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 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 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/shiningpanda9142818272622819760.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-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/3084ec99/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/3084ec99/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/3084ec99/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/3084ec99/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/3084ec99/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1061, in _validate_conn
conn.connect()
File "/home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/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/3084ec99/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 0x7ff3bdfec8b0>: 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/3084ec99/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py", line 489, in send
resp = conn.urlopen(
File "/home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py", line 802, in urlopen
retries = retries.increment(
File "/home/cmiss/Jenkins/shiningpanda/jobs/3084ec99/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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7ff3bdfec8b0>: 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 Dev/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/3084ec99/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/3084ec99/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/3084ec99/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/3084ec99/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/3084ec99/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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7ff3bdfec8b0>: Failed to establish a new connection: [Errno -2] Name or service not known'))
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #1095 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE