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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/SciCrunch Knowledge Testing [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/alan-wu/scicrunch-knowledge-testing.git > git init /home/cmiss/Jenkins/workspace/SciCrunch Knowledge Testing # timeout=10 Fetching upstream changes from https://github.com/alan-wu/scicrunch-knowledge-testing.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/alan-wu/scicrunch-knowledge-testing.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/alan-wu/scicrunch-knowledge-testing.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/main^{commit} # timeout=10 Checking out Revision 3d05adb35e4bcf1e06033cba3e971c2ec60eb068 (refs/remotes/origin/main) > git config core.sparsecheckout # timeout=10 > git checkout -f 3d05adb35e4bcf1e06033cba3e971c2ec60eb068 # timeout=10 Commit message: "Merge pull request #17 from alan-wu/main" > git rev-list --no-walk 3d05adb35e4bcf1e06033cba3e971c2ec60eb068 # timeout=10 [SciCrunch Knowledge Testing] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9 /home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/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/d0cfff48/virtualenvs/d41d8cd9/bin/python3.9 Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/bin/python Installing setuptools, pip, wheel...done. [SciCrunch Knowledge Testing] $ /bin/sh -xe /tmp/shiningpanda7738524618895448813.sh + export PENNSIEVE_API_HOST=https://api.pennsieve.io/discover + export SCICRUNCH_API_HOST=https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_pr + pip install -r requirements.txt Collecting mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl (from -r requirements.txt (line 5)) Downloading https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl (18 kB) Collecting requests==2.28.1 (from -r requirements.txt (line 1)) Using cached requests-2.28.1-py3-none-any.whl.metadata (4.6 kB) Collecting algoliasearch==2.6.2 (from -r requirements.txt (line 2)) Using cached algoliasearch-2.6.2-py2.py3-none-any.whl.metadata (4.4 kB) Collecting boto3==1.17.67 (from -r requirements.txt (line 3)) Using cached boto3-1.17.67-py2.py3-none-any.whl.metadata (6.2 kB) Collecting ftfy==6.1.1 (from -r requirements.txt (line 4)) Using cached ftfy-6.1.1-py3-none-any.whl.metadata (6.1 kB) Collecting charset-normalizer<3,>=2 (from requests==2.28.1->-r requirements.txt (line 1)) Using cached charset_normalizer-2.1.1-py3-none-any.whl.metadata (11 kB) Collecting idna<4,>=2.5 (from requests==2.28.1->-r requirements.txt (line 1)) Using cached idna-3.8-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<1.27,>=1.21.1 (from requests==2.28.1->-r requirements.txt (line 1)) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting certifi>=2017.4.17 (from requests==2.28.1->-r requirements.txt (line 1)) Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB) Collecting botocore<1.21.0,>=1.20.67 (from boto3==1.17.67->-r requirements.txt (line 3)) Using cached botocore-1.20.112-py2.py3-none-any.whl.metadata (5.6 kB) Collecting jmespath<1.0.0,>=0.7.1 (from boto3==1.17.67->-r requirements.txt (line 3)) Using cached jmespath-0.10.0-py2.py3-none-any.whl.metadata (8.0 kB) Collecting s3transfer<0.5.0,>=0.4.0 (from boto3==1.17.67->-r requirements.txt (line 3)) Using cached s3transfer-0.4.2-py2.py3-none-any.whl.metadata (1.5 kB) Collecting wcwidth>=0.2.5 (from ftfy==6.1.1->-r requirements.txt (line 4)) Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) Collecting networkx<3.0.0,>=2.8.8 (from mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) Using cached networkx-2.8.8-py3-none-any.whl.metadata (5.1 kB) Collecting rdflib<7.0.0,>=6.2.0 (from mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) Using cached rdflib-6.3.2-py3-none-any.whl.metadata (11 kB) Collecting python-dateutil<3.0.0,>=2.1 (from botocore<1.21.0,>=1.20.67->boto3==1.17.67->-r requirements.txt (line 3)) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting isodate<0.7.0,>=0.6.0 (from rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) Using cached isodate-0.6.1-py2.py3-none-any.whl.metadata (9.6 kB) Collecting pyparsing<4,>=2.1.0 (from rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) Using cached pyparsing-3.1.4-py3-none-any.whl.metadata (5.1 kB) Collecting six (from isodate<0.7.0,>=0.6.0->rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Using cached requests-2.28.1-py3-none-any.whl (62 kB) Using cached algoliasearch-2.6.2-py2.py3-none-any.whl (35 kB) Using cached boto3-1.17.67-py2.py3-none-any.whl (131 kB) Using cached ftfy-6.1.1-py3-none-any.whl (53 kB) Using cached botocore-1.20.112-py2.py3-none-any.whl (7.7 MB) Using cached certifi-2024.8.30-py3-none-any.whl (167 kB) Using cached charset_normalizer-2.1.1-py3-none-any.whl (39 kB) Using cached idna-3.8-py3-none-any.whl (66 kB) Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB) Using cached networkx-2.8.8-py3-none-any.whl (2.0 MB) Using cached rdflib-6.3.2-py3-none-any.whl (528 kB) Using cached s3transfer-0.4.2-py2.py3-none-any.whl (79 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Using cached isodate-0.6.1-py2.py3-none-any.whl (41 kB) Using cached pyparsing-3.1.4-py3-none-any.whl (104 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Installing collected packages: wcwidth, urllib3, six, pyparsing, networkx, jmespath, idna, ftfy, charset-normalizer, certifi, requests, python-dateutil, isodate, rdflib, botocore, algoliasearch, s3transfer, mapknowledge, boto3 Successfully installed algoliasearch-2.6.2 boto3-1.17.67 botocore-1.20.112 certifi-2024.8.30 charset-normalizer-2.1.1 ftfy-6.1.1 idna-3.8 isodate-0.6.1 jmespath-0.10.0 mapknowledge-0.13.1 networkx-2.8.8 pyparsing-3.1.4 python-dateutil-2.9.0.post0 rdflib-6.3.2 requests-2.28.1 s3transfer-0.4.2 six-1.16.0 urllib3-1.26.20 wcwidth-0.2.13 + python -m unittest tests/nightly_tests/test_comparison.py .F ====================================================================== FAIL: test_doi_information (tests.nightly_tests.test_comparison.ComparisonTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/SciCrunch Knowledge Testing/tests/nightly_tests/test_comparison.py", line 107, in test_doi_information checkResult(self, discover_doi, scicrunch_doi, name_doi_map, 'Pennsieve vs SciCrunch') File "/home/cmiss/Jenkins/workspace/SciCrunch Knowledge Testing/tests/nightly_tests/test_comparison.py", line 40, in checkResult client.assertEqual([], not_found_doi, name) AssertionError: Lists differ: [] != ['10.26275/pu3x-uisf', '10.26275/ofgg-9x6j[63 chars]pb8'] Second list contains 5 additional elements. First extra element 0: '10.26275/pu3x-uisf' - [] + ['10.26275/pu3x-uisf', + '10.26275/ofgg-9x6j', + '10.26275/onuv-fhmt', + '10.26275/4tn2-3i3j', + '10.26275/2nyl-vpb8'] : Pennsieve vs SciCrunch ---------------------------------------------------------------------- Ran 2 tests in 18.420s FAILED (failures=1) Pennsieve vs SciCrunch: Not found datasets report: 95 - 10.26275/pu3x-uisf - Generic human colon scaffold 154 - 10.26275/ofgg-9x6j - Generic human brainstem scaffold 144 - 10.26275/onuv-fhmt - Generic human bladder scaffold 94 - 10.26275/4tn2-3i3j - Generic cat bladder scaffold 402 - 10.26275/2nyl-vpb8 - 3D segmentation of myelinated afferents of the rat bladder in the pelvic nerve Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1065 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE