Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 940ed5f5dd1f34456d81513db8bbf0a66476e683 https://github.com/galaxyproject/galaxy/commit/940ed5f5dd1f34456d81513db8bbf... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: cb97f89d129cf7f0b7cf7146c0c15309b3dcb0c7 https://github.com/galaxyproject/galaxy/commit/cb97f89d129cf7f0b7cf7146c0c15... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: 9b19d5c267900409b5aace9f2c554b2da13ce8e7 https://github.com/galaxyproject/galaxy/commit/9b19d5c267900409b5aace9f2c554... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: fd16302d65193f13eb04456b610044343ca54adb https://github.com/galaxyproject/galaxy/commit/fd16302d65193f13eb04456b61004... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: 258ccb89bd5190e703f9d1705ec888b65ce77724 https://github.com/galaxyproject/galaxy/commit/258ccb89bd5190e703f9d1705ec88... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: fc06a7a168d5d36fabb3f6f420a4ef0b12363f2c https://github.com/galaxyproject/galaxy/commit/fc06a7a168d5d36fabb3f6f420a4e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: 178486b840b64c2bfb1b4cffefd44c945a8ccb3e https://github.com/galaxyproject/galaxy/commit/178486b840b64c2bfb1b4cffefd44... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/history_query.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6278 from mvdbeek/fix_paired_mapping_over Various fixes for mapping over collections Compare: https://github.com/galaxyproject/galaxy/compare/cd2feb7dcb81...178486b840b6 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.