- 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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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 client/galaxy/scripts/mvc/toolshed/repository-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-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.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/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.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 M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py 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 M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py 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/proteomics.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py 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/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/__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/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.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/data/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py A lib/galaxy/tools/repositories.py M lib/galaxy/util/biostar.py M lib/galaxy/util/permutations.py A lib/galaxy/util/renamed_temporary_file.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/api/workflows.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 R lib/galaxy/webapps/reports/controllers/sample_tracking.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/api/tools.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/controllers/upload.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.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/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/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml 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/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.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/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.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/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/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/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/repository-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-canvas.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-terminals.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/ja/locale.js M static/scripts/nls/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.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 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 M templates/display_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 M templates/webapps/galaxy/workflow/editor.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/api/test_tools_upload.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/functional/webhooks/phdcomics/helper/__init__.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample 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 A test/unit/tools/test_tool_validation.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tag_limit_size Commit: d2d0e4169c93223f645a5e647862a105d9f93d47 https://github.com/galaxyproject/galaxy/commit/d2d0e4169c93223f645a5e647862… 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/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 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-canvas.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/job_conf.xml.sample_advanced M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M 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

1 0

[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

1 0

[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

1 0

[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

1 0

[galaxyproject/galaxy] 0cf38e: Force window jquery access for charts.mako. This ...
by GitHub 17 Dec '17

17 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0cf38e5d52c9eb9120dcc0e6971355402c95128a https://github.com/galaxyproject/galaxy/commit/0cf38e5d52c9eb9120dcc0e69713… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Force window jquery access for charts.mako. This isn't great, but charts *and* the rest of the viz framework are being refactored into bundles that will avoid this hackery. Commit: 6fc9296d5359afecdfff8c3a3b5af9bace14ac6b https://github.com/galaxyproject/galaxy/commit/6fc9296d5359afecdfff8c3a3b5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-17 (Sun, 17 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Merge pull request #5210 from dannon/fix_charts_jquery_usage Force window jquery access for charts Compare: https://github.com/galaxyproject/galaxy/compare/02b6ff3492ef...6fc9296d5359

1 0

[galaxyproject/galaxy] f9969e: Remove API scripts for axed APIs.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9969ee97acfb985c82c98946f08f522c232e654 https://github.com/galaxyproject/galaxy/commit/f9969ee97acfb985c82c98946f08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: 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 Log Message: ----------- Remove API scripts for axed APIs. Commit: 02b6ff3492efca986e34c769cc5a4869167332fb https://github.com/galaxyproject/galaxy/commit/02b6ff3492efca986e34c769cc5a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: 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 Log Message: ----------- Merge pull request #5230 from jmchilton/axed_api_scripts Remove API scripts for axed API (requests, samples...) Compare: https://github.com/galaxyproject/galaxy/compare/94dae3b7de18...02b6ff3492ef

1 0

[galaxyproject/galaxy] d5e39c: Python3: fix list.sort() and sorted() to use `key`...
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5e39c873e9aed6a2b0822b0f7187aa8a73430be https://github.com/galaxyproject/galaxy/commit/d5e39c873e9aed6a2b0822b0f718… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` xref. https://github.com/galaxyproject/galaxy/issues/1715 xref. https://github.com/galaxyproject/galaxy/issues/5216 Commit: 94dae3b7de180303427d4bfd0b1cbd4ee183469c https://github.com/galaxyproject/galaxy/commit/94dae3b7de180303427d4bfd0b1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Merge pull request #5225 from nsoranzo/fix_sort_sorted Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` Compare: https://github.com/galaxyproject/galaxy/compare/6d3eadedbd70...94dae3b7de18

1 0

[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Commit: 90ba35a9a49f583a1fe2a173c1239be86d71125a https://github.com/galaxyproject/galaxy/commit/90ba35a9a49f583a1fe2a173c123… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_17.09' into merge_1709 Commit: 6d3eadedbd7093fc19553d7812152293960f3f14 https://github.com/galaxyproject/galaxy/commit/6d3eadedbd7093fc19553d781215… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5227 from jmchilton/merge_1709 Merge 17.09. Compare: https://github.com/galaxyproject/galaxy/compare/717b5bbce9c5...6d3eadedbd70

1 0

[galaxyproject/galaxy] 3b9d28: Add check_py3_compatibility Travis job
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b9d2881618ca47f2135e3d226262ff736994260 https://github.com/galaxyproject/galaxy/commit/3b9d2881618ca47f2135e3d22626… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Add check_py3_compatibility Travis job Commit: 717b5bbce9c552de5d28d783bc8620c9396f269c https://github.com/galaxyproject/galaxy/commit/717b5bbce9c552de5d28d783bc86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Merge pull request #5228 from nsoranzo/add_check_py3_compatibility_travis_job Add check_py3_compatibility Travis job Compare: https://github.com/galaxyproject/galaxy/compare/7e7dc249ab93...717b5bbce9c5

1 0

[galaxyproject/galaxy] 18221a: paster.pid/log to galaxy.pid/log reference update
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18221ae931b22187a5978bd89222a8e84ed400f0 https://github.com/galaxyproject/galaxy/commit/18221ae931b22187a5978bd89222… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/first_startup.sh M contrib/galaxy.fedora-init M doc/source/admin/production.md M scripts/summarize_timings.py Log Message: ----------- paster.pid/log to galaxy.pid/log reference update Fix errors in `first_startup` jobs: https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029 Introduced in https://github.com/galaxyproject/galaxy/pull/4475 Commit: 7e7dc249ab93e66e405abf830782bcf78c0788c5 https://github.com/galaxyproject/galaxy/commit/7e7dc249ab93e66e405abf830782… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/first_startup.sh M contrib/galaxy.fedora-init M doc/source/admin/production.md M scripts/summarize_timings.py Log Message: ----------- Merge pull request #5226 from nsoranzo/fix_paster.log_pid paster.pid/log to galaxy.pid/log reference update Compare: https://github.com/galaxyproject/galaxy/compare/5b6eaac4a06c...7e7dc249ab93

1 0

[galaxyproject/galaxy] 710177: Add API tests for history uploads from URL
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Compare: https://github.com/galaxyproject/galaxy/compare/42c572f34469...44635eae1dc1

1 0

[galaxyproject/galaxy] 6f7228: Python3: fix moved imports
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f722861cfd4c36f93348048fe6e6c83305fcc9f https://github.com/galaxyproject/galaxy/commit/6f722861cfd4c36f93348048fe6e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M contrib/nagios/check_galaxy.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/util/biostar.py M test/base/driver_util.py M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- Python3: fix moved imports Add `.ci/check_py3_compatibility.sh` script to find library modules that have been moved in Python3. Fix errors found by the script. Commit: 5b6eaac4a06cfcd714dd4b578cdbf3239868ca28 https://github.com/galaxyproject/galaxy/commit/5b6eaac4a06cfcd714dd4b578cdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M contrib/nagios/check_galaxy.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/util/biostar.py M test/base/driver_util.py M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- Merge pull request #5221 from nsoranzo/python3 Python3: fix moved imports Compare: https://github.com/galaxyproject/galaxy/compare/ad0459d81840...5b6eaac4a06c

1 0

[galaxyproject/galaxy] d1be0a: Allow shells with different parameters to co-exist
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1be0a20eded8a31d5c514fcc7e370a96d0a01e9 https://github.com/galaxyproject/galaxy/commit/d1be0a20eded8a31d5c514fcc7e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py Log Message: ----------- Allow shells with different parameters to co-exist Commit: 86d9b64ec88a601f51607f09b4363cfe02388328 https://github.com/galaxyproject/galaxy/commit/86d9b64ec88a601f51607f09b436… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use absolute import for Bunch Commit: ad0459d81840464a03730f1cad90a860416e51c4 https://github.com/galaxyproject/galaxy/commit/ad0459d81840464a03730f1cad90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #5223 from mvdbeek/fix_second_submit_host Allow shell plugins with different parameters to co-exist Compare: https://github.com/galaxyproject/galaxy/compare/0d8520fe2df1...ad0459d81840

1 0

[galaxyproject/galaxy] ab4db8: rewrite Admin/DataTables with Vue
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab4db8925cc895e90972de8b22f1919d25423a12 https://github.com/galaxyproject/galaxy/commit/ab4db8925cc895e90972de8b22f1… Author: Evgeny Anatskiy <evgeny.anatskiy(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 A client/galaxy/scripts/components/admin/base-grid.vue A client/galaxy/scripts/components/admin/data-manager-grid.vue A client/galaxy/scripts/components/admin/data-tables-grid.vue A client/galaxy/scripts/components/admin/data-tables.vue A client/galaxy/scripts/components/message.vue M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- rewrite Admin/DataTables with Vue Commit: 4516958e9d56ae78fbb606dbeb7664f57cf242b6 https://github.com/galaxyproject/galaxy/commit/4516958e9d56ae78fbb606dbeb76… 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 Log Message: ----------- Minor formatting. Commit: 44a1c0bcbcf51dff72d3132f36e2ab106a121ad0 https://github.com/galaxyproject/galaxy/commit/44a1c0bcbcf51dff72d3132f36e2… 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 A client/galaxy/scripts/components/Message.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 R client/galaxy/scripts/components/admin/base-grid.vue R client/galaxy/scripts/components/admin/data-manager-grid.vue R client/galaxy/scripts/components/admin/data-tables-grid.vue R client/galaxy/scripts/components/admin/data-tables.vue R client/galaxy/scripts/components/message.vue Log Message: ----------- Rename new .vue components. Commit: fe8c009f48d9ed39bd8a7af41d26dc61b1219717 https://github.com/galaxyproject/galaxy/commit/fe8c009f48d9ed39bd8a7af41d26… 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 R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue Log Message: ----------- Move UserAPIKeys to components/admin Commit: 0e13c14e9ebca17c385f09df977cb58653be424e https://github.com/galaxyproject/galaxy/commit/0e13c14e9ebca17c385f09df977c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/tours.js 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 client/galaxy/scripts/onload.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js 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 lib/galaxy/webapps/galaxy/controllers/root.py 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/library.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 A static/scripts/libs/bibtex.js M static/scripts/mvc/tours.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 static/scripts/onload.js M templates/webapps/galaxy/workflow/editor.mako A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py 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 admin_data_tables_vue Commit: 203630c509be0eca1fb150bfa680b8c0b152aa11 https://github.com/galaxyproject/galaxy/commit/203630c509be0eca1fb150bfa680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 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/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-canvas.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/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/security/__init__.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/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 M templates/display_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 admin_data_tables_vue Commit: f9d84f876f1c782b0d1580c23aea3b8465ed826c https://github.com/galaxyproject/galaxy/commit/f9d84f876f1c782b0d1580c23aea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 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 Log Message: ----------- Build client. Commit: 0d8520fe2df1c24c625d27ee8308b4daff0565dc https://github.com/galaxyproject/galaxy/commit/0d8520fe2df1c24c625d27ee8308… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.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 lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.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 Log Message: ----------- Merge pull request #5191 from dannon/admin_data_tables_vue Admin data tables vue Compare: https://github.com/galaxyproject/galaxy/compare/9aa596df8b68...0d8520fe2df1

1 0

[galaxyproject/galaxy] 12ce4e: Strip legacy request helpers
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12ce4e7266b2fb5985e8384eda62ff764930e60e https://github.com/galaxyproject/galaxy/commit/12ce4e7266b2fb5985e8384eda62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Strip legacy request helpers Commit: 67cf6944894f71a1408e0b596558039d00306f68 https://github.com/galaxyproject/galaxy/commit/67cf6944894f71a1408e0b596558… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove field value helper Commit: de5d29a6f2e66bf2792c4cde0a7eb2a56e018234 https://github.com/galaxyproject/galaxy/commit/de5d29a6f2e66bf2792c4cde0a7e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: A lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Move grid helper to reports Commit: 7961dcc75ca8f9932b0c1f674347dbaf91190ce6 https://github.com/galaxyproject/galaxy/commit/7961dcc75ca8f9932b0c1f674347… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Strip mako support from galaxy grid helper Commit: f600a1dd99998e9415215a045bafd3a47ffb4975 https://github.com/galaxyproject/galaxy/commit/f600a1dd99998e9415215a045baf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Remove comma from root controller config dict Commit: 24cd0893e5f9ad5aab1befa2aa311ba9b597302a https://github.com/galaxyproject/galaxy/commit/24cd0893e5f9ad5aab1befa2aa31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Link jobs mako to legacy reports module Commit: a8f59df445cbe36f9cdc281f2fe5aa91a809be5c https://github.com/galaxyproject/galaxy/commit/a8f59df445cbe36f9cdc281f2fe5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Same for worflows grid in reports Commit: 47578b641fadee5b9dd2d0e65fe06da1dfb5ccfd https://github.com/galaxyproject/galaxy/commit/47578b641fadee5b9dd2d0e65fe0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Redirect for admin toolshed grids Commit: b726cda3a7abbc49a0532b942fcf6923475d51df https://github.com/galaxyproject/galaxy/commit/b726cda3a7abbc49a0532b942fcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- More redirects for toolshed grids Commit: d4dda34f1214df3389d779e9b835d7557a7499c8 https://github.com/galaxyproject/galaxy/commit/d4dda34f1214df3389d779e9b835… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: R templates/webapps/reports/grid.mako Log Message: ----------- Remove reports default grid mako Commit: d930b114558814945bd0d5f054904318c2f83b35 https://github.com/galaxyproject/galaxy/commit/d930b114558814945bd0d5f05490… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: R templates/grid_base.mako R templates/grid_base_async.mako A templates/webapps/reports/grid_base.mako A templates/webapps/reports/grid_base_asyn.mako Log Message: ----------- Move grid makos from galaxy to reports app Commit: 6c974dd81b0f6fb2dec6c65d1a0c3a98983cda5b https://github.com/galaxyproject/galaxy/commit/6c974dd81b0f6fb2dec6c65d1a0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_asyn.mako A templates/webapps/reports/grid_base_async.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 Log Message: ----------- Redirect makos to new grid helper location in reports Commit: d2752dc7b7977f6d887fe7b7c88f53141a2b46bf https://github.com/galaxyproject/galaxy/commit/d2752dc7b7977f6d887fe7b7c88f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: A lib/galaxy/webapps/reports/framework/__init__.py Log Message: ----------- Add init file to framework module Commit: 96b9b151aea1236cc754bdabc9c1ebe29f23533c https://github.com/galaxyproject/galaxy/commit/96b9b151aea1236cc754bdabc9c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove dict format from legacy grid helper Commit: c9783de884db11c77c05303fbf36591fba84030a https://github.com/galaxyproject/galaxy/commit/c9783de884db11c77c05303fbf36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/config.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py 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 Log Message: ----------- Merge branch 'clear_sample_tracking' into remove_gridhelper Commit: 1c8ed722c221de5baaf437085c0b3e84b1ee5689 https://github.com/galaxyproject/galaxy/commit/1c8ed722c221de5baaf437085c0b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js R static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/grid_base.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Copy legacy grid code to reports app, redirect imports Commit: f01a597480909c53ca3fadd3a1e01922ccf430b3 https://github.com/galaxyproject/galaxy/commit/f01a597480909c53ca3fadd3a1e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py M templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Fix imports to new mako location Commit: cbe7cab090398695431acc3b87b11e2c0e66a36b https://github.com/galaxyproject/galaxy/commit/cbe7cab090398695431acc3b87b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix grids used within Galaxy's admin interface Commit: f2d12a5d699b30532e5a73ea24a0f599ebe42481 https://github.com/galaxyproject/galaxy/commit/f2d12a5d699b30532e5a73ea24a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove async attribute from grid helper Commit: d12e65652e7eb001b9e274de5ccff2665276ec7c https://github.com/galaxyproject/galaxy/commit/d12e65652e7eb001b9e274de5ccf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove async attribute from grids Commit: e32d965034f791756b3107cf6f6055ae0784ffab https://github.com/galaxyproject/galaxy/commit/e32d965034f791756b3107cf6f60… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove async flag handling from grid client Commit: 134b3cc47fd3f1f94fb896f8c7a4d5843d8f2280 https://github.com/galaxyproject/galaxy/commit/134b3cc47fd3f1f94fb896f8c7a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Remove dict format flag from grid client Commit: efbd02743ed3be506c608662ae6e649f1695d675 https://github.com/galaxyproject/galaxy/commit/efbd02743ed3be506c608662ae6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.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/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove dict format from controllers Commit: 7624ce25ed1f224f3df1423fa30f88e02186012c https://github.com/galaxyproject/galaxy/commit/7624ce25ed1f224f3df1423fa30f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/viz/trackster.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js Log Message: ----------- Repack client Commit: 0f7bc19e30d37acb3a2b7da14972ba6c046d4112 https://github.com/galaxyproject/galaxy/commit/0f7bc19e30d37acb3a2b7da14972… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.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/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- Remove unused preserve state attribute from grids Commit: 1bb521b8ed693775e7e52322737f58c1867f9552 https://github.com/galaxyproject/galaxy/commit/1bb521b8ed693775e7e52322737f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A client/galaxy/scripts/reports/grid/grid-model.js A client/galaxy/scripts/reports/grid/grid-template.js A client/galaxy/scripts/reports/grid/grid-view.js A static/scripts/reports/grid/grid-model.js A static/scripts/reports/grid/grid-template.js A static/scripts/reports/grid/grid-view.js Log Message: ----------- Add separated grid client for reports and toolshed Commit: 52ce746b64457d46ea8f6f7c72d90cb9b851243b https://github.com/galaxyproject/galaxy/commit/52ce746b64457d46ea8f6f7c72d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/reports/framework/grids.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Remove unused imports, fix import order Commit: 85fef66272014df1ad944117a017368253253b9f https://github.com/galaxyproject/galaxy/commit/85fef66272014df1ad944117a017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused expose attribute from grid helper Commit: 73749b748276802c66a112cf181723036fcbef0f https://github.com/galaxyproject/galaxy/commit/73749b748276802c66a112cf1817… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove unused pass_through_operations from grid helper Commit: ced73c02e8acdebda9523ef6f3054eeea7845dd0 https://github.com/galaxyproject/galaxy/commit/ced73c02e8acdebda9523ef6f305… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Remove flags from legacy grid helper in reports Commit: b703a4c525911dd9bf98a847b549417a589ad299 https://github.com/galaxyproject/galaxy/commit/b703a4c525911dd9bf98a847b549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: R templates/panels.mako Log Message: ----------- Remove legacy panels mako for grids Commit: 6586ce2b6dcab1ac866062e0e4c486daf489afc6 https://github.com/galaxyproject/galaxy/commit/6586ce2b6dcab1ac866062e0e4c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove legacy comment Commit: 644977c6a538db4829c33a0cd7d0827138a8f8e6 https://github.com/galaxyproject/galaxy/commit/644977c6a538db4829c33a0cd7d0… Author: guerler <aysam.guerler(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-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 M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js 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 branch 'dev' into remove_gridhelper Commit: 5c12a9a9bdbf6da453edf0259dcd1eb3400cbaed https://github.com/galaxyproject/galaxy/commit/5c12a9a9bdbf6da453edf0259dcd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Log Message: ----------- Merge branch 'dev' into remove_gridhelper Commit: 4411189f2589ca366098f93dfc48942b0d2cb7a9 https://github.com/galaxyproject/galaxy/commit/4411189f2589ca366098f93dfc48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Log Message: ----------- Merge branch 'dev' into remove_gridhelper Commit: 364804f40a176ab5bf2350c85a62bcb72a3cdddc https://github.com/galaxyproject/galaxy/commit/364804f40a176ab5bf2350c85a62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/user/user-preferences.js M templates/user/openid_manage.mako Log Message: ----------- Use client side grid builder for openids table Commit: 200d8a229a7f51cb7a1a3fbade94fca0412d492e https://github.com/galaxyproject/galaxy/commit/200d8a229a7f51cb7a1a3fbade94… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add error message if openids are disabled Commit: 241de16c327c6e92d8127382770b8e1d9bdaf715 https://github.com/galaxyproject/galaxy/commit/241de16c327c6e92d8127382770b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add delete operation to new openid controller Commit: f2fd3b1626ee86d228102d9a5368f67b94ae6bbd https://github.com/galaxyproject/galaxy/commit/f2fd3b1626ee86d228102d9a5368… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove previous delete operation caller Commit: 7fd3bfb36566ad5d18814c081b136e0e13d688f9 https://github.com/galaxyproject/galaxy/commit/7fd3bfb36566ad5d18814c081b13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Prepare openid creation form Commit: 8e4ab4012620fc4a28d6baa0eb2ca2bb186ba01b https://github.com/galaxyproject/galaxy/commit/8e4ab4012620fc4a28d6baa0eb2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/openid_manage.mako Log Message: ----------- Remove table view from manage mako Commit: cf7cc197e7fd16bf6fb0619d08b449ca3f051d4c https://github.com/galaxyproject/galaxy/commit/cf7cc197e7fd16bf6fb0619d08b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/openid_manage.mako Log Message: ----------- Use mako to display add account form Commit: e942e4b3e2ccea0505dcfaef6d8a11444238485a https://github.com/galaxyproject/galaxy/commit/e942e4b3e2ccea0505dcfaef6d8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Show openid form in center panel Commit: 87777cf52db6b811a99691a7bd2104decd7eecb5 https://github.com/galaxyproject/galaxy/commit/87777cf52db6b811a99691a7bd21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/index.mako Log Message: ----------- Fix redirects to new client side route Commit: 7bc92610a25db4d1480130a3022905eea8f27234 https://github.com/galaxyproject/galaxy/commit/7bc92610a25db4d1480130a30229… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Fix delete operation, remove unused route to client form Commit: 74d4ea8eef26cb83ede4a3f53be617cc9872b6e1 https://github.com/galaxyproject/galaxy/commit/74d4ea8eef26cb83ede4a3f53be6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/user/openid_manage.mako Log Message: ----------- Remove unused mako properties Commit: 1952e738a703afab2db0cffe615498536f74bb31 https://github.com/galaxyproject/galaxy/commit/1952e738a703afab2db0cffe6154… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/user/user-preferences.js M templates/user/index.mako M templates/user/openid_manage.mako Log Message: ----------- Merge branch 'replace_openid_table' into remove_gridhelper Commit: d0a5a35dfd567ea8ce13fec38d1761fd44cd0ff2 https://github.com/galaxyproject/galaxy/commit/d0a5a35dfd567ea8ce13fec38d17… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Require only regular login to create openids Commit: f239ef45465149964b30438b717cc30e7b2716ca https://github.com/galaxyproject/galaxy/commit/f239ef45465149964b30438b717c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js Log Message: ----------- Move reports app to reports Commit: 52cee726621e0281fde10c9ebb2820e8cc94a083 https://github.com/galaxyproject/galaxy/commit/52cee726621e0281fde10c9ebb28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R client/galaxy/scripts/mvc/grid/grid-model.js R client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/grid/grid-template.js R client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/reports/grid/grid-model.js A client/galaxy/scripts/reports/grid/grid-shared.js A client/galaxy/scripts/reports/grid/grid-template.js A client/galaxy/scripts/reports/grid/grid-view.js Log Message: ----------- Move legacy grid client to reports Commit: 5ed7b143eb457695bf230c5912e48dfabbfa7fb0 https://github.com/galaxyproject/galaxy/commit/5ed7b143eb457695bf230c5912e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/reports/grid/grid-shared.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.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/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 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/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.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 static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/grid/grid-model.js A static/scripts/reports/grid/grid-template.js A static/scripts/reports/grid/grid-view.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 R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako R templates/webapps/reports/grid.mako A templates/webapps/reports/grid_base.mako A templates/webapps/reports/grid_base_async.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 Log Message: ----------- Merge branch 'remove_gridhelper' into remove_gridhelper_001 Commit: 170b2431c9f61ea320a19ed04834e2f836f1c740 https://github.com/galaxyproject/galaxy/commit/170b2431c9f61ea320a19ed04834… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js A client/galaxy/scripts/mvc/grid/grid-template.js A client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Add grid modules Commit: 6e8100f274648cb57fe5f2cda34dd22806b540ac https://github.com/galaxyproject/galaxy/commit/6e8100f274648cb57fe5f2cda34d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: A static/scripts/reports/grid/grid-shared.js Log Message: ----------- Pack client Commit: c19ef1aacea869b33651fa3352970531150b0e07 https://github.com/galaxyproject/galaxy/commit/c19ef1aacea869b33651fa335297… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R client/galaxy/scripts/reports/grid/grid-shared.js R static/scripts/reports/grid/grid-shared.js Log Message: ----------- Remove shared grid view Commit: cbc4e55fda91dde884c9be474d7a95c62ccd98c7 https://github.com/galaxyproject/galaxy/commit/cbc4e55fda91dde884c9be474d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Client format. Commit: 85ba7c56e8ff0f2f6797a0e2b25f577ff7ee0071 https://github.com/galaxyproject/galaxy/commit/85ba7c56e8ff0f2f6797a0e2b25f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: 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 R client/galaxy/scripts/reports/grid/grid-model.js R client/galaxy/scripts/reports/grid/grid-template.js R client/galaxy/scripts/reports/grid/grid-view.js Log Message: ----------- Relocate to legacy* templates to be very clear on the status of this code. Commit: 8ecb6ecdfb6c7943b627bc63299d606fefe21c49 https://github.com/galaxyproject/galaxy/commit/8ecb6ecdfb6c7943b627bc63299d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-view.js Log Message: ----------- Correct legacy grid* to point to the correct copied code (this was broken before the shift to legacy -- instead pointing back to the mvc version instead of the reports version Commit: 8db84bea66615687d1ffba2f6b0af1fd770883b5 https://github.com/galaxyproject/galaxy/commit/8db84bea66615687d1ffba2f6b0a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/webapps/reports/framework/grids.py A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/repository_review/grid.mako Log Message: ----------- Move templates (commonly used legacy grid code) from reports to legacy Commit: 28653132bec89eab6bd3cdebebb334bd3fcb1345 https://github.com/galaxyproject/galaxy/commit/28653132bec89eab6bd3cdebebb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 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/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.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/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.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/handler.py M lib/galaxy/jobs/runners/chronos.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/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/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/controllers/admin.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/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/tool_dependencies/recipe/step_handler.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/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/libs.bundled.js R static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-base.js M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into remove_gridhelper_001 Commit: bb6e58b40dbc64b77dcf31291c28d1af7138e42a https://github.com/galaxyproject/galaxy/commit/bb6e58b40dbc64b77dcf31291c28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-template.js Log Message: ----------- Formatting in grid-template Commit: 985c65e677eb1dee5190685e85a429c8d1eab842 https://github.com/galaxyproject/galaxy/commit/985c65e677eb1dee5190685e85a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/legacy/grid/grid-model.js M client/galaxy/scripts/legacy/grid/grid-template.js Log Message: ----------- Remove a little cruft in now-legacy grids. Commit: e08a2839867b5214e830fe6a3df84dddca66521f https://github.com/galaxyproject/galaxy/commit/e08a2839867b5214e830fe6a3df8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Remove the same cruft from the mvc/grid/grid-template. Commit: b832fec9e71694caf233627dd09c2f8921841534 https://github.com/galaxyproject/galaxy/commit/b832fec9e71694caf233627dd09c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M static/scripts/bundled/libs.bundled.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 M static/scripts/mvc/grid/grid-template.js R static/scripts/reports/grid/grid-model.js R static/scripts/reports/grid/grid-template.js R static/scripts/reports/grid/grid-view.js A static/scripts/reports/run_stats.js Log Message: ----------- Build client Commit: 609020da0fa8b2d3171e157bf609b30dd4b54067 https://github.com/galaxyproject/galaxy/commit/609020da0fa8b2d3171e157bf609… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-14 (Thu, 14 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/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-template.js M client/galaxy/scripts/mvc/history/hdca-li.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/workflow/workflow-canvas.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 R client/galaxy/scripts/reports/grid/grid-model.js R client/galaxy/scripts/reports/grid/grid-template.js R client/galaxy/scripts/reports/grid/grid-view.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.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/handler.py M lib/galaxy/jobs/runners/chronos.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/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/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/controllers/admin.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/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M 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/tool_dependencies/recipe/step_handler.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/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/libs.bundled.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-template.js M static/scripts/mvc/tool/tool-form-base.js R static/scripts/reports/grid/grid-model.js R static/scripts/reports/grid/grid-template.js R static/scripts/reports/grid/grid-view.js A static/scripts/reports/run_stats.js A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/webapps/reports/grid_base.mako R templates/webapps/reports/grid_base_async.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/repository_review/grid.mako M test/selenium_tests/test_tool_form.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #23 from dannon/remove_gridhelper_001 Some fixes and cleanup, makes the merge clean. Commit: 9aa596df8b6853bcf63635fdbd38790f634a0888 https://github.com/galaxyproject/galaxy/commit/9aa596df8b6853bcf63635fdbd38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.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/history-list.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.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 lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.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/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 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/controllers/repository.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.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 static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.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 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/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 Log Message: ----------- Merge pull request #5212 from guerler/remove_gridhelper_001 Remove html producing grid helpers Compare: https://github.com/galaxyproject/galaxy/compare/b96c428cde5e...9aa596df8b68

1 0

[galaxyproject/galaxy] 504343: Selenium - little pause to let extension form in u...
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5043439df2ca694254623887d351905be1d9b698 https://github.com/galaxyproject/galaxy/commit/5043439df2ca694254623887d351… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - little pause to let extension form in upload dialog render. xref https://github.com/galaxyproject/galaxy/issues/5169 Commit: 6fd6595238b5189e89f54ad01079b4d34fbcfea7 https://github.com/galaxyproject/galaxy/commit/6fd6595238b5189e89f54ad01079… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Another try to fix flakey tool form Selenium test. Commit: b96c428cde5e9786376d0ecd5eba5f5233b6fec2 https://github.com/galaxyproject/galaxy/commit/b96c428cde5e9786376d0ecd5eba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #5211 from jmchilton/selenium_test_fixes Mark transiently failing test_run_data as flakey. Compare: https://github.com/galaxyproject/galaxy/compare/3b7f40198e96...b96c428cde5e

1 0

[galaxyproject/galaxy] 14259b: Python3: finish first pass on whole codebase
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14259b11d9a5f6238153556ed5a28bf89468e2b4 https://github.com/galaxyproject/galaxy/commit/14259b11d9a5f6238153556ed5a2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.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/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.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/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/controllers/admin.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/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.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 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 tools/genomespace/genomespace_importer.py Log Message: ----------- Python3: finish first pass on whole codebase Commit: 820d1e259c625f2472f79ee46654bbf91b19dea4 https://github.com/galaxyproject/galaxy/commit/820d1e259c625f2472f79ee46654… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Mercurial does not support Python3 yet Commit: 3b7f40198e968d7c2bbda533551686688cfd8f48 https://github.com/galaxyproject/galaxy/commit/3b7f40198e968d7c2bbda5335516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.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/handler.py M lib/galaxy/jobs/runners/chronos.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/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.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/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/controllers/admin.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/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.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 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 tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #5215 from nsoranzo/python3 Python3: finish first pass on whole codebase Compare: https://github.com/galaxyproject/galaxy/compare/fd4f0e6aa6f7...3b7f40198e96

1 0

[galaxyproject/galaxy] dda410: #3002 update to newer version of virtualenv.
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dda410da63ef26c7d86a40bd764adadb19cbbcd5 https://github.com/galaxyproject/galaxy/commit/dda410da63ef26c7d86a40bd764a… Author: Peter Selten <peter.selten98(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- #3002 update to newer version of virtualenv. Commit: fd4f0e6aa6f7178639c3af556da86a0805460808 https://github.com/galaxyproject/galaxy/commit/fd4f0e6aa6f7178639c3af556da8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #5202 from selten/dev #3002 update to newer version of virtualenv. Compare: https://github.com/galaxyproject/galaxy/compare/7b04c834e0ff...fd4f0e6aa6f7

1 0

[galaxyproject/galaxy] 6eaa73: Swap to vue via node_module; no staging.
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6eaa73e37ee5f795d8b96c9abe274403dfa62753 https://github.com/galaxyproject/galaxy/commit/6eaa73e37ee5f795d8b96c9abe27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/gulpfile.js M client/webpack.config.js R static/scripts/libs/vue.js Log Message: ----------- Swap to vue via node_module; no staging. Commit: 1a6065b0c3ee7178acbf96028672a33ee32bb195 https://github.com/galaxyproject/galaxy/commit/1a6065b0c3ee7178acbf96028672… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: R static/scripts/libs/bibtex.js Log Message: ----------- Remove old bibtex.js cruft. Commit: 662f35df490c66c2d9443f9815820c2041ee7fdd https://github.com/galaxyproject/galaxy/commit/662f35df490c66c2d9443f981582… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade vue. Commit: 2ca7b90262a6ef5e833df0c65da4c3a5a45a6d9b https://github.com/galaxyproject/galaxy/commit/2ca7b90262a6ef5e833df0c65da4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade webpack to 3.10 Commit: 0a92f5b80bea2b593a9d37ab9d606e5ac97c2e71 https://github.com/galaxyproject/galaxy/commit/0a92f5b80bea2b593a9d37ab9d60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Update vue-template-compiler Commit: 8cd62168d8eda3e5480ffcfb25e87c62b44163c6 https://github.com/galaxyproject/galaxy/commit/8cd62168d8eda3e5480ffcfb25e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade minor devDependencies. Commit: 4dbe7c420e6f6c1515183bf44838a4f2ed3fa453 https://github.com/galaxyproject/galaxy/commit/4dbe7c420e6f6c1515183bf44838… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade prettier 1.7->1.9 Commit: a363d81b7314bd41fba5ea15b2ff432a9bc83dad https://github.com/galaxyproject/galaxy/commit/a363d81b7314bd41fba5ea15b2ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.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.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-view.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Rerun new version of prettier. Commit: c09643d57bac206bc101434f4623c0d63d75ca16 https://github.com/galaxyproject/galaxy/commit/c09643d57bac206bc101434f4623… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Build client. Commit: 7b04c834e0ff03eddedd81303ea0242d0e44fbc6 https://github.com/galaxyproject/galaxy/commit/7b04c834e0ff03eddedd81303ea0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hdca-li.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/workflow/workflow-canvas.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 M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5190 from dannon/vue_dep_tweaks Client dependency upgrades, changes. Compare: https://github.com/galaxyproject/galaxy/compare/fce9f13eba7f...7b04c834e0ff

1 0