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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/SCKAN Connectivity [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/SCKAN Connectivity # 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 [SCKAN Connectivity] $ /bin/sh -xe /tmp/shiningpanda3079738039211252318.sh + 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 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/5a3744f0/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/5a3744f0/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/5a3744f0/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/5a3744f0/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/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2.0.12) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2022.9.24) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (1.26.12) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (3.4) Requirement already satisfied: s3transfer<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.4.2) Requirement already satisfied: botocore<1.21.0,>=1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/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/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.10.0) Requirement already satisfied: wcwidth>=0.2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from ftfy==6.1.1->-r requirements.txt (line 4)) (0.2.6) Requirement already satisfied: networkx<3.0.0,>=2.8.8 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/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/5a3744f0/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)) (6.2.0) Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from botocore<1.21.0,>=1.20.67->boto3==1.17.67->-r requirements.txt (line 3)) (2.8.2) Requirement already satisfied: pyparsing in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/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)) (3.0.9) Requirement already satisfied: isodate in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/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: setuptools in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/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)) (65.6.0) Requirement already satisfied: six>=1.5 in /home/cmiss/Jenkins/shiningpanda/jobs/5a3744f0/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.21.0,>=1.20.67->boto3==1.17.67->-r requirements.txt (line 3)) (1.16.0) [notice] A new release of pip available: 22.3.1 -> 24.1.2 [notice] To update, run: pip install --upgrade pip + python -m unittest tests/nightly_tests/test_connectivity.py WARNING:root:Couldn't access https://scicrunch.org/api/1/sckan-scigraph/dynamic/demos/apinat/neru-7/ilxtr:neuron-type-keast-5.json: Exception: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sckan-scigraph/dynamic/demos/apinat/neru-7/ilxtr:neuron-type-keast-5.json?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&limit=9999 (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f315d166e20>, 'Connection to scicrunch.org timed out. (connect timeout=30)')) WARNING:root:Unknown anatomical entity: ilxtr:neuron-type-keast-5 FWARNING:root:Couldn't access https://scicrunch.org/api/1/sckan-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https%3A%2F%2Fapinatomy.org%2Furis%2Fmodels%2Fkeast-bladder.json: Exception: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sckan-scigraph/dynamic/demos/apinat/modelPopulationsReferences/https%3A%2F%2Fapinatomy.org%2Furis%2Fmodels%2Fkeast-bladder.json?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&limit=9999 (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f315d18f8b0>, 'Connection to scicrunch.org timed out. (connect timeout=30)')) WARNING:root:Unknown anatomical entity: https://apinatomy.org/uris/models/keast-bladder E ====================================================================== ERROR: test_connectivity_neurons (tests.nightly_tests.test_connectivity.ConnectivityTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/SCKAN Connectivity/tests/nightly_tests/test_connectivity.py", line 117, in test_connectivity_neurons assert len(knowledge.get('paths')) == 20, 'Wrong number of neuron paths for Keast bladder model' TypeError: object of type 'NoneType' has no len() ====================================================================== FAIL: test_connectivity_neuron_group (tests.nightly_tests.test_connectivity.ConnectivityTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/SCKAN Connectivity/tests/nightly_tests/test_connectivity.py", line 122, in test_connectivity_neuron_group assert len(knowledge.get('connectivity', [])) == len(KEAST_NEURON_PATH_5['connectivity']), 'Incorrect number of nodes for Keast neuron path 5' AssertionError: Incorrect number of nodes for Keast neuron path 5 ---------------------------------------------------------------------- Ran 2 tests in 60.555s FAILED (failures=1, errors=1) Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #597 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE