Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: eb506b25b9cc02e828442ecb9772cc0d4bcc029b https://github.com/galaxyproject/galaxy/commit/eb506b25b9cc02e828442ecb9772c... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-01-30 (Tue, 30 Jan 2018)
Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
Log Message: ----------- Allow map-over when discovering dataset collections
This would affect for example the mapping over of fastq-dump (and all other tools in the sra-toolkit).
If one had attempted this previously the discovery phase would fail with: ``` galaxy.tools.parameters.output_collect ERROR 2018-01-30 08:56:46,369 Problem gathering output collection. Traceback (most recent call last): File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 169, in collect_dynamic_collections collection File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/managers/collections.py", line 216, in collection_builder_for return builder.BoundCollectionBuilder(dataset_collection, collection_type_description) File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/dataset_collections/builder.py", line 84, in __init__ raise Exception("Cannot reset elements of an already populated dataset collection.") Exception: Cannot reset elements of an already populated dataset collection. ```
Instead we force the collection state to be new when we are discovering output collection datasets, which seems reasonable to me. This includes an API testcase that would have failed previously.
Commit: cad17b07c36ded48d3f1eaded98f0ea8e9dfd0c6 https://github.com/galaxyproject/galaxy/commit/cad17b07c36ded48d3f1eaded98f0... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-01-30 (Tue, 30 Jan 2018)
Changed paths: M test/api/test_workflows.py
Log Message: ----------- Revert "Revert extra assertions that are causing unrelated issues to surface."
This reverts commit 4925660ab4aa2974c6ac8e94180180bac7db9781.
Commit: 54e07568bef2687be10e317cd668d68ba68777bf https://github.com/galaxyproject/galaxy/commit/54e07568bef2687be10e317cd668d... Author: John Chilton jmchilton@gmail.com Date: 2018-01-30 (Tue, 30 Jan 2018)
Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
Log Message: ----------- Merge pull request #5413 from mvdbeek/fix_dynamic_collection_output_18_01
Allow map-over when discovering dataset collections
Compare: https://github.com/galaxyproject/galaxy/compare/b1c5186e1cb4...54e07568bef2