- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] eb406c: Fix install operation in installed_repository_grid
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb406cc210b556a9218d778383451916d7cd1ecf https://github.com/galaxyproject/galaxy/commit/eb406cc210b556a9218d77838345… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix install operation in installed_repository_grid The incoming url keywords look like this: ``` operation=install&id=ebfb8f50c6abde6d?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=install&id=ebfb8f50c6abde6d ``` and the id parameter gets parsed into a list: ``` ['ebfb8f50c6abde6d?async=false', 'ebfb8f50c6abde6d'] ``` Obviously there's something wrong in the grid or mako, but this works fine. Fixes https://github.com/galaxyproject/galaxy/issues/5619 Commit: 6a660e9893b6fc5eb9bb0f3225fdeb9fb9ad763f https://github.com/galaxyproject/galaxy/commit/6a660e9893b6fc5eb9bb0f3225fd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid [18.09] Fix install operation in installed_repository_grid Commit: dc6ec1ed3dec5663aeb127b85bb4b1aa724afb9f https://github.com/galaxyproject/galaxy/commit/dc6ec1ed3dec5663aeb127b85bb4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 Commit: 0b95564789c37e7b0aba2d32b9442e96d7cb786d https://github.com/galaxyproject/galaxy/commit/0b95564789c37e7b0aba2d32b944… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/53017d6be489...0b95564789c3 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] eb406c: Fix install operation in installed_repository_grid
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: eb406cc210b556a9218d778383451916d7cd1ecf https://github.com/galaxyproject/galaxy/commit/eb406cc210b556a9218d77838345… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix install operation in installed_repository_grid The incoming url keywords look like this: ``` operation=install&id=ebfb8f50c6abde6d?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=install&id=ebfb8f50c6abde6d ``` and the id parameter gets parsed into a list: ``` ['ebfb8f50c6abde6d?async=false', 'ebfb8f50c6abde6d'] ``` Obviously there's something wrong in the grid or mako, but this works fine. Fixes https://github.com/galaxyproject/galaxy/issues/5619 Commit: 6a660e9893b6fc5eb9bb0f3225fdeb9fb9ad763f https://github.com/galaxyproject/galaxy/commit/6a660e9893b6fc5eb9bb0f3225fd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid [18.09] Fix install operation in installed_repository_grid Commit: dc6ec1ed3dec5663aeb127b85bb4b1aa724afb9f https://github.com/galaxyproject/galaxy/commit/dc6ec1ed3dec5663aeb127b85bb4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/7b08e98ffce5...dc6ec1ed3dec **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] eb406c: Fix install operation in installed_repository_grid
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: eb406cc210b556a9218d778383451916d7cd1ecf https://github.com/galaxyproject/galaxy/commit/eb406cc210b556a9218d77838345… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix install operation in installed_repository_grid The incoming url keywords look like this: ``` operation=install&id=ebfb8f50c6abde6d?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=install&id=ebfb8f50c6abde6d ``` and the id parameter gets parsed into a list: ``` ['ebfb8f50c6abde6d?async=false', 'ebfb8f50c6abde6d'] ``` Obviously there's something wrong in the grid or mako, but this works fine. Fixes https://github.com/galaxyproject/galaxy/issues/5619 Commit: 6a660e9893b6fc5eb9bb0f3225fdeb9fb9ad763f https://github.com/galaxyproject/galaxy/commit/6a660e9893b6fc5eb9bb0f3225fd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid [18.09] Fix install operation in installed_repository_grid Compare: https://github.com/galaxyproject/galaxy/compare/f0bd2df6d4f3...6a660e9893b6 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] b12357: Changed logout behavior to automatically redirect ...
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b123579a48823b912fdb03f85323525dc73b6da3 https://github.com/galaxyproject/galaxy/commit/b123579a48823b912fdb03f85323… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M templates/user/logout.mako Log Message: ----------- Changed logout behavior to automatically redirect home Commit: 53017d6be489ee298ac7ede8c39cb5a6f35467ca https://github.com/galaxyproject/galaxy/commit/53017d6be489ee298ac7ede8c39c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M client/galaxy/scripts/layout/menu.js M templates/user/logout.mako Log Message: ----------- Merge pull request #7255 from Nerdinacan/fix_logout_behavior_7249 Changed logout behavior to automatically redirect home Compare: https://github.com/galaxyproject/galaxy/compare/840d85dfb503...53017d6be489 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 65cab1: Mount a volume on galaxy06 for InfluxDB
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 65cab126f183b24fb00c873e2df64ebb876b8c4d https://github.com/galaxyproject/infrastructure-playbook/commit/65cab126f18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M env/tacc/host_vars/galaxy06.tacc.utexas.edu.yml Log Message: ----------- Mount a volume on galaxy06 for InfluxDB **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 5adfa8: Update sqlalchemy-migrate requirement to 0.12.0
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5adfa81a8b6366467d003a9e7b2a551255fdfb20 https://github.com/galaxyproject/galaxy/commit/5adfa81a8b6366467d003a9e7b2a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update sqlalchemy-migrate requirement to 0.12.0 Fix https://github.com/galaxyproject/galaxy/issues/7159 Commit: f0bd2df6d4f314c449937dff6878720e83d060bb https://github.com/galaxyproject/galaxy/commit/f0bd2df6d4f314c449937dff6878… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #7265 from nsoranzo/release_18.09_sqlalchemy-migrate_0.12.0 [18.09] Update sqlalchemy-migrate requirement to 0.12.0 Commit: 7b08e98ffce50a1f99fca392ac6e1462fd97ed7e https://github.com/galaxyproject/galaxy/commit/7b08e98ffce50a1f99fca392ac6e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 840d85dfb5030896c1e796355a713a65b6d0e2fc https://github.com/galaxyproject/galaxy/commit/840d85dfb5030896c1e796355a71… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/84c2138794ab...840d85dfb503 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 5adfa8: Update sqlalchemy-migrate requirement to 0.12.0
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5adfa81a8b6366467d003a9e7b2a551255fdfb20 https://github.com/galaxyproject/galaxy/commit/5adfa81a8b6366467d003a9e7b2a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update sqlalchemy-migrate requirement to 0.12.0 Fix https://github.com/galaxyproject/galaxy/issues/7159 Commit: f0bd2df6d4f314c449937dff6878720e83d060bb https://github.com/galaxyproject/galaxy/commit/f0bd2df6d4f314c449937dff6878… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #7265 from nsoranzo/release_18.09_sqlalchemy-migrate_0.12.0 [18.09] Update sqlalchemy-migrate requirement to 0.12.0 Compare: https://github.com/galaxyproject/galaxy/compare/1a4c1ec51402...f0bd2df6d4f3 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 687c99: Remove duplicated entry in ``.gitignore``
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 687c99c0094d1ff0ee91ef581fb340a7f09e2404 https://github.com/galaxyproject/galaxy/commit/687c99c0094d1ff0ee91ef581fb3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M .gitignore Log Message: ----------- Remove duplicated entry in ``.gitignore`` Commit: 9207b56eebaa06eed0614fdb877abc9b6744cf44 https://github.com/galaxyproject/galaxy/commit/9207b56eebaa06eed0614fdb877a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M lib/galaxy/datatypes/isa.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/util/filelock.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M tools/filters/sff_extract.py Log Message: ----------- Fix "occured" typo everywhere Fix https://github.com/galaxyproject/galaxy/issues/7264 Commit: 84c2138794ab564f46736edc6dc25baded663a6c https://github.com/galaxyproject/galaxy/commit/84c2138794ab564f46736edc6dc2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M .gitignore M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M lib/galaxy/datatypes/isa.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/util/filelock.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M tools/filters/sff_extract.py Log Message: ----------- Merge pull request #7266 from nsoranzo/occured Fix "occured" typo everywhere Compare: https://github.com/galaxyproject/galaxy/compare/3f02d30c5070...84c2138794ab **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 31c71f: strip() text when loading xml
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31c71fbd6fb65cc4a4358e8b415d48885e73e7de https://github.com/galaxyproject/galaxy/commit/31c71fbd6fb65cc4a4358e8b415d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- strip() text when loading xml Should fix https://github.com/galaxyproject/galaxy/issues/7250. Commit: 920f07369dc553a31a848fe044b563b83bd0f2dc https://github.com/galaxyproject/galaxy/commit/920f07369dc553a31a848fe044b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing [18.09] strip() text when parsing xml Commit: 35fe3bf716e4f527755f75ebb99b9dbdb777e37d https://github.com/galaxyproject/galaxy/commit/35fe3bf716e4f527755f75ebb99b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Not all workflow outputs have a UUID Commit: f2a454c776bea547967c867e47a827a9a969f67c https://github.com/galaxyproject/galaxy/commit/f2a454c776bea547967c867e47a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix output uuid comparison Commit: 1a4c1ec514024bb5ee71997afe54158083ca5222 https://github.com/galaxyproject/galaxy/commit/1a4c1ec514024bb5ee71997afe54… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access [18.09] Not all workflow outputs have a UUID Commit: f9ca90a2288acbbc7de5d5e3b903d143519f1174 https://github.com/galaxyproject/galaxy/commit/f9ca90a2288acbbc7de5d5e3b903… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py M test/unit/test_utils.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 3f02d30c50704ebd1dda9e85567f600d20341e58 https://github.com/galaxyproject/galaxy/commit/3f02d30c50704ebd1dda9e85567f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py M test/unit/test_utils.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/599f5d5a3346...3f02d30c5070 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 31c71f: strip() text when loading xml
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 31c71fbd6fb65cc4a4358e8b415d48885e73e7de https://github.com/galaxyproject/galaxy/commit/31c71fbd6fb65cc4a4358e8b415d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- strip() text when loading xml Should fix https://github.com/galaxyproject/galaxy/issues/7250. Commit: 920f07369dc553a31a848fe044b563b83bd0f2dc https://github.com/galaxyproject/galaxy/commit/920f07369dc553a31a848fe044b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing [18.09] strip() text when parsing xml Commit: 35fe3bf716e4f527755f75ebb99b9dbdb777e37d https://github.com/galaxyproject/galaxy/commit/35fe3bf716e4f527755f75ebb99b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Not all workflow outputs have a UUID Commit: f2a454c776bea547967c867e47a827a9a969f67c https://github.com/galaxyproject/galaxy/commit/f2a454c776bea547967c867e47a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix output uuid comparison Commit: 1a4c1ec514024bb5ee71997afe54158083ca5222 https://github.com/galaxyproject/galaxy/commit/1a4c1ec514024bb5ee71997afe54… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access [18.09] Not all workflow outputs have a UUID Commit: f9ca90a2288acbbc7de5d5e3b903d143519f1174 https://github.com/galaxyproject/galaxy/commit/f9ca90a2288acbbc7de5d5e3b903… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/workflow/modules.py M test/unit/test_utils.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/bdd340cf1c2e...f9ca90a2288a **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/galaxy] 35fe3b: Not all workflow outputs have a UUID
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 35fe3bf716e4f527755f75ebb99b9dbdb777e37d https://github.com/galaxyproject/galaxy/commit/35fe3bf716e4f527755f75ebb99b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Not all workflow outputs have a UUID Commit: f2a454c776bea547967c867e47a827a9a969f67c https://github.com/galaxyproject/galaxy/commit/f2a454c776bea547967c867e47a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix output uuid comparison Commit: 1a4c1ec514024bb5ee71997afe54158083ca5222 https://github.com/galaxyproject/galaxy/commit/1a4c1ec514024bb5ee71997afe54… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access [18.09] Not all workflow outputs have a UUID Compare: https://github.com/galaxyproject/galaxy/compare/920f07369dc5...1a4c1ec51402 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 703c07: Update .loc paths for gemini.
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 703c07670970ff2c473e7c6fcf4b36d032ad1f0f https://github.com/galaxyproject/usegalaxy-playbook/commit/703c07670970ff2c… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update .loc paths for gemini. **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] 1e558f: Update ProFTPD role
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e558f777516658157f489347a2227dfe500f439 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e558f7775166581… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/meta/.galaxy_install_info M roles/galaxyproject.proftpd/tasks/tls.yml Log Message: ----------- Update ProFTPD role **NOTE:** This service has 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.

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[galaxyproject/usegalaxy-playbook] 7fa74f: Update gemini wrappers and binary to version 0.20....
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7fa74f8832275444e1d88582765026c8d986dea8 https://github.com/galaxyproject/usegalaxy-playbook/commit/7fa74f8832275444… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update gemini wrappers and binary to version 0.20.1 **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 7f6bf0: make it a list
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 7f6bf00101efb5f5b48a20e894988b2664c1059f https://github.com/galaxyproject/ansible-galaxy/commit/7f6bf00101efb5f5b48a… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M README.md Log Message: ----------- make it a list **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 008f65: fix condition again
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 008f65ba431ddf7d3c7526727e7d7bcdd8278ab3 https://github.com/galaxyproject/ansible-galaxy/commit/008f65ba431ddf7d3c75… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M tasks/main.yml Log Message: ----------- fix condition again **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 44b6d2: fix condition
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 44b6d2e5daac3637e99cf234f38a0e8224ca4f0b https://github.com/galaxyproject/ansible-galaxy/commit/44b6d2e5daac3637e99c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M tasks/main.yml Log Message: ----------- fix condition **NOTE:** This service has 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.

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[galaxyproject/galaxy] be7628: Remove unneeded conditional requirements
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be7628531927ca826e1b0d05f435da19e721ea8d https://github.com/galaxyproject/galaxy/commit/be7628531927ca826e1b0d05f435… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Remove unneeded conditional requirements They are already included in `requirements.txt` . `ConditionalDependencies.check_python_openid()` was already removed in commit f31d61b71c739c03e5068bff188a56f175a18297 . Commit: d0373c6a956cea15618db2021f3501117078a23f https://github.com/galaxyproject/galaxy/commit/d0373c6a956cea15618db2021f35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- ``make config-rebuild`` Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 . Commit: d5b306dd216e1b8d0f2ed34c52e562df643c8069 https://github.com/galaxyproject/galaxy/commit/d5b306dd216e1b8d0f2ed34c52e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M doc/source/admin/authentication.md M doc/source/admin/config.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst Log Message: ----------- Remove OpenID auth from docs Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 . Commit: 599f5d5a334627451e78cf7349aec55035fcb8f9 https://github.com/galaxyproject/galaxy/commit/599f5d5a334627451e78cf7349ae… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/authentication.md M doc/source/admin/config.rst M doc/source/admin/galaxy_options.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7247 from nsoranzo/unneeded_conditional_reqs Remove unneeded conditional requirements Compare: https://github.com/galaxyproject/galaxy/compare/c58f9acf7fe2...599f5d5a3346 **NOTE:** This service has 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.

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[galaxyproject/galaxy] 31c71f: strip() text when loading xml
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 31c71fbd6fb65cc4a4358e8b415d48885e73e7de https://github.com/galaxyproject/galaxy/commit/31c71fbd6fb65cc4a4358e8b415d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- strip() text when loading xml Should fix https://github.com/galaxyproject/galaxy/issues/7250. Commit: 920f07369dc553a31a848fe044b563b83bd0f2dc https://github.com/galaxyproject/galaxy/commit/920f07369dc553a31a848fe044b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing [18.09] strip() text when parsing xml Compare: https://github.com/galaxyproject/galaxy/compare/889c1026c089...920f07369dc5 **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 4d873f: add common startup task
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 4d873f72e958d9768244933c075ecf0c8ef4abc1 https://github.com/galaxyproject/ansible-galaxy/commit/4d873f72e958d9768244… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: A tasks/build_client.yml M tasks/main.yml Log Message: ----------- add common startup task **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 3ea2aa: fix role name / add contributor
by GitHub 21 Jan '19

21 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3ea2aad4c93de829b8b89e91517dd722e5fb6a54 https://github.com/galaxyproject/ansible-galaxy/commit/3ea2aad4c93de829b8b8… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M README.md Log Message: ----------- fix role name / add contributor **NOTE:** This service has 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.

1 0

[galaxyproject/galaxy] 2aa8ed: fix tag_using_filenames not converted to bool
by GitHub 21 Jan '19

21 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2aa8ed4efbcf1224d335593e9d64966b8b173bac https://github.com/galaxyproject/galaxy/commit/2aa8ed4efbcf1224d335593e9d64… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- fix tag_using_filenames not converted to bool Commit: 3fa43dfecea37a5f56e3675afad0bd65d3196f56 https://github.com/galaxyproject/galaxy/commit/3fa43dfecea37a5f56e3675afad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Swap to normal event bindings for multipanel drop. get(0) isn't great, but we'll overhaul this more in the future. Commit: 7c13cdf006733182b4bfb07ced24df729600e670 https://github.com/galaxyproject/galaxy/commit/7c13cdf006733182b4bfb07ced24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #7218 from dannon/fix_multipanel_drop [19.01] Swap to normal event bindings for multipanel drag/drop. Commit: 54aecb3f31812c86d370034cf557537780efbcdf https://github.com/galaxyproject/galaxy/commit/54aecb3f31812c86d370034cf557… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Properly deal with missing tools in subworkflows If a subworkflow is missing tools the entire parent workflow couldn't be loaded into the editor, because we raised an exception. This is now only logged as an error. On the user side we now prevent running and saving such workflows by actually implementing the `get_errors` method for the SubWorkflowModule class. This should fix https://github.com/galaxyproject/galaxy/issues/7140. Commit: 6ff84684bd577ea4610d63213cc090b86d983aa8 https://github.com/galaxyproject/galaxy/commit/6ff84684bd577ea4610d63213cc0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix displaying tool help images on python 3 Commit: ab8ea1ee40c2a7de3a7cc6e6aaafba95f451a6c6 https://github.com/galaxyproject/galaxy/commit/ab8ea1ee40c2a7de3a7cc6e6aaaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add error listener for input elements, utilize to highlight numeric value range adjustments Commit: 48c2807e2ebecf7fd01bd56e102ccaaa25947a29 https://github.com/galaxyproject/galaxy/commit/48c2807e2ebecf7fd01bd56e102c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Fix name of error handler helper function Commit: d20c6f6d8c1cfdd677afa04ad70c10e11c7228f4 https://github.com/galaxyproject/galaxy/commit/d20c6f6d8c1cfdd677afa04ad70c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Remove unused default error message Commit: ef02c60f792a8aeadcaa58d8e0a4ac71d65aa42b https://github.com/galaxyproject/galaxy/commit/ef02c60f792a8aeadcaa58d8e0a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move local slider helper variables into score/statement Commit: 8534ef5d5cef95bad2dbb882b8285a44deb0dca6 https://github.com/galaxyproject/galaxy/commit/8534ef5d5cef95bad2dbb882b828… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Move field error binding to input element wrapper Commit: 48811d4c0c79b5dfdba2e51471f71d9d9fa0b34e https://github.com/galaxyproject/galaxy/commit/48811d4c0c79b5dfdba2e51471f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Use listento caller to bind input element error listener Commit: 97651462212b2a08a18b67b9fe2d731732b3d1c3 https://github.com/galaxyproject/galaxy/commit/97651462212b2a08a18b67b9fe2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Add additional validation to slider out-of-range error detection Commit: b1b1d848d35816cfa344aeb687c78c7a0c93e66f https://github.com/galaxyproject/galaxy/commit/b1b1d848d35816cfa344aeb687c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix loading subworkflows Commit: 24f97f6917da606f8b9c1fc1fb4faef5c54f1933 https://github.com/galaxyproject/galaxy/commit/24f97f6917da606f8b9c1fc1fb4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Open files in binary mode when sending data Commit: 7a9422600c76ad49515844d582bf6d5f507076e8 https://github.com/galaxyproject/galaxy/commit/7a9422600c76ad49515844d582bf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M test/api/test_galaxy_interactor.py Log Message: ----------- Fix ``GalaxyInteractorBackwardCompatTestCase.test_local_test_data_download`` API test Broken in commit bf851269c30996876c0614e7a5b57da495c44ac9 . Commit: d460d218ad898242046c2422aa211fe6a4830462 https://github.com/galaxyproject/galaxy/commit/d460d218ad898242046c2422aa21… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #7229 from mvdbeek/backport_sliding_validator [19.01] Backport #7183 input element listener Commit: ed6011755cf7cf5c7232bd43365dd01ab0b12af5 https://github.com/galaxyproject/galaxy/commit/ed6011755cf7cf5c7232bd43365d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M