September 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 3e60d5: init travis script and test playbook
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3e60d5801b0577e0e3574a514838ce13e65a3d4c https://github.com/galaxyproject/ansible-galaxy/commit/3e60d5801b0577e0e357… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: A .travis.yml A tests/test_playbook.yml Log Message: ----------- init travis script and test playbook Commit: 2f9de4a553d3561743b47cff34b579f2fce03c3e https://github.com/galaxyproject/ansible-galaxy/commit/2f9de4a553d3561743b4… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M defaults/main.yml Log Message: ----------- Added variables for folder ownership and permissions Commit: 85b579c12319ec4d9d14a81992157aa2875e2213 https://github.com/galaxyproject/ansible-galaxy/commit/85b579c12319ec4d9d14… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/database.yml Log Message: ----------- Added become statements and setting database dir ownership & permissions Commit: 5febd3ca7e3a879ec20eb7b0bded8d5077e2e7b9 https://github.com/galaxyproject/ansible-galaxy/commit/5febd3ca7e3a879ec20e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Added become statements Commit: 26871a0cc59083a21fe9c098c9ac73fed3d00ef4 https://github.com/galaxyproject/ansible-galaxy/commit/26871a0cc59083a21fe9… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/mutable_setup.yml Log Message: ----------- Added become statements and setting config & shed tools dir ownership & permissions Commit: e01155439ed882666d7d663e39b537aa2f076582 https://github.com/galaxyproject/ansible-galaxy/commit/e01155439ed882666d7d… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Added become statements Commit: 0745f52b597067844c27afac52277e020226764d https://github.com/galaxyproject/ansible-galaxy/commit/0745f52b597067844c27… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/clone.yml Log Message: ----------- Added become statements and setting galaxy dir ownership & permissions Commit: cac16f1209e2e02b4a8167801c7cc41610585703 https://github.com/galaxyproject/ansible-galaxy/commit/cac16f1209e2e02b4a81… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- removed unnecessary docker lines Commit: dafe6ad12abf0f471d2954d2ed0be8d193bcac10 https://github.com/galaxyproject/ansible-galaxy/commit/dafe6ad12abf0f471d29… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml Log Message: ----------- added become statements which apply outside of travis Commit: 78d9bd9754c57258c5a13af1c873ef4509de0d16 https://github.com/galaxyproject/ansible-galaxy/commit/78d9bd9754c57258c5a1… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Update .travis.yml Commit: 1b54661490b9660f554b2a681fdb040aa9ba816f https://github.com/galaxyproject/ansible-galaxy/commit/1b54661490b9660f554b… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- pinning Ansible version to 2.4 https://github.com/galaxyproject/ansible-galaxy/pull/38/files/dafe6ad12abf0… Commit: 838cd85876d7bd6e3d3e10dde6b377ac6a3ab02b https://github.com/galaxyproject/ansible-galaxy/commit/838cd85876d7bd6e3d3e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install an upgraded pip and virtualenv Commit: fccea6b2cde19e3c961e2c7d2d9672d5d12f57ae https://github.com/galaxyproject/ansible-galaxy/commit/fccea6b2cde19e3c961e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install git Commit: a74e098c29917cf7c5120e5bec6f788238a4d7a5 https://github.com/galaxyproject/ansible-galaxy/commit/a74e098c29917cf7c512… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Drop unnecessary become Commit: bdafc7e265a16fec35e74a30a47e557e46b38e06 https://github.com/galaxyproject/ansible-galaxy/commit/bdafc7e265a16fec35e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tests/test_playbook.yml Log Message: ----------- Add become on play level Commit: cbd0201114858f0af391c03ddd9f3f54a8e70fa0 https://github.com/galaxyproject/ansible-galaxy/commit/cbd0201114858f0af391… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml M tests/test_playbook.yml Log Message: ----------- Merge pull request #5 from mvdbeek/drop_become Thank you! Commit: f606476bbaa96fbfc472a973dadd023fbebaad0c https://github.com/galaxyproject/ansible-galaxy/commit/f606476bbaa96fbfc472… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M defaults/main.yml M tasks/clone.yml M tasks/database.yml M tasks/mutable_setup.yml M tasks/static_setup.yml Log Message: ----------- drop unnecessary file and variable Commit: 9ee412e2d63d706437134f3a307774af7eeb8fd8 https://github.com/galaxyproject/ansible-galaxy/commit/9ee412e2d63d70643713… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: A .travis.yml M tasks/clone.yml M tasks/static_setup.yml A tests/test_playbook.yml Log Message: ----------- Merge pull request #38 from eslerm/travis Travis-CI Compare: https://github.com/galaxyproject/ansible-galaxy/compare/fa0df02a3eaf...9ee4… **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] eae35f: Deduplicate pgcleanup.py
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eae35fab3304224ab6d55ffeae40d6b6611a99cb https://github.com/galaxyproject/galaxy/commit/eae35fab3304224ab6d55ffeae40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Deduplicate pgcleanup.py Commit: 7b8af87091eb5686ad390073f678d9088f6af10b https://github.com/galaxyproject/galaxy/commit/7b8af87091eb5686ad390073f678… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Add a pgcleanup function for purging error HDAs Commit: 7481d97a33ba7fb2a003ae2ad51414c04ae826b0 https://github.com/galaxyproject/galaxy/commit/7481d97a33ba7fb2a003ae2ad514… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6736 from natefoo/pgcleanup pgcleanup.py enhancements Compare: https://github.com/galaxyproject/galaxy/compare/bae08f3ca226...7481d97a33ba **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] 649390: Increase Toolshed uWSGI proxy timeout
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6493903ab85efa59019c9b9e056e2ae97319d300 https://github.com/galaxyproject/usegalaxy-playbook/commit/6493903ab85efa59… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- Increase Toolshed uWSGI proxy timeout **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] b5e221: Fix page editor height for flex panels.
