Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf4923... Author: Dave B dave@bx.psu.edu Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py
Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950)
* Fix the cause of toolshed test 1400 failing.
* Fix handling of repositories without tool dependencies.
* Fix tool dependency retrieval.
In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue.
* Correct the logic that returns an empty string for an empty dict.
* Fix getting latest revision with tool dependencies.
* Use self.app instead of trans.app
Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py
Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe567... Author: Martin Cech cech.marten@gmail.com Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py
Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b3... Author: Martin Cech cech.marten@gmail.com Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message: ----------- correct the method call
Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e043... Author: Martin Cech cech.marten@gmail.com Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message: ----------- bump freebayes in test (since it was updated)
Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341ddc... Author: John Chilton jmchilton@gmail.com Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message: ----------- Merge pull request #2959 from martenson/release_16.04
[16.04] backport of model tool dependencies fix
Compare: https://github.com/galaxyproject/galaxy/compare/b748250193a2...45e6949eeae8