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] $ /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/shiningpanda15754688282908024608.sh + pwd + export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API + pip install -r requirements.txt Collecting autopep8==2.0.2 (from -r requirements.txt (line 1)) Using cached autopep8-2.0.2-py2.py3-none-any.whl (45 kB) Collecting fastapi==0.80.0 (from -r requirements.txt (line 2)) Using cached fastapi-0.80.0-py3-none-any.whl (54 kB) Collecting fastapi-utils==0.2.1 (from -r requirements.txt (line 3)) Using cached fastapi_utils-0.2.1-py3-none-any.whl (16 kB) Collecting gen3==4.19.1 (from -r requirements.txt (line 4)) Obtaining dependency information for gen3==4.19.1 from https://files.pythonhosted.org/packages/0e/61/ad7c94df55dab5663b45ea689a9252231bd179e5dc61eed9ce00bb4ff44d/gen3-4.19.1-py3-none-any.whl.metadata Downloading gen3-4.19.1-py3-none-any.whl.metadata (1.3 kB) Collecting gunicorn==20.1.0 (from -r requirements.txt (line 5)) Using cached gunicorn-20.1.0-py3-none-any.whl (79 kB) Collecting PyJWT==2.7.0 (from -r requirements.txt (line 6)) Using cached PyJWT-2.7.0-py3-none-any.whl (22 kB) Collecting python-dotenv==0.20.0 (from -r requirements.txt (line 7)) Using cached python_dotenv-0.20.0-py3-none-any.whl (17 kB) Collecting python-irodsclient==1.1.8 (from -r requirements.txt (line 8)) Obtaining dependency information for python-irodsclient==1.1.8 from https://files.pythonhosted.org/packages/83/b2/bd7fc36926ad7cf8a6fcb390902479c6fd18620b4360a377f402d2c8a8da/python_irodsclient-1.1.8-py2.py3-none-any.whl.metadata Downloading python_irodsclient-1.1.8-py2.py3-none-any.whl.metadata (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 4.8 MB/s eta 0:00:00 Collecting sgqlc==16.3 (from -r requirements.txt (line 9)) Obtaining dependency information for sgqlc==16.3 from https://files.pythonhosted.org/packages/3c/82/18f202b0891bc41e556e48e72e3ec9e83362f28cfbb4744dd9bd77a3d192/sgqlc-16.3-py3-none-any.whl.metadata Downloading 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 (57 kB) Collecting pycodestyle>=2.10.0 (from autopep8==2.0.2->-r requirements.txt (line 1)) Obtaining dependency information for pycodestyle>=2.10.0 from https://files.pythonhosted.org/packages/31/c2/e1508ed4395793f69e40fd8c6b5a690e1d568e649aae9492076a7b6befb4/pycodestyle-2.11.0-py2.py3-none-any.whl.metadata Downloading pycodestyle-2.11.0-py2.py3-none-any.whl.metadata (4.5 kB) Collecting tomli (from autopep8==2.0.2->-r requirements.txt (line 1)) Using cached tomli-2.0.1-py3-none-any.whl (12 kB) Collecting starlette==0.19.1 (from fastapi==0.80.0->-r requirements.txt (line 2)) Using cached starlette-0.19.1-py3-none-any.whl (63 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 2)) Obtaining dependency information for pydantic!=1.7,!=1.7.1,!=1.7.2,!=1.7.3,!=1.8,!=1.8.1,<2.0.0,>=1.6.2 from https://files.pythonhosted.org/packages/02/bd/2c6a34eeffcc437fca7d5c4b6cf7745fcc806842de5fced482d4cdba55f0/pydantic-1.10.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading pydantic-1.10.12-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (149 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.3/149.3 kB 14.3 MB/s eta 0:00:00 Collecting sqlalchemy<2.0.0,>=1.3.12 (from fastapi-utils==0.2.1->-r requirements.txt (line 3)) Obtaining dependency information for sqlalchemy<2.0.0,>=1.3.12 from https://files.pythonhosted.org/packages/1b/21/3aa5406575603c15a9eb1e76d5f6a7c7d29682eedb9f643a43e54e8c4f29/SQLAlchemy-1.4.49-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading SQLAlchemy-1.4.49-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 4)) Using cached aiofiles-0.8.0-py3-none-any.whl (13 kB) Collecting aiohttp (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for aiohttp from https://files.pythonhosted.org/packages/5b/8d/821fcb268cfc056964a75da3823896b17eabaa4968a2414121bc93b0c501/aiohttp-3.8.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading aiohttp-3.8.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB) Collecting backoff (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached backoff-2.2.1-py3-none-any.whl (15 kB) Collecting cdislogging<2.0.0,>=1.1.0 (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached cdislogging-1.1.1-py3-none-any.whl Collecting click (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for click from https://files.pythonhosted.org/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/click-8.1.7-py3-none-any.whl.metadata Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Collecting dataclasses-json (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for dataclasses-json from