January 2019 - galaxy-commits - lists.galaxyproject.org

[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.

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[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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[galaxyproject/galaxy] f663e0: Use regular font-size in popovers by default
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f663e09b29dd166e846268468e4f088d05e3f85d https://github.com/galaxyproject/galaxy/commit/f663e09b29dd166e846268468e4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Use regular font-size in popovers by default Commit: 9a6ae4d9d64f338a7069d736dd7b0026d02db865 https://github.com/galaxyproject/galaxy/commit/9a6ae4d9d64f338a7069d736dd7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Use multistring for composite upload row template Commit: 73e027b8a6429e8882fb606f184a0108ae70daa5 https://github.com/galaxyproject/galaxy/commit/73e027b8a6429e8882fb606f184a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Use multistring for composite upload view template Commit: 4c0df7ef1ff4c39632c915de25ea37f861970566 https://github.com/galaxyproject/galaxy/commit/4c0df7ef1ff4c39632c915de25ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- Use multistring for collection upload view template Commit: 7e4a0518e59cdd11568b550440e549b6668808c7 https://github.com/galaxyproject/galaxy/commit/7e4a0518e59cdd11568b550440e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix font size handling in upload view Commit: ca4e5677db9044b993fe7ac552c1b0dbf5dd4e2c https://github.com/galaxyproject/galaxy/commit/ca4e5677db9044b993fe7ac552c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix footer styles in upload view Commit: bdc2584d1206a785b522c08e859a7b1fb3b70e29 https://github.com/galaxyproject/galaxy/commit/bdc2584d1206a785b522c08e859a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M .travis.yml M Makefile A client/.eslintignore A client/.eslintrc.js M client/galaxy/scripts/app/galaxy.js M client/galaxy/scripts/components/Alert.vue M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/Masthead/index.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/entry/admin/index.js M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js R client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.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-librarylist-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/package.json A client/prettier.config.js M client/yarn.lock R config/openid_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py A lib/galaxy/metadata/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py R lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy_ext/metadata/set_metadata.py M templates/user/index.mako M templates/user/login.mako R templates/user/openid_associate.mako R templates/user/openid_manage.mako M tox.ini Log Message: ----------- Merge branch 'dev' into upload_view_fixes Commit: bf27a7c99364d634182554c7126ad957c915203f https://github.com/galaxyproject/galaxy/commit/bf27a7c99364d634182554c7126a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/scss/upload.scss Log Message: ----------- Use regular font size throughout uploader Commit: 43409ce5cb3e76648d31c4e4d09db260a28b6a69 https://github.com/galaxyproject/galaxy/commit/43409ce5cb3e76648d31c4e4d09d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix collection uploaders table header alignment Commit: 1cacdb76eb92927ed69b2ba0ae6af123a08fd685 https://github.com/galaxyproject/galaxy/commit/1cacdb76eb92927ed69b2ba0ae6a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Apply suggestions from code review Co-Authored-By: dannon <dannon.baker(a)gmail.com> Commit: 67136670cf96ab19ffee3e8096b7e3bb3ad000bc https://github.com/galaxyproject/galaxy/commit/67136670cf96ab19ffee3e8096b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Adjust info message padding for uploader, convert nav-tabs margin from fixed pixels to ems Commit: 7742bed9c9f3246da8ccc4fcf1f6084116643fe4 https://github.com/galaxyproject/galaxy/commit/7742bed9c9f3246da8ccc4fcf1f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Leave a block element in upload-top-info for consistent spacing. The other three tabs already start with info there. Commit: ce113af1fc86650401f95bcdb90fa0d6927d3a57 https://github.com/galaxyproject/galaxy/commit/ce113af1fc86650401f95bcdb90f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Merge pull request #7232 from guerler/upload_view_fixes Use regular font-size and styling in uploader Compare: https://github.com/galaxyproject/galaxy/compare/40003111b3cc...ce113af1fc86 **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] 3040e9: Strip openid features from user controller
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3040e9f7a3cf7d761b3c258d377a8efb62341cc2 https://github.com/galaxyproject/galaxy/commit/3040e9f7a3cf7d761b3c258d377a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Strip openid features from user controller Commit: c9846391b2d4aa0e1e4f798a11c7258896c87705 https://github.com/galaxyproject/galaxy/commit/c9846391b2d4aa0e1e4f798a11c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/openid_associate.mako R templates/user/openid_manage.mako Log Message: ----------- Remove openid related makos Commit: 260d2240134d6ea730ab22b9117fc290209c94e3 https://github.com/galaxyproject/galaxy/commit/260d2240134d6ea730ab22b9117f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove openid access links from preferences Commit: 62cc4e27e56f27ca5a293ca3f9f616623519fecc https://github.com/galaxyproject/galaxy/commit/62cc4e27e56f27ca5a293ca3f9f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Remove openid feature from login form Commit: 73f75aeb11bd657819ce73f4509995a5c283418c https://github.com/galaxyproject/galaxy/commit/73f75aeb11bd657819ce73f45099… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/user/index.mako Log Message: ----------- Remove openid feature from legacy toolshed preference view Commit: 4b678daab8c9c686ccc07a51d40062ba905dc87b https://github.com/galaxyproject/galaxy/commit/4b678daab8c9c686ccc07a51d400… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/app.py Log Message: ----------- Strip openid manager and providers from app Commit: 2f942eefb407b3449a90ef780181393041da7e6b https://github.com/galaxyproject/galaxy/commit/2f942eefb407b3449a90ef780181… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R config/openid_conf.xml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Remove openid options from config schema Commit: 3fa2409de4355e7c1b88ef43cb540fb459b1923b https://github.com/galaxyproject/galaxy/commit/3fa2409de4355e7c1b88ef43cb54… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- Remove openid from schema and controller endpoints Commit: 6fecb4a07aa079ed1a1430cf34562b53fda9d1ea https://github.com/galaxyproject/galaxy/commit/6fecb4a07aa079ed1a1430cf3456… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Remove openid manager and routes Commit: bd3c37f06506066c96a1d939ce87627e4d4918c6 https://github.com/galaxyproject/galaxy/commit/bd3c37f06506066c96a1d939ce87… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Remove openid settings from config and toolshed Commit: b9af75567c298944c026930892fd16ebbd9510ab https://github.com/galaxyproject/galaxy/commit/b9af75567c298944c026930892fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R lib/galaxy/openid/__init__.py R lib/galaxy/openid/providers.py Log Message: ----------- Remove openid service modules Commit: 8b9082ac19e43394f513f27dbf3ccf939c06c226 https://github.com/galaxyproject/galaxy/commit/8b9082ac19e43394f513f27dbf3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove openid check in dependencies Commit: f591999738d3e99c8f10abefd11c79515878cc98 https://github.com/galaxyproject/galaxy/commit/f591999738d3e99c8f10abefd11c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Strip openid from data model Commit: 4f0b1fbd79df9232cbde99d11d9089e323a37092 https://github.com/galaxyproject/galaxy/commit/4f0b1fbd79df9232cbde99d11d90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove unused imports Commit: 5426f3b5533417ba4fd6043dd6bdb6f81e8db678 https://github.com/galaxyproject/galaxy/commit/5426f3b5533417ba4fd6043dd6bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/login/Login.vue Log Message: ----------- Add login vue component Commit: 92011492413a5ead7b8f1680d81096b28ae7e400 https://github.com/galaxyproject/galaxy/commit/92011492413a5ead7b8f1680d810… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Add Password vue component Commit: ee465276d1d7537eca424302cb68f537c0832687 https://github.com/galaxyproject/galaxy/commit/ee465276d1d7537eca424302cb68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/apps/login.js Log Message: ----------- Revise login app to load vue components Commit: d78b5903388379f0642861b86731e08ba3e7c3b6 https://github.com/galaxyproject/galaxy/commit/d78b5903388379f0642861b86731… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Revise masthead routes Commit: a7ba7788a48af98febd890ddad6f84d033c7b15b https://github.com/galaxyproject/galaxy/commit/a7ba7788a48af98febd890ddad6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Remove unused parameter from auth manager Commit: 3065d7c5879d0831d4355f59613aea1c6266b9c0 https://github.com/galaxyproject/galaxy/commit/3065d7c5879d0831d4355f59613a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Move authentication logic to user manager Commit: 98a1dede27d3996b9450ae8c2f4bae23fab099ba https://github.com/galaxyproject/galaxy/commit/98a1dede27d3996b9450ae8c2f4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove CreatesUsersMixin from base controller Commit: 1bcb02da2071996de1637469b3b8df40379f9d65 https://github.com/galaxyproject/galaxy/commit/1bcb02da2071996de1637469b3b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Reuse shared user manager features in user api Commit: a7bb8db3a966f87c2f472c3bc34768fe135cb6f1 https://github.com/galaxyproject/galaxy/commit/a7bb8db3a966f87c2f472c3bc347… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Revise user controller, user shared manager features Commit: 273e91a563bb74626e239490c6ce693408f59a87 https://github.com/galaxyproject/galaxy/commit/273e91a563bb74626e239490c6ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Align toolshed user controller Commit: 644d612083b94d7571c75792133585b26d7411bc https://github.com/galaxyproject/galaxy/commit/644d612083b94d7571c757921335… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/user/change_password.mako M templates/webapps/tool_shed/user/index.mako Log Message: ----------- Adjust toolshed makos Commit: 14912d72d00fb96c05786e82edcd6a23239d32a1 https://github.com/galaxyproject/galaxy/commit/14912d72d00fb96c05786e82edcd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/login.mako R templates/user/reset_password.mako A templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/reset_password.