test/api/test_galaxy_interactor.py Log Message: ----------- Merge pull request #7228 from mvdbeek/fix_image_display_py3 [19.01] Fix displaying tool help images on python 3 Commit: 06aa30ffdca0fe092fa2d094aa23da34b10a1667 https://github.com/galaxyproject/galaxy/commit/06aa30ffdca0fe092fa2d094aa23… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/actions/library.py Log Message: ----------- disable tag_using_filenames by default (consistent with #5115) Commit: 8d99791afb6a699e987bd1e25aaea8582f7f7065 https://github.com/galaxyproject/galaxy/commit/8d99791afb6a699e987bd1e25aae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M tools/data_source/data_source.py Log Message: ----------- Fix data_source tools on python 3 Commit: b0b5fb44d282b52391becdac1b190ebbd075168d https://github.com/galaxyproject/galaxy/commit/b0b5fb44d282b52391becdac1b19… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Merge pull request #7204 from abretaud/tag_fn [19.01] Data library: fix tag_using_filenames not properly converted to bool Commit: 7b14c3099876d5991ebdea85ff18c027de434be8 https://github.com/galaxyproject/galaxy/commit/7b14c3099876d5991ebdea85ff18… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Reduce duplicated code Commit: e92e978ca179870d586e08f16a0542b9dd499a2a https://github.com/galaxyproject/galaxy/commit/e92e978ca179870d586e08f16a05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Drop use of col1_startswith Contigs may start with whatever sequence you like. Luckily this isn't essential to the datatypes. Leaving data.col1_startswith in case toolshed datatypes import this. Commit: 6f861dec7e897bbc06b2cffbb33b2fdd9e6ac11a https://github.com/galaxyproject/galaxy/commit/6f861dec7e897bbc06b2cffbb33b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/exceptions/__init__.py Log Message: ----------- Overridde __init__ for ToolMissingException Commit: d2d87625f0a5989c40c40a8d50857efb5dc21c36 https://github.com/galaxyproject/galaxy/commit/d2d87625f0a5989c40c40a8d5085… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #7237 from mvdbeek/datatype_fixes [19.01] Interval datatype fixes Commit: 9467d0261cab5712d15dfcfa7ca5d7cdb765f631 https://github.com/galaxyproject/galaxy/commit/9467d0261cab5712d15dfcfa7ca5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M tools/data_source/data_source.py Log Message: ----------- Merge pull request #7236 from mvdbeek/data_source_fix [19.01] Fix data_source tools on python 3 Commit: 889c1026c0893636b4fc6375443408c0ec2b4a8a https://github.com/galaxyproject/galaxy/commit/889c1026c0893636b4fc63754434… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving [18.09] Properly deal with missing tools in workflows Commit: 5c90e02d3665caec50369baf0918e58f043af6e4 https://github.com/galaxyproject/galaxy/commit/5c90e02d3665caec50369baf0918… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow save_as functionality Fixes https://github.com/galaxyproject/galaxy/issues/7240, broken in https://github.com/galaxyproject/galaxy/pull/7019, where it was renamed from `build_workflow_from_dict` to `build_workflow_from_raw_description`. Commit: 8862b9311b000b83a733ed216130f0a7cfe7d4ba https://github.com/galaxyproject/galaxy/commit/8862b9311b000b83a733ed216130… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use update_workflow_from_raw_description method not build_workflow_from_raw_description Co-Authored-By: mvdbeek <m.vandenbeek(a)gmail.com> Commit: b4e450cff021b68831337a8e0bf12c892f54eb8c https://github.com/galaxyproject/galaxy/commit/b4e450cff021b68831337a8e0bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: f24176d95060288a0973ef78dab43bf552efb3ba https://github.com/galaxyproject/galaxy/commit/f24176d95060288a0973ef78dab4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7245 from nsoranzo/release_19.01 Merge branch 'release_18.09' into release_19.01 Commit: bdd340cf1c2e31a5a8c82995bad26d07c7ed5adb https://github.com/galaxyproject/galaxy/commit/bdd340cf1c2e31a5a8c82995bad2… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #7241 from mvdbeek/fix_workflow_save_as [19.01] Fix workflow save_as functionality Commit: c58f9acf7fe2cf515ab7440c835257c24b0440cd https://github.com/galaxyproject/galaxy/commit/c58f9acf7fe2cf515ab7440c8352… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/actions/library.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M tools/data_source/data_source.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ce113af1fc86...c58f9acf7fe2 **NOTE:** This service has 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.

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[galaxyproject/galaxy] 5c90e0: Fix workflow save_as functionality
by GitHub 21 Jan '19

21 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 5c90e02d3665caec50369baf0918e58f043af6e4 https://github.com/galaxyproject/galaxy/commit/5c90e02d3665caec50369baf0918… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow save_as functionality Fixes https://github.com/galaxyproject/galaxy/issues/7240, broken in https://github.com/galaxyproject/galaxy/pull/7019, where it was renamed from `build_workflow_from_dict` to `build_workflow_from_raw_description`. Commit: 8862b9311b000b83a733ed216130f0a7cfe7d4ba https://github.com/galaxyproject/galaxy/commit/8862b9311b000b83a733ed216130… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use update_workflow_from_raw_description method not build_workflow_from_raw_description Co-Authored-By: mvdbeek <m.vandenbeek(a)gmail.com> Commit: bdd340cf1c2e31a5a8c82995bad26d07c7ed5adb https://github.com/galaxyproject/galaxy/commit/bdd340cf1c2e31a5a8c82995bad2… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #7241 from mvdbeek/fix_workflow_save_as [19.01] Fix workflow save_as functionality Compare: https://github.com/galaxyproject/galaxy/compare/f24176d95060...bdd340cf1c2e **NOTE:** This service has 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.

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[galaxyproject/galaxy] 54aecb: Properly deal with missing tools in subworkflows
by GitHub 21 Jan '19

21 Jan '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 54aecb3f31812c86d370034cf557537780efbcdf https://github.com/galaxyproject/galaxy/commit/54aecb3f31812c86d370034cf557… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Properly deal with missing tools in subworkflows If a subworkflow is missing tools the entire parent workflow couldn't be loaded into the editor, because we raised an exception. This is now only logged as an error. On the user side we now prevent running and saving such workflows by actually implementing the `get_errors` method for the SubWorkflowModule class. This should fix https://github.com/galaxyproject/galaxy/issues/7140. Commit: b1b1d848d35816cfa344aeb687c78c7a0c93e66f https://github.com/galaxyproject/galaxy/commit/b1b1d848d35816cfa344aeb687c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix loading subworkflows Commit: 6f861dec7e897bbc06b2cffbb33b2fdd9e6ac11a https://github.com/galaxyproject/galaxy/commit/6f861dec7e897bbc06b2cffbb33b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M lib/galaxy/exceptions/__init__.py Log Message: ----------- Overridde __init__ for ToolMissingException Commit: 889c1026c0893636b4fc6375443408c0ec2b4a8a https://github.com/galaxyproject/galaxy/commit/889c1026c0893636b4fc63754434… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving [18.09] Properly deal with missing tools in workflows Commit: b4e450cff021b68831337a8e0bf12c892f54eb8c https://github.com/galaxyproject/galaxy/commit/b4e450cff021b68831337a8e0bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: f24176d95060288a0973ef78dab43bf552efb3ba https://github.com/galaxyproject/galaxy/commit/f24176d95060288a0973ef78dab4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7245 from nsoranzo/release_19.01 Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/9467d0261cab...f24176d95060 **NOTE:** This service has 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.

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[galaxyproject/ansible-galaxy] 9033be: Ensure consistent sorting for nicer diffs
by GitHub 21 Jan '19

21 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 9033be3db99c9288fc34f70ab503c65931bb5415 https://github.com/galaxyproject/ansible-galaxy/commit/9033be3db99c9288fc34… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M templates/galaxy.ini.j2 Log Message: ----------- Ensure consistent sorting for nicer diffs Commit: f8995d91b363bc30bed6ed33b852d0acf3e9f093 https://github.com/galaxyproject/ansible-galaxy/commit/f8995d91b363bc30bed6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M tasks/database.yml Log Message: ----------- Permit running with --check Commit: 257b15c4d0ec4f4f0ed1717a47407c06bb2dd974 https://github.com/galaxyproject/ansible-galaxy/commit/257b15c4d0ec4f4f0ed1… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M tasks/clone.yml Log Message: ----------- Another --check commit Commit: aa6ea9991c73a3544c472e5fbb893f798b9a6421 https://github.com/galaxyproject/ansible-galaxy/commit/aa6ea9991c73a3544c47… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M defaults/main.yml M tasks/static_setup.yml Log Message: ----------- Permit disabling backups Compare: https://github.com/galaxyproject/ansible-galaxy/compare/9033be3db99c^...aa6… **NOTE:** This service has 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.

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