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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 Dev [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 Dev # 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 d3d7b0041f71b26c4bc267594945f0758e855311 (refs/remotes/origin/main) > git config core.sparsecheckout # timeout=10 > git checkout -f d3d7b0041f71b26c4bc267594945f0758e855311 # timeout=10 Commit message: "Merge pull request #20 from ddjnw1yu/testing-script" > git rev-list --no-walk d3d7b0041f71b26c4bc267594945f0758e855311 # timeout=10 [SciCrunch Knowledge Testing Dev] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/virtualenvs/d41d8cd9 /home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/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/3084ec99/virtualenvs/d41d8cd9/bin/python3.9 Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/virtualenvs/d41d8cd9/bin/python Installing setuptools, pip, wheel...done. [SciCrunch Knowledge Testing Dev] $ /bin/sh -xe /tmp/shiningpanda9238952729812249108.sh + export PENNSIEVE_API_HOST=https://api.pennsieve.io/discover + export SCICRUNCH_API_HOST=https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_dev + 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-3.10-py3-none-any.whl.metadata (10 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-2025.1.31-py3-none-any.whl.metadata (2.5 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-3.2.1-py3-none-any.whl.metadata (5.0 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-1.17.0-py2.py3-none-any.whl.metadata (1.7 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-2025.1.31-py3-none-any.whl (166 kB) Using cached charset_normalizer-2.1.1-py3-none-any.whl (39 kB) Using cached idna-3.10-py3-none-any.whl (70 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-3.2.1-py3-none-any.whl (107 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached six-1.17.0-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-2025.1.31 charset-normalizer-2.1.1 ftfy-6.1.1 idna-3.10 isodate-0.6.1 jmespath-0.10.0 mapknowledge-0.13.1 networkx-2.8.8 pyparsing-3.2.1 python-dateutil-2.9.0.post0 rdflib-6.3.2 requests-2.28.1 s3transfer-0.4.2 six-1.17.0 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 Dev/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 Dev/tests/nightly_tests/test_comparison.py", line 40, in checkResult client.assertEqual([], not_found_doi, name) AssertionError: Lists differ: [] != ['10.26275/xjgh-9rrj'] Second list contains 1 additional elements. First extra element 0: '10.26275/xjgh-9rrj' - [] + ['10.26275/xjgh-9rrj'] : Pennsieve vs SciCrunch ---------------------------------------------------------------------- Ran 2 tests in 9.940s FAILED (failures=1) Pennsieve vs SciCrunch: Not found datasets report: 425 - 10.26275/xjgh-9rrj - Using in vivo calcium imaging to examine joint neuron spontaneous activity and home cage analysis to monitor activity changes in mouse models of arthritis Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1211 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE