Arvados

Reviewing updates at 0c817f2f9

Followed guide on https://dev.arvados.org/issues/11948#note-4 to run conformance tests on a local arvbox instance, and many tests failed:

Test [108/108] 
40 tests passed, 64 failures, 4 unsupported features

1 tool tests failed

Ran some failing tests manually, this is what I got:

(venv)lucas@curoverse:~/common-workflow-language$ /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmpGUvLgn --debug v1.0/shellchar2.cwl v1.0/empty.json
2017-07-27 17:10:41 cwltool INFO: /home/lucas/venv/bin/arvados-cwl-runner 0c817f2f98fc9f15bf36ec226da2e72afb34edd5 1.0.20170727113430, arvados-python-client 0.1.20170717175001, cwltool 1.0.20170727112954
2017-07-27 17:10:41 cwltool DEBUG: Search path is ['/home/lucas/common-workflow-language/v1.0/shellchar2.cwl', '/home/lucas/.local/share/commonwl/v1.0/shellchar2.cwl', '/usr/share/xfce4/commonwl/v1.0/shellchar2.cwl', '/usr/local/share/commonwl/v1.0/shellchar2.cwl', '/usr/share/commonwl/v1.0/shellchar2.cwl', '/usr/share/commonwl/v1.0/shellchar2.cwl']
2017-07-27 17:10:41 cwltool INFO: Resolved 'v1.0/shellchar2.cwl' to 'file:///home/lucas/common-workflow-language/v1.0/shellchar2.cwl'
2017-07-27 17:10:41 cwltool ERROR: Tool definition failed initialization:
[Errno 2] No such file or directory: '/home/lucas/common-workflow-language/v1.0/shellchar2.cwl'
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/cwltool/main.py", line 795, in main
    fetcher_constructor=fetcher_constructor)
  File "build/bdist.linux-x86_64/egg/cwltool/load_tool.py", line 66, in fetch_document
    workflowobj = document_loader.fetch(fileuri)
  File "build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py", line 868, in fetch
    text = self.fetch_text(url)
  File "build/bdist.linux-x86_64/egg/arvados_cwl/fsaccess.py", line 173, in fetch_text
    return super(CollectionFetcher, self).fetch_text(url)
  File "build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py", line 154, in fetch_text
    raise RuntimeError(six.text_type(e))
RuntimeError: [Errno 2] No such file or directory: '/home/lucas/common-workflow-language/v1.0/shellchar2.cwl'
(venv)lucas@curoverse:~/common-workflow-language$ find . -name shellchar2.cwl
./v1.1.0-dev1/v1.1.0-dev1/shellchar2.cwl
./v1.0/v1.0/shellchar2.cwl

(venv)lucas@curoverse:~/common-workflow-language$ /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmpsevmdA --debug v1.0/null-defined.cwl v1.0/empty.json
2017-07-27 17:25:19 cwltool INFO: /home/lucas/venv/bin/arvados-cwl-runner 0c817f2f98fc9f15bf36ec226da2e72afb34edd5 1.0.20170727113430, arvados-python-client 0.1.20170717175001, cwltool 1.0.20170727112954
2017-07-27 17:25:19 cwltool DEBUG: Search path is ['/home/lucas/common-workflow-language/v1.0/null-defined.cwl', '/home/lucas/.local/share/commonwl/v1.0/null-defined.cwl', '/usr/share/xfce4/commonwl/v1.0/null-defined.cwl', '/usr/local/share/commonwl/v1.0/null-defined.cwl', '/usr/share/commonwl/v1.0/null-defined.cwl', '/usr/share/commonwl/v1.0/null-defined.cwl']
2017-07-27 17:25:19 cwltool INFO: Resolved 'v1.0/null-defined.cwl' to 'file:///home/lucas/common-workflow-language/v1.0/null-defined.cwl'
2017-07-27 17:25:19 cwltool ERROR: Tool definition failed initialization:
[Errno 2] No such file or directory: '/home/lucas/common-workflow-language/v1.0/null-defined.cwl'
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/cwltool/main.py", line 795, in main
    fetcher_constructor=fetcher_constructor)
  File "build/bdist.linux-x86_64/egg/cwltool/load_tool.py", line 66, in fetch_document
    workflowobj = document_loader.fetch(fileuri)
  File "build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py", line 868, in fetch
    text = self.fetch_text(url)
  File "build/bdist.linux-x86_64/egg/arvados_cwl/fsaccess.py", line 173, in fetch_text
    return super(CollectionFetcher, self).fetch_text(url)
  File "build/bdist.linux-x86_64/egg/schema_salad/ref_resolver.py", line 154, in fetch_text
    raise RuntimeError(six.text_type(e))
RuntimeError: [Errno 2] No such file or directory: '/home/lucas/common-workflow-language/v1.0/null-defined.cwl'
(venv)lucas@curoverse:~/common-workflow-language$ find . -name null-defined.cwl
./v1.0/v1.0/null-defined.cwl

Is this some cwl mistake or something is wrongly configured on my local setup?

You need to cd in to the "v1.0" directory before you paste the command line.

Adding environment information.

pip freeze returns:

CacheControl==0.11.7
argparse==1.2.1
arvados-cwl-runner==1.0.20170727113430
arvados-python-client==0.1.20170717175001
avro==1.8.1
certifi==2017.7.27.1
chardet==3.0.4
ciso8601==1.0.3
cwltest==1.0.20170721135308
cwltool==1.0.20170727112954
future==0.16.0
futures==3.1.1
google-api-python-client==1.6.2
httplib2==0.10.3
idna==2.5
isodate==0.5.4
junit-xml==1.7
lockfile==0.12.2
mistune==0.7.4
oauth2client==4.1.2
pyasn1==0.3.1
pyasn1-modules==0.0.10
pycurl==7.43.0
pyparsing==2.2.0
rdflib==4.2.2
rdflib-jsonld==0.4.0
requests==2.18.2
rsa==3.4.2
ruamel.ordereddict==0.4.13
ruamel.yaml==0.13.7
schema-salad==2.6.20170712194300
shellescape==3.4.1
six==1.10.0
typing==3.5.3.0
uritemplate==3.0.0
urllib3==1.22
ws4py==0.3.5
wsgiref==0.1.2

Trying run the conformance tests from cwl repo, commit ffd2dbfc4a73937c91cfa05afa079f1609eff583

So the issue is that it is missing a Docker image tagged arvados/jobs:latest, compounded by the a logging bug that obscured the issue a bit.

It will now pull arvados/jobs:latest image if necessay. Now 12037-cwl-v1.0.1 @ d69024a630b907c930070fbfd24e61aad1070a70

All conformance tests now worked for me.
LGTM, thanks!