could not connect to specified host and port: 130.216.216.128:1247 =========================== short test summary info ============================ FAILED tests/test_api/test_access_api.py::test_create_access - assert 500 == 400 FAILED tests/test_api/test_access_api.py::test_create_one_off_access - KeyErr... FAILED tests/test_api/test_access_api.py::test_revoke_access - KeyError: 'acc... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_record - KeyError: 'acc... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_query - KeyErro... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_graphql_pagination - Ke... FAILED tests/test_api/test_gen3_api.py::test_get_gen3_filter - KeyError: 'acc... FAILED tests/test_api/test_irods_api.py::test_get_irods_collection - KeyError... FAILED tests/test_data/test_gen3_data.py::test_experiment_node - KeyError: 'a... FAILED tests/test_data/test_gen3_data.py::test_dataset_description_node - Key... FAILED tests/test_data/test_gen3_data.py::test_manifest_node - KeyError: 'acc... FAILED tests/test_data/test_gen3_data.py::test_case_node - KeyError: 'access_... FAILED tests/test_data/test_irods_data.py::test_irods_collection - KeyError: ... ERROR tests/test_api/test_irods_api.py::test_get_irods_data_file - KeyError: ... ==================== 13 failed, 25 passed, 1 error in 3.97s ==================== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #2183 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE