https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422017-07-26T14:46:29ZArvadosArvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537222017-07-26T14:46:29ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>In Progress</i></li><li><strong>Assigned To</strong> set to <i>Peter Amstutz</i></li></ul> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537712017-07-27T21:27:22ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>Reviewing updates at <a class="changeset" title="12037: Fix tests. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curoverse.com>" href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/0c817f2f98fc9f15bf36ec226da2e72afb34edd5">0c817f2f9</a></p>
<p>Followed guide on <a class="external" href="https://dev.arvados.org/issues/11948#note-4">https://dev.arvados.org/issues/11948#note-4</a> to run conformance tests on a local arvbox instance, and many tests failed:</p>
<pre>
Test [108/108]
40 tests passed, 64 failures, 4 unsupported features
1 tool tests failed
</pre>
<p>Ran some failing tests manually, this is what I got:</p>
<pre>
(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
</pre>
<pre>
(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
</pre>
<p>Is this some cwl mistake or something is wrongly configured on my local setup?</p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537732017-07-28T13:07:44ZPeter Amstutzpeter.amstutz@curii.com
<ul></ul><p>You need to cd in to the "v1.0" directory before you paste the command line.</p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537762017-07-28T14:11:51ZLucas Di Pentimalucas.dipentima@curii.com
<ul><li><strong>File</strong> <a href="/attachments/1763">container.json</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/1763/container.json">container.json</a> added</li><li><strong>File</strong> <a href="/attachments/1764">crunch-run.txt</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/1764/crunch-run.txt">crunch-run.txt</a> added</li><li><strong>File</strong> <a href="/attachments/1765">crunchstat.txt</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/1765/crunchstat.txt">crunchstat.txt</a> added</li><li><strong>File</strong> <a href="/attachments/1767">node-info.txt</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/1767/node-info.txt">node-info.txt</a> added</li><li><strong>File</strong> <a href="/attachments/1766">stderr.txt</a> <a class="icon-only icon-download" title="Download" href="/attachments/download/1766/stderr.txt">stderr.txt</a> added</li></ul><p>Attaching log files from a failed conformance test run on my arvbox setup</p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537812017-07-28T15:32:26ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>Adding environment information.</p>
<p><code>pip freeze</code> returns:<br /><pre>
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
</pre></p>
<p>Trying run the conformance tests from cwl repo, commit <code>ffd2dbfc4a73937c91cfa05afa079f1609eff583</code></p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537872017-07-28T19:54:17ZPeter Amstutzpeter.amstutz@curii.com
<ul></ul><p>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.</p>
<p>It will now pull arvados/jobs:latest image if necessay. Now 12037-cwl-v1.0.1 @ <a class="changeset" title="12037: Pull default arvados/jobs:latest image as needed. Arvados-DCO-1.1-Signed-off-by: Peter Am..." href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/d69024a630b907c930070fbfd24e61aad1070a70">d69024a630b907c930070fbfd24e61aad1070a70</a></p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537932017-07-28T21:14:47ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>All conformance tests now worked for me.<br />LGTM, thanks!</p> Arvados - Idea #12037: [CWL] Pass conformance for v1.0.1https://dev.arvados.org/issues/12037?journal_id=537952017-07-29T14:15:05ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>In Progress</i> to <i>Resolved</i></li></ul><p>Applied in changeset arvados|commit:386e1eefaac2021805f73732b10e9f543c221593.</p>