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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/shiningpanda13932907563946272031.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-3.10-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-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-3.2.0-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-1.16.0-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-3.10-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-3.2.0-py3-none-any.whl (106 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-3.10 isodate-0.6.1 jmespath-0.10.0 mapknowledge-0.13.1 networkx-2.8.8 pyparsing-3.2.0 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 Traceback (most recent call last): File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn conn = connection.create_connection( File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py", line 72, in create_connection for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): File "/usr/lib/python3.9/socket.py", line 966, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno -2] Name or service not known During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 716, in urlopen httplib_response = self._make_request( File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 404, in _make_request self._validate_conn(conn) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1061, in _validate_conn conn.connect() File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 363, in connect self.sock = conn = self._new_conn() File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py", line 186, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6476f968b0>: Failed to establish a new connection: [Errno -2] Name or service not known During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 489, in send resp = conn.urlopen( File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 802, in urlopen retries = retries.increment( File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/retry.py", line 594, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6476f968b0>: Failed to establish a new connection: [Errno -2] Name or service not known')) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/usr/lib/python3.9/unittest/__main__.py", line 18, in <module> main(module=None) File "/usr/lib/python3.9/unittest/main.py", line 100, in __init__ self.parseArgs(argv) File "/usr/lib/python3.9/unittest/main.py", line 147, in parseArgs self.createTests() File "/usr/lib/python3.9/unittest/main.py", line 158, in createTests self.test = self.testLoader.loadTestsFromNames(self.testNames, File "/usr/lib/python3.9/unittest/loader.py", line 220, in loadTestsFromNames suites = [self.loadTestsFromName(name, module) for name in names] File "/usr/lib/python3.9/unittest/loader.py", line 220, in <listcomp> suites = [self.loadTestsFromName(name, module) for name in names] File "/usr/lib/python3.9/unittest/loader.py", line 191, in loadTestsFromName return self.loadTestsFromModule(obj) File "/usr/lib/python3.9/unittest/loader.py", line 124, in loadTestsFromModule tests.append(self.loadTestsFromTestCase(obj)) File "/usr/lib/python3.9/unittest/loader.py", line 93, in loadTestsFromTestCase loaded_suite = self.suiteClass(map(testCaseClass, testCaseNames)) File "/usr/lib/python3.9/unittest/suite.py", line 24, in __init__ self.addTests(tests) File "/usr/lib/python3.9/unittest/suite.py", line 57, in addTests for test in tests: File "/home/cmiss/Jenkins/workspace/SciCrunch Knowledge Testing/tests/nightly_tests/test_comparison.py", line 53, in __init__ scicrunch_response = requests.post(urljoin(scicrunch_host, '_search'), json=SCICRUNCH_DOI_AGGREGATION, params=params, headers=headers) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 115, in post return request("post", url, data=data, json=json, **kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 587, in request resp = self.send(prep, **send_kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py", line 701, in send r = adapter.send(request, **kwargs) File "/home/cmiss/Jenkins/shiningpanda/jobs/d0cfff48/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 565, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6476f968b0>: Failed to establish a new connection: [Errno -2] Name or service not known')) Build step 'Virtualenv Builder' marked build as failure [Slack Notifications] found #1144 as previous completed, non-aborted build [Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it Finished: FAILURE