Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b114f3f7b9d483509e7d684aa8be54e769fddbf7 https://github.com/galaxyproject/galaxy/commit/b114f3f7b9d483509e7d684aa8be5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt Log Message: ----------- Add tool that tags collection elements from a file This tags collection elements (but not collections). Commit: b2be7b51814a4354307e8f0a0df0c8885ef73bb0 https://github.com/galaxyproject/galaxy/commit/b2be7b51814a4354307e8f0a0df0c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/managers/taggable.py Log Message: ----------- Sort tags when serializing them Commit: f9664a0863b24ff738aefcbe520f033e5f53e76d https://github.com/galaxyproject/galaxy/commit/f9664a0863b24ff738aefcbe520f0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/base/interactor.py Log Message: ----------- Make presence of tags testable Commit: fd373501c78dee268844e82fa1a56a108d34cf23 https://github.com/galaxyproject/galaxy/commit/fd373501c78dee268844e82fa1a56... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add tag from file tool to samples_tool_conf.xml Commit: e306a447c080f8d252a9a7fe49f4d36f6a8de4a9 https://github.com/galaxyproject/galaxy/commit/e306a447c080f8d252a9a7fe49f4d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/tag_collection_from_file.xml Log Message: ----------- Switch tag tool to use select and add remove mode Commit: d14bae73f72cd454ef41bb1815cf1dfc9256db5d https://github.com/galaxyproject/galaxy/commit/d14bae73f72cd454ef41bb1815cf1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/tools/tag_collection_from_file.xml M test-data/new_tags_1.txt Log Message: ----------- Flush once per tag Not sure this is the right thing to do (maybe there is a better way to get an ID?), but it avoids ``` IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" DETAIL: Key (name)=(group) already exists. [SQL: 'INSERT INTO tag (type, parent_id, name) VALUES (%(type)s, %(parent_id)s, %(name)s) RETURNING tag.id'] [parameters: {'parent_id': None, 'type': 0, 'name': u'group'}] galaxy.tools.execute WARNING 2018-02-06 15:22:38,808 [p:2122,w:1,m:0] [uWSGIWorker1Core1] There was a failure executing a job for tool [__TAG_FROM_FILE__] - Error executing tool: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" ``` Commit: 6d00958d43eab15bf2c94bc9088dfa5f162ce3c9 https://github.com/galaxyproject/galaxy/commit/6d00958d43eab15bf2c94bc9088df... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5462 from mvdbeek/tag_collection_from_files Tool that adds/sets tags for collection elements from a file Compare: https://github.com/galaxyproject/galaxy/compare/0367a356d528...6d00958d43ea