https://files.pythonhosted.org/packages/13/75/82ce74880711ced796fd5a32e4d40c5a32dbea3f1c5e219a8b0544b7bd8c/dataclasses_json-0.6.0-py3-none-any.whl.metadata Downloading dataclasses_json-0.6.0-py3-none-any.whl.metadata (24 kB) Collecting drsclient<0.3.0,>=0.2.2 (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached drsclient-0.2.3-py3-none-any.whl Collecting httpx (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for httpx from https://files.pythonhosted.org/packages/ec/91/e41f64f03d2a13aee7e8c819d82ee3aa7cdc484d18c0ae859742597d5aa0/httpx-0.24.1-py3-none-any.whl.metadata Downloading httpx-0.24.1-py3-none-any.whl.metadata (7.4 kB) Collecting humanfriendly (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB) Collecting indexclient (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached indexclient-2.2.1-py3-none-any.whl Collecting jsonschema (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for jsonschema from https://files.pythonhosted.org/packages/2b/ff/af59fd34bc4d7ac3e6e0cd1f3c10317d329b6c1aee179e8b24ad9a79fbac/jsonschema-4.19.0-py3-none-any.whl.metadata Downloading jsonschema-4.19.0-py3-none-any.whl.metadata (8.2 kB) Collecting pandas<2.0.0,>=1.4.2 (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) Collecting pypfb<1.0.0 (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for pypfb<1.0.0 from https://files.pythonhosted.org/packages/87/55/243988a1ed6208f6299a10ed74cc399af42af6d323f8cf20d8a6108ad690/pypfb-0.5.26-py3-none-any.whl.metadata Downloading pypfb-0.5.26-py3-none-any.whl.metadata (775 bytes) Collecting python-dateutil (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting requests (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for requests from https://files.pythonhosted.org/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl.metadata 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 4)) Obtaining dependency information for tqdm<5.0.0,>=4.61.2 from https://files.pythonhosted.org/packages/00/e5/f12a80907d0884e6dff9c16d0c0114d81b8cd07dc3ae54c5e962cc83037e/tqdm-4.66.1-py3-none-any.whl.metadata Downloading tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 5.6 MB/s eta 0:00:00 Collecting urllib3<2.0.0 (from gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for urllib3<2.0.0 from https://files.pythonhosted.org/packages/c5/05/c214b32d21c0b465506f95c4f28ccbcba15022e000b043b72b3df7728471/urllib3-1.26.16-py2.py3-none-any.whl.metadata Using cached urllib3-1.26.16-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 4)) Using cached xmltodict-0.13.0-py2.py3-none-any.whl (10.0 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 5)) (68.1.2) Collecting PrettyTable>=0.7.2 (from python-irodsclient==1.1.8->-r requirements.txt (line 8)) Obtaining dependency information for PrettyTable>=0.7.2 from https://files.pythonhosted.org/packages/25/1e/4c284713b092ec384fad4399452f43f6446ad9aabc9c0b3c3c0920cc53b6/prettytable-3.8.0-py3-none-any.whl.metadata Downloading prettytable-3.8.0-py3-none-any.whl.metadata (26 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 (25 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 (11 kB) Collecting graphql-core<4.0.0,>=3.1.7 (from sgqlc==16.3->-r requirements.txt (line 9)) Using cached graphql_core-3.2.3-py3-none-any.whl (202 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 (58 kB) Collecting anyio<5,>=3.4.0 (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 2)) Obtaining dependency information for anyio<5,>=3.4.0 from https://files.pythonhosted.org/packages/36/55/ad4de788d84a630656ece71059665e01ca793c04294c463fd84132f40fe6/anyio-4.0.0-py3-none-any.whl.metadata Downloading anyio-4.0.0-py3-none-any.whl.metadata (4.5 kB) Collecting typing-extensions>=3.10.0 (from starlette==0.19.1->fastapi==0.80.0->-r requirements.txt (line 2)) Obtaining dependency information for typing-extensions>=3.10.0 from https://files.pythonhosted.org/packages/ec/6b/63cc3df74987c36fe26157ee12e09e8f9db4de771e0f3404263117e75b95/typing_extensions-4.7.1-py3-none-any.whl.metadata Downloading typing_extensions-4.7.1-py3-none-any.whl.metadata (3.1 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 4)) Using cached asyncio-3.4.3-py3-none-any.whl (101 kB) Collecting backoff (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached backoff-1.11.1-py2.py3-none-any.whl (13 kB) Collecting httpx (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached httpx-0.23.3-py3-none-any.whl (71 kB) Collecting certifi (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for certifi from https://files.pythonhosted.org/packages/4c/dd/2234eab22353ffc7d94e8d13177aaa050113286e93e7b40eae01fbf7c3d9/certifi-2023.7.22-py3-none-any.whl.metadata Using cached certifi-2023.7.22-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 