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

[galaxyproject/galaxy] 56f5bf: Make newer unit tests more robust with a looped wa...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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: 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... Compare: https://github.com/galaxyproject/galaxy/compare/5eb7e5ce6f16...d312c48ea768 **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/release_18.09 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/7a22f38a2e52...5eb7e5ce6f16 **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 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.05 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/840041744505...d014469f070e **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] 420f43: map the favicon in uwsgi config
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 420f43645af9b37c32eb126f89c4266f36f6edb0 https://github.com/galaxyproject/galaxy/commit/420f43645af9b37c32eb126f89c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/uwsgi_schema.yml M scripts/get_uwsgi_args.py Log Message: ----------- map the favicon in uwsgi config Commit: b45c3531dedc71b4ea8142fe5aa9f17f10bfb997 https://github.com/galaxyproject/galaxy/commit/b45c3531dedc71b4ea8142fe5aa9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- dispose of tooltip when the delete is being called Commit: 33eb06c9b872f75fd22e06297a2043f8685d1df2 https://github.com/galaxyproject/galaxy/commit/33eb06c9b872f75fd22e06297a20… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- remove something that should have never been where it was look at me, I do not know what I am doing Commit: b64754dee94c571112c79ccb15fe515545337e15 https://github.com/galaxyproject/galaxy/commit/b64754dee94c571112c79ccb15fe… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #6743 from martenson/fix-favicon-uwsgi [18.09] fix favicon.ico for uwsgi deployments Commit: 7a22f38a2e5229ebca109836396b17bf8785af37 https://github.com/galaxyproject/galaxy/commit/7a22f38a2e5229ebca109836396b… Author: Dannon <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: ----------- Merge pull request #6744 from martenson/dispose-tooltip-on-delete [18.09] dispose of dataset tooltip when the delete is being called Commit: 101f2009f81d3c884ac1343a6d369be5fdfb03d4 https://github.com/galaxyproject/galaxy/commit/101f2009f81d3c884ac1343a6d36… 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 config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4723ad6672fe...101f2009f81d **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] b45c35: dispose of tooltip when the delete is being called
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b45c3531dedc71b4ea8142fe5aa9f17f10bfb997 https://github.com/galaxyproject/galaxy/commit/b45c3531dedc71b4ea8142fe5aa9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- dispose of tooltip when the delete is being called Commit: 7a22f38a2e5229ebca109836396b17bf8785af37 https://github.com/galaxyproject/galaxy/commit/7a22f38a2e5229ebca109836396b… Author: Dannon <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: ----------- Merge pull request #6744 from martenson/dispose-tooltip-on-delete [18.09] dispose of dataset tooltip when the delete is being called Compare: https://github.com/galaxyproject/galaxy/compare/b64754dee94c...7a22f38a2e52 **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] 420f43: map the favicon in uwsgi config
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 420f43645af9b37c32eb126f89c4266f36f6edb0 https://github.com/galaxyproject/galaxy/commit/420f43645af9b37c32eb126f89c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/uwsgi_schema.yml M scripts/get_uwsgi_args.py Log Message: ----------- map the favicon in uwsgi config Commit: 33eb06c9b872f75fd22e06297a2043f8685d1df2 https://github.com/galaxyproject/galaxy/commit/33eb06c9b872f75fd22e06297a20… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- remove something that should have never been where it was look at me, I do not know what I am doing Commit: b64754dee94c571112c79ccb15fe515545337e15 https://github.com/galaxyproject/galaxy/commit/b64754dee94c571112c79ccb15fe… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #6743 from martenson/fix-favicon-uwsgi [18.09] fix favicon.ico for uwsgi deployments Compare: https://github.com/galaxyproject/galaxy/compare/4ce8086c2052...b64754dee94c **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] 4fc9fe: Fix target update for rule collection builder afte...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 5121275c1d5e7c724edbc3cef531f3401aea5225 https://github.com/galaxyproject/galaxy/commit/5121275c1d5e7c724edbc3cef531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove stray debug statement. Commit: 1cdcb80fe88cd076f5c966b0b6a4acab37841877 https://github.com/galaxyproject/galaxy/commit/1cdcb80fe88cd076f5c966b0b6a4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6739 from jmchilton/remove_debug [18.09] Remove stray debug statement. Commit: 5635a05a2a70c3e8887c32b1a8675f124808fd49 https://github.com/galaxyproject/galaxy/commit/5635a05a2a70c3e8887c32b1a867… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: f7fe3418d63683a998425b99f4688872fef07b09 https://github.com/galaxyproject/galaxy/commit/f7fe3418d63683a998425b99f468… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: a52ee84aede53ff2cb5a3e667e4ef03df1fd3acb https://github.com/galaxyproject/galaxy/commit/a52ee84aede53ff2cb5a3e667e4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: 29f07f0b0ad49b86b50c34e9890eb2117e067a2b https://github.com/galaxyproject/galaxy/commit/29f07f0b0ad49b86b50c34e9890e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6741 from jmchilton/backport_type_source [18.09] Backport #6732 Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Commit: 4ce8086c2052a1abee4824456ddfd48ee5cb7c6a https://github.com/galaxyproject/galaxy/commit/4ce8086c2052a1abee4824456ddf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 4723ad6672fef064a75934604ab03150ec14e872 https://github.com/galaxyproject/galaxy/commit/4723ad6672fef064a75934604ab0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9f2361e8e1f...4723ad6672fe **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] 4fc9fe: Fix target update for rule collection builder afte...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Commit: 4ce8086c2052a1abee4824456ddfd48ee5cb7c6a https://github.com/galaxyproject/galaxy/commit/4ce8086c2052a1abee4824456ddf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/29f07f0b0ad4...4ce8086c2052 **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] 18d99d: Decode tool id and version in the client, not in t...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Compare: https://github.com/galaxyproject/galaxy/compare/6993dbb6fcd1...840041744505 **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] 5635a0: Look up collection_type if collection_type_source ...
by GitHub 19 Sep '18

19 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5635a05a2a70c3e8887c32b1a8675f124808fd49 https://github.com/galaxyproject/galaxy/commit/5635a05a2a70c3e8887c32b1a867… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: f7fe3418d63683a998425b99f4688872fef07b09 https://github.com/galaxyproject/galaxy/commit/f7fe3418d63683a998425b99f468… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: a52ee84aede53ff2cb5a3e667e4ef03df1fd3acb https://github.com/galaxyproject/galaxy/commit/a52ee84aede53ff2cb5a3e667e4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: 29f07f0b0ad49b86b50c34e9890eb2117e067a2b https://github.com/galaxyproject/galaxy/commit/29f07f0b0ad49b86b50c34e9890e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6741 from jmchilton/backport_type_source [18.09] Backport #6732 Compare: https://github.com/galaxyproject/galaxy/compare/1cdcb80fe88c...29f07f0b0ad4 **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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