Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c26... Author: John Chilton jmchilton@gmail.com Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_1.txt M test/functional/tools/samples_tool_conf.xml
Log Message: ----------- 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.
Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331 https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e9878... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_2.txt
Log Message: ----------- Add possibility to rename collection items from a tabular file
Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8 https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffca... Author: John Chilton jmchilton@gmail.com Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths: M lib/galaxy/tools/relabel_from_file.xml
Log Message: ----------- Fix failing test case in relable_from_file based on comment from @mvdbeek.
Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47 https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8c... Author: John Chilton jmchilton@gmail.com Date: 2017-04-13 (Thu, 13 Apr 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_1.txt
Log Message: ----------- 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,
Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8 https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d0... Author: John Chilton jmchilton@gmail.com Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_2.txt
Log Message: ----------- Fix relabel_from_file collection operation error handling if duplicate identifiers.
Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df6... Author: John Chilton jmchilton@gmail.com Date: 2017-04-17 (Mon, 17 Apr 2017)
Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt M test/functional/tools/samples_tool_conf.xml
Log Message: ----------- Implement collection operation for filtering lists from a file.
Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0 https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eecd... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml A lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/functional/tools/samples_tool_conf.xml
Log Message: ----------- Merge pull request #3940 from jmchilton/collection_op_filter_from_file
Collection Operation - Filtering from a File
Compare: https://github.com/galaxyproject/galaxy/compare/9f4fd7c44964...01b3eb42d88b