Bug #13140

[CWL] Update cwltool for latest cwl conformance tests

Added by Peter Amstutz over 1 year ago. Updated about 1 year ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
03/02/2018
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-
Release relationship:
Auto

Description

Some conformance tests are failing. Update arvados-cwl-runner to pass.


Subtasks

Task #13154: Update cwltool & ensure passing testsResolvedPeter Amstutz

Task #13161: Review 13140-cwl-conformanceResolvedPeter Amstutz

Associated revisions

Revision 9c983060
Added by Peter Amstutz over 1 year ago

Merge branch '13140-cwl-conformance' refs #13140

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

Revision 1a3fb9d7 (diff)
Added by Peter Amstutz over 1 year ago

Update version of cwltest package refs #13140

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

Revision 50223437 (diff)
Added by Peter Amstutz over 1 year ago

Fix packaging for python-cwltest. refs #13140

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

Revision a75460e1 (diff)
Added by Peter Amstutz over 1 year ago

Fix packaging for python-cwltest. refs #13140

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

History

#1 Updated by Peter Amstutz over 1 year ago

  • Status changed from New to In Progress

#2 Updated by Peter Amstutz over 1 year ago

  • Subject changed from [CWL] Update cwltool to [CWL] Update cwltool for latest cwl conformance tests

#3 Updated by Peter Amstutz over 1 year ago

  • Description updated (diff)

#4 Updated by Peter Amstutz over 1 year ago

  • Status changed from In Progress to New
  • Assigned To set to Peter Amstutz

#5 Updated by Lucas Di Pentima over 1 year ago

Just to keep the record of what we already chatted:

Tried to run the conformance tests on arvbox and got errors similar to:

Test [13/127] 
Test failed: /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmp0wBPwn --quiet v1.0/cat4-tool.cwl v1.0/cat-job.json
Test command execution in Docker with stdin and stdout redirection
Returned non-zero
2018-03-02 16:04:26 cwltool ERROR: Workflow error, try again with --debug for more information:
v1.0/cat4-tool.cwl:7:5: 'module' object has no attribute 'get_image'

There are also some tests failing, don't know if they're related: https://ci.curoverse.com/job/developer-run-tests/626/

#6 Updated by Peter Amstutz over 1 year ago

Thanks.

Updated with fix 13140-cwl-conformance @ cde5fc115a5d543eb6522fdad6e651dfbe857656

#7 Updated by Lucas Di Pentima over 1 year ago

I'm having problems when trying to run the conformance tests on arvbox:

(venv) lucas@veritas:~/common-workflow-language$ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse" 
--- Running conformance test v1.0 on /home/lucas/venv/bin/arvados-cwl-runner ---
/home/lucas/venv/bin/arvados-cwl-runner 1.0.20180302211217, arvados-python-client 0.1.20180223161544, cwltool 1.0.20180225105849
Test [1/127] 
Test timed out: /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmp_fJ2Wz --quiet v1.0/bwa-mem-tool.cwl v1.0/bwa-mem-job.json
General test of command line generation
Test [2/127] 

Maybe it's a local issue, I tried resetting the arvbox instance from scratch, re-building the image, but it's not working for me. On workbench the jobs appear as Queued and are kept that way after the timeout.

#8 Updated by Lucas Di Pentima over 1 year ago

As suggested by Peter I asked for the crunch-dispatch-local logs and I'm seeing this error:

[...]
2018-03-05_19:01:10.61051 # git.curoverse.com/arvados.git/services/crunch-run
2018-03-05_19:01:10.61054 src/git.curoverse.com/arvados.git/services/crunch-run/crunchrun.go:1777: cannot use docker (type *client.Client) as type ThinDockerClient in argument to NewContaine
rRunner:
2018-03-05_19:01:10.61055       *client.Client does not implement ThinDockerClient (wrong type for ContainerAttach method)
2018-03-05_19:01:10.61055               have ContainerAttach("github.com/docker/docker/vendor/golang.org/x/net/context".Context, string, types.ContainerAttachOptions) (types.HijackedResponse
, error)
2018-03-05_19:01:10.61055               want ContainerAttach("golang.org/x/net/context".Context, string, types.ContainerAttachOptions) (types.HijackedResponse, error)
[...]

#9 Updated by Peter Amstutz over 1 year ago

Lucas Di Pentima wrote:

As suggested by Peter I asked for the crunch-dispatch-local logs and I'm seeing this error:

[...]

arvbox has "reset" and "destroy". The "reset" option only deletes arvados data (database, keep, git repos, etc) whereas the "destroy" option deletes the whole thing including the package caches. This looks like a problem in your go libraries (maybe arvbox isn't using govendor properly? not sure) you can try deleting ~/.arvbox/arvbox/gopath or using "arvbox destroy" to wipe out the whole thing.

#10 Updated by Peter Amstutz over 1 year ago

  • Status changed from New to Feedback

Also I think our cwltest package needs to be updated, I believe that is why it is failing on some clusters but not others.

#11 Updated by Peter Amstutz over 1 year ago

  • Status changed from Feedback to Resolved

Finally everything is blue again.

#12 Updated by Tom Morris about 1 year ago

  • Release set to 17

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