- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d97a74: #5187
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d97a74e9783863270697ab9a329f7dc247df1e37 https://github.com/galaxyproject/galaxy/commit/d97a74e9783863270697ab9a329f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 63e2964c2e161baf268a848e0abb8d2b35f3858b https://github.com/galaxyproject/galaxy/commit/63e2964c2e161baf268a848e0abb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5233 from NCEichner/#5187 #5187: altered conda version number for using '--offline' option again Compare: https://github.com/galaxyproject/galaxy/compare/b3a8f5f54b74...63e2964c2e16

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[galaxyproject/galaxy] 49f0cf: remove dead code, the object is always nonempty
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49f0cf86f05d161be9614258bdee80916444524a https://github.com/galaxyproject/galaxy/commit/49f0cf86f05d161be9614258bdee… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/layout/router.js Log Message: ----------- remove dead code, the object is always nonempty Commit: e6215dd495649e2255d0d72115eb47bcd11706a9 https://github.com/galaxyproject/galaxy/commit/e6215dd495649e2255d0d72115eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/layout/router.js Log Message: ----------- Build client. Commit: b3a8f5f54b7433bc1fcc6578f928db2e02c1c254 https://github.com/galaxyproject/galaxy/commit/b3a8f5f54b7433bc1fcc6578f928… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/layout/router.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/layout/router.js Log Message: ----------- Merge branch 'router-mods' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7eae6bf06185...b3a8f5f54b74

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[galaxyproject/galaxy] 71380d: Add chinese support
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71380da4cf9d2da114487b6567f29b6612d20c05 https://github.com/galaxyproject/galaxy/commit/71380da4cf9d2da114487b6567f2… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Add chinese support Add simplified chinese support Commit: c89967f9a4a1322dd7ea85956be6264058779937 https://github.com/galaxyproject/galaxy/commit/c89967f9a4a1322dd7ea85956be6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Client-format (TODO: Set this up as a build pipeline using .po's as the canonical source, building to these bundles...) Commit: 1b301ba604723e36530d323c79d5378516e95d0c https://github.com/galaxyproject/galaxy/commit/1b301ba604723e36530d323c79d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/nls/zh/locale.js Log Message: ----------- Build client Commit: 7eae6bf06185164f1a9184bd45a48badd45882af https://github.com/galaxyproject/galaxy/commit/7eae6bf06185164f1a9184bd45a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js M static/scripts/bundled/libs.bundled.js M static/scripts/nls/zh/locale.js Log Message: ----------- Merge branch 'patch-1' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ee6512ee8a59...7eae6bf06185

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[galaxyproject/galaxy] d42eef: convert to arrow functions, eliminate self and tha...
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d42eef992df528f1591d6513a68a13f53171f954 https://github.com/galaxyproject/galaxy/commit/d42eef992df528f1591d6513a68a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- convert to arrow functions, eliminate self and that Commit: e8e12a6026289420757488bd72e726aedea87bbd https://github.com/galaxyproject/galaxy/commit/e8e12a6026289420757488bd72e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/library.css Log Message: ----------- remove styles for the removed old library interface Commit: 96565e9b84cc064ab717580b143bacd8672b2e70 https://github.com/galaxyproject/galaxy/commit/96565e9b84cc064ab717580b143b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/style/blue/library.css M test/galaxy_selenium/navigation.yml Log Message: ----------- wip on importing from library to history as a collection + various es6 additions; cleanup; refactoring I tried to separate it into more commits but it kept growing too fast, sorry Commit: 88d9c669d06f5503f8337ce4d187ed83a6295ab9 https://github.com/galaxyproject/galaxy/commit/88d9c669d06f5503f8337ce4d187… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- implement support for paired and list:paired collections Commit: e344de3660a02501467fd769883cc17d359b8223 https://github.com/galaxyproject/galaxy/commit/e344de3660a02501467fd769883c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- finish the list:paired modal invocation Commit: 2f90fd87663924f39d6c264e45c66ebb80bd3bf0 https://github.com/galaxyproject/galaxy/commit/2f90fd87663924f39d6c264e45c6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- re enable and enhance the collection validator Commit: 2dfdbb645bebf4834606e8534181970a79508bb0 https://github.com/galaxyproject/galaxy/commit/2dfdbb645bebf4834606e8534181… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- refactor modal to bind closing event at different time this allows chaining modals after each other with closing events working Commit: e4d0788a28da6f2007de700dae3f35400f7abdb0 https://github.com/galaxyproject/galaxy/commit/e4d0788a28da6f2007de700dae3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Improvements to library testing. - Add tests for creating a collection from a library. - Add more class names to library GUI to improve selectors for tests. - Automatically select whichever radio box makes sense in library collection builder dialog based on whether there is a selection or not. Commit: d0a9d6619d1970a6de9b2c5567f0a927d16bcded https://github.com/galaxyproject/galaxy/commit/d0a9d6619d1970a6de9b2c5567f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- hide source items by default in all library-collection creators Commit: d806cf7b3776f048b97fd7254a37c4a763894579 https://github.com/galaxyproject/galaxy/commit/d806cf7b3776f048b97fd7254a37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #26 from jmchilton/lib-to-colllection Improvements to library testing. Commit: fb256b7aa330e43feae5a27aff72bd0b82661a21 https://github.com/galaxyproject/galaxy/commit/fb256b7aa330e43feae5a27aff72… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- fix the modal backdrop listener to respect the config Commit: 498de3e830220556a838f71a20505b6d58794a31 https://github.com/galaxyproject/galaxy/commit/498de3e830220556a838f71a2050… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the selenium test that expects the class to be here Commit: 00e31c13f516206ff979cc0798d2dd69f044495c https://github.com/galaxyproject/galaxy/commit/00e31c13f516206ff979cc0798d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix more selenium library tests. Commit: 9dda0ed3f117a3b29c6962713efb6543e2b30e0d https://github.com/galaxyproject/galaxy/commit/9dda0ed3f117a3b29c6962713efb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/history.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection Commit: 9a14f7c835bbfdb013a5860eac41e8064bc2570b https://github.com/galaxyproject/galaxy/commit/9a14f7c835bbfdb013a5860eac41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 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/galaxy.library.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Rebuild client. Commit: ee6512ee8a592a4ab44c0827bff8ee04949a7b2d https://github.com/galaxyproject/galaxy/commit/ee6512ee8a592a4ab44c0827bff8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.library.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/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/style/less/library.less 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/galaxy.library.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css M static/style/blue/library.css M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5080 from martenson/lib-to-colllection Libraries to collections Compare: https://github.com/galaxyproject/galaxy/compare/77d77a935fa0...ee6512ee8a59

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[galaxyproject/galaxy] e6b650: Pages entrypoint; eliminate require.
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6b650b6b872d50c9b2a57a9d31fed7b6b110d3d https://github.com/galaxyproject/galaxy/commit/e6b650b6b872d50c9b2a57a9d31f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Pages entrypoint; eliminate require. Commit: 81bfe11fbd3ce51ae3e2d01a16620c58211c6799 https://github.com/galaxyproject/galaxy/commit/81bfe11fbd3ce51ae3e2d01a1662… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js Log Message: ----------- WYM needs this global space, this fixes the loaders in a better way (for us) than the export loaders. Compatibility fix for the ~8 year old wymeditor. We should look into newer options. Commit: 7722a2151ae6f0b1910aaf9670de6efce65c9c5e https://github.com/galaxyproject/galaxy/commit/7722a2151ae6f0b1910aaf9670de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/phyloviz.mako Log Message: ----------- Convert phyloviz loading to bundle instead of require. Commit: d8bbeae47313eb37a97f8fe301c46f182120e65e https://github.com/galaxyproject/galaxy/commit/d8bbeae47313eb37a97f8fe301c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Bundle and use createTabularDatasetChunkedView entrypoint. Commit: 00770e28090125595a0f21332be775f2672af438 https://github.com/galaxyproject/galaxy/commit/00770e28090125595a0f21332be7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- History multiview bundle/entry. Commit: 5f514d44a551d0a3521cca4345788a8da390191e https://github.com/galaxyproject/galaxy/commit/5f514d44a551d0a3521cca434578… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view.mako Log Message: ----------- History view and view-edit bundling into extended UI. Refactored some of the bootstrapping. We really need a Galaxy singleton for logging/etc. Commit: fc37c728e9ac7eecc652fe4fe085d1090db60f03 https://github.com/galaxyproject/galaxy/commit/fc37c728e9ac7eecc652fe4fe085… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Temporary-ish fix for logging in extended bundle (add logging to whatever Galaxy object exists on the window) Commit: d795bc229bd3f76ea2b1b5737067b474e5f55b87 https://github.com/galaxyproject/galaxy/commit/d795bc229bd3f76ea2b1b5737067… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Only strap in logging when it's not already there. Commit: 32537e136e5bec6651004c5594dc67ecf51fce35 https://github.com/galaxyproject/galaxy/commit/32537e136e5bec6651004c5594dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/dataset/display.mako Log Message: ----------- Use bundles for dataset/display; we really probably want to get rid of dataset/display_by_username_and_slug, because 1) there is no slug, and 2) username isn't used... Commit: 4c54c9dfb99e3b9f7d8f972554fbd022852d836e https://github.com/galaxyproject/galaxy/commit/4c54c9dfb99e3b9f7d8f972554fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: f5dad8810fcca9fba5e8965d82555a6a4c4031e4 https://github.com/galaxyproject/galaxy/commit/f5dad8810fcca9fba5e8965d8255… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster globals, argh. Needs more refactoring, but I'd like to get it working again first. Commit: f440586738284dba5ccee86ee9668368a1e45395 https://github.com/galaxyproject/galaxy/commit/f440586738284dba5ccee86ee966… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix circster loading error> Commit: 7f107e8e8b318db89e9fcbd94cc0c8816086cc28 https://github.com/galaxyproject/galaxy/commit/7f107e8e8b318db89e9fcbd94cc0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Swap to default d3 for circster. Commit: 4d6ab294339924b3930673e914929ddd6247442d https://github.com/galaxyproject/galaxy/commit/4d6ab294339924b3930673e91492… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix d3 event handling in circster. Commit: 55afdb1b25437dfb033367caf0f50604b6a63137 https://github.com/galaxyproject/galaxy/commit/55afdb1b25437dfb033367caf0f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Attach toplevel or global viz stuff to window (force_left_panel, force_right_panel, galaxy_config). Commit: 3543cd31748c3a4906e71dfcf339597d11041b4c https://github.com/galaxyproject/galaxy/commit/3543cd31748c3a4906e71dfcf339… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Embedded page entrypoints, bundling. Commit: 30f98eac21fc838ab4ba4cf0e007223fce1872c6 https://github.com/galaxyproject/galaxy/commit/30f98eac21fc838ab4ba4cf0e007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Formatting in workflow canvas and trackster Commit: 993c0b7341ab2f1515d727b0b3c44b7fbf8e4b75 https://github.com/galaxyproject/galaxy/commit/993c0b7341ab2f1515d727b0b3c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- More bundling, always bundling. Commit: e69c047bd8e1df1d6cbb178b3de8488600aa076f https://github.com/galaxyproject/galaxy/commit/e69c047bd8e1df1d6cbb178b3de8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/display.mako Log Message: ----------- Trackster external display bundling. Commit: b9862425acbed31c905448c76573d266ba7cb28b https://github.com/galaxyproject/galaxy/commit/b9862425acbed31c905448c76573… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/display_common.mako Log Message: ----------- Remove SampleDataset and RequestType references from display_common; this prevents any use of this mako currently. Commit: a3b25a345f02a4dab99e57e93549ea21e3c1a563 https://github.com/galaxyproject/galaxy/commit/a3b25a345f02a4dab99e57e93549… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- More request type cruft; seems to be unused and it'd blow up if tried to use Commit: f02895705d2bd171e3f51a34928e050f4563e87b https://github.com/galaxyproject/galaxy/commit/f02895705d2bd171e3f51a34928e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Bundle sweepster. Commit: d31868ad32bb237f4f72c4e2b10d75fa69b0913a https://github.com/galaxyproject/galaxy/commit/d31868ad32bb237f4f72c4e2b10d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M templates/webapps/galaxy/history/display.mako Log Message: ----------- History display mako swapped to use existing bundled javascript. Commit: 2e59e92a0b0f888c709695d130a1643d68ab3492 https://github.com/galaxyproject/galaxy/commit/2e59e92a0b0f888c709695d130a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Bundle structure view (still has a bug, but that's not new) Commit: 2d2726456c1377f12faeb5ab389ae1c6bd9b0a54 https://github.com/galaxyproject/galaxy/commit/2d2726456c1377f12faeb5ab389a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Bundle history structure view. Commit: 560b2e0b963e697c51fbf90fce8446d724d7484c https://github.com/galaxyproject/galaxy/commit/560b2e0b963e697c51fbf90fce84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Package GalaxyApp in extended bundle for bootstrapping outside the primary entrypoints; TODO: Refactor this to be import-based and keep a singleton Commit: ed274a7ca562ad170d86aa2f21748693c8a54e46 https://github.com/galaxyproject/galaxy/commit/ed274a7ca562ad170d86aa2f2174… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M 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 M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.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/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py R openid/yahoo.xml M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.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 A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/bibtex.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/common/select_template.mako R templates/common/template_common.mako R templates/form.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: a4899ae9b32ea081bac02dbc7e4b93c64ae6c6f6 https://github.com/galaxyproject/galaxy/commit/a4899ae9b32ea081bac02dbc7e4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako M templates/webapps/galaxy/base_panels.mako Log Message: ----------- Some bundle import reorg in old-style 'base' templates; we basically always want to load the bundle entrypoints here. Commit: e2e271d81a23d9c8a0db716f3f2d6f3d198f0bb2 https://github.com/galaxyproject/galaxy/commit/e2e271d81a23d9c8a0db716f3f2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/legacy/grid_base.mako Log Message: ----------- Use bundle entrypoint for legacy grid_base Commit: 38ecceb4c5ba877658b28cce8523afa5d7bc9b29 https://github.com/galaxyproject/galaxy/commit/38ecceb4c5ba877658b28cce8523… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Expose LegacyGridView via extended application bundle. Commit: 8e650ff29bb98f347439c6e808ea919ea974b5c7 https://github.com/galaxyproject/galaxy/commit/8e650ff29bb98f347439c6e808ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Remove unused dependencies from ui-select-library Commit: 90ea47e1dae07ab7a9ddd3f0477c57d552660be5 https://github.com/galaxyproject/galaxy/commit/90ea47e1dae07ab7a9ddd3f0477c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Slight logic clarification in ui-select-library. Commit: 1b39f2d1311cc86164818bc86524a039ead85a28 https://github.com/galaxyproject/galaxy/commit/1b39f2d1311cc86164818bc86524… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.js Log Message: ----------- Add a temporary workaround for Galaxy not being accessible at static build time Commit: 4ef30c89f43a8d266fc575fda64c8e8573aa7cbf https://github.com/galaxyproject/galaxy/commit/4ef30c89f43a8d266fc575fda64c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js Log Message: ----------- Remove unused dependencies from dataset/data.js Commit: 3f1f1727c63c682ff959e5e5ee2f32f92e52fe31 https://github.com/galaxyproject/galaxy/commit/3f1f1727c63c682ff959e5e5ee2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Swap reports run_stats to extended bundle entrypoint. Commit: 9290a7e5c3cc7b20dd51a655838a3af234b7b700 https://github.com/galaxyproject/galaxy/commit/9290a7e5c3cc7b20dd51a655838a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Drop debug statement Commit: ddc5f90907094e5b5ebb5bfc41144c2a168b8acc https://github.com/galaxyproject/galaxy/commit/ddc5f90907094e5b5ebb5bfc4114… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js Log Message: ----------- Merge builds gxy/shed Commit: 759014e15e2a5a383c8f280c18eba4554b3e7a1d https://github.com/galaxyproject/galaxy/commit/759014e15e2a5a383c8f280c18eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/GruntFile.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js Log Message: ----------- Consolidate to the one grunt task. Commit: db1f00fa3cf8ab65d37af776b72e46b70940ee3f https://github.com/galaxyproject/galaxy/commit/db1f00fa3cf8ab65d37af776b72e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Format toolshed js Commit: 426884284508f6ca949469cec06755d61631647d https://github.com/galaxyproject/galaxy/commit/426884284508f6ca949469cec067… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js R client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Lots of incremental toolshed js/ groups refactoring, bundling. Commit: 1159c342280a82a804c2192fdd58e11095108f34 https://github.com/galaxyproject/galaxy/commit/1159c342280a82a804c2192fdd58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- More incremental es6'ing of toolshed client code. Commit: bfb2d049a1a22c474337ca5a614220f5f7d31f93 https://github.com/galaxyproject/galaxy/commit/bfb2d049a1a22c474337ca5a6142… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Remove unused group-model import. Commit: 17e074068ac7c8fff25334ac555a8ff9984ffa6b https://github.com/galaxyproject/galaxy/commit/17e074068ac7c8fff25334ac555a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js Log Message: ----------- Toolshed client refactoring, fixing, etc. Commit: d79b5fff559e029a33180ab214699def343aa86b https://github.com/galaxyproject/galaxy/commit/d79b5fff559e029a33180ab21469… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Toolshed groups actually work now. Commit: c0eb0fadd8ebd8773d8be743d41667c16700074e https://github.com/galaxyproject/galaxy/commit/c0eb0fadd8ebd8773d8be743d416… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/README.md Log Message: ----------- Remove toolshed build info (part of the standard client build now) Commit: c2b709ae1c5d270f8d671b6ff8892b9aa1fc31ba https://github.com/galaxyproject/galaxy/commit/c2b709ae1c5d270f8d671b6ff889… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Old debug cruft removal in structure.mako Commit: 648d4bd5d34ea81bd55e1239c8aea47d112ba9fe https://github.com/galaxyproject/galaxy/commit/648d4bd5d34ea81bd55e1239c8ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js Log Message: ----------- Toolshed artifacts initial commit (hopefully we don't do this much more...) Commit: 20fa0e73f2aace2bc872cd49137f4cc23fa8f5d0 https://github.com/galaxyproject/galaxy/commit/20fa0e73f2aace2bc872cd49137f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 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.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js Log Message: ----------- Build client, including toolshed. Commit: e589f1e8bd5b575aaea7992a8769322d722ffe75 https://github.com/galaxyproject/galaxy/commit/e589f1e8bd5b575aaea7992a8769… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R static/scripts/bundled/adminToolshed.bundled.js R static/scripts/bundled/library.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js Log Message: ----------- Remove old, unused bundles. Commit: 77d77a935fa0b4f4c7476e871189a5fb8ecbe54f https://github.com/galaxyproject/galaxy/commit/77d77a935fa0b4f4c7476e871189… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge branch 'require_elimination' into dev Compare: https://github.com/galaxyproject/galaxy/compare/62a3a5c5968c...77d77a935fa0

