Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a701a718a0c7675f21a063b225aa31cc54a0d4b4 https://github.com/galaxyproject/galaxy/commit/a701a718a0c7675f21a063b225aa3... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py Log Message: ----------- More correct, more efficient collection operations. We were copying datasets and not assigning them new HIDs in some cases (the newer collection operations apply_rules, tag_from_file were doing the right thing here but it looks like we didn't go back and fix older operations). With the uniform handling of dataset copying in place - I used the much more efficient history.add_datasets instead of history.add_dataset. This also optimizes the actual HDA copying by eliminating some extra flushes. hda.copy() would flush to get an HDA before copying metadata but this is only needed if there are FileParameter metadata types (e.g. bams) so I made that flush conditional as well as the final one. So for most datatypes - this eliminates two extra flushes per dataset copied. Rebased with fix for issue pointed out by @nsoranzo - cleaned up _add_datasets_to_history to just consume values directly. Using itervalues since these methods have performance issues and these lists can be quite large. Commit: db5b368668265a5fcbd147d9db76cc64156bb6f7 https://github.com/galaxyproject/galaxy/commit/db5b368668265a5fcbd147d9db76c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Don't rely on the order of history contents in test_map_over_collection_structured_like Commit: a10aab8f4f59d12c0d97fd45f1625576287e4a48 https://github.com/galaxyproject/galaxy/commit/a10aab8f4f59d12c0d97fd45f1625... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove copy-paste mistakes. Commit: db036c6f51e53b537d6b88e872c2ecae74b72b44 https://github.com/galaxyproject/galaxy/commit/db036c6f51e53b537d6b88e872c2e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Another typo fix. Commit: 04b69d399b708aaab5b4166acfae89924cf8af7e https://github.com/galaxyproject/galaxy/commit/04b69d399b708aaab5b4166acfae8... Author: Dannon <dannon.baker@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6370 from jmchilton/collection_operations_opt More correct, more efficient collection operations. Compare: https://github.com/galaxyproject/galaxy/compare/704f956306bb...04b69d399b70 **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.