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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 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/shiningpanda1674815880197003032.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)) Using cached fastapi-0.80.0-py3-none-any.whl.metadata (25 kB) Collecting fastapi-utils==0.2.1 (from -r requirements.txt (line 2)) Using cached fastapi_utils-0.2.1-py3-none-any.whl.metadata (4.8 kB) Collecting gen3==4.19.1 (from -r requirements.txt (line 3)) Using cached gen3-4.19.1-py3-none-any.whl.metadata (1.3 kB) Collecting gunicorn==20.1.0 (from -r requirements.txt (line 4)) Using cached gunicorn-20.1.0-py3-none-any.whl.metadata (3.8 kB) Collecting PyJWT==2.7.0 (from -r requirements.txt (line 5)) Using cached PyJWT-2.7.0-py3-none-any.whl.metadata (4.1 kB) Collecting pyorthanc==1.11.5 (from -r requirements.txt (line 6)) Using cached pyorthanc-1.11.5-py3-none-any.whl.metadata (7.6 kB) Collecting python-dotenv==0.20.0 (from -r requirements.txt (line 7)) Using cached python_dotenv-0.20.0-py3-none-any.whl.metadata (19 kB) Collecting python-irodsclient==1.1.8 (from -r requirements.txt (line 8)) Using cached python_irodsclient-1.1.8-py2.py3-none-any.whl.metadata (54 kB) Collecting sgqlc==16.3 (from -r requirements.txt (line 9)) Using cached sgqlc-16.3-py3-none-any.whl.metadata (18 kB) Collecting uvicorn==0.18.2 (from -r requirements.txt (line 10)) Using cached 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)) Using cached 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-1.10.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (152 kB) Collecting sqlalchemy<2.0.0,>=1.3.12 (from fastapi-utils==0.2.1->-r requirements.txt (line 2)) Downloading SQLAlchemy-1.4.54-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)) Using cached 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-3.10.5-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)) Using cached 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-0.6.7-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-0.27.2-py3-none-any.whl.metadata (7.1 kB) Collecting humanfriendly (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) Collecting indexclient (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading indexclient-2.3.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting jsonschema (from gen3==4.19.1->-r requirements.txt (line 3)) Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB) Collecting pandas<2.0.0,>=1.4.2 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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)) Using cached 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-2.32.3-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-4.66.5-py3-none-any.whl.metadata (57 kB) Collecting urllib3<2.0.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting xmltodict<0.14.0,>=0.13.0 (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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)) (74.1.2) Collecting httpx (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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)) Using cached 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-3.11.0-py3-none-any.whl.metadata (30 kB) Collecting defusedxml (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) Using cached 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-3.2.4-py3-none-any.whl.metadata (10 kB) Collecting h11>=0.8 (from uvicorn==0.18.2->-r requirements.txt (line 10)) Using cached 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-4.4.0-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-4.12.2-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)) Using cached asyncio-3.4.3-py3-none-any.whl.metadata (1.7 kB) Collecting backoff (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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-2024.8.30-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)) Using cached 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)) Using cached 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)) Using cached 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-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) 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-6.0.2-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)) Using cached dictionaryutils-3.4.10-py3-none-any.whl Collecting fastavro<1.9.0,>=1.8.2 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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)) Using cached gen3dictionary-2.0.3-py3-none-any.whl 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 aiohappyeyeballs>=2.3.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading aiohappyeyeballs-2.4.0-py3-none-any.whl.metadata (5.9 kB) Collecting aiosignal>=1.1.2 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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-24.2.0-py3-none-any.whl.metadata (11 kB) Collecting frozenlist>=1.1.1 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.0 kB) Collecting yarl<2.0,>=1.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Downloading yarl-1.11.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (48 kB) Collecting async-timeout<5.0,>=4.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 3)) Using cached 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-3.8-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-3.1.0-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-3.22.0-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)) Using cached 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)) Using cached 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-0.35.1-py3-none-any.whl.metadata (2.8 kB) Collecting rpds-py>=0.7.1 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) Downloading rpds_py-0.