Comments (5)
Weird, are they getting passed through a shell at some layer...?
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(Pdb) pp image
'samuelgerber/utm'
(Pdb) pp entrypoint
None
(Pdb) pp volumes
{'/tmp/tmpqbclifh4': {'bind': '/mnt/girder_worker/faa3b3626a104b19a115b7579abae1f6',
'mode': 'rw'}}
(Pdb) pp container_args
['/mnt/girder_worker/faa3b3626a104b19a115b7579abae1f6/5bf5717f89f99f119ce51703/UTM '
'2018-11-21T14:53:51.104Z',
'/mnt/girder_worker/faa3b3626a104b19a115b7579abae1f6/5bfea50989f99f119ce51d80/variables.csv',
'--workingfolder',
'/mnt/girder_worker/faa3b3626a104b19a115b7579abae1f6/__results__']
Invoked by:
return docker_run.delay('samuelgerber/utm', container_args=[
GirderFolderIdToVolume(folder['_id']),
GirderFileIdToVolume(paramsFile['_id']),
'--workingfolder', outpath
], girder_job_title='UTM: ' + folder['name'], girder_result_hooks=[
GirderUploadVolumePathToFolder(outpath, outputFolder['_id'])
]).job
from girder_worker.
@zachmullen i'm working on a failing test now
from girder_worker.
Turns out the string '/mnt/girder_worker/faa3b3626a104b19a115b7579abae1f6/5bf5717f89f99f119ce51703/UTM 2018-11-21T14:53:51.104Z'
is not actually being split on the whitespace, pdb is choosing to split the string when printing. The issue is the underlying container entrypoint script does not handle paths with spaces.
from girder_worker.
For posterity, the entrypoint in question is this R script.
I don't know anything about R arg parsing, but from a quick glance, I'm guessing it's actually the result of how that R script makes subprocess calls internally to other R scripts (via the system2
command).
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Related Issues (20)
- RFC: Consider cache configuration in new girder worker tasks HOT 2
- Girder worker integration test plugin is not compatible with girder 3.
- Create "How to write an integration test" documentation for girder worker
- Check if Celery Pinning is still necessary HOT 24
- Docker in docker permission issue HOT 1
- Girder Client 2.4.0 breaking integration test HOT 7
- girder_plugin settings for worker.api_url, worker.broker, worker.backend are not being picked up correctly HOT 3
- Using kwargs in chained tasks fails to create Job object
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- girder_result_hooks cleanup methods are not called after task is done
- File paths from docker transforms should be wrapped in quotes HOT 1
- Document job event binding and output reference kwargs. HOT 7
- Running NVidia dockers
- docker_run can't process non-string arguments HOT 3
- Exceptions are silently ignored during plugin load
- Girder plugin: use setting default HOT 1
- Pin celery version in requirements.in HOT 1
- How can I pass env variables from within DSA to a image that is being added through slicer web task
- Is the "DIRECT_PATH" checkbox actually used ? HOT 2
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