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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/Segmentation test [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/scicrunch-knowledge-testing.git > git init /home/cmiss/Jenkins/workspace/Segmentation test # timeout=10 Fetching upstream changes from https://github.com/ABI-Software/scicrunch-knowledge-testing.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/ABI-Software/scicrunch-knowledge-testing.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/ABI-Software/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 [Segmentation test] $ /bin/sh -xe /tmp/shiningpanda8149440745647884298.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) Requirement already satisfied: requests==2.28.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (2.28.1) Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 2)) (2.6.2) Requirement already satisfied: boto3==1.17.67 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.17.67) Requirement already satisfied: ftfy==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (6.1.1) Requirement already satisfied: charset-normalizer<3,>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2.1.1) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (3.7) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (1.26.19) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2024.7.4) Requirement already satisfied: botocore<1.21.0,>=1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (1.20.112) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.10.0) Requirement already satisfied: s3transfer<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.4.2) Requirement already satisfied: wcwidth>=0.2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from ftfy==6.1.1->-r requirements.txt (line 4)) (0.2.13) Requirement already satisfied: networkx<3.0.0,>=2.8.8 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (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)) (2.8.8) Requirement already satisfied: rdflib<7.0.0,>=6.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (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)) (6.3.2) Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from botocore<1.21.0,>=1.20.67->boto3==1.17.67->-r requirements.txt (line 3)) (2.9.0.post0) Requirement already satisfied: isodate<0.7.0,>=0.6.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (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)) (0.6.1) Requirement already satisfied: pyparsing<4,>=2.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (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)) (3.1.2) Requirement already satisfied: six in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (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)) (1.16.0) [notice] A new release of pip is available: 24.1.2 -> 24.3.1 [notice] To update, run: pip install --upgrade pip + python -m unittest tests/slow_tests/segmentation_tests.py Reports generated for 17 Reports generated for 30 Reports generated for 78 Reports generated for 7 Reports generated for 8 Reports generated for 171 Reports generated for 261 Reports generated for 303 Reports generated for 305 Reports generated for 229 Reports generated for 257 Reports generated for 270 Reports generated for 294 Reports generated for 211 Reports generated for 22 Reports generated for 210 Reports generated for 296 Reports generated for 143 Reports generated for 20 Reports generated for 259 Reports 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for 205 Reports generated for 21 Reports generated for 153 Reports generated for 242 Reports generated for 24 Reports generated for 320 Reports generated for 97 Reports generated for 32 Reports generated for 271 Reports generated for 28 Reports generated for 85 Reports generated for 162 Reports generated for 89 Reports generated for 239 Reports generated for 376 Reports generated for 369 Reports generated for 375 Reports generated for 354 Reports generated for 29 Reports generated for 357 Reports generated for 132 Reports generated for 292 Reports generated for 182 Reports generated for 367 Reports generated for 373 Reports generated for 65 Reports generated for 388 Reports generated for 386 Reports generated for 316 Reports generated for 161 Reports generated for 55 Reports generated for 165 Reports generated for 204 Reports generated for 59 Reports generated for 138 Reports generated for 108 Reports generated for 106 Reports generated for 283 Reports generated for 317 Reports generated for 48 Reports generated for 293 Reports generated for 88 Reports generated for 178 Reports generated for 208 Reports generated for 382 Reports generated for 385 Reports generated for 225 Reports generated for 226 Reports generated for 378 Reports generated for 118 Reports generated for 372 Reports generated for 41 Reports generated for 324 Reports generated for 333 Reports generated for 287 Reports generated for 119 Reports generated for 392 Reports generated for 221 Reports generated for 395 Reports generated for 396 Reports generated for 397 Reports generated for 398 Reports generated for 307 Reports generated for 173 Reports generated for 166 F ====================================================================== FAIL: test_files_information (tests.slow_tests.segmentation_tests.SegmentationDatasetFilesTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/Segmentation test/tests/slow_tests/segmentation_tests.py", line 440, in test_files_information self.assertEqual(0, len(reports['FailedIds'])) AssertionError: 0 != 12 ---------------------------------------------------------------------- Ran 1 test in 522.734s FAILED (failures=1) Reports generated for 76 Reports generated for 98 Reports generated for 232 Reports generated for 99 Reports generated for 155 Reports generated for 102 Reports generated for 218 Reports generated for 409 Reports generated for 380 Reports generated for 154 Reports generated for 135 Number of datasets tested: 328 Number of dataset with erros: 12 Failed Datasets: ['31', '64', '43', '314', '120', '125', '230', '60', '347', '225', '226', '221'] Full report has been generated at reports/segmentation_reports.json Build step 'Virtualenv Builder' marked build as failure Archiving artifacts Finished: FAILURE