Input naming flexibility - tracking the input name throughout the analysis

[zipho]

In using Galaxy, I would like to be able to keep track of the input dataset name down the analysis chain.

This is a similar if not the same issue raised by @erasche in #2752, to which they propose in the context of a workflow that, "the rename dataset action should support usage of all the dataset names from Input Dataset elements, rather than just input files to the particular tool." Please see the issue for more details.

There are other similar issues raise scattered all over regarding the same issues:

Enhancements:

1. Ability to name datasets using the element identifier: Expose element_identifier as a workflow parameter variable. #2006
2. Ability to define the collection name in a workflow: Enhancement: Ability to name collection in a workflow #2398
3. Name datasets according to both collection name and element identifier: Feature request - Filenames based on dataset collection identifier #2140, Download files in a list of datasets with the name from the list #2023

Bug Fixes:

1. Renaming using the input from paired dataset collections: Rename output in workflow fails on paired dataset collection #1675, Rename output file on workflow #1686

If there any work currently being done in this area? Can there be a consensus on how best to address these requests/proposals ideally with clear milestones?

Can the Galaxy devs please assist regarding the above questions?

[jmchilton]

So here are my thoughts if someone wants like an only moderately difficult entrance into this:

• The downloaded filename of collection items is pretty bad and seems fairly fixable. It targets an endpoint that I believe lets you chose a filename - so the client code just needs to figure out what that should be and it should have the context. I don't know exactly when the download button for these datasets was added - but it might have been in this PR ([15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… #854). It is a good place to start.

• PostJobActions for mapped over output collections. #1680 This would be a clear win - the rename post job action should apply to collection name (not element identifiers though IMO). Some relevant pieces of code include:

  • https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/execute.py#L92
  • https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/execute.py#L131
  • https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/workflow/modules.py#L1083
  • https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/__init__.py#L1052

  The trick here I think is to figure out what PJA can easily be applied ahead of time during collection creation and then apply them. In general there is no ... synchronization point in Galaxy that says after I have executed all the jobs that go into creating this collection ... do something. So that is a bit tricky in general but I think stuff like rename can be applied ahead of time.

• This Expose element_identifier as a workflow parameter variable. #2006 to my mind is a bit more questionable but it should be not to complicated to implement. The most relevant piece of code is probably https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/actions/post.py#L137 or that whole function. As well as the tool wrapper and model code that grabs the element_identifier from the database.

[zipho]

Thanks @jmchilton
For our purposes, issues #2752 and #1680 are of priority.