4)) Using cached httpcore-0.16.3-py3-none-any.whl (69 kB) Collecting rfc3986[idna2008]<2,>=1.3 (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) Using cached rfc3986-1.5.0-py2.py3-none-any.whl (31 kB) Collecting sniffio (from httpx->gen3==4.19.1->-r requirements.txt (line 4)) Using cached sniffio-1.3.0-py3-none-any.whl (10 kB) Collecting pytz>=2020.1 (from pandas<2.0.0,>=1.4.2->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for pytz>=2020.1 from https://files.pythonhosted.org/packages/32/4d/aaf7eff5deb402fd9a24a1449a8119f00d74ae9c2efa79f8ef9994261fc2/pytz-2023.3.post1-py2.py3-none-any.whl.metadata Downloading pytz-2023.3.post1-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 4)) Obtaining dependency information for numpy>=1.20.3 from https://files.pythonhosted.org/packages/69/1f/c95b1108a9972a52d7b1b63ed8ca70466b59b8c1811bd121f1e667cc45d8/numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB) Collecting wcwidth (from PrettyTable>=0.7.2->python-irodsclient==1.1.8->-r requirements.txt (line 8)) Using cached wcwidth-0.2.6-py2.py3-none-any.whl (29 kB) Collecting PyYAML<6.0.0,>=5.3.1 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) Using cached PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl (630 kB) Collecting click (from gen3==4.19.1->-r requirements.txt (line 4)) Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting dictionaryutils<4.0.0,>=3.4.3 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) Using cached dictionaryutils-3.4.6-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 4)) Obtaining dependency information for fastavro<1.9.0,>=1.8.2 from https://files.pythonhosted.org/packages/d1/32/12202e93d0cac2fe6a38066a1264391fdbfd8fcfea446846d9dff4f68c53/fastavro-1.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading fastavro-1.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB) Collecting gdcdictionary<2.0.0,>=1.2.0 (from pypfb<1.0.0->gen3==4.19.1->-r requirements.txt (line 4)) Using cached gdcdictionary-1.2.0-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 4)) Using cached python_json_logger-0.1.11-py2.py3-none-any.whl Collecting attrs>=17.3.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) Using cached attrs-23.1.0-py3-none-any.whl (61 kB) Collecting charset-normalizer<4.0,>=2.0 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for charset-normalizer<4.0,>=2.0 from 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yarl-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (269 kB) Collecting frozenlist>=1.1.1 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for frozenlist>=1.1.1 from https://files.pythonhosted.org/packages/b5/03/7dec2e257bd173b5ca1f74477863b97d322149f6f0284d7decead8c5ceeb/frozenlist-1.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata Downloading frozenlist-1.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.2 kB) Collecting aiosignal>=1.1.2 (from aiohttp->gen3==4.19.1->-r requirements.txt (line 4)) Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB) Collecting idna<4,>=2.5 (from requests->gen3==4.19.1->-r requirements.txt (line 4)) Using cached idna-3.4-py3-none-any.whl (61 kB) Collecting greenlet!=0.4.17 (from sqlalchemy<2.0.0,>=1.3.12->fastapi-utils==0.2.1->-r requirements.txt (line 3)) Using cached greenlet-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (610 kB) Collecting marshmallow<4.0.0,>=3.18.0 (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for marshmallow<4.0.0,>=3.18.0 from https://files.pythonhosted.org/packages/ed/3c/cebfdcad015240014ff08b883d1c0c427f2ba45ae8c6572851b6ef136cad/marshmallow-3.20.1-py3-none-any.whl.metadata Downloading marshmallow-3.20.1-py3-none-any.whl.metadata (7.8 kB) Collecting typing-inspect<1,>=0.4.0 (from dataclasses-json->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for typing-inspect<1,>=0.4.0 from https://files.pythonhosted.org/packages/65/f3/107a22063bf27bdccf2024833d3445f4eea42b2e598abfbd46f6a63b6cb0/typing_inspect-0.9.0-py3-none-any.whl.metadata 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 4)) Obtaining dependency information for jsonschema-specifications>=2023.03.6 from https://files.pythonhosted.org/packages/1c/24/83349ac2189cc2435e84da3f69ba3c97314d3c0622628e55171c6798ed80/jsonschema_specifications-2023.7.1-py3-none-any.whl.metadata Downloading jsonschema_specifications-2023.7.1-py3-none-any.whl.metadata (2.8 kB) Collecting referencing>=0.28.4 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for referencing>=0.28.4 from https://files.pythonhosted.org/packages/be/8e/56d6f1e2d591f4d6cbcba446cac4a1b0dc4f584537e2071d9bcee8eeab6b/referencing-0.30.2-py3-none-any.whl.metadata Downloading referencing-0.30.2-py3-none-any.whl.metadata (2.6 kB) Collecting rpds-py>=0.7.1 (from jsonschema->gen3==4.19.1->-r requirements.txt (line 4)) Obtaining dependency information for rpds-py>=0.7.1 from 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frozenlist-1.