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Compare: https://github.com/galaxyproject/galaxy/compare/287648f5d9f9...9b5045a05c88 **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] 2209c3: Minor cleanup.
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 2209c3171de52dbe83683d2644b0ec6befbaa763 https://github.com/galaxyproject/galaxy/commit/2209c3171de52dbe83683d2644b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor cleanup. Commit: 037ddfeab5decd47d4d2bd8771e975dc1857703a https://github.com/galaxyproject/galaxy/commit/037ddfeab5decd47d4d2bd8771e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Fix active content setting for views with explicitly defined models Commit: 96593cb444063d6cc6819dd77d7b2fb89c250054 https://github.com/galaxyproject/galaxy/commit/96593cb444063d6cc6819dd77d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Import cleanup and documentation for dataset-li-edit. Commit: 11b5157825ee318b763f6c48b674b968f114aebb https://github.com/galaxyproject/galaxy/commit/11b5157825ee318b763f6c48b674… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use standard faIconButton for visualize. Commit: 4aa2b8f919f28b798ba9a2401c602990287338b6 https://github.com/galaxyproject/galaxy/commit/4aa2b8f919f28b798ba9a2401c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Disentangle this/self/frames in scratchbook's events. Commit: 077f3088ece5c8617b044d53764aebff1768b34f https://github.com/galaxyproject/galaxy/commit/077f3088ece5c8617b044d53764a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Correct visualization link to use router or scratchbook as appropriate. Commit: 3f29d32898efd121f315b2147e917584e9dec28f https://github.com/galaxyproject/galaxy/commit/3f29d32898efd121f315b2147e91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Strip unused function, cleanup. Commit: 0018ab989b117c953dd2b02e1e06cc80af1ddff2 https://github.com/galaxyproject/galaxy/commit/0018ab989b117c953dd2b02e1e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Add event hook for non-bb-view center panel id setting, use it for dataset visualization. Commit: d17ea03442448472f1e5e5d4e12e73459f1736e7 https://github.com/galaxyproject/galaxy/commit/d17ea03442448472f1e5e5d4e12e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor formatting tweaks. Commit: 87ecf1428e841bced376e504d1d468319a7853c9 https://github.com/galaxyproject/galaxy/commit/87ecf1428e841bced376e504d1d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use pre-fetched dataset id Commit: 287648f5d9f95ccd1b625037e30de0ab3e62e7f5 https://github.com/galaxyproject/galaxy/commit/287648f5d9f95ccd1b625037e30d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Merge pull request #6725 from dannon/fix_active_highlight [18.09] Fix active highlight Compare: https://github.com/galaxyproject/galaxy/compare/30728899054d...287648f5d9f9 **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/infrastructure-playbook] ff7351: Decrease stratum1 squid memory to hopefully preven...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ff7351e512d9471167b39de5438a331aae05981e https://github.com/galaxyproject/infrastructure-playbook/commit/ff7351e512d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M env/galaxy/group_vars/cvmfsstratum1servers/vars.yml Log Message: ----------- Decrease stratum1 squid memory to hopefully prevent squid from dying on cvmfs1-iu0 **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/infrastructure-playbook] 75ae1d: Attempted slurmscale fix
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 75ae1d079a7ed28e9d5172f82b786d9c145f7aee https://github.com/galaxyproject/infrastructure-playbook/commit/75ae1d079a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M roles/slurmscale/files/resume.yml Log Message: ----------- Attempted slurmscale fix **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] 806bea: Test that newest version will be returned if tool ...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Commit: 30728899054dde65ddd9fe99dc8424166ee0c5ad https://github.com/galaxyproject/galaxy/commit/30728899054dde65ddd9fe99dc84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/d312c48ea768...30728899054d **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] 806bea: Test that newest version will be returned if tool ...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Compare: https://github.com/galaxyproject/galaxy/compare/d014469f070e...02c177152bd7 **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] f5dcf6: Fix and test anonymous error reports
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5dcf60561703086a070a2b59ad3918df68cbd0e https://github.com/galaxyproject/galaxy/commit/f5dcf60561703086a070a2b59ad3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix and test anonymous error reports Fixes https://github.com/galaxyproject/galaxy/issues/6675 Commit: 56f5bf743a50afadc74e253bc95fcef4bb6d599d https://github.com/galaxyproject/galaxy/commit/56f5bf743a50afadc74e253bc95f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Make newer unit tests more robust with a looped wait... ... instead of raw sleep. Commit: d014469f070e62a0b3dc8bdbd93128e4c7a308f8 https://github.com/galaxyproject/galaxy/commit/d014469f070e62a0b3dc8bdbd931… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6742 from mvdbeek/fix_error_reporting [18.05] Fix and test anonymous error reports Commit: 5eb7e5ce6f16e4e6978e44637b419ff3fb1b8e87 https://github.com/galaxyproject/galaxy/commit/5eb7e5ce6f16e4e6978e44637b41… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: d312c48ea76876bd4219f544b8c03e2e909ac6f5 https://github.com/galaxyproject/galaxy/commit/d312c48ea76876bd4219f544b8c0… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6748 from jmchilton/1809_robust_sleep [18.09] Make newer unit tests more robust with a looped wait... Commit: bae08f3ca226711e14256258ed34b916ef73c83f https://github.com/galaxyproject/galaxy/commit/bae08f3ca226711e14256258ed34… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/101f2009f81d...bae08f3ca226 **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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