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Collection Operation - Filtering from a File #3940
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bgruening
merged 6 commits into
galaxyproject:dev
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jmchilton:collection_op_filter_from_file
Apr 20, 2017
Merged
Collection Operation - Filtering from a File #3940
bgruening
merged 6 commits into
galaxyproject:dev
from
jmchilton:collection_op_filter_from_file
Apr 20, 2017
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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.
- 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,
mvdbeek
reviewed
Apr 17, 2017
@@ -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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Did you forget to add this file?
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Rebased with that file - seems important.
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Thanks @jmchilton! |
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Builds on #3603 (relabelling a collection from a supplied file).