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[17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool #4644

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@mvdbeek
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commented Sep 19, 2017

If the job metadata isn't embedded in the job the registry.xml file wouldn't be written to the tool working directory, causing the upload tool to fail. Reported by @mblue9 on gitter.

@mvdbeek mvdbeek added this to the 17.09 milestone Sep 19, 2017

@mvdbeek mvdbeek changed the base branch from dev to release_17.05 Sep 19, 2017

if job.tool_id == 'upload1':
# We usually write the 'registry.xml' file together with the metadata tool,
# but if `embed_metadata_in_job` is set to false 'registry.xml' will not be available
# to the u[load tool, which will then fail.

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@nsoranzo

nsoranzo Sep 19, 2017

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s/u[load/upload/

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@mvdbeek

mvdbeek Sep 19, 2017

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I rebased the commit with this change.

@mvdbeek mvdbeek force-pushed the mvdbeek:upload_tool_registry_xml_failure branch from 08fbc04 to a3ff129 Sep 19, 2017

@jmchilton

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commented Sep 19, 2017

I believe data source tools use this also right?

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commented Sep 19, 2017

Yes, you're right, and it has always been available as $__datatypes_config__ for tools to consume. Should we just write it out for every job then ?

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commented Sep 19, 2017

In 17.05 yes I think so, longer term we should add a property to Tool like tool.requires_datatypes_conf and prevent tools from getting access to this by default.

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commented Sep 19, 2017

Actually we could reuse preserve_python_environment since that registry is probably worthless without the Galaxy environment on the PATH.

Yeah - can we do this - use that property to determine if it should be written? We've put a lot of work into that so I feel like it should be a safe indicator for 17.05.

mvdbeek added some commits Sep 19, 2017

Write registry.xml for all tools that require galaxy's python env
This should cover the upload and data_source tools.
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commented Sep 19, 2017

Wonderful - thanks @mvdbeek !

@natefoo natefoo merged commit 5d7b524 into galaxyproject:release_17.05 Sep 21, 2017

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@mvdbeek mvdbeek deleted the mvdbeek:upload_tool_registry_xml_failure branch Aug 16, 2018

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