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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/cd1454c40a43...a0eae9510c9e

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Compare: https://github.com/galaxyproject/galaxy/compare/eab30c96522a...86ab6fd227b6

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[galaxyproject/galaxy] 934542: Fix duplicate import of _l in workflows
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 934542dd1113cefb19840f68b465f8604a0fd4c9 https://github.com/galaxyproject/galaxy/commit/934542dd1113cefb19840f68b465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix duplicate import of _l in workflows Commit: 8a3c3c15a43f64b615bceba9cf4449f5f230b9a2 https://github.com/galaxyproject/galaxy/commit/8a3c3c15a43f64b615bceba9cf44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Client format. Commit: 440aba01b4cc87d472f9871999378233181a3f22 https://github.com/galaxyproject/galaxy/commit/440aba01b4cc87d472f987199937… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js Log Message: ----------- Client build. Commit: 6055de286d6c8d36a5c29f960390c5ac65c1c3b5 https://github.com/galaxyproject/galaxy/commit/6055de286d6c8d36a5c29f960390… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5156 from dannon/fix_localization_and_build Fix localization and build client. Compare: https://github.com/galaxyproject/galaxy/compare/c8d45dd4b37c...6055de286d6c

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[galaxyproject/galaxy] b7be41: Re-allow workflow outputs that aren't produced dur...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7be4162bd2f5ea43b318dc7ea3f552b6475d9a2 https://github.com/galaxyproject/galaxy/commit/b7be4162bd2f5ea43b318dc7ea3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Re-allow workflow outputs that aren't produced during workflow scheduling. These are sort of an error in the workflow definition but we don't have a means to competently display this information to the user via the UI so I think we need to just allow this to happen. I've attached a test case that exhibits this behavior and passes under 17.09 but fails under the current dev branch without these fixes. This was broken in https://github.com/galaxyproject/galaxy/commit/d5f98f49045bca351e982f17cac9… when we started to actually persist pointers to workflow invocation outputs (as part of https://github.com/galaxyproject/galaxy/pull/5013) Commit: 4925660ab4aa2974c6ac8e94180180bac7db9781 https://github.com/galaxyproject/galaxy/commit/4925660ab4aa2974c6ac8e941801… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Revert extra assertions that are causing unrelated issues to surface. The unrelated issues are serious problems though and I've created an issue to track them https://github.com/galaxyproject/galaxy/issues/5146. Commit: c8d45dd4b37c707d8ebe1d104c8a3e72d016bb9d https://github.com/galaxyproject/galaxy/commit/c8d45dd4b37c707d8ebe1d104c8a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5143 from jmchilton/fix_missing_outputs Re-allow workflow outputs that aren't produced during workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/c8937c8929a5...c8d45dd4b37c

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[galaxyproject/galaxy] b1d6c0: Fixes for handling delayed steps within subworkflo...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1d6c017d03a1202c7fbc17f4e3ec3872d8f57b4 https://github.com/galaxyproject/galaxy/commit/b1d6c017d03a1202c7fbc17f4e3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Fixes for handling delayed steps within subworkflows. With new test case to verify this fix is needed. The previous test case that was verifying collection mapping and rescheduling of subworkflows turned out to really be testing the connections with respect to the outer workflow since only the last step of the subworkflow required rescheduling iterations. This newer test case verifies the connections within the subworkflow also - in addition to re-testing the connections and mapping in the outer workflow. Commit: c8937c8929a5d582a8d8ed033e07cd38432342d3 https://github.com/galaxyproject/galaxy/commit/c8937c8929a5d582a8d8ed033e07… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5145 from jmchilton/subworkflow_delayed_handling Fixes for handling delayed steps within subworkflows. Compare: https://github.com/galaxyproject/galaxy/compare/d042f446a4c2...c8937c8929a5

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[galaxyproject/galaxy] 743441: Rebuild fr locale.js file to match basic locale....
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7434411e14039d035f3f2309f0ff1a5de7bdc498 https://github.com/galaxyproject/galaxy/commit/7434411e14039d035f3f2309f0ff… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Rebuild fr locale.js file to match basic locale.js Commit: 886aded175c7f870152305480856a8a8c287b3f8 https://github.com/galaxyproject/galaxy/commit/886aded175c7f870152305480856… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.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/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.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/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/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.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.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Add new title entries basic locale.js and fr Commit: 3fba0d049ac589d1306c211cc59dd22f5ea1a40c https://github.com/galaxyproject/galaxy/commit/3fba0d049ac589d1306c211cc59d… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Add new description entries in basic locale.js and fr Commit: a8fc967df2ff52aeaf9fb938aa16de79a40008e3 https://github.com/galaxyproject/galaxy/commit/a8fc967df2ff52aeaf9fb938aa16… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Add new help entries in basic locale.js and fr Commit: f8a5108d6db32917f9aaca73db6ac37643be765d https://github.com/galaxyproject/galaxy/commit/f8a5108d6db32917f9aaca73db6a… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add new tooltip entries in basic locale.js and fr Commit: b9461e32b8731eeb46b13271a5a10187a18e7632 https://github.com/galaxyproject/galaxy/commit/b9461e32b8731eeb46b13271a5a1… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.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/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.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/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/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.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.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- remove labels entries and useless translation Commit: 12f2f74db3ab29d3cbeaab9b4c1e6c05456c61b6 https://github.com/galaxyproject/galaxy/commit/12f2f74db3ab29d3cbeaab9b4c1e… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Remove translation of name Commit: 05aae3c69c8eb744d87931c632dc785d0b57166c https://github.com/galaxyproject/galaxy/commit/05aae3c69c8eb744d87931c632dc… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Drop changes in qunit files Commit: 9d16aacfe1d069e8d41792494d49b9b99b89e158 https://github.com/galaxyproject/galaxy/commit/9d16aacfe1d069e8d41792494d49… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Add and remove one comma Commit: d042f446a4c27d1358c394ef485b71ef7c2b8134 https://github.com/galaxyproject/galaxy/commit/d042f446a4c27d1358c394ef485b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.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/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.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/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/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.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.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5089 from ValentinChCloud/dev i18n improvements French localization the sequel Compare: https://github.com/galaxyproject/galaxy/compare/3a9d63c69005...d042f446a4c2

