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Collection Operation - Filtering from a File #3940

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merged 6 commits into from Apr 20, 2017

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commented Apr 17, 2017

Builds on #3603 (relabelling a collection from a supplied file).

jmchilton and others added some commits Feb 13, 2017

Start work on a relabelling collection operation.
I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:

 - Validate uniqueness of identifiers and provide nice messages if they are not unique.
 - Validate that at least the required number of lines are present in the file and provide a nice message if not.
 - Add strict mode to ensure exactly the correct number of lines is added.
 - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
 - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
 - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
Various improvements to relabel from file collection operation.
- Better error handling (check for bad characters when creating collections).
- Implement a strict mode parameter to do even more validation.
- Rework tabular vs txt mode to be explicit user choice.
- Mirror fix in release_17.01 for datasets not having a history,
@@ -36,6 +36,8 @@
<tool file="${model_tools_path}/filter_failed_collection.xml" />
<tool file="${model_tools_path}/flatten_collection.xml" />
<tool file="${model_tools_path}/merge_collection.xml" />
<tool file="${model_tools_path}/relabel_from_file.xml" />
<tool file="${model_tools_path}/filter_from_file.xml" />

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@mvdbeek

mvdbeek Apr 17, 2017

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Did you forget to add this file?

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@jmchilton

jmchilton Apr 17, 2017

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Rebased with that file - seems important.

@jmchilton jmchilton force-pushed the jmchilton:collection_op_filter_from_file branch from 7366666 to 49abfce Apr 17, 2017

@bgruening

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commented Apr 20, 2017

Thanks @jmchilton!

@bgruening bgruening merged commit 01b3eb4 into galaxyproject:dev Apr 20, 2017

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