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/shiningpanda3234544881648589648.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) + python -m unittest tests/slow_tests/segmentation_tests.py Build was aborted Aborted by David J. Yu Archiving artifacts Finished: ABORTED