1 0

[galaxyproject/galaxy] 38ec39: Fix revision selection during installation
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38ec399d56f07e40c64f37342b099fab65c746d7 https://github.com/galaxyproject/galaxy/commit/38ec399d56f07e40c64f37342b09… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix revision selection during installation Without this the model would be refetched and would remain at the initial changeset revision. Commit: 7bbd2dbd758cf685978dee4deb50d047b648b9fe https://github.com/galaxyproject/galaxy/commit/7bbd2dbd758cf685978dee4deb50… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Order the metadata revisions Commit: 41e2558ed5d228cd4b5b3c45b59d80ff7dcb7f8b https://github.com/galaxyproject/galaxy/commit/41e2558ed5d228cd4b5b3c45b59d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix undefined variable error in repository installation queue Commit: fd16b3d3b46dde3d11ab357704755915149cb8d8 https://github.com/galaxyproject/galaxy/commit/fd16b3d3b46dde3d11ab35770475… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix key error for non-tool workflow steps (i.e collection input) Commit: 39912e8c5beba8daa82078aa3a9626cedded5277 https://github.com/galaxyproject/galaxy/commit/39912e8c5beba8daa82078aa3a96… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M static/maps/mvc/toolshed/repository-view.js.map M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Add static JS Commit: d95ad427618ae6dae88c58e5eaed29aa7e16393b https://github.com/galaxyproject/galaxy/commit/d95ad427618ae6dae88c58e5eaed… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Fix KeyError in beta repository installation Repository metadata may not include tool dependencies. Commit: ec81d16585e43335cd54d4d5c3f415e861db6522 https://github.com/galaxyproject/galaxy/commit/ec81d16585e43335cd54d4d5c3f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M README.rst M client/README.md M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.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/collection-view.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/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M 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test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/microbial_import.xml M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into beta_tool_install_fixes and repack. Commit: 3a9d63c69005602d32212208c69729bc4813ad5e https://github.com/galaxyproject/galaxy/commit/3a9d63c69005602d32212208c697… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Merge pull request #4944 from mvdbeek/beta_tool_install_fixes Fix revision selection during (beta) repository installation Compare: https://github.com/galaxyproject/galaxy/compare/c0b1337f26b4...3a9d63c69005

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[galaxyproject/galaxy] 143a2d: Implement Multilingualization support on workflow ...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 143a2db7adf05ba8e34d145327c0aaa467e1a460 https://github.com/galaxyproject/galaxy/commit/143a2db7adf05ba8e34d145327c0… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Implement Multilingualization support on workflow page Commit: 81bf05494bc0a29ff0bcb6b1ebe741e910ff1886 https://github.com/galaxyproject/galaxy/commit/81bf05494bc0a29ff0bcb6b1ebe7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M .gitignore M Makefile M client/README.md R client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R 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test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/test_toolbox.py M test/functional/tools/bibtex.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/config_vars.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/identifier_in_actions.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py M test/integration/test_local_job_cancellation.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_mules_as_job_handlers.py M test/integration/test_workflow_handler_configuration.py A test/integration/test_workflow_scheduling_options.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample M test/unit/dataset_collections/test_matching.py M test/unit/jobs/test_job_configuration.py A test/unit/tools/test_tool_validation.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into workflow_page_translation Commit: e93821152432081dcfa08b1550e6c4d11e22abf7 https://github.com/galaxyproject/galaxy/commit/e93821152432081dcfa08b1550e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/ja/locale.js Log Message: ----------- Repack to merge PR. Commit: c0b1337f26b4072dca8cdf0144a28799b524d3c0 https://github.com/galaxyproject/galaxy/commit/c0b1337f26b4072dca8cdf0144a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/ja/locale.js Log Message: ----------- Merge pull request #5077 from manabuishii/workflow_page_translation Implement Multilingualization support on workflow page Compare: https://github.com/galaxyproject/galaxy/compare/30e2736cc4fc...c0b1337f26b4

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[galaxyproject/galaxy] f7820e: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7820e82380f7ea69ba56037a3f463352ef36807 https://github.com/galaxyproject/galaxy/commit/f7820e82380f7ea69ba56037a3f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: a2b8e445d85b50265da52c06f017c9c78be953b6 https://github.com/galaxyproject/galaxy/commit/a2b8e445d85b50265da52c06f017… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: d44a20cef098abf905f8525c42eb7f37d39f4ad9 https://github.com/galaxyproject/galaxy/commit/d44a20cef098abf905f8525c42eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Use a temporary ToolDataTableManager when generating metadata Otherwise loaded data tables bleed into the app-wide data tables. This can be seen with lots of data tables pointing to (non-existing, at that point) temporary files after a metadata reset in the galaxy admin panel, but it can also cause failure to install tools with entirely new data tables. Commit: 561f71ec50ee6708913d57955456faa1932c4cac https://github.com/galaxyproject/galaxy/commit/561f71ec50ee6708913d57955456… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Avoid manipulating global toll data tables Commit: c02d9363c45b7272f8b507f6c46aecf867faee5d https://github.com/galaxyproject/galaxy/commit/c02d9363c45b7272f8b507f6c46a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix copying of loc.sample files `filename` should be joined with the tool_path, as evidenced by other uses of copy_sample_file. Commit: fe6033fb22a23d4004a70de101e3f9597d0c6912 https://github.com/galaxyproject/galaxy/commit/fe6033fb22a23d4004a70de101e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Avoid global changes to app.config.tool_data_path Commit: 7df9dce63d635d66a0a9ce5045135ab49b7ef506 https://github.com/galaxyproject/galaxy/commit/7df9dce63d635d66a0a9ce504513… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py Log Message: ----------- Rename the ToolDataTableManager that deals with repository data to ShedToolDataTableManager to avoid confusion Commit: b03f16ed49074ef98ba7ecd7ed9f70123e196ace https://github.com/galaxyproject/galaxy/commit/b03f16ed49074ef98ba7ecd7ed9f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Load tools directly from source and avoid loading via toolbox Commit: c0887d72f8d37ee7c608fa0e41d2455956e6791a https://github.com/galaxyproject/galaxy/commit/c0887d72f8d37ee7c608fa0e41d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix missing index file check Commit: 55e458262b4184557842312c77f70dc1f5f3903c https://github.com/galaxyproject/galaxy/commit/55e458262b4184557842312c77f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: A lib/galaxy/util/miniapp.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Add miniapp to avoid manipulating global settings Commit: ab21f303af8d53fe543974ed48e7d0614db2de22 https://github.com/galaxyproject/galaxy/commit/ab21f303af8d53fe543974ed48e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/util/miniapp.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Always use MiniApp when using ToolValidator Commit: f08f4733050922c4177d84ec6f2550dd53cc8fcb https://github.com/galaxyproject/galaxy/commit/f08f4733050922c4177d84ec6f25… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Only parse citations if app has citations_manager Commit: d3261096c831a8539aeeae5ccf4e6734593f91a1 https://github.com/galaxyproject/galaxy/commit/d3261096c831a8539aeeae5ccf4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/util/miniapp.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Fix linting issues and fix data manager installation Commit: c1630c244fc4700998e0d23130f7120344b303b2 https://github.com/galaxyproject/galaxy/commit/c1630c244fc4700998e0d23130f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: A lib/galaxy/tools/repositories/validationcontext.py R lib/galaxy/util/miniapp.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Move and rename MiniApp to ValidationContext This better describes what it used for and since it is tool specific, fits better here that in utils. Thanks @jmchilton for the suggestion. Commit: 93442f621bea51bd242f2b67e7d201bc409f9fe9 https://github.com/galaxyproject/galaxy/commit/93442f621bea51bd242f2b67e7d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: A lib/galaxy/tools/repositories.py R lib/galaxy/tools/repositories/validationcontext.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Move ValidationContext to right path Commit: 482c9cce76c56bee840a87f25b0a17b8937444f5 https://github.com/galaxyproject/galaxy/commit/482c9cce76c56bee840a87f25b0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Remove more unused variables Commit: db88175b9fffe76cfd9013a6e6d6cfb9c573c354 https://github.com/galaxyproject/galaxy/commit/db88175b9fffe76cfd9013a6e6d6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py Log Message: ----------- Use ValidationContext data tables instead of separately passing in relevant data tables Commit: fd4737d0ecade2dd3f13d51756f90899920ef2a4 https://github.com/galaxyproject/galaxy/commit/fd4737d0ecade2dd3f13d51756f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Don't reload tools, new indexes and data tables are recognized without a reload Commit: f97774be82108d94fecc29dcf98f1fe833a4ece0 https://github.com/galaxyproject/galaxy/commit/f97774be82108d94fecc29dcf98f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Change ValidationContext.build_file_path to be file Also simplify cleanup code. Commit: 1b48ff3dd15ebde13382afdb41cfb200a3c883cc https://github.com/galaxyproject/galaxy/commit/1b48ff3dd15ebde13382afdb41cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Skip format parsing if datatypes registry contains no datatypes Commit: 78e1478c7f9c6f3c232c6c91263c7bb28dec5c88 https://github.com/galaxyproject/galaxy/commit/78e1478c7f9c6f3c232c6c91263c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Remove unnecessary tool data table resets Commit: e65a2490c108929043a685eeca6bb89b6ade0b9c https://github.com/galaxyproject/galaxy/commit/e65a2490c108929043a685eeca6b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/galaxy/tools/repositories.py M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Linting fixes Commit: 4f162f28041d6c0ee3b551d589339d4048b5b7e1 https://github.com/galaxyproject/galaxy/commit/4f162f28041d6c0ee3b551d58933… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-03 (Sun, 03 Dec 2017) Changed paths: M lib/galaxy/tools/__init__.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Add unit test for ValidationContext and ToolValidator Commit: 30e2736cc4fc82cdf32437c60934a0e8e6bac453 https://github.com/galaxyproject/galaxy/commit/30e2736cc4fc82cdf32437c60934… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/repositories.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Merge pull request #5119 from mvdbeek/dev_toolshed_install_improvements_2 Improve tool validation and metadata generation Compare: https://github.com/galaxyproject/galaxy/compare/a901264ca745...30e2736cc4fc

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[galaxyproject/galaxy] 4a7045: Merge remote-tracking branch 'origin/release_17.05...
by GitHub 06 Dec '17

06 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534 https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/ui.less M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/compression_utils.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tours.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/datatypes_conf.xml.sample M create_db.sh M extract_dataset_parts.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' Commit: 15372f7369137b964534e9ddb8e81fb150dc2677 https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-31 (Tue, 31 Oct 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.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/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M 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client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-model.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-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M 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test/shed_functional/functional/test_0040_repository_circular_dependencies.py M test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0070_invalid_tool.py M test/shed_functional/functional/test_0080_advanced_circular_dependencies.py M test/shed_functional/functional/test_0090_tool_search.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py M test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_0130_datatype_converters.py M test/shed_functional/functional/test_0140_tool_help_images.py M test/shed_functional/functional/test_0150_prior_installation_required.py M test/shed_functional/functional/test_0160_circular_prior_installation_required.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_0430_browse_utilities.py M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py M test/shed_functional/functional/test_0460_upload_to_repository.py M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py M test/shed_functional/functional/test_0490_export_import_repositories.py M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py M 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test/shed_functional/functional/test_1070_invalid_tool.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1160_tool_help_images.py M test/shed_functional/functional/test_1170_prior_installation_required.py M test/shed_functional/functional/test_1180_circular_prior_installation_required.py M 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test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py A test/unit/test_remote_shell.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M 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tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'release_17.09' Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Migrate documentation for setting up a production instance to Galaxy. This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance). This content currently includes: - the production configuration page - the cluster configuration page - the job configuration page - the scaling information page - the ftp configuration page - the top-level nginx page (for external auth content still linking out to the hub) - the top-level apache page (for external auth content still linking out to the hub) - the job metrics configuration page Includes small tweaks to sphinx documentation generation. - Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs. - Use AutoStructify for better Markdown integration. Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including: - Update the job configuration page with information about XML macros. - Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore). - Updated list of dynamic job runner configuration parameters. - Mention the ``raw`` attribute for ``env`` directives in the job configuration page. - Mention the ``total_walltime`` limit added in #3217. - Drop mentions of older URL-based job conf configuration stuff. - Mention newer Local and Paramiko based shell runners in CLI section. - Mention newer slurm job styles in CLI section. - Improved Pulsar links. - Fix dataset security link in Apache display sites config. - Update job metrics page to link to a new Github issue instead of old Trello issues. Commit: befa077cc444115e0cac738c2bd3ee786f7425d2 https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Rework headings in jobs docs. Thanks to comment from @erasche review. Commit: b0c03240fd96ace2b25680e753fed0237264ec98 https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Merge pull request #5135 from jmchilton/17.09_admin_docs [17.09] Migrate documentation for setting up a production instance to Galaxy. Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43 https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Log Message: ----------- Merge pull request #5141 from jmchilton/master [17.09] Re-merge master into release_17.09. Commit: a901264ca74594f358b4d95862cb0ccd29346fcf https://github.com/galaxyproject/galaxy/commit/a901264ca74594f358b4d95862cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4d30b4f9cc5c...a901264ca745

1 0

[galaxyproject/galaxy] b7e05a: otherwise it will overwrite linking source file
by GitHub 06 Dec '17

06 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: b7e05a012cb8dd3bf90f31f5c5a7df44587e97c0 https://github.com/galaxyproject/galaxy/commit/b7e05a012cb8dd3bf90f31f5c5a7… Author: Ignacio Eguinoa <igegu(a)psb.ugent.be> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- otherwise it will overwrite linking source file Commit: 19e5478cb8ffbd9d97db663bb1d04e52bed721a0 https://github.com/galaxyproject/galaxy/commit/19e5478cb8ffbd9d97db663bb1d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4911 from jmchilton/backport_4858 [17.09] Backport #4858 Commit: e3be7c31d59b69571bcee04599bdac6693426b89 https://github.com/galaxyproject/galaxy/commit/e3be7c31d59b69571bcee04599bd… Author: Wolfgang Maier <wolfgang.maier(a)biologie.uni-freiburg.de> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- fix broken link in 17.09 announcement Commit: 222ece4eabb6d080c6b8a0e327f8cf617b8a194f https://github.com/galaxyproject/galaxy/commit/222ece4eabb6d080c6b8a0e327f8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4927 from wm75/patch-2 fix broken link in 17.09 announcement Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3 https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. Commit: 0207b0186ac7c3d61004718ff7b91c3ea0c52165 https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Specify TagAssociation class when copying a tag This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags. Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377 https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Encode file content with utf-8 There shouldn't be any disadvantages over doing this only for specific elements. This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378. I have tested this with unicode strings in the name and info fields. Commit: b978acbe62053596e5c2ae736c848a62dc936591 https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Revert "Remove downloading workflows through controller" This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa. This is used when downloading workflows with the save icom from "pages". Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3 https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Open files in text-mode (thx @nsoranzo) Commit: 6915007f85482648999768eecb9920da57b42e59 https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759 https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4987 from mvdbeek/history_import_bug [17.09][Bug] Encode file content with utf-8 Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0 https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 3b523260551d15241de5dce3d1023790dcfd2250 https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d102… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #4988 from jmchilton/revert_export_to_file [17.09] Revert export to file Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6 https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags [17.05][BUG] Specify TagAssociation class when copying a tag Commit: 1a412bfb1b0497d9e3e2b8f9c348d7aa0f2478d6 https://github.com/galaxyproject/galaxy/commit/1a412bfb1b0497d9e3e2b8f9c348… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 06e9509d3868c885d41d94e455d7245f4af10156 https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Allow get_history calls with create=False when evaluation workflows. No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history. Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing ipaddress requirement Broken in https://github.com/galaxyproject/galaxy/pull/4289 . Fix https://github.com/galaxyproject/galaxy/issues/4999 . Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- remove the default override since it is wrong and ignores the access permissions Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2 https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Do not attempt to visit parameters of invalid conditionals Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8 https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Check for key/value errors only when testing conditional cases Commit: 75f84bfc476ea94c22a38097d20f694265fcded6 https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test cases to cover version changes Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check [16.07] history contents api - remove the default flag override Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD Commit: eab30c96522a5a558de4232320c87c1ef102d2d2 https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7 https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into HEAD Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Remove unnecessary name setting for non-group parameters Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116 https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix comments Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement [17.09] Add missing ipaddress requirement Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix workflow editor output attributes. Commit: 5dc2254417667216dab982a4bc375a85d3b55316 https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4997 from jmchilton/allow_create_false_in_work_context [17.09] Allow get_history calls with create=False when evaluation workflows. Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8 https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #5022 from dannon/workflow_editor_fix_backport [17.09] Fix workflow editor output attributes. Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add ICM datatype for glimmer Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- copy paste mistake... Commit: f60a75c285830bff963bd31120f3420e9815dbe2 https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f3… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- extraneous %s Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0 https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #5048 from erasche/fix-ufr-6206 Remove extraneous %s in condor logging Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38 https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e388… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Bug fix - expose proper element_identifier in tool action template expansions. (#5049) xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3… Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't read too much Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Closes https://github.com/galaxyproject/galaxy/issues/2645. Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ``` Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix metadata setting for Otu datatypes I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard. Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes [BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade [BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation [BUG][17.09] Fix metadata setting for Otu datatypes Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446 https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix exception in admin panel TypeError: Non-hexadecimal digit found File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories return self.repository_installation_grid(trans, **kwd) File "galaxy/web/framework/helpers/grids.py", line 85, in __call__ query = self.build_initial_query(trans, **kwargs) File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id)) File "galaxy/web/security/__init__.py", line 107, in decode_id return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!")) File "encodings/hex_codec.py", line 42, in hex_decode output = binascii.a2b_hex(input) This is due to `tool_shed_repository_ids` being a json dump of a list in certain consitions (noticed this after installing a new repository). Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt [17.09] Add ICM datatype for glimmer Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix [17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045 [17.09] Backport #5045 Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03 https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #5010 from guerler/fix_pages_workflows [17.09] Do not visit child inputs of invalid conditionals Commit: a82d325d18375797ce8ab53366320f3c9a772ab7 https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab5336632… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Merge pull request #5079 from mvdbeek/admin_panel_exception_fix [17.09] Fix exception in admin panel Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Migrate documentation for setting up a production instance to Galaxy. This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance). This content currently includes: - the production configuration page - the cluster configuration page - the job configuration page - the scaling information page - the ftp configuration page - the top-level nginx page (for external auth content still linking out to the hub) - the top-level apache page (for external auth content still linking out to the hub) - the job metrics configuration page Includes small tweaks to sphinx documentation generation. - Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs. - Use AutoStructify for better Markdown integration. Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including: - Update the job configuration page with information about XML macros. - Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore). - Updated list of dynamic job runner configuration parameters. - Mention the ``raw`` attribute for ``env`` directives in the job configuration page. - Mention the ``total_walltime`` limit added in #3217. - Drop mentions of older URL-based job conf configuration stuff. - Mention newer Local and Paramiko based shell runners in CLI section. - Mention newer slurm job styles in CLI section. - Improved Pulsar links. - Fix dataset security link in Apache display sites config. - Update job metrics page to link to a new Github issue instead of old Trello issues. Commit: befa077cc444115e0cac738c2bd3ee786f7425d2 https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Rework headings in jobs docs. Thanks to comment from @erasche review. Commit: b0c03240fd96ace2b25680e753fed0237264ec98 https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Merge pull request #5135 from jmchilton/17.09_admin_docs [17.09] Migrate documentation for setting up a production instance to Galaxy. Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43 https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Log Message: ----------- Merge pull request #5141 from jmchilton/master [17.09] Re-merge master into release_17.09. Compare: https://github.com/galaxyproject/galaxy/compare/15372f736913...cd1454c40a43

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[galaxyproject/galaxy] 4a7045: Merge remote-tracking branch 'origin/release_17.05...
by GitHub 06 Dec '17

06 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534 https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-24 (Mon, 24 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/ui.less M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/compression_utils.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tours.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/datatypes_conf.xml.sample M create_db.sh M extract_dataset_parts.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' Commit: 15372f7369137b964534e9ddb8e81fb150dc2677 https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-31 (Tue, 31 Oct 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.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/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/options-menu.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-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-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M 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client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-model.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-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less M 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test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py A test/unit/test_remote_shell.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/joiner.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'release_17.09' Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43 https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Log Message: ----------- Merge pull request #5141 from jmchilton/master [17.09] Re-merge master into release_17.09. Compare: https://github.com/galaxyproject/galaxy/compare/b0c03240fd96...cd1454c40a43

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[galaxyproject/galaxy] d24b54: Migrate documentation for setting up a production ...
by GitHub 06 Dec '17

06 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Migrate documentation for setting up a production instance to Galaxy. This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance). This content currently includes: - the production configuration page - the cluster configuration page - the job configuration page - the scaling information page - the ftp configuration page - the top-level nginx page (for external auth content still linking out to the hub) - the top-level apache page (for external auth content still linking out to the hub) - the job metrics configuration page Includes small tweaks to sphinx documentation generation. - Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs. - Use AutoStructify for better Markdown integration. Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including: - Update the job configuration page with information about XML macros. - Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore). - Updated list of dynamic job runner configuration parameters. - Mention the ``raw`` attribute for ``env`` directives in the job configuration page. - Mention the ``total_walltime`` limit added in #3217. - Drop mentions of older URL-based job conf configuration stuff. - Mention newer Local and Paramiko based shell runners in CLI section. - Mention newer slurm job styles in CLI section. - Improved Pulsar links. - Fix dataset security link in Apache display sites config. - Update job metrics page to link to a new Github issue instead of old Trello issues. Commit: befa077cc444115e0cac738c2bd3ee786f7425d2 https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Rework headings in jobs docs. Thanks to comment from @erasche review. Commit: b0c03240fd96ace2b25680e753fed0237264ec98 https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py Log Message: ----------- Merge pull request #5135 from jmchilton/17.09_admin_docs [17.09] Migrate documentation for setting up a production instance to Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/22aa02f59496...b0c03240fd96