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (228 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 228.0/228.0 kB 21.9 MB/s eta 0:00:00 Downloading marshmallow-3.20.1-py3-none-any.whl (49 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.4/49.4 kB 5.6 MB/s eta 0:00:00 Downloading numpy-1.25.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.3/18.3 MB 52.0 MB/s eta 0:00:00 Downloading pytz-2023.3.post1-py2.py3-none-any.whl (502 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.5/502.5 kB 33.7 MB/s eta 0:00:00 Using cached typing_extensions-4.7.1-py3-none-any.whl (33 kB) Using cached typing_inspect-0.9.0-py3-none-any.whl (8.8 kB) Downloading exceptiongroup-1.1.3-py3-none-any.whl (14 kB) Installing collected packages: wcwidth, rfc3986, pytz, cdislogging, asyncio, xmltodict, urllib3, typing-extensions, tqdm, tomli, sniffio, six, PyYAML, python-json-logger, python-dotenv, pyrsistent, PyJWT, pycodestyle, 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, autopep8, anyio, aiosignal, starlette, pandas, indexclient, httpcore, dictionaryutils, dataclasses-json, aiohttp, httpx, gdcdictionary, fastapi, fastapi-utils, drsclient, pypfb, gen3 Successfully installed PrettyTable-3.8.0 PyJWT-2.7.0 PyYAML-5.4.1 aiofiles-0.8.0 aiohttp-3.8.5 aiosignal-1.3.1 anyio-4.0.0 async-timeout-4.0.3 asyncio-3.4.3 attrs-23.1.0 autopep8-2.0.2 backoff-1.11.1 cdislogging-1.1.1 certifi-2023.7.22 charset-normalizer-3.2.0 click-7.1.2 dataclasses-json-0.6.0 defusedxml-0.7.1 dictionaryutils-3.4.6 drsclient-0.2.3 exceptiongroup-1.1.3 fastapi-0.80.0 fastapi-utils-0.2.1 fastavro-1.8.2 frozenlist-1.4.0 gdcdictionary-1.2.0 gen3-4.19.1 graphql-core-3.2.3 greenlet-2.0.2 gunicorn-20.1.0 h11-0.14.0 httpcore-0.16.3 httpx-0.23.3 humanfriendly-10.0 idna-3.4 indexclient-2.2.1 jsonschema-3.2.0 marshmallow-3.20.1 multidict-6.0.4 mypy-extensions-1.0.0 numpy-1.25.2 packaging-23.1 pandas-1.5.3 pycodestyle-2.11.0 pydantic-1.10.12 pypfb-0.5.26 pyrsistent-0.19.3 python-dateutil-2.8.2 python-dotenv-0.20.0 python-irodsclient-1.1.8 python-json-logger-0.1.11 pytz-2023.3.post1 requests-2.31.0 rfc3986-1.5.0 sgqlc-16.3 six-1.16.0 sniffio-1.3.0 sqlalchemy-1.4.49 starlette-0.19.1 tomli-2.0.1 tqdm-4.66.1 typing-extensions-4.7.1 typing-inspect-0.9.0 urllib3-1.26.16 uvicorn-0.18.2 wcwidth-0.2.6 xmltodict-0.13.0 yarl-1.9.2 + 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 (297 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 (12 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)) (23.1.0) Collecting iniconfig (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 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)) (23.1) Collecting pluggy<2.0,>=0.12 (from pytest==7.1.2->-r requirements-dev.txt (line 1)) Obtaining dependency information for pluggy<2.0,>=0.12 from https://files.pythonhosted.org/packages/05/b8/42ed91898d4784546c5f06c60506400548db3f7a4b3fb441cba4e5c17952/pluggy-1.3.0-py3-none-any.whl.metadata Downloading pluggy-1.3.0-py3-none-any.whl.metadata (4.3 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 (98 kB) 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) Downloading pluggy-1.3.0-py3-none-any.whl (18 kB) Installing collected packages: py, pluggy, iniconfig, pytest, pytest-timeout Successfully installed iniconfig-2.0.0 pluggy-1.3.0 py-1.11.0 pytest-7.1.2 pytest-timeout-2.1.0 + pytest ============================= test session starts ============================== platform linux -- Python 3.9.18, pytest-7.1.2, pluggy-1.3.0 rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API plugins: timeout-2.1.0, anyio-4.0.0 collected 16 items tests/test_api.py EEEEEEEEEEE [ 68%] tests/test_data.py EEEEE [100%] ==================================== ERRORS ==================================== __________________ ERROR at setup of test_create_gen3_access ___________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392d88b0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError __________________ ERROR at setup of test_revoke_gen3_access ___________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392d8a30> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError __________________ ERROR at setup of test_get_gen3_dictionary __________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392df6d0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _________________ ERROR at setup of test_get_gen3_node_records _________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392e8b20> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError ____________________ ERROR at setup of test_get_gen3_record ____________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392d8970> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _____________________ ERROR at setup of test_graphql_query _____________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa39472fd0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError __________________ ERROR at setup of test_graphql_pagination ___________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa394ce8e0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError ______________________ ERROR at setup of test_get_filter _______________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392e10d0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError ______________ ERROR at setup of test_download_gen3_metadata_file ______________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa39493c70> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _________________ ERROR at setup of test_get_irods_collection __________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa394ce2e0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError __________________ ERROR at setup of test_get_irods_data_file __________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_api.py:11: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392e1370> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError ____________________ ERROR at setup of test_experiment_node ____________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_data.py:10: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa394ddd60> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _______________ ERROR at setup of test_dataset_description_node ________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_data.py:10: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa3949d7c0> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _____________________ ERROR at setup of test_manifest_node _____________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_data.py:10: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa394ce880> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError _______________________ ERROR at setup of test_case_node _______________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_data.py:10: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392df940> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError ___________________ ERROR at setup of test_irods_collection ____________________ @pytest.fixture def client(): > with TestClient(app) as client: tests/test_data.py:10: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <starlette.testclient.TestClient object at 0x7ffa392e8160> def __enter__(self) -> "TestClient": with contextlib.ExitStack() as stack: self.portal = portal = stack.enter_context( > anyio.start_blocking_portal(**self.async_backend) ) E AttributeError: module 'anyio' has no attribute 'start_blocking_portal' ../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/starlette/testclient.py:518: AttributeError =========================== short test summary info ============================ ERROR tests/test_api.py::test_create_gen3_access - AttributeError: module 'an... ERROR tests/test_api.py::test_revoke_gen3_access - AttributeError: module 'an... ERROR tests/test_api.py::test_get_gen3_dictionary - AttributeError: module 'a... ERROR tests/test_api.py::test_get_gen3_node_records - AttributeError: module ... ERROR tests/test_api.py::test_get_gen3_record - AttributeError: module 'anyio... ERROR tests/test_api.py::test_graphql_query - AttributeError: module 'anyio' ... ERROR tests/test_api.py::test_graphql_pagination - AttributeError: module 'an... ERROR tests/test_api.py::test_get_filter - AttributeError: module 'anyio' has... ERROR tests/test_api.py::test_download_gen3_metadata_file - AttributeError: m... ERROR tests/test_api.py::test_get_irods_collection - AttributeError: module '... ERROR tests/test_api.py::test_get_irods_data_file - AttributeError: module 'a... ERROR tests/test_data.py::test_experiment_node - AttributeError: module 'anyi... ERROR tests/test_data.py::test_dataset_description_node - AttributeError: mod... ERROR tests/test_data.py::test_manifest_node - AttributeError: module 'anyio'... ERROR tests/test_data.py::test_case_node - AttributeError: module 'anyio' has... ERROR tests/test_data.py::test_irods_collection - AttributeError: module 'any... ============================== 16 errors in 1.59s ============================== Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1119 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE