[galaxy-commits] [galaxyproject/galaxy] 9b3c06: [16.07] Fix tool dependencies handling in Tool She...

GitHub noreply at github.com
Fri Sep 23 12:53:17 EDT 2016


  Branch: refs/heads/release_16.07
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e
      https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492396b9e07464e
  Author: Dave B <dave at 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/a78b8bcd2aa02abf787f0974fe567ab4f70f41a1
  Author: Martin Cech <cech.marten at 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/c06f8c29968971c6c1e0dfc6847b3baf755f3a96
  Author: Martin Cech <cech.marten at 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/5e7ee28e0d6937fa53f39b350e04357b554ce9ae
  Author: Martin Cech <cech.marten at 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/45e6949eeae88c0d3c4c3f6341ddc5695d329bb2
  Author: John Chilton <jmchilton at 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


  Commit: 3b3e2e3358aa73a5374345686581310d37349ff9
      https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581310d37349ff9
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-09-23 (Fri, 23 Sep 2016)

  Changed paths:
    M test/shed_functional/functional/test_1400_review_migration_stages.py

  Log Message:
  -----------
  Merge branch 'release_16.04' into release_16.07

Conflicts:
	lib/galaxy/webapps/tool_shed/controllers/repository.py
	lib/galaxy/webapps/tool_shed/model/__init__.py


Compare: https://github.com/galaxyproject/galaxy/compare/c0e8a7608351...3b3e2e3358aa


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