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[galaxyproject/galaxy] 2db85b: Swaps nametags to a div, sets a max-height (intent...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2db85b3dd9ede81691ebff7d72d58acfa38524c7 https://github.com/galaxyproject/galaxy/commit/2db85b3dd9ede81691ebff7d72d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Swaps nametags to a div, sets a max-height (intentionally such that it clips a second line of tags, promoting curiosity to find the scroll Commit: 79465fd13cb2902aa3bb9f284e6e3fc0c86460d1 https://github.com/galaxyproject/galaxy/commit/79465fd13cb2902aa3bb9f284e6e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Add tooltip with number of nametags. Commit: 067d1c2abe391fe5d3f1794ce8945d9e4ea1b4e7 https://github.com/galaxyproject/galaxy/commit/067d1c2abe391fe5d3f1794ce894… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Constrain nametags in select2 boxes to 5 matching tags. Commit: cb635d22fb2ad93d13fe67bef7865cf3102f7f7f https://github.com/galaxyproject/galaxy/commit/cb635d22fb2ad93d13fe67bef786… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add an 'extra tags' block in the select interface since we're so limited on space. Commit: 21c18b5a30243c7b107bdc0168115da24e2f7fb3 https://github.com/galaxyproject/galaxy/commit/21c18b5a30243c7b107bdc016811… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js Log Message: ----------- Refactor tag templating, changes order of operations and filtering to improve performance issues noticeable with many tags Commit: ee1655307ddb152f8289f42e3fa67e371fd33288 https://github.com/galaxyproject/galaxy/commit/ee1655307ddb152f8289f42e3fa6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Attempt to fix matched tags counting in select2 (internal state is shared and wonky here). Some cleanup to help see what's going on. Commit: c389a84d71caf5850d101940c132580a17059673 https://github.com/galaxyproject/galaxy/commit/c389a84d71caf5850d101940c132… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix select2 tag filtering, counting, indication of extra tags. Commit: 35e1d18c06def858a8ee96986074eb14e2fccb66 https://github.com/galaxyproject/galaxy/commit/35e1d18c06def858a8ee96986074… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- More fat arrow functions and elimination of self in uiselectdefault Commit: 3fcc3c970078f5adc789569a1b80ef47e9c206e2 https://github.com/galaxyproject/galaxy/commit/3fcc3c970078f5adc789569a1b80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.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/grid/grid-model.js M 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 M client/galaxy/scripts/mvc/history/hdca-li.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-library-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 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Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Rebuild client after upstream/dev merge. Commit: 62a3a5c5968c5eeca27fd9e25f05bd718666a70b https://github.com/galaxyproject/galaxy/commit/62a3a5c5968c5eeca27fd9e25f05… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/history.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #5155 from dannon/tag_limit_size Dataset hashtag display improvements Compare: https://github.com/galaxyproject/galaxy/compare/be44b9b5eb5c...62a3a5c5968c

1 0

[galaxyproject/galaxy] 7a1d7f: download behaves badly on firefox, preventing righ...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a1d7fcaf4672c0a3ad382b07362b969180797d2 https://github.com/galaxyproject/galaxy/commit/7a1d7fcaf4672c0a3ad382b07362… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- download behaves badly on firefox, preventing right clicking to copy the url here Commit: 0ab21a2f4ed195711d0a55fa369dbc2fc09b123a https://github.com/galaxyproject/galaxy/commit/0ab21a2f4ed195711d0a55fa369d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- We preventdefault on this anyway, so the void(0) doesn't do anything. This allows right click copy on primary dataset regardless of whether or not there are extra meta files. Commit: ab084ffd4b9a797d3ccee35ffcdc1953970b88a0 https://github.com/galaxyproject/galaxy/commit/ab084ffd4b9a797d3ccee35ffcdc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Convert download blob to template literals instead of array concats. Commit: d3d6e723539618bea80a9f18b1895cc82aee280b https://github.com/galaxyproject/galaxy/commit/d3d6e723539618bea80a9f18b189… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Use the local var for urls.download Commit: ca8ec7395860f82a3622a5c21821a9341a3e1267 https://github.com/galaxyproject/galaxy/commit/ca8ec7395860f82a3622a5c21821… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A 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lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/util/biostar.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py 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 A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository_review/grid.mako M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/populators.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into download_fixes Commit: d93a2b437972d08c3df38f2c8020b04fb659f696 https://github.com/galaxyproject/galaxy/commit/d93a2b437972d08c3df38f2c8020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Client-format. Commit: 202305687abcf887541d6d16fc71e96f9afb63d9 https://github.com/galaxyproject/galaxy/commit/202305687abcf887541d6d16fc71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Rebuild client again. Commit: be44b9b5eb5c87eb79e561c2ebceba75106bf5b3 https://github.com/galaxyproject/galaxy/commit/be44b9b5eb5c87eb79e561c2ebce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Merge pull request #5125 from dannon/download_fixes Download fixes Compare: https://github.com/galaxyproject/galaxy/compare/1880230e5fdf...be44b9b5eb5c

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[galaxyproject/galaxy] 13c470: related to #4937 - add option to check file permis...
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13c4701f947d5f993f74bf9a37aeed9a2766a58b https://github.com/galaxyproject/galaxy/commit/13c4701f947d5f993f74bf9a37ae… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- related to #4937 - add option to check file permissions for the user library imports Commit: b17e7ecffa924bab244128cf91b5bb5c2931c55b https://github.com/galaxyproject/galaxy/commit/b17e7ecffa924bab244128cf91b5… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- fix linting errors Commit: a5c705e6741cb27d305c2eda2b55d457a8cb0a28 https://github.com/galaxyproject/galaxy/commit/a5c705e6741cb27d305c2eda2b55… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- right import order? Commit: 3294eba7c02bebecd61f181584cb5a9e8200cf98 https://github.com/galaxyproject/galaxy/commit/3294eba7c02bebecd61f181584cb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- fix flake8 errors Commit: 1880230e5fdfffe89f10806debe422d1e3471afe https://github.com/galaxyproject/galaxy/commit/1880230e5fdfffe89f10806debe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5154 from scholtalbers/feature/add_permission_check_to_user_lib_import add option to check file permissions for the user library imports Compare: https://github.com/galaxyproject/galaxy/compare/6bf5d663b4f3...1880230e5fdf

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[galaxyproject/galaxy] 09f51f: Upload optimization - eliminate second call to che...
by GitHub 18 Dec '17

18 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09f51f59af9290cd4c93345c6e0f682d32af052e https://github.com/galaxyproject/galaxy/commit/09f51f59af9290cd4c93345c6e0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload optimization - eliminate second call to check_binary in upload.py. Commit: cafac19f65020ef29cd8d73d226c43e901318616 https://github.com/galaxyproject/galaxy/commit/cafac19f65020ef29cd8d73d226c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload refactor - make link_data_only a bool. Since it is a bool. Commit: 2528ef33cdd4f7b5b07c9de6e6adc5a35a7851b3 https://github.com/galaxyproject/galaxy/commit/2528ef33cdd4f7b5b07c9de6e6ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Upload refactor - supply reasonable defaults to sniff methods making it easier to use. Commit: 7e1bff7d69b0bc25056c6e2b18ccd2a689654c0e https://github.com/galaxyproject/galaxy/commit/7e1bff7d69b0bc25056c6e2b18cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload refactor - change upload.py to use exceptions. Make decomposing and reuse of this easier downstream and feels cleaner to me. Commit: 6bf5d663b4f3cc448b25df50f486dfb383fbd267 https://github.com/galaxyproject/galaxy/commit/6bf5d663b4f3cc448b25df50f486… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5229 from jmchilton/upload_refactor Refactor upload.py toward reuse Compare: https://github.com/galaxyproject/galaxy/compare/21dc271bf014...6bf5d663b4f3

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[galaxyproject/galaxy] 1253ef: Adds k8s support for CPU and memory resource setti...
by GitHub 18 Dec '17

18 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1253eff2f5737183dbd702382534e920b32b2270 https://github.com/galaxyproject/galaxy/commit/1253eff2f5737183dbd702382534… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds k8s support for CPU and memory resource settings. Commit: 3145509b7a870d3ff06a2ad6037d5c5ce20eb559 https://github.com/galaxyproject/galaxy/commit/3145509b7a870d3ff06a2ad6037d… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Avoids cleaning up container name when destination id is not str, probably applicable for dynamic destinations. Commit: ca2e121fa67443797436189387e7ff6733cfc6b9 https://github.com/galaxyproject/galaxy/commit/ca2e121fa67443797436189387e7… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Minor code formatting for tox tests Commit: 7654935f031afdd852df3a800f2f012a89bdb08f https://github.com/galaxyproject/galaxy/commit/7654935f031afdd852df3a800f2f… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- k8s runner: Adds ability to detect OOMKilled jobs and signals it for resubmission. Commit: ac477fc0216c9c22af659eb9f1de7622c9207779 https://github.com/galaxyproject/galaxy/commit/ac477fc0216c9c22af659eb9f1de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Rework k8s resource request parameters. xref https://github.com/galaxyproject/galaxy/pull/4751#issuecomment-341196780 Commit: ec6011c23815355cdc35acc3246f473d9b2a98d9 https://github.com/galaxyproject/galaxy/commit/ec6011c23815355cdc35acc3246f… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #19 from jmchilton/feature/k8s-resources-requests-limits Rework k8s resource request parameters and docs Commit: 21dc271bf014889de3c4b2a3c1124c55811e4e22 https://github.com/galaxyproject/galaxy/commit/21dc271bf014889de3c4b2a3c112… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #4751 from phnmnl/feature/k8s-resources-requests-limits Kubernetes resources requests/limits support Compare: https://github.com/galaxyproject/galaxy/compare/6fc9296d5359...21dc271bf014

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