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[galaxyproject/galaxy] 28cdb6: Postpone depends_list generation
by GitHub 06 Dec '17

06 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28cdb6d165293060458e5336d7ab4b9972c0a826 https://github.com/galaxyproject/galaxy/commit/28cdb6d165293060458e5336d7ab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Postpone depends_list generation No need to calculate it if a converted dataset already exists. Commit: 4d30b4f9cc5c580637af3a1bd9aaca8932d465f1 https://github.com/galaxyproject/galaxy/commit/4d30b4f9cc5c580637af3a1bd9aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5137 from nsoranzo/datatype_conversion_fixes Postpone depends_list generation Compare: https://github.com/galaxyproject/galaxy/compare/211121877c3a...4d30b4f9cc5c

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[galaxyproject/galaxy] 0dfe73: Determine dynamically if an extension corresponds ...
by GitHub 05 Dec '17

05 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0dfe73a54cebb1e4fd7a02d9ff05ca585d034244 https://github.com/galaxyproject/galaxy/commit/0dfe73a54cebb1e4fd7a02d9ff05… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Determine dynamically if an extension corresponds to an unsniffable binary datatype Remove the need to call `Binary.register_unsniffable_binary_ext()` for each unsniffable binary datatype. Fix https://github.com/galaxyproject/galaxy/issues/3441 , where the upload of files of a datatype defined in datatypes_conf.xml as subclass of an unsniffable binary datatype ended up with "The uploaded binary file contains inappropriate content" because it was not possible to register the subclassed datatype as unsniffable. Also remove unused `stop_err()` function in upload.py . Commit: 211121877c3a579e3c9cbd05c0933017177f26a8 https://github.com/galaxyproject/galaxy/commit/211121877c3a579e3c9cbd05c093… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5109 from nsoranzo/deprecate_register_unsniffable_binary_ext Determine dynamically if an extension corresponds to an unsniffable binary datatype Compare: https://github.com/galaxyproject/galaxy/compare/f09944a8229b...211121877c3a

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[galaxyproject/galaxy] 706221: Some workflow formatting.
by GitHub 05 Dec '17

05 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7062219d2a0d7545ce894b7a4ac542345a2c73d3 https://github.com/galaxyproject/galaxy/commit/7062219d2a0d7545ce894b7a4ac5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Some workflow formatting. Commit: ea386b394763b69da1427e766f52cfe2e9917337 https://github.com/galaxyproject/galaxy/commit/ea386b394763b69da1427e766f52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Cleanup, fix linting in workflow-canvas.js Commit: dcadf30148e8aa13301151b06efcad1db11857bb https://github.com/galaxyproject/galaxy/commit/dcadf30148e8aa13301151b06efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Add passthroughs for copy/paste in workflow editor event bindings. Commit: 4d3abb5eb11f36537550526b4b9c2a100ce19907 https://github.com/galaxyproject/galaxy/commit/4d3abb5eb11f36537550526b4b9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- window.getSelection is a function. Commit: be6b52df307197d75ad15e1cea1b8d3b14ee1ca6 https://github.com/galaxyproject/galaxy/commit/be6b52df307197d75ad15e1cea1b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- On node change, we need to blur() here; otherwise the active input is still potentially a hidden input field behind the scenes. Amazing this hasn't been a bug before now? Commit: 32afe8fab56d7f609fac0994f10f40e9f5ab6644 https://github.com/galaxyproject/galaxy/commit/32afe8fab56d7f609fac0994f10f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Clear active node is a more appropriate place for this blur. Commit: 0096a5851cd3513e3674341f89f556f710758d20 https://github.com/galaxyproject/galaxy/commit/0096a5851cd3513e3674341f89f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Blur on canvas click, too. Commit: 0e346735ab6b3256a2d4d6589308bab6113b6bdb https://github.com/galaxyproject/galaxy/commit/0e346735ab6b3256a2d4d6589308… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Build client. Commit: f09944a8229bf835ad838c7579a7a2b2b425c638 https://github.com/galaxyproject/galaxy/commit/f09944a8229bf835ad838c7579a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Merge pull request #5124 from dannon/workflow_tool_copy_cleanup Workflow tool copy tweaks Compare: https://github.com/galaxyproject/galaxy/compare/3744730a9bcd...f09944a8229b

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[galaxyproject/galaxy] 1f210c: Improve resilience of filter detection
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f210c98f895b75d10010df2f702f6cc0d20fde5 https://github.com/galaxyproject/galaxy/commit/1f210c98f895b75d10010df2f702… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Improve resilience of filter detection Commit: bc24621e81baba35727f7b4593a7cc6a3a766d06 https://github.com/galaxyproject/galaxy/commit/bc24621e81baba35727f7b4593a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Raise log level for missing filter to warning Commit: 39bf7814f8b9caf5f12983a3786643ad8046f6b2 https://github.com/galaxyproject/galaxy/commit/39bf7814f8b9caf5f12983a37866… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Check filter function before adding it on initialization Commit: 62d1f5459a3596641e823de9207e2406a9cf865f https://github.com/galaxyproject/galaxy/commit/62d1f5459a3596641e823de9207e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix warning message Commit: f47fde8dc0b6e4469c74fe8357fbaf6e4e060b9b https://github.com/galaxyproject/galaxy/commit/f47fde8dc0b6e4469c74fe8357fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix user preference identifiers for section and label filters Commit: f3f40b5a6d1baa47c44a60b714d413069422ffc9 https://github.com/galaxyproject/galaxy/commit/f3f40b5a6d1baa47c44a60b714d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Highlight filter inputs with missing modules Commit: 05daad94421bf2fa8282ca7b7beec9e98a82cf7f https://github.com/galaxyproject/galaxy/commit/05daad94421bf2fa8282ca7b7bee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add criteria to existing statement Commit: 7469b6483ba8d6aa58e35a04a0640a465e5677b7 https://github.com/galaxyproject/galaxy/commit/7469b6483ba8d6aa58e35a04a064… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Avoid building prefix string if not needed Commit: 225008ccf073b1ec925060c28f9fcbba9dff82dc https://github.com/galaxyproject/galaxy/commit/225008ccf073b1ec925060c28f9f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Add module name to error log Commit: 15928b544c3542a06b727a5d12246a073a1cc3cd https://github.com/galaxyproject/galaxy/commit/15928b544c3542a06b727a5d1224… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Improve error message Commit: 3744730a9bcd015589099920b8bce434d96ae7a7 https://github.com/galaxyproject/galaxy/commit/3744730a9bcd015589099920b8bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Merge remote-tracking branch 'guerler/improve_filter_resilience' into dev Compare: https://github.com/galaxyproject/galaxy/compare/43c518a6e951...3744730a9bcd

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[galaxyproject/galaxy] 4d94fb: start work on workflow tool cloning
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d94fb58d4b13562a58c2353b0778d94f1ea4f3e https://github.com/galaxyproject/galaxy/commit/4d94fb58d4b13562a58c2353b077… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/yarn.lock M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- start work on workflow tool cloning Commit: 021a5eb2e3b02c07b01887a66f1f1e4522a8a645 https://github.com/galaxyproject/galaxy/commit/021a5eb2e3b02c07b01887a66f1f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- preserve params on copy Commit: 8fcb7578ab9dcf963ad50d8190832be9fe055d3b https://github.com/galaxyproject/galaxy/commit/8fcb7578ab9dcf963ad50d819083… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- fix a bug when a tool couldn't be copied Commit: 1173ce6cf9fc2b46da127e1177fd12a2bbc60bb0 https://github.com/galaxyproject/galaxy/commit/1173ce6cf9fc2b46da127e1177fd… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- add copy&paste feature Commit: 43c518a6e9519efbd23c0c831b9475cc9fca206d https://github.com/galaxyproject/galaxy/commit/43c518a6e9519efbd23c0c831b94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/yarn.lock M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge remote-tracking branch 'anatskiy/workflow_tools_copying' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8c87b2c401f6...43c518a6e951

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[galaxyproject/galaxy] 1a0800: Remove unused import, self from ui-tabs; named exp...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a08005847d8a722262602e44c5d1d895295f89a https://github.com/galaxyproject/galaxy/commit/1a08005847d8a722262602e44c5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Remove unused import, self from ui-tabs; named export for the View. Commit: 243855cfd4e3a3a96f93e092e4a47325ebf183b2 https://github.com/galaxyproject/galaxy/commit/243855cfd4e3a3a96f93e092e4a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Minor cleanup; named exports for these common utils functions which we can expect external consumers of. Commit: 5e05aa114b45341cba02329ef8c20ba71e6d5994 https://github.com/galaxyproject/galaxy/commit/5e05aa114b45341cba02329ef8c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Named exports, cleanup for ui-misc. Includes a note about eliminating the practice of re-exporting stuff, but that's another project that'll have to fix downstream consumers. Commit: 5877d0c43e5adc8fb4342062d6577adcc6a6ea6b https://github.com/galaxyproject/galaxy/commit/5877d0c43e5adc8fb4342062d657… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js Log Message: ----------- Import/Export refactoring in mvc/form and mvc/ui; adjust charts usage to fix require-based entry. Lots of cleanup, too. Commit: 1c587117b04d6f5322bcdd1d60c609e19a4c313d https://github.com/galaxyproject/galaxy/commit/1c587117b04d6f5322bcdd1d60c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Charts cleanup, formatting. Commit: df1083c541f6130b2a1de9e8ad99ba03b8a4d5af https://github.com/galaxyproject/galaxy/commit/df1083c541f6130b2a1de9e8ad99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/Gruntfile.js Log Message: ----------- Drop sudo reference (local npm, non-root), elaborate comment in scatterplot gruntfile. Commit: b6509f402fe7d33fd807501a5253daa18ff22876 https://github.com/galaxyproject/galaxy/commit/b6509f402fe7d33fd807501a5253… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Scatterplot was missing require? Did not dig to see how this ever worked before, yet. Commit: c23c2324bc6c84d1f09e0dc2651c1775f1cc2ca5 https://github.com/galaxyproject/galaxy/commit/c23c2324bc6c84d1f09e0dc2651c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/package.json R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Scatterplot overhaul progress. Should just need to fix bootstrap tooltip loading and it's good to go. Commit: 7ebe68d770e20abfd21d32d30566abab25e75205 https://github.com/galaxyproject/galaxy/commit/7ebe68d770e20abfd21d32d30566… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Cleanup in scatterplot. Commit: 3a532ad8e8fee5045a5d31e9f5e06d714216bb69 https://github.com/galaxyproject/galaxy/commit/3a532ad8e8fee5045a5d31e9f5e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/package.json M client/yarn.lock M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Bootstrap.js bug was preventing loading the 'correct' way; resolved with an update. Commit: 2083ce9ea0a513b3e3345c56a94fa0971d3381b1 https://github.com/galaxyproject/galaxy/commit/2083ce9ea0a513b3e3345c56a94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/package.json M client/yarn.lock M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- jquery-ui does not like loading. jquery-ui-bundle handles this better, can easily be used as an import (we probably want to get rid of this stuff eventually, but it works for now) Commit: 6fbaced59b525466d381c1ad632626bcd8695daf https://github.com/galaxyproject/galaxy/commit/6fbaced59b525466d381c1ad6326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Remove (now-unused) i18n loader from scatterplot's webpack config (was there for utils) Commit: 52e65537ed76b59da2bcfe2be2d53e3033860ef8 https://github.com/galaxyproject/galaxy/commit/52e65537ed76b59da2bcfe2be2d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js Log Message: ----------- Scatterplot lives! Commit: 50870d5ab6904d096312c97c6790281036a31f53 https://github.com/galaxyproject/galaxy/commit/50870d5ab6904d096312c97c6790… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/utils/utils.js Log Message: ----------- Rebuild client. Commit: 8c87b2c401f6d70cdda3c1d2c567cf13ce9a90f0 https://github.com/galaxyproject/galaxy/commit/8c87b2c401f6d70cdda3c1d2c567… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.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-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/utils/utils.js M client/package.json M client/yarn.lock M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/webpack.config.js R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #5081 from dannon/fix-charts-packing Viz plugin loading fixes Compare: https://github.com/galaxyproject/galaxy/compare/b3e207095848...8c87b2c401f6

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[galaxyproject/galaxy] 6d6313: Reorg bundling into standalone apps and a 'kitchen...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d63130fbfbd63922bdfe9080c886309a686870b https://github.com/galaxyproject/galaxy/commit/6d63130fbfbd63922bdfe9080c88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: R client/galaxy/scripts/apps/admin-toolshed.js A client/galaxy/scripts/apps/interface_ext.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R client/galaxy/scripts/apps/viz.js R client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Reorg bundling into standalone apps and a 'kitchensink' type bundle as discussed for a catchall migration target as we refactor. Commit: 24e5afc5b9b7c0d5eb95dd264acd235310d18168 https://github.com/galaxyproject/galaxy/commit/24e5afc5b9b7c0d5eb95dd264acd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/interface_ext.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js Log Message: ----------- Rebuild client with new bundles. Commit: dba22f3fe868c0ab39f8e8293454494b6b586019 https://github.com/galaxyproject/galaxy/commit/dba22f3fe868c0ab39f8e8293454… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/interface_ext.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py A static/scripts/bundled/extended.bundled.js R static/scripts/bundled/interface_ext.bundled.js M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Swap interface_ext to 'extended', and fix a masthead bug. Commit: 0a5c7aaa7a49f53f9dad52e24b63934a17557a9c https://github.com/galaxyproject/galaxy/commit/0a5c7aaa7a49f53f9dad52e24b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Beta Admin Toolshed entrypoint fix. Commit: b3e207095848ffa584d91d849825fdf19421acf9 https://github.com/galaxyproject/galaxy/commit/b3e207095848ffa584d91d849825… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: R client/galaxy/scripts/apps/admin-toolshed.js A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R client/galaxy/scripts/apps/viz.js R client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #5093 from dannon/bundle-refactoring Bundle refactoring Compare: https://github.com/galaxyproject/galaxy/compare/358cfc14af7c...b3e207095848

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[galaxyproject/galaxy] 2e288e: Fix attribute error that was missed during refacto...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e288ef60f6a461cbd0bb4c5d82f7e6cee0f9fc8 https://github.com/galaxyproject/galaxy/commit/2e288ef60f6a461cbd0bb4c5d82f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix attribute error that was missed during refactor Commit: 358cfc14af7c025bcf00d614fafe68ae90ef8437 https://github.com/galaxyproject/galaxy/commit/358cfc14af7c025bcf00d614fafe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5122 from erasche/fix-attr-error Fix attribute error that was missed during refactor of sentry Compare: https://github.com/galaxyproject/galaxy/compare/72ed629c2a33...358cfc14af7c

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[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Commit: 72ed629c2a333de1adaac6892642e39aba7478c8 https://github.com/galaxyproject/galaxy/commit/72ed629c2a333de1adaac6892642… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: config/datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/7c59b8a33be9...72ed629c2a33

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[galaxyproject/galaxy] d73bb6: Fix ICM datatype sniffer config
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Compare: https://github.com/galaxyproject/galaxy/compare/c41fc0a4275a...22aa02f59496

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[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 02 Dec '17

02 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Compare: https://github.com/galaxyproject/galaxy/compare/a82d325d1837...c41fc0a4275a

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[galaxyproject/galaxy] 85bf39: change the default ot not add tags based on filena...
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85bf398fc33fb7ca230c51b09661176382923796 https://github.com/galaxyproject/galaxy/commit/85bf398fc33fb7ca230c51b09661… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- change the default ot not add tags based on filename this is fairly confusing if you do not expect it and there is no way to revert Commit: 7c59b8a33be920c72eac187ba35d0fdbba0b8e0e https://github.com/galaxyproject/galaxy/commit/7c59b8a33be920c72eac187ba35d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5115 from martenson/change-libimport-tagdefault change the default to not add tags based on filename Compare: https://github.com/galaxyproject/galaxy/compare/dad11b8ef6d7...7c59b8a33be9

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