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Move toolshed makos, adjust test cases Commit: 0ced7d393d05b011e101e25ff135956a4d45026f https://github.com/galaxyproject/galaxy/commit/0ced7d393d05b011e101e25ff135… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M test/unit/managers/test_HDAManager.py M test/unit/managers/test_UserManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Add test cases for user manager Commit: 86b6786e0856ecb7c6e5618e5a5f5672a84e5960 https://github.com/galaxyproject/galaxy/commit/86b6786e0856ecb7c6e5618e5a5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/index.mako Log Message: ----------- Remove unused user index mako Commit: 4e2192963879c61e65a450d8126878e1a951ed08 https://github.com/galaxyproject/galaxy/commit/4e2192963879c61e65a450d81268… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Remove openid use case from toolshed login controller Commit: f8db566f4e476eaf2a82d4277e4d18ba5d29f4b0 https://github.com/galaxyproject/galaxy/commit/f8db566f4e476eaf2a82d4277e4d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R templates/user/info.mako M templates/webapps/tool_shed/user/manage_info.mako Log Message: ----------- Remove user info mako Commit: b1ba31ea90f8239c03938c108045239a255702b0 https://github.com/galaxyproject/galaxy/commit/b1ba31ea90f8239c03938c108045… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py 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scripts/grt/grt.yml.sample R templates/admin/tool_errors.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/message.mako M templates/no_access.mako M templates/refresh_frames.mako M templates/slug_editing_js.mako M templates/tagging_common.mako M templates/user/logout.mako R templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/display.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/page/wymiframe.mako M templates/webapps/galaxy/root/redirect.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/browse_repository.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako M templates/webapps/tool_shed/user/login.mako A test/api/test_galaxy_interactor.py M test/api/test_histories.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/integration_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh A test/functional/tools/collection_creates_pair_y.yml M test/functional/tools/composite_output_tests.xml M test/functional/tools/for_workflows/head.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/multi_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_10.xml A test/functional/tools/tool_provided_metadata_11.xml A test/functional/tools/tool_provided_metadata_12.xml A test/integration/handler_template_job_conf.xml A test/integration/resubmission_pulsar_job_conf.xml A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py A test/integration/test_handler_assignment_methods.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/integration/test_scripts.py A test/integration/test_workflow_sync.py M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/grouping.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Merge branch 'dev' into remove_openid_login_mako Commit: 6bd675e0396166e92bc305b0b04ae9d1403461c5 https://github.com/galaxyproject/galaxy/commit/6bd675e0396166e92bc305b0b04a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: R client/galaxy/scripts/apps/login.js Log Message: ----------- Remove previous login.js file Commit: 6ae064d903a366088715d31de5f49cabc15acd2d https://github.com/galaxyproject/galaxy/commit/6ae064d903a366088715d31de5f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Load galaxy instance in password vue component Commit: a38eec9c063f17aa189d7509507264f9205b62f1 https://github.com/galaxyproject/galaxy/commit/a38eec9c063f17aa189d75095072… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Use urlroot and galaxy instance in password component Commit: 26ffce5fa1c6944001af6edec58acfb0dd011d4c https://github.com/galaxyproject/galaxy/commit/26ffce5fa1c6944001af6edec58a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Fix galaxy instance access in password vue Commit: f5f5f432ad18cbef1c221d7661ec3c5e39ed39c6 https://github.com/galaxyproject/galaxy/commit/f5f5f432ad18cbef1c221d7661ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Fix error message for password token validation Commit: 9926bbfb0e4e9be29803addb51b3f2c57477d2a7 https://github.com/galaxyproject/galaxy/commit/9926bbfb0e4e9be29803addb51b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py Log Message: ----------- Add host to password reset email Commit: e264c48399202a3e7a30672a24a3e1a741d2fed0 https://github.com/galaxyproject/galaxy/commit/e264c48399202a3e7a30672a24a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Remove legacy mako-based login variation Commit: 75435cb8f974e82b240d6365f0b6dc112e97dc21 https://github.com/galaxyproject/galaxy/commit/75435cb8f974e82b240d6365f0b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Password.vue Log Message: ----------- Move alert message in password component to the top Commit: a276e5befebf65fa5633a2f28c49424b260be38f https://github.com/galaxyproject/galaxy/commit/a276e5befebf65fa5633a2f28c49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Restore login redirects to galaxy resources Commit: 905a7d0aa5461efd9e23929606fedbfdf8cac5a4 https://github.com/galaxyproject/galaxy/commit/905a7d0aa5461efd9e23929606fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Fix message content test in user manager test case Commit: bad54ea5dbc9dd08c11bfa2cd3462d391f65346f https://github.com/galaxyproject/galaxy/commit/bad54ea5dbc9dd08c11bfa2cd346… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-01-10 (Thu, 10 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix url for in unit login test case Commit: 70dacdd4d2706e46c22a04bbf0f7986b684f57ef https://github.com/galaxyproject/galaxy/commit/70dacdd4d2706e46c22a04bbf0f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Remove unused imports in login/index.js Commit: 0ad0de987dae7bb6b34ffa9c9a4fa4e13e413469 https://github.com/galaxyproject/galaxy/commit/0ad0de987dae7bb6b34ffa9c9a4f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-16 (Wed, 16 Jan 2019) Changed paths: M client/galaxy/scripts/components/login/Login.vue M client/galaxy/scripts/components/login/Password.vue M client/galaxy/scripts/entry/login/index.js Log Message: ----------- Minor formatting tweaks (prettier update) Commit: 40003111b3cc28a7eba0994767ecf50d49f80363 https://github.com/galaxyproject/galaxy/commit/40003111b3cc28a7eba0994767ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: A client/galaxy/scripts/components/login/Login.vue A client/galaxy/scripts/components/login/Password.vue R client/galaxy/scripts/entry/login/LoginPage.js M client/galaxy/scripts/entry/login/index.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/auth/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/info.mako R templates/user/login.mako R templates/user/reset_password.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/user/change_password.mako M templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/login.mako M templates/webapps/tool_shed/user/manage_info.mako A templates/webapps/tool_shed/user/reset_password.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_login.py M test/shed_functional/base/twilltestcase.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_UserManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'remove_openid_login_mako' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4044704f131d...40003111b3cc **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] bad8cf: Verify .venv's node version is in line with what w...
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bad8cffdbca2afbd2e5653041326abdfde3673bd https://github.com/galaxyproject/galaxy/commit/bad8cffdbca2afbd2e5653041326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Verify .venv's node version is in line with what we've specified as being locked, rather than just checking if node exists. Commit: 4044704f131d713372c4db7a8e10064a91ce20fa https://github.com/galaxyproject/galaxy/commit/4044704f131d713372c4db7a8e10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7220 from dannon/node-version-upgrades Verify/update .venv's node version Compare: https://github.com/galaxyproject/galaxy/compare/91fc612af677...4044704f131d **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] 54aecb: Properly deal with missing tools in subworkflows
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/release_18.09 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 Compare: https://github.com/galaxyproject/galaxy/compare/105a1d8a61ef...889c1026c089 **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] 42be5b: Add galaxycloudrunner as a conditional dependency.
by GitHub 18 Jan '19

18 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 42be5b61f2bf67a579cc1841630328e6244003fe https://github.com/galaxyproject/galaxy/commit/42be5b61f2bf67a579cc18416303… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add galaxycloudrunner as a conditional dependency. Commit: c14c358ce23ae90b2e51c01802296d0a987e0295 https://github.com/galaxyproject/galaxy/commit/c14c358ce23ae90b2e51c0180229… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Rename dynamic_destination_plugins to job_rule_modules Commit: e822f95fcbc4768d145858d7841c935aeed36cf9 https://github.com/galaxyproject/galaxy/commit/e822f95fcbc4768d145858d7841c… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Added galaxycloudrunner config example and pipfile dependency Commit: 76ac19839911cfebf4ef8facf2f364f8a509cb1a https://github.com/galaxyproject/galaxy/commit/76ac19839911cfebf4ef8facf2f3… Author: Nuwan Goonasekera <2070605+nuwang(a)users.noreply.github.com> Date: 2019-01-17 (Thu, 17 Jan 2019) Changed paths: M .travis.yml M Makefile A client/.eslintignore A client/.eslintrc.js M client/galaxy/scripts/app/galaxy.js M client/galaxy/scripts/components/Alert.vue M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/Masthead/index.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/components/admin/DisplayApplications.vue M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/entry/admin/index.js M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M 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client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js R client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.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-librarylist-view.js M 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lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py R lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy_ext/metadata/set_metadata.py M templates/user/index.mako M templates/user/login.mako R templates/user/openid_associate.mako R templates/user/openid_manage.mako M tox.ini Log Message: ----------- Merge pull request #2 from dannon/conditional_galaxycloudrunner Conditional galaxycloudrunner Commit: 91fc612af67725beb31830624d448e2c1a74bd20 https://github.com/galaxyproject/galaxy/commit/91fc612af67725beb31830624d44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7226 from nuwang/add_galaxy_cloud_runner Added galaxy cloud runner Compare: https://github.com/galaxyproject/galaxy/compare/f2ccea2ded16...91fc612af677 **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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