Arvados

Bug #17008

Updated by Michael Crusoe over 3 years ago

From running CWL v1.0 conformance tests against https://workbench.covid19workflows-vu.surf-hosted.nl 

 <pre> 
 Test 47 failed: /home/michael/common-workflow-language/arvenv3.6/bin/arvados-cwl-runner --compute-checksum --project-uuid=testc-j7d0g-n7la9srj0ycdvix --outdir=/tmp/tmpc8__hhgl --quiet v1.0/env-wf2.cwl v1.0/env-job.json 
 Test requirements override hints 
 Returned non-zero 
 ERROR [container env-wf2.cwl] (testc-dz642-uych2j0mwa6vm49) error log: 

   2020-10-15T14:52:21.285202240Z stderr       for res in _socket.getaddrinfo(host, port, family, type, proto, flags): 
   2020-10-15T14:52:21.285202240Z stderr socket.gaierror: [Errno -3] Temporary failure in name resolution 
   2020-10-15T14:52:21.285202240Z stderr 
   2020-10-15T14:52:21.285202240Z stderr During handling of the above exception, another exception occurred: 
   2020-10-15T14:52:21.285202240Z stderr 
   2020-10-15T14:52:21.285202240Z stderr Traceback (most recent call last): 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/api.py", line 85, in _intercept_http_request 
   2020-10-15T14:52:21.285202240Z stderr       return self.orig_http_request(uri, method, headers=headers, **kwargs) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/httplib2/__init__.py", line 1994, in request 
   2020-10-15T14:52:21.285202240Z stderr       cachekey, 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/httplib2/__init__.py", line 1651, in _request 
   2020-10-15T14:52:21.285202240Z stderr       conn, request_uri, method, body, headers 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/httplib2/__init__.py", line 1564, in _conn_request 
   2020-10-15T14:52:21.285202240Z stderr       raise ServerNotFoundError("Unable to find the server at %s" % conn.host) 
   2020-10-15T14:52:21.285202240Z stderr httplib2.ServerNotFoundError: Unable to find the server at hackathon.covid19workflows-vu.surf-hosted.nl 
   2020-10-15T14:52:21.285202240Z stderr 
   2020-10-15T14:52:21.285202240Z stderr During handling of the above exception, another exception occurred: 
   2020-10-15T14:52:21.285202240Z stderr 
   2020-10-15T14:52:21.285202240Z stderr Traceback (most recent call last): 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/__init__.py", line 297, in main 
   2020-10-15T14:52:21.285202240Z stderr       keep_params={"num_retries": 4}) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/safeapi.py", line 33, in __init__ 
   2020-10-15T14:52:21.285202240Z stderr       self.localapi() 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/safeapi.py", line 40, in localapi 
   2020-10-15T14:52:21.285202240Z stderr       **self.api_params) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/api.py", line 278, in api_from_config 
   2020-10-15T14:52:21.285202240Z stderr       return api(version=version, host=host, token=token, insecure=insecure, **kwargs) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/api.py", line 236, in api 
   2020-10-15T14:52:21.285202240Z stderr       svc = apiclient_discovery.build('arvados', version, cache_discovery=False, **kwargs) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/googleapiclient/_helpers.py", line 130, in positional_wrapper 
   2020-10-15T14:52:21.285202240Z stderr       return wrapped(*args, **kwargs) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/googleapiclient/discovery.py", line 222, in build 
   2020-10-15T14:52:21.285202240Z stderr       requested_url, discovery_http, cache_discovery, cache) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/googleapiclient/discovery.py", line 269, in _retrieve_discovery_doc 
   2020-10-15T14:52:21.285202240Z stderr       resp, content = http.request(actual_url) 
   2020-10-15T14:52:21.285202240Z stderr     File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados/api.py", line 99, in _intercept_http_request 
   2020-10-15T14:52:21.285202240Z stderr       except httplib2.SSLHandshakeError as e: 
   2020-10-15T14:52:21.285202240Z stderr AttributeError: module 'httplib2' has no attribute 'SSLHandshakeError' 
   2020-10-15T14:52:21.610802843Z crunch-run Container exited with code: 1 
   2020-10-15T14:52:21.753959895Z crunch-run Complete 
 ERROR Overall process status is permanentFail 
 WARNING Final process status is permanentFail 

 </pre> 

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