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB) Collecting exceptiongroup>=1.0.2 (from anyio<5,>=3.4.0->starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 1)) Using cached exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB) Collecting jsonschema (from gen3==4.19.1->-r requirements.txt (line 3)) Using cached jsonschema-3.2.0-py2.py3-none-any.whl.metadata (7.8 kB) Collecting pyrsistent>=0.14.0 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 3)) Using cached pyrsistent-0.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (27 kB) Collecting packaging>=17.0 (from marshmallow<4.0.0,>=3.18.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB) Collecting mypy-extensions>=0.3.0 (from typing-inspect<1,>=0.4.0->dataclasses-json->gen3==4.19.1->-r requirements.txt (line 3)) Using cached mypy_extensions-1.0.0-py3-none-any.whl.metadata (1.1 kB) Using cached fastapi-0.80.0-py3-none-any.whl (54 kB) Using cached fastapi_utils-0.2.1-py3-none-any.whl (16 kB) Using cached gen3-4.19.1-py3-none-any.whl (144 kB) Using cached gunicorn-20.1.0-py3-none-any.whl (79 kB) Using cached PyJWT-2.7.0-py3-none-any.whl (22 kB) Using cached pyorthanc-1.11.5-py3-none-any.whl (85 kB) Using cached python_dotenv-0.20.0-py3-none-any.whl (17 kB) Using cached python_irodsclient-1.1.8-py2.py3-none-any.whl (199 kB) Using cached sgqlc-16.3-py3-none-any.whl (81 kB) Using cached uvicorn-0.18.2-py3-none-any.whl (57 kB) Using cached starlette-0.19.1-py3-none-any.whl (63 kB) Using cached aiofiles-0.8.0-py3-none-any.whl (13 kB) Using cached click-8.1.7-py3-none-any.whl (97 kB) Using cached backoff-1.11.1-py2.py3-none-any.whl (13 kB) Downloading graphql_core-3.2.4-py3-none-any.whl (203 kB) Using cached h11-0.14.0-py3-none-any.whl (58 kB) Using cached httpx-0.23.3-py3-none-any.whl (71 kB) Using cached pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) Downloading prettytable-3.11.0-py3-none-any.whl (28 kB) Downloading pydantic-1.10.18-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 78.6 MB/s eta 0:00:00 Using cached pydicom-2.4.4-py3-none-any.whl (1.8 MB) Using cached pypfb-0.5.29-py3-none-any.whl (28 kB) Downloading aiohttp-3.10.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 51.6 MB/s eta 0:00:00 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Downloading requests-2.32.3-py3-none-any.whl (64 kB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Downloading SQLAlchemy-1.4.54-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 61.4 MB/s eta 0:00:00 Downloading tqdm-4.66.5-py3-none-any.whl (78 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached xmltodict-0.13.0-py2.py3-none-any.whl (10.0 kB) Downloading dataclasses_json-0.6.7-py3-none-any.whl (28 kB) Using cached defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB) Downloading aiohappyeyeballs-2.4.0-py3-none-any.whl (12 kB) Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB) Downloading anyio-4.4.0-py3-none-any.whl (86 kB) Using cached async_timeout-4.0.3-py3-none-any.whl (5.7 kB) Using cached asyncio-3.4.3-py3-none-any.whl (101 kB) Using cached attrs-24.2.0-py3-none-any.whl (63 kB) Using cached certifi-2024.8.30-py3-none-any.whl (167 kB) Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB) Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Using cached fastavro-1.8.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB) Using cached frozenlist-1.4.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (240 kB) Downloading greenlet-3.1.0-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (615 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 616.0/616.0 kB 25.3 MB/s eta 0:00:00 Using cached httpcore-0.16.3-py3-none-any.whl (69 kB) Using cached sniffio-1.3.1-py3-none-any.whl (10 kB) Using cached idna-3.8-py3-none-any.whl (66 kB) Downloading marshmallow-3.22.0-py3-none-any.whl (49 kB) Downloading multidict-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (124 kB) Downloading numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.5/19.5 MB 93.7 MB/s eta 0:00:00 Using cached pyrsistent-0.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (117 kB) Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB) Downloading PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 737.4/737.4 kB 22.5 MB/s eta 0:00:00 Using cached rfc3986-1.5.0-py2.py3-none-any.whl (31 kB) Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB) Using cached typing_inspect-0.9.0-py3-none-any.whl (8.8 kB) Downloading yarl-1.11.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (453 kB) Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Using cached exceptiongroup-1.2.2-py3-none-any.whl (16 kB) Using cached mypy_extensions-1.0.0-py3-none-any.whl (4.7 kB) Using cached packaging-24.1-py3-none-any.whl (53 kB) Building wheels for collected packages: indexclient Building wheel for indexclient (setup.py): started Building wheel for indexclient (setup.py): finished with status 'done' Created wheel for indexclient: filename=indexclient-2.3.1-py3-none-any.whl size=17881 sha256=0533cc9d99ab04029f9913bda9ab9efdedc8e82a08247376d85c457e2bee7db3 Stored in directory: /home/cmiss/.cache/pip/wheels/af/04/e4/4a68c4c05e5c98749b463c23c06d0e2e1abebe506bd68ab75b Successfully built indexclient 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, idna, humanfriendly, h11, gunicorn, greenlet, graphql-core, frozenlist, fastavro, exceptiongroup, defusedxml, click, charset-normalizer, certifi, backoff, attrs, async-timeout, aiohappyeyeballs, aiofiles, uvicorn, typing-inspect, sqlalchemy, sgqlc, requests, python-irodsclient, python-dateutil, pydantic, multidict, marshmallow, jsonschema, anyio, aiosignal, yarl, starlette, pandas, indexclient, httpcore, dictionaryutils, dataclasses-json, httpx, gen3dictionary, fastapi, aiohttp, pyorthanc, fastapi-utils, drsclient, pypfb, gen3 Successfully installed PrettyTable-3.11.0 PyJWT-2.7.0 PyYAML-6.0.2 aiofiles-0.8.0 aiohappyeyeballs-2.4.0 aiohttp-3.10.5 aiosignal-1.3.1 anyio-4.4.0 async-timeout-4.0.3 asyncio-3.4.3 attrs-24.2.0 backoff-1.11.1 cdislogging-1.1.1 certifi-2024.8.30 charset-normalizer-3.3.2 click-8.1.7 dataclasses-json-0.6.7 defusedxml-0.7.1 dictionaryutils-3.4.10 drsclient-0.2.3 exceptiongroup-1.2.2 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-3.2.4 greenlet-3.1.0 gunicorn-20.1.0 h11-0.14.0 httpcore-0.16.3 httpx-0.23.3 humanfriendly-10.0 idna-3.8 indexclient-2.3.1 jsonschema-3.2.0 marshmallow-3.22.0 multidict-6.1.0 mypy-extensions-1.0.0 numpy-2.0.2 packaging-24.1 pandas-1.5.3 pydantic-1.10.18 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-2.32.3 rfc3986-1.5.0 sgqlc-16.3 six-1.16.0 sniffio-1.3.1 sqlalchemy-1.4.54 starlette-0.19.1 tqdm-4.66.5 typing-extensions-4.12.2 typing-inspect-0.9.0 urllib3-1.26.20 uvicorn-0.18.2 wcwidth-0.2.13 xmltodict-0.13.0 yarl-1.11.1 + pip install -r requirements-dev.txt Collecting pytest==7.1.2 (from -r requirements-dev.txt (line 1)) Using cached pytest-7.1.2-py3-none-any.whl.metadata (7.8 kB) Collecting pytest-timeout==2.1.0 (from -r requirements-dev.txt (line 2)) Using cached pytest_timeout-2.1.0-py3-none-any.whl.metadata (16 kB) Collecting anyio==3.6.2 (from -r requirements-dev.txt (line 3)) Using cached 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)) (24.2.0) 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)) (24.1) Collecting pluggy<2.0,>=0.12 (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Using cached 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)) (3.8) 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) Using cached pytest-7.1.2-py3-none-any.whl (297 kB) Using cached pytest_timeout-2.1.0-py3-none-any.whl (12 kB) Using cached anyio-3.6.2-py3-none-any.whl (80 kB) Using cached 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 4.4.0 Uninstalling anyio-4.4.0: Successfully uninstalled anyio-4.4.0 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 3.9.20, 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 23 items / 6 errors ==================================== ERRORS ==================================== ______________ ERROR collecting tests/test_api/test_access_api.py ______________ tests/test_api/test_access_api.py:4: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject _______________ ERROR collecting tests/test_api/test_gen3_api.py _______________ tests/test_api/test_gen3_api.py:4: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject ______________ ERROR collecting tests/test_api/test_irods_api.py _______________ tests/test_api/test_irods_api.py:4: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject _____________ ERROR collecting tests/test_api/test_orthanc_api.py ______________ tests/test_api/test_orthanc_api.py:4: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject ______________ ERROR collecting tests/test_data/test_gen3_data.py ______________ tests/test_data/test_gen3_data.py:5: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject _____________ ERROR collecting tests/test_data/test_irods_data.py ______________ tests/test_data/test_irods_data.py:4: in <module> from app.main import app app/main.py:57: in <module> from services.external_service import ExternalService services/external_service.py:7: in <module> from services.gen3.gen3_service import Gen3Service services/gen3/gen3_service.py:16: in <module> from gen3.submission import Gen3Submission ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module> import pandas as pd ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module> from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module> from pandas.compat.numpy import ( ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module> from pandas.util.version import Version ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module> from pandas.util._decorators import ( # noqa:F401 ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module> from pandas._libs.properties import cache_readonly ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module> from pandas._libs.interval import Interval pandas/_libs/interval.pyx:1: in init pandas._libs.interval ??? E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject =========================== short test summary info ============================ ERROR tests/test_api/test_access_api.py - ValueError: numpy.dtype size change... ERROR tests/test_api/test_gen3_api.py - ValueError: numpy.dtype size changed,... ERROR tests/test_api/test_irods_api.py - ValueError: numpy.dtype size changed... ERROR tests/test_api/test_orthanc_api.py - ValueError: numpy.dtype size chang... ERROR tests/test_data/test_gen3_data.py - ValueError: numpy.dtype size change... ERROR tests/test_data/test_irods_data.py - ValueError: numpy.dtype size chang... !!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!! ============================== 6 errors in 1.39s =============================== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #2656 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE