- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 41a56e: Fix list collection creator being cutoff by restor...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator being cutoff by restoring height: 100% Commit: 94b049926d844a8aa54017b6d7a9983b94203316 https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% Compare: https://github.com/galaxyproject/galaxy/compare/7d4eac1535fc...94b049926d84

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[galaxyproject/usegalaxy-playbook] 082bb6: update Main
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 082bb67d5aa95a845016ffbc76c6f8c17e9f3e34 https://github.com/galaxyproject/usegalaxy-playbook/commit/082bb67d5aa95a84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- update Main

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[galaxyproject/galaxy] f08d51: Use fixed path to sync like in dev.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534 https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. Commit: e186b6a0cfeada4d7852d4661530dec30f73685f https://github.com/galaxyproject/galaxy/commit/e186b6a0cfeada4d7852d4661530… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. Commit: 7d4eac1535fcdc46bea5e407ca74902128dbee18 https://github.com/galaxyproject/galaxy/commit/7d4eac1535fcdc46bea5e407ca74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Commit: bcf8ddfbd0a966fd3d6fad157f8ca87702e9c61a https://github.com/galaxyproject/galaxy/commit/bcf8ddfbd0a966fd3d6fad157f8c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/galaxy/jobs/runners/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/01a919ce6a7c...bcf8ddfbd0a9

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[galaxyproject/galaxy] f08d51: Use fixed path to sync like in dev.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534 https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8 https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Add the missing "amqp_ack_republish_time" param for the Pulsar runner (it's available in the Pulsar client lib). Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603 https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #1234 from natefoo/pulsar-missing-param [15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. Commit: e186b6a0cfeada4d7852d4661530dec30f73685f https://github.com/galaxyproject/galaxy/commit/e186b6a0cfeada4d7852d4661530… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. Commit: 7d4eac1535fcdc46bea5e407ca74902128dbee18 https://github.com/galaxyproject/galaxy/commit/7d4eac1535fcdc46bea5e407ca74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Compare: https://github.com/galaxyproject/galaxy/compare/516b079ab97d...7d4eac1535fc

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[galaxyproject/galaxy] 732b57: Do not mess with galaxy_config_file, if provided.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 732b5722ae7c668634185209171fa55288e19985 https://github.com/galaxyproject/galaxy/commit/732b5722ae7c668634185209171f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Do not mess with galaxy_config_file, if provided. Commit: 01a919ce6a7cc29556e257fd0af46f5071310748 https://github.com/galaxyproject/galaxy/commit/01a919ce6a7cc29556e257fd0af4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1253 from nsoranzo/dev_verify_tools Tool migration: do not mess with galaxy_config_file, if provided. Compare: https://github.com/galaxyproject/galaxy/compare/371125bc870a...01a919ce6a7c

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[galaxyproject/galaxy] 71b27b: Select2 for sharing
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71b27b0f018c6bc3997099137ff2c80ca088981d https://github.com/galaxyproject/galaxy/commit/71b27b0f018c6bc3997099137ff2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Select2 for sharing This adjusts the default 'share' template to use the select2/exposed user list implemented in 60ad9e934b3e4c50389a624a28578aa9fc326f32. As previously, if the email list is not exposed then you may still enter an email address manually. If usernames are exposed but not emails (e.g. public galaxies) we currently just hide those results even if searches match. Fixes #977 Commit: 86bb4aeaca80b9fbf98ef89f92c1ce2a5bfc6208 https://github.com/galaxyproject/galaxy/commit/86bb4aeaca80b9fbf98ef89f92c1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Patch other share implementation to handle case of undefined emails more gracefully Commit: 944df4a5647a71304bab12185b708b4bb28da049 https://github.com/galaxyproject/galaxy/commit/944df4a5647a71304bab12185b70… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Followup to #1109, #1110, add f_any to user API Commit: 9516b7179d541953ebaea4061300440d02f11bb7 https://github.com/galaxyproject/galaxy/commit/9516b7179d541953ebaea4061300… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Documented API call Commit: 371125bc870a29371fba8656d3c93538a50a63ab https://github.com/galaxyproject/galaxy/commit/371125bc870a29371fba8656d3c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #1111 from erasche/user-search-name Add search on username/any for API calls to user, use Select2 for sharing workflows/pages/histories Compare: https://github.com/galaxyproject/galaxy/compare/3a023f4cae6b...371125bc870a

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[galaxyproject/galaxy] d0a011: Enable lookup of tools from other tool sheds.
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0a011675323ba7e8deba588ae0ae6ed9c23f0fe https://github.com/galaxyproject/galaxy/commit/d0a011675323ba7e8deba588ae0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Enable lookup of tools from other tool sheds. Commit: c040a18b4b164e58a45d1c4f6da65f1eacf18ed5 https://github.com/galaxyproject/galaxy/commit/c040a18b4b164e58a45d1c4f6da6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Modify get_tool() directly instead of using decorator. Commit: 2d168a2c07798ab736676a1eb865ae6976b48464 https://github.com/galaxyproject/galaxy/commit/2d168a2c07798ab736676a1eb865… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove whitespaces in blank line. Commit: 1be4f85404c75be364cb20b3c460ea3f51c4dae2 https://github.com/galaxyproject/galaxy/commit/1be4f85404c75be364cb20b3c460… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Add messages inform users of changes in the tool_id. 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static/maps/galaxy.base.js.map R static/maps/galaxy.frame.js.map A static/maps/galaxy.js.map M static/maps/galaxy.library.js.map R static/maps/galaxy.masthead.js.map R static/maps/galaxy.menu.js.map M static/maps/galaxy.pages.js.map R static/maps/galaxy.panels.js.map R static/maps/galaxy.tools.js.map R static/maps/galaxy.ui.scrollPanel.js.map R static/maps/galaxy.workflows.js.map A static/maps/layout/masthead.js.map A static/maps/layout/menu.js.map A static/maps/layout/modal.js.map A static/maps/layout/page.js.map A static/maps/layout/panel.js.map A static/maps/layout/scratchbook.js.map R static/maps/libs/IE/IE7.js.map R static/maps/libs/IE/IE8.js.map R static/maps/libs/IE/excanvas.js.map R static/maps/libs/IE/ie7-recalc.js.map A static/maps/libs/backbone.js.map A static/maps/libs/common-libs.js.map A static/maps/mvc/annotation.js.map R static/maps/mvc/annotations.js.map R static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/app/app-login.js.map R 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R static/maps/mvc/history/history-panel-annotated.js.map R static/maps/mvc/history/history-panel-edit-current.js.map R static/maps/mvc/history/history-panel-edit.js.map R static/maps/mvc/history/history-panel.js.map A static/maps/mvc/history/history-view-annotated.js.map A static/maps/mvc/history/history-view-edit-current.js.map A static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map A static/maps/mvc/list/list-view.js.map A static/maps/mvc/tag.js.map R static/maps/mvc/tags.js.map A static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tool/tools-form-workflow.js.map A static/maps/mvc/tool/tools-form.js.map A static/maps/mvc/tool/tools-jobs.js.map A static/maps/mvc/tool/tools-template.js.map A static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map A static/maps/onload.js.map A static/maps/polyfills.js.map R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.js.map A static/maps/ui/autocom_tagging.js.map A static/maps/ui/editable-text.js.map A static/maps/ui/popupmenu.js.map A static/maps/ui/scroll-panel.js.map A static/maps/utils/async-save-text.js.map M static/maps/utils/localization.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map R static/scripts/base.js A static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map R static/scripts/galaxy-app-base.js R static/scripts/galaxy.autocom_tagging.js R static/scripts/galaxy.base.js R static/scripts/galaxy.frame.js A static/scripts/galaxy.js M static/scripts/galaxy.library.js R static/scripts/galaxy.masthead.js R static/scripts/galaxy.menu.js M static/scripts/galaxy.pages.js R static/scripts/galaxy.panels.js R static/scripts/galaxy.tools.js R static/scripts/galaxy.ui.scrollPanel.js R static/scripts/galaxy.workflows.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/modal.js A static/scripts/layout/page.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js R static/scripts/libs/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js A static/scripts/libs/backbone.js A static/scripts/libs/common-libs.js A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.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/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into cross_toolshed_tool_fetching Commit: 77f034019b93bdd539a495a89318bcb1e51b3993 https://github.com/galaxyproject/galaxy/commit/77f034019b93bdd539a495a89318… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing api test Commit: 3a023f4cae6b9b6b25c1d389b9ba2ad7223cb24a https://github.com/galaxyproject/galaxy/commit/3a023f4cae6b9b6b25c1d389b9ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #818 from mvdbeek/cross_toolshed_tool_fetching Look up installed tools from different toolshed(s) Compare: https://github.com/galaxyproject/galaxy/compare/4fe36f8d6a15...3a023f4cae6b

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[galaxyproject/galaxy] 563e36: Tool optimization - don't set state to queued twic...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 563e363478258cb1d08802e16586c42efe511e6a https://github.com/galaxyproject/galaxy/commit/563e363478258cb1d08802e16586… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - don't set state to queued twice. Just keep the dataset in the correct NEW state until it has actually been queued. Addresses FIXME comment added by James 7 years ago in https://github.com/galaxyproject/galaxy/commit/4c3db1af95fb0520960046ae5494…. This behavior feels correct to me, but it does have ramifications in the GUI. I had previously never actually seen a dataset in the "NEW" state. Saves an extra flush per dataset, on sqlite this translates to 50ms per dataset for me. Commit: 0ac7c33522cfeb51b89ec8d14fbb2d716f956450 https://github.com/galaxyproject/galaxy/commit/0ac7c33522cfeb51b89ec8d14fbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization and comment improvement. Commit: 2b8a1423f7e9ae6bdf09571b8992493dc30e035c https://github.com/galaxyproject/galaxy/commit/2b8a1423f7e9ae6bdf09571b8992… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - remove another seemingly needless flush. Saves around a teenth of a second per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 13:00:56,984 Tool [cat1] created job [24] (435.468 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:17,296 Tool [cat1] created job [25] (341.687 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:32,896 Tool [cat1] created job [26] (354.138 ms) After - - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) Commit: 81799bd3a72b3e704be6c12e89b85eb5bd077428 https://github.com/galaxyproject/galaxy/commit/81799bd3a72b3e704be6c12e89b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Micro-optimizations for adding many datasets to history... ... during tool execution. Build method once instead of in each function call, use imap instead of map since we don't need a list, remove some duplicated checks. Frankly this is all stuff Python is probably doing anyway - but in case it doesn't and just so the eye doesn't jump to these optimizations again. Timings before and after for a section of tool action execute that includes this additon show that this might have a small effect. Before: - galaxy.tools.actions INFO 2015-12-01 13:11:39,446 Add outputs to history (127.379 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:06,598 Add outputs to history (137.029 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:23,931 Add outputs to history (118.489 ms) After: - galaxy.tools.actions INFO 2015-12-01 13:13:09,999 Add outputs to history (99.456 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:38,573 Add outputs to history (126.131 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:54,538 Add outputs to history (137.643 ms) - galaxy.tools.actions INFO 2015-12-01 13:14:12,516 Add outputs to history (101.451 ms) Commit: bd6a34e279f8d612185fe9d8aa27084efe246e2d https://github.com/galaxyproject/galaxy/commit/bd6a34e279f8d612185fe9d8aa27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization comments for future reference. Including replacing a log statement with a comment. Commit: 59c3acfbf56e14c8f691946932be71b81774de0e https://github.com/galaxyproject/galaxy/commit/59c3acfbf56e14c8f691946932be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool execution optimization - remove another unneeded flush. Flush the job and its output datasets all at the same time in one transaction. Inuitively it makes sense that this should work and the timings seem to improve, triming another quater or third of the submission time per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) After: - galaxy.tools.execute DEBUG 2015-12-01 13:22:00,649 Tool [cat1] created job [39] (265.547 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:27,720 Tool [cat1] created job [40] (214.905 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:21:40,225 Tool [cat1] created job [38] (198.936 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:44,076 Tool [cat1] created job [41] (213.096 ms) Commit: 3bf466c8f5d554f583dfc2fe8f7b95397278b2d9 https://github.com/galaxyproject/galaxy/commit/3bf466c8f5d554f583dfc2fe8f7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Micro optimization in tool execute - eliminate repeated trans.app fetch. Commit: e72604be7c0c0a88c6267140b6433fcde88f1d01 https://github.com/galaxyproject/galaxy/commit/e72604be7c0c0a88c6267140b643… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Instrument upload action for timing. - Checked and cleanup datasets ~500ms - Create job ~200ms - Persisting ~20 ms Commit: 2c6819cd87520fb43f4ebea96eea5fb151787edb https://github.com/galaxyproject/galaxy/commit/2c6819cd87520fb43f4ebea96eea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - eliminate repeated role generation. For cat1 with 5 inputs - this shaves about 100 ms off of job execution time. Before: galaxy.tools.execute DEBUG 2015-12-01 15:08:56,745 Tool [cat1] created job [171] (545.776 ms) galaxy.tools.execute DEBUG 2015-12-01 15:08:31,871 Tool [cat1] created job [170] (478.813 ms) After : galaxy.tools.execute DEBUG 2015-12-01 15:07:11,401 Tool [cat1] created job [168] (371.722 ms) galaxy.tools.execute DEBUG 2015-12-01 15:07:42,060 Tool [cat1] created job [169] (333.296 ms) Commit: 836b0dfc1504357b738375b109b22243dd58efe7 https://github.com/galaxyproject/galaxy/commit/836b0dfc1504357b738375b109b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix location of timer generation for fairer comparison in next commit. Commit: c14c45be46a4a3b08b3cb0b5132cbbdf151d5100 https://github.com/galaxyproject/galaxy/commit/c14c45be46a4a3b08b3cb0b5132c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Further cache user roles across batched tool executions. Commit: 53354c7e361cc769f42c7eae42de0eca1769e9a4 https://github.com/galaxyproject/galaxy/commit/53354c7e361cc769f42c7eae42de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix collection output for less flushing in tool action handle_output. Commit: 4fe36f8d6a151536267e3aeace2414cc148e18e8 https://github.com/galaxyproject/galaxy/commit/4fe36f8d6a151536267e3aeace24… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #1199 from jmchilton/tool_opts_4 Yet More Tool Execution Optimizations Compare: https://github.com/galaxyproject/galaxy/compare/beb4a67fb0a4...4fe36f8d6a15

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[galaxyproject/galaxy] b55635: Client, upload: fix passing of nginx_upload_path a...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b55635f71b7fd3bba8393a3c267408d6dd248f99 https://github.com/galaxyproject/galaxy/commit/b55635f71b7fd3bba8393a3c2674… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Client, upload: fix passing of nginx_upload_path and ftp_upload_site to upload-view, fix default nginx_upload_path in configuration serializer Commit: beb4a67fb0a4b879b732fd05b35d03019481ea90 https://github.com/galaxyproject/galaxy/commit/beb4a67fb0a4b879b732fd05b35d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1250 from carlfeberhard/fix.upload Client, upload: fix passing of nginx_upload_path and ftp_upload_site … Compare: https://github.com/galaxyproject/galaxy/compare/91d348a73fd4...beb4a67fb0a4

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[galaxyproject/galaxy] 1fdde2: Refactor generic side workflow editor panel toward...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fdde2cb4d3d685916dc82a8fc846079a8066cd5 https://github.com/galaxyproject/galaxy/commit/1fdde2cb4d3d685916dc82a8fc84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Refactor generic side workflow editor panel toward backbone. Commit: 91d348a73fd49453c9cde5fb6116c3b230a2f162 https://github.com/galaxyproject/galaxy/commit/91d348a73fd49453c9cde5fb6116… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1247 from jmchilton/editor_refactor Refactor generic side workflow editor panel toward backbone. Compare: https://github.com/galaxyproject/galaxy/compare/e12179b0160d...91d348a73fd4

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[galaxyproject/galaxy] 4fdea5: Enhance the VTK datatypes to support cell data in ...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fdea55f81756a27bff8ef66b3fe27d4bda36905 https://github.com/galaxyproject/galaxy/commit/4fdea55f81756a27bff8ef66b3fe… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Enhance the VTK datatypes to support cell data in addition to point data. Replaces https://github.com/galaxyproject/galaxy/pull/1189. Commit: 9b085740dfddfcb67f6a2e21a51503cd2ac0741e https://github.com/galaxyproject/galaxy/commit/9b085740dfddfcb67f6a2e21a515… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: d2ce6d4d2b03fc7ad0a40ac4b0194f8636350f52 https://github.com/galaxyproject/galaxy/commit/d2ce6d4d2b03fc7ad0a40ac4b019… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 3069e12ca741245563b9e372bf581747861fce6e https://github.com/galaxyproject/galaxy/commit/3069e12ca741245563b9e372bf58… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A 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static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.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/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_tools.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: e12179b0160d242be870b15b8da5a46e294063bf https://github.com/galaxyproject/galaxy/commit/e12179b0160d242be870b15b8da5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Merge pull request #1211 from gregvonkuster/dev Enhance the VTK datatypes to support cell data in addition to point Compare: https://github.com/galaxyproject/galaxy/compare/fef8ce2a762b...e12179b0160d

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[galaxyproject/galaxy] cae457: Fail maxseconds test tool if sleep is interrupted.
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cae457d8c18ded2abf03a0a6c3fb027735e1b5ef https://github.com/galaxyproject/galaxy/commit/cae457d8c18ded2abf03a0a6c3fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: fef8ce2a762b82480d5f7304c345cc3168e10036 https://github.com/galaxyproject/galaxy/commit/fef8ce2a762b82480d5f7304c345… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Merge pull request #1248 from jmchilton/maxseconds_debug_2 Attempt to fix transiently failing tool test on Jenkins Compare: https://github.com/galaxyproject/galaxy/compare/df6470654411...fef8ce2a762b

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[galaxyproject/galaxy] df781d: Fix missing assertion pointed out @nsoranzo.
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df781dcc188193ff044a625540dc02961a8c5640 https://github.com/galaxyproject/galaxy/commit/df781dcc188193ff044a625540dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: df6470654411bfa8ce997f932e92b4c2d644c685 https://github.com/galaxyproject/galaxy/commit/df6470654411bfa8ce997f932e92… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Merge pull request #1237 from jmchilton/test_jobs_fix Fix missing assertion pointed out @nsoranzo. Compare: https://github.com/galaxyproject/galaxy/compare/4d252119fd00...df6470654411

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[galaxyproject/galaxy] e186b6: Fix for getting shed_config_dict when an old/inval...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: e186b6a0cfeada4d7852d4661530dec30f73685f https://github.com/galaxyproject/galaxy/commit/e186b6a0cfeada4d7852d4661530… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. Commit: 7d4eac1535fcdc46bea5e407ca74902128dbee18 https://github.com/galaxyproject/galaxy/commit/7d4eac1535fcdc46bea5e407ca74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Compare: https://github.com/galaxyproject/galaxy/compare/f34d70101910...7d4eac1535fc

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[galaxyproject/galaxy] 599440: Fix for workflow progress unit testing.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59944046b7f16d13886928eb6928a7d67446c1e6 https://github.com/galaxyproject/galaxy/commit/59944046b7f16d13886928eb6928… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Fix for workflow progress unit testing. Commit: bed421fbc98583fdc00db57d3bb787450766576b https://github.com/galaxyproject/galaxy/commit/bed421fbc98583fdc00db57d3bb7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Introduce model abstractions for dealing with workflow steps. Three methods to provide higher-level access and reasoning about steps than just a flat array. Commit: da6051922e51ecc43c2f5b973adf5ba2dbf7554b https://github.com/galaxyproject/galaxy/commit/da6051922e51ecc43c2f5b973adf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Unroll input connection logic. Need to extend it downstream and the one-liner is fun but not easy to extend or particularily readable. Commit: d97d8a203c7c09123f7298627ad394d6c96e5b1c https://github.com/galaxyproject/galaxy/commit/d97d8a203c7c09123f7298627ad3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Better error messages in workflow running code. Commit: 296971c5ded17367d2a14a32a072678b727ddf05 https://github.com/galaxyproject/galaxy/commit/296971c5ded17367d2a14a32a072… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: 93bfa1992cc23a411e46437547581843c0e7b952 https://github.com/galaxyproject/galaxy/commit/93bfa1992cc23a411e4643754758… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Make more workflow methods properties. As suggested by @nsoranzo. Commit: 4d252119fd0057b9b9433a4d874784c86f96d42e https://github.com/galaxyproject/galaxy/commit/4d252119fd0057b9b9433a4d8747… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #1216 from jmchilton/workflow_tweaks_1 More small workflow tweaks. Compare: https://github.com/galaxyproject/galaxy/compare/6126bd0e93e1...4d252119fd00

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[galaxyproject/galaxy] 4a279f: Allow inputs section for Format 2 workflow definit...
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a279ffb64576258f2f2755f182430e1ccbacbc2 https://github.com/galaxyproject/galaxy/commit/4a279ffb64576258f2f2755f1824… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Allow inputs section for Format 2 workflow definitions. Arguably a more natural way to define inputs, regardless it allows more CWL-like input definitions for workflows. Commit: b0b26e69019162e335ea5a331ab21009c882f0d1 https://github.com/galaxyproject/galaxy/commit/b0b26e69019162e335ea5a331ab2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py Log Message: ----------- Allow specifying Format 2 workflow by path. This will allow importing workflow relative resources in subsequent passes at this. Commit: 70a9f213932947758f9882776140727eb6c0e246 https://github.com/galaxyproject/galaxy/commit/70a9f213932947758f9882776140… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py Log Message: ----------- Update workflow format 2 code with infrastructure for nesting runnables. In downstream work this is used for subworkflows and nested tools. Not sure which of these would potentially hit main line Galaxy first so setting this all up in its own commit. Commit: 1bd0a4e9703406223f0e9bfe31df4c801998f400 https://github.com/galaxyproject/galaxy/commit/1bd0a4e9703406223f0e9bfe31df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Refactoring and more testing of format 2 workflow implementation code... ... toward more reusable design. Commit: a597e0e8349f33d4d2c642d2e0a74e3da64b156b https://github.com/galaxyproject/galaxy/commit/a597e0e8349f33d4d2c642d2e0a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Implement workflow outputs for format 2 workflow definitions. Copy CWL style of specifying a outputs specification block at the top-level of the workflow specification and within that use the "source" attribute to specify the output. Reuse the specification used by "$link"s to describe this output - namely <label_or_order_index>[#<output_name=output>]. Commit: 3d0723c812632a276102748ec6a754bbec0b9d9a https://github.com/galaxyproject/galaxy/commit/3d0723c812632a276102748ec6a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- JS Model abstractions for dealing workflow outputs. Need to modify how these are represented so I want the logic centralized in the model... also the logic should be centralized in the model. Commit: 7b3fa824b67c0c7f881a514ae5b6598ede62e14c https://github.com/galaxyproject/galaxy/commit/7b3fa824b67c0c7f881a514ae5b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Update worklfow editor representation of workflow outputs. Modified this for the workflow export representation but this needed to be updated for the workflow editor because they shared some code in the manager. This was going to be needed downstream when I add labels and uuids to workflow outputs anyway. Commit: cee9d4d1b30633689d8dd5fde715aed528e578a1 https://github.com/galaxyproject/galaxy/commit/cee9d4d1b30633689d8dd5fde715… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Grunt the workflow JS. Commit: 40e6932a25f71c240e038e4e6dc9be6a19ff8459 https://github.com/galaxyproject/galaxy/commit/40e6932a25f71c240e038e4e6dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Fix workflow API tests for workflow output changes. Commit: 6126bd0e93e17c2d9cd6512ec068f806cc9da72d https://github.com/galaxyproject/galaxy/commit/6126bd0e93e17c2d9cd6512ec068… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1214 from jmchilton/format_2_1 Small enhancements in workflow inputs and outputs Compare: https://github.com/galaxyproject/galaxy/compare/d7f5dbe4ca1b...6126bd0e93e1

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[galaxyproject/galaxy] e9e73f: Remove dated comment.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9e73f4828f7926a1a36654ed48325828992bed3 https://github.com/galaxyproject/galaxy/commit/e9e73f4828f7926a1a36654ed483… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js Log Message: ----------- Remove dated comment. Commit: c91a2eb33947a64ed8c03115d1de9ccf746cc195 https://github.com/galaxyproject/galaxy/commit/c91a2eb33947a64ed8c03115d1de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Multi data parameter improvements. Allow multiple collections to be fed to a multi data parameter in one reduction step. Fixes #750 and will really simplify certain classes of tools. Rebased original with fixes for rerun of such reductions. Manually tested workflow execution and everything seems fine. The workflow editor already thought this was possible, so that is another bug corrected by this enhancement. To run the associated API test, execute the following command: ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_reduce_multiple_lists_on_multi_data Conflicts: static/maps/mvc/dataset/dataset-choice.js.map static/maps/mvc/form/form-select-content.js.map static/scripts/mvc/form/form-select-content.js Commit: 62a26516cd7a3a6d1ad6441dc8d63efafa25d8d0 https://github.com/galaxyproject/galaxy/commit/62a26516cd7a3a6d1ad6441dc8d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix PR #805 for changes in PR #1153. Commit: 17851ba0ea9572f1c387ff1fea1012b7af737855 https://github.com/galaxyproject/galaxy/commit/17851ba0ea9572f1c387ff1fea10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- And fix unit test for b036adcaa166153e544935c12123877c69a7450f. Commit: d7f5dbe4ca1bc0943e3d3edbddd88d1c226ff5e5 https://github.com/galaxyproject/galaxy/commit/d7f5dbe4ca1bc0943e3d3edbddd8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #805 from jmchilton/multi_data_param_enhance Allow multiple collections to be supplied to a multiple data parameter. Compare: https://github.com/galaxyproject/galaxy/compare/b0c1cd7460f1...d7f5dbe4ca1b

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[galaxyproject/galaxy] bab7ae: Improved logging related tool test timeouts.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bab7ae099845f4503a2e41c939abc2aca9dc7a66 https://github.com/galaxyproject/galaxy/commit/bab7ae099845f4503a2e41c939ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Improved logging related tool test timeouts. There are transient failures of maxseconds.xml's tool test on Jenkins that I can't reproduce locally, hopefully improved logging will help. https://jenkins.galaxyproject.org/job/docker-framework/1309/testReport/juni… Commit: b0c1cd7460f13075c565750298f9d4c3cb89bb80 https://github.com/galaxyproject/galaxy/commit/b0c1cd7460f13075c565750298f9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Merge pull request #1243 from jmchilton/maxseconds_debug Improved logging related tool test timeouts. Compare: https://github.com/galaxyproject/galaxy/compare/f7a2acdcabdf...b0c1cd7460f1

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[galaxyproject/galaxy] 092489: Fix up merge issue with double underscore shim.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0924891e31f3f215323fe7030e0d6c167f596878 https://github.com/galaxyproject/galaxy/commit/0924891e31f3f215323fe7030e0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Fix up merge issue with double underscore shim. Commit: f7a2acdcabdfb0d2368e00c4959712bf7d5c98f2 https://github.com/galaxyproject/galaxy/commit/f7a2acdcabdfb0d2368e00c49597… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Merge pull request #1246 from jmchilton/test-commons Fix up merge issue with double underscore shim. Compare: https://github.com/galaxyproject/galaxy/compare/9f8eb465e718...f7a2acdcabdf

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[galaxyproject/galaxy] 0c03f6: Client build, webpack: prototype commit
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c03f69c3952ab4dda8c09b39bf5caea97cd10d6 https://github.com/galaxyproject/galaxy/commit/0c03f69c3952ab4dda8c09b39bf5… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: A client/galaxy/scripts/apps/history-app.js A client/galaxy/scripts/apps/libs.js A client/galaxy/scripts/galaxy-app-webpack.js A client/galaxy/scripts/libs/common-libs.js A client/galaxy/scripts/utils/webpack-localization.js A client/webpack.config.js M lib/galaxy/web/base/controller.py A static/maps/apps/history-app.js.map A static/maps/apps/libs.js.map A static/maps/galaxy-app-webpack.js.map A static/maps/libs/common-libs.js.map A static/maps/utils/webpack-localization.js.map A static/scripts/apps/history-app.js A static/scripts/apps/libs.js A static/scripts/bundled/common.js A static/scripts/bundled/history.bundled.js A static/scripts/bundled/libs.bundled.js A static/scripts/galaxy-app-webpack.js A static/scripts/libs/common-libs.js A static/scripts/utils/webpack-localization.js A templates/js-app.mako Log Message: ----------- Client build, webpack: prototype commit Commit: 25770f4c7cf8c7dfb4f50692fbe2154b4053a484 https://github.com/galaxyproject/galaxy/commit/25770f4c7cf8c7dfb4f50692fbe2… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy-app-webpack.js M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controller.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy-app-webpack.js.map M static/scripts/bundled/history.bundled.js M static/scripts/galaxy-app-base.js M static/scripts/galaxy-app-webpack.js Log Message: ----------- Client build, webpack: move app-webpack closer to app-base for replacement/inheritance, fix bootstrapping of configuration and use managers Commit: 1fd38fb3ee467473d5326ef8c197cedcd9472d53 https://github.com/galaxyproject/galaxy/commit/1fd38fb3ee467473d5326ef8c197… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/package.json M static/scripts/bundled/history.bundled.js Log Message: ----------- Client build: update webpack versions in package.json; recompile Commit: 0235eceb57101d03f6027a28980535a4accd02a6 https://github.com/galaxyproject/galaxy/commit/0235eceb57101d03f6027a289805… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-23 (Fri, 23 Oct 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M 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tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/grouping.py M tools/visualization/LAJ.xml M tox.ini Log Message: ----------- (merge dev) Commit: 5dfb3ffbecf18c9bc1275a4aae7024f69e5ef303 https://github.com/galaxyproject/galaxy/commit/5dfb3ffbecf18c9bc1275a4aae70… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: A client/galaxy/scripts/apps/analysis.js A 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static/scripts/libs/common-libs.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/tools.js M static/scripts/mvc/user/user-model.js M static/scripts/templates/compiled/tool_form.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/root/index.mako Log Message: ----------- Webpack: test index page (Analyze Data) working, original working, history app working Commit: cebfdd2745b4695f7d61e6d5b95984dee0f3eba6 https://github.com/galaxyproject/galaxy/commit/cebfdd2745b4695f7d61e6d5b959… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/libs/common-libs.js.map M static/maps/mvc/tools.js.map M static/scripts/libs/common-libs.js M static/scripts/mvc/tools.js M static/scripts/templates/compiled/tool_form.js Log Message: ----------- Webpack: restore original page scripts Commit: 7bfbb71b27af3147a18beaf2fdd889c7e1c7455d https://github.com/galaxyproject/galaxy/commit/7bfbb71b27af3147a18beaf2fdd8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M .gitignore A lib/galaxy/webapps/galaxy/controllers/test.py Log Message: ----------- Webpack: temp add test controller, add bundled webpack directory to gitignore Commit: 2513e766be2ac2a37b87ff7682dff83688bed815 https://github.com/galaxyproject/galaxy/commit/2513e766be2ac2a37b87ff7682df… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: A static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/common.js A static/scripts/bundled/common.js.map A static/scripts/bundled/galaxy.bundled.js A static/scripts/bundled/galaxy.bundled.js.map A static/scripts/bundled/history.bundled.js A static/scripts/bundled/history.bundled.js.map A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Webpack: adding production bundles Commit: 4ce8b3d96a0922483de24afe8c02e221ef142f57 https://github.com/galaxyproject/galaxy/commit/4ce8b3d96a0922483de24afe8c02… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/test.py M templates/js-app.mako Log Message: ----------- Managers, users: change serialize_current_anonymous_user to return None when no history present; Webpack: move jsAppLauncher test controller into root controller, replace index method Commit: 790c2f5954fbb30ad4c3c0362bbd01ab85de9e3a https://github.com/galaxyproject/galaxy/commit/790c2f5954fbb30ad4c3c0362bbd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/test.py Log Message: ----------- Webpack: remove test controller Commit: 1b89d839aed4c14c5cf62e4b6f3c9b4816f419d2 https://github.com/galaxyproject/galaxy/commit/1b89d839aed4c14c5cf62e4b6f3c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: fix newlibs jquery Commit: 9a659d85d6896dffa280005e66cc72abc0dcbab1 https://github.com/galaxyproject/galaxy/commit/9a659d85d6896dffa280005e66cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/common.js M static/scripts/bundled/common.js.map M 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config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/main.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/pulsar/client/transport/curl.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh M run_tests.sh A scripts/binary_compatibility.py M scripts/common_startup.sh A scripts/galaxy-main M scripts/tools/maf/check_loc_file.py M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.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/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/reports_webapp/run_stats.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/style/blue/base.css M static/welcome.html.sample M test/qunit/tests/galaxy-app-base.js M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- (merge dev) Commit: d80d74c8880c8194dc2c727b7fc9dbf2297483f0 https://github.com/galaxyproject/galaxy/commit/d80d74c8880c8194dc2c727b7fc9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/common-libs.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/user/user-model.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.panels.js.map A static/maps/libs/backbone.js.map M static/maps/libs/common-libs.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/user/user-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/common.js R static/scripts/bundled/common.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/bundled/history.bundled.js R static/scripts/bundled/history.bundled.js.map R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.base.js M static/scripts/galaxy.panels.js A static/scripts/libs/backbone.js M static/scripts/libs/common-libs.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/user/user-model.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.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/visualization/display.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Client libs: move backbone down into /libs (not backbone/backbone); Webpack: move to non-entry vendor bundling for libraries, clean up assoc. Commit: 4f242151e7f6519e27ecae04632bdbbccddb2879 https://github.com/galaxyproject/galaxy/commit/4f242151e7f6519e27ecae04632b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: R client/galaxy/scripts/apps/history-app.js R client/galaxy/scripts/apps/libs.js R client/galaxy/scripts/libs/common-libs.js R static/maps/apps/history-app.js.map R static/maps/apps/libs.js.map M static/maps/galaxy-app-base.js.map M static/maps/galaxy.base.js.map R static/scripts/apps/history-app.js R static/scripts/apps/libs.js M static/scripts/galaxy-app-base.js M static/scripts/galaxy.base.js M static/scripts/mvc/base-mvc.js Log Message: ----------- Webpack: remove libs and history apps, grunt:pack scripts Commit: e59d08f85631eacb83eada88c3351e4c19bcd667 https://github.com/galaxyproject/galaxy/commit/e59d08f85631eacb83eada88c335… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy-app-webpack.js A client/galaxy/scripts/galaxy-async.js R client/galaxy/scripts/galaxy.autocom_tagging.js M client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/galaxy.panels.js A client/galaxy/scripts/modal.js M client/galaxy/scripts/mvc/annotations.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/collection/collection-panel-edit.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/polyfills.js A client/galaxy/scripts/ui/autocom_tagging.js A client/galaxy/scripts/ui/editable-text.js A client/galaxy/scripts/ui/popupmenu.js A client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/webpack.config.js R static/maps/galaxy-app-webpack.js.map A static/maps/galaxy-async.js.map R static/maps/galaxy.autocom_tagging.js.map M static/maps/galaxy.base.js.map M static/maps/galaxy.pages.js.map M static/maps/galaxy.panels.js.map A static/maps/modal.js.map M static/maps/mvc/annotations.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/collection/collection-panel-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/workflow/workflow-view.js.map A static/maps/polyfills.js.map A static/maps/ui/autocom_tagging.js.map A static/maps/ui/editable-text.js.map A static/maps/ui/popupmenu.js.map A static/maps/utils/async-save-text.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy-app-webpack.js A static/scripts/galaxy-async.js R static/scripts/galaxy.autocom_tagging.js M static/scripts/galaxy.base.js M static/scripts/galaxy.pages.js M static/scripts/galaxy.panels.js A static/scripts/modal.js M static/scripts/mvc/annotations.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/collection/collection-panel-edit.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/polyfills.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/utils/async-save-text.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Webpack: move vendor to libs; break up galaxy.panels to panels and modal; break up galaxy.base to polyfills, galaxy-async, ui/popupmenu, ui/editable-text, and utils/async-save-text; move reset_tool_search into workflow-view; move commatize into trackster/util; move galaxy.autocom_tagging to ui/autocom_tagging Commit: 9c35d35c52eca6638e25459293ac9a28e40f9d63 https://github.com/galaxyproject/galaxy/commit/9c35d35c52eca6638e25459293ac… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/app/app-view.js A client/galaxy/scripts/onload.js A client/galaxy/scripts/panel.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/webpack.config.js R static/maps/galaxy.base.js.map R static/maps/galaxy.panels.js.map M static/maps/mvc/app/app-view.js.map A static/maps/onload.js.map A static/maps/panel.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.base.js R static/scripts/galaxy.panels.js M static/scripts/mvc/app/app-view.js A static/scripts/onload.js A static/scripts/panel.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/util.js Log Message: ----------- Webpack: make autocom_tagging into a module, export commatize, rename galaxy.base to onload and galaxy.panels to panels Commit: 649a83c1aa8026160f8d77cb423547ecb76cda28 https://github.com/galaxyproject/galaxy/commit/649a83c1aa8026160f8d77cb4235… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: (shoulda been 2 sep. commits) re-add minimal DOM for 1,2,3 panel layouts via server-side/js-app.mako, correct noscript tag styling; Instantiate galaxy.frame and galaxy.menu from galaxy.masthead (currently the only user), reverse dependencies in them (masthead imports them), and move GalaxyMastheadTab into galaxy.menu and GalaxyMastheadIcon into galaxy.frame - allowing a single import of galaxy.masthead Commit: a639b0c996b13d45412115009615af826ca38ed8 https://github.com/galaxyproject/galaxy/commit/a639b0c996b13d45412115009615… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.frame.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/app/app-view.js R client/galaxy/scripts/panel.js M client/webpack.config.js R static/maps/galaxy.frame.js.map R static/maps/galaxy.masthead.js.map R static/maps/galaxy.menu.js.map A static/maps/layout/masthead.js.map A static/maps/layout/menu.js.map A static/maps/layout/panel.js.map A static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-view.js.map R static/maps/panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.frame.js R static/scripts/galaxy.masthead.js R static/scripts/galaxy.menu.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-view.js R static/scripts/panel.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: move galaxy.masthead and galaxy.menu to layout/masthead and layout/menu, panel to layout/panel, and rename galaxy.frame to layout/scratchbook Commit: b1266b45dc4ddd63a2b2ae1cc9c28ba9d43a2bc0 https://github.com/galaxyproject/galaxy/commit/b1266b45dc4ddd63a2b2ae1cc9c2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/galaxy.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/onload.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy-app-base.js.map A static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/tools.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js A static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/tools.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: move panel to Backbone, implement ToolPanel and HistoryPanel; simplify js-app.mako (by removing alternate layouts); clean up debugging info, make Galaxy less chatty before logging setup Commit: c1cc3bd483fc2197b43048f467be6e80f80babea https://github.com/galaxyproject/galaxy/commit/c1cc3bd483fc2197b43048f467be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: fix masthead in libraries; update Panel usage in base_panels.mako, galaxy.panels.mako Commit: a4edf159be9996d09bb029d2098d9c0d39fb2975 https://github.com/galaxyproject/galaxy/commit/a4edf159be9996d09bb029d2098d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M .gitignore M CONTRIBUTORS.md M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run.sh A scripts/check_eggs.py A scripts/fetch_eggs.py M static/maps/galaxy-app-base.js.map M static/maps/libs/jquery/select2.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/libs/jquery/select2.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/api/helpers.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml M test/unit/jobs/test_job_output_checker.py M tools/filters/wig_to_bigwig.xml M tools/stats/gsummary.py Log Message: ----------- (merge dev) Commit: dc0b960ea1242ae3ec34e7d00c5f8619e06f7b59 https://github.com/galaxyproject/galaxy/commit/dc0b960ea1242ae3ec34e7d00c5f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/onload.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: lowercase DD-helper throughout project to reflect changes in 7717659 Commit: 78e6253178b51afa77346b259801f221eb9c201e https://github.com/galaxyproject/galaxy/commit/78e6253178b51afa77346b259801… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: A client/galaxy/scripts/layout/modal.js R client/galaxy/scripts/modal.js M client/galaxy/scripts/onload.js M client/webpack.config.js A static/maps/layout/modal.js.map R static/maps/modal.js.map A static/scripts/layout/modal.js R static/scripts/modal.js Log Message: ----------- Webpack: move old school modal into layout/ Commit: 215391f571f72725a87f45b556be10e8446db8a9 https://github.com/galaxyproject/galaxy/commit/215391f571f72725a87f45b556be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy-async.js R static/maps/galaxy-async.js.map R static/scripts/galaxy-async.js Log Message: ----------- Webpack: remove galaxy-async Commit: 350a53f1ef9c686ad3617cc37f037251a79a28ef https://github.com/galaxyproject/galaxy/commit/350a53f1ef9c686ad3617cc37f03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/base.js M client/galaxy/scripts/viz/trackster.js R static/maps/base.js.map M static/maps/viz/trackster.js.map R static/scripts/base.js M static/scripts/viz/trackster.js Log Message: ----------- Webpack: move base.Base to trackster (which uses it) Commit: f971e17f95d62662eaec47a96da88f1b45d823ce https://github.com/galaxyproject/galaxy/commit/f971e17f95d62662eaec47a96da8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/ui/scroll-panel.js R static/maps/galaxy.ui.scrollPanel.js.map A static/maps/ui/scroll-panel.js.map R static/scripts/galaxy.ui.scrollPanel.js A static/scripts/ui/scroll-panel.js Log Message: ----------- Webpack: move galaxy.ui.scrollPanel into ui/scroll-panel Commit: 93629bb29e35340618aca2d1b420d948b56c695b https://github.com/galaxyproject/galaxy/commit/93629bb29e35340618aca2d1b420… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map Log Message: ----------- Webpack: add handlebars loader, update tools.js Commit: 2f0b64613770c8e59613bb46218e12565d260038 https://github.com/galaxyproject/galaxy/commit/2f0b64613770c8e59613bb46218e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/tools.js A client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js R static/maps/mvc/tools.js.map A static/maps/mvc/tools/tools.js.map R static/scripts/mvc/tools.js A static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: move tools.js into mvc/tools/ Commit: 372c2e9e43854b0e5e576abcead50e22f00923d9 https://github.com/galaxyproject/galaxy/commit/372c2e9e43854b0e5e576abcead5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M static/maps/galaxy.tools.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/data.js.map A static/maps/mvc/dataset/data.js.map M static/maps/mvc/tools/tools.js.map M static/maps/onload.js.map M static/maps/ui/scroll-panel.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.tools.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/tools/tools.js M static/scripts/onload.js M static/scripts/ui/scroll-panel.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Webpack: move data.js into dataset/data.js; pack scripts Commit: 6d0ab669ecbd12e75cf38f8c914bbf5954caac20 https://github.com/galaxyproject/galaxy/commit/6d0ab669ecbd12e75cf38f8c914b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/webpack.config.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Webpack: correctly load jQuery-ui, require bibtex in citations, and move polyfills to first loaded Commit: c66bc7ab766e2af197a668a76e15e1dc21cfb9fa https://github.com/galaxyproject/galaxy/commit/c66bc7ab766e2af197a668a76e15… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/mvc/collection/collection-panel-edit.js R client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/collection-view-edit.js A client/galaxy/scripts/mvc/collection/collection-view.js R client/galaxy/scripts/mvc/history/history-panel-annotated.js R client/galaxy/scripts/mvc/history/history-panel-edit-current.js R client/galaxy/scripts/mvc/history/history-panel-edit.js R client/galaxy/scripts/mvc/history/history-panel.js A client/galaxy/scripts/mvc/history/history-view-annotated.js A client/galaxy/scripts/mvc/history/history-view-edit-current.js A client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/history/history-view.js M client/webpack.config.js R static/maps/mvc/collection/collection-panel-edit.js.map R static/maps/mvc/collection/collection-panel.js.map A static/maps/mvc/collection/collection-view-edit.js.map A static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/history/history-panel-annotated.js.map R static/maps/mvc/history/history-panel-edit-current.js.map R static/maps/mvc/history/history-panel-edit.js.map R static/maps/mvc/history/history-panel.js.map A static/maps/mvc/history/history-view-annotated.js.map A static/maps/mvc/history/history-view-edit-current.js.map A static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/history/history-view.js.map R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js Log Message: ----------- Webpack: normalize history and panel module names with other mvc modules (history-panel is not a panel - just a view) Commit: 55068dea285c82232bd9dbf024de580013c5f3d8 https://github.com/galaxyproject/galaxy/commit/55068dea285c82232bd9dbf024de… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Webpack: normalize 'panel' names part-2: history and collection modules Commit: 8efabbbcd5546441182cbff1cc66e525cf6abf48 https://github.com/galaxyproject/galaxy/commit/8efabbbcd5546441182cbff1cc66… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Webpack: fix load order in embedded grids by removing autocom_tagging script tag (it's in the libs.bundle), remove it from other mako templates as well; remove bibtex script from workflow/editor.mako (unused) Commit: c3f4b54b686ba93b3bb8f65d17f3961d344b9d7c https://github.com/galaxyproject/galaxy/commit/c3f4b54b686ba93b3bb8f65d17f3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/utils/localization.js R client/galaxy/scripts/utils/webpack-localization.js M client/package.json M client/webpack.config.js M static/maps/galaxy-app-base.js.map M static/maps/utils/localization.js.map R static/maps/utils/webpack-localization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/utils/localization.js R static/scripts/utils/webpack-localization.js Log Message: ----------- Webpack, localization: support both requirejs and webpack i18n by including the amdi18n-loader (both now share the utils/localization file) Commit: 6f754216a4100969b18185aa705065b03a215628 https://github.com/galaxyproject/galaxy/commit/6f754216a4100969b18185aa7050… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js R client/galaxy/scripts/mvc/list/list-panel.js A client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/history/history-view.js.map R static/maps/mvc/list/list-panel.js.map A static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/history/history-view.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js Log Message: ----------- Webpack: normalize list-panel to list-view Commit: d285c01108f59d1b054955f312b16c3b978aa97a https://github.com/galaxyproject/galaxy/commit/d285c01108f59d1b054955f312b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js A client/galaxy/scripts/mvc/tag.js R client/galaxy/scripts/mvc/tags.js A client/galaxy/scripts/mvc/tool/tools-form-base.js A client/galaxy/scripts/mvc/tool/tools-form-workflow.js A client/galaxy/scripts/mvc/tool/tools-form.js A client/galaxy/scripts/mvc/tool/tools-jobs.js A client/galaxy/scripts/mvc/tool/tools-template.js A client/galaxy/scripts/mvc/tool/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js R client/galaxy/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (the names of) Commit: 894af4c5deadc75d2f1a5e11e26abc9c3f4f7256 https://github.com/galaxyproject/galaxy/commit/894af4c5deadc75d2f1a5e11e26a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A static/maps/mvc/annotation.js.map R static/maps/mvc/annotations.js.map A static/maps/mvc/tag.js.map R static/maps/mvc/tags.js.map A static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tool/tools-form-workflow.js.map A static/maps/mvc/tool/tools-form.js.map A static/maps/mvc/tool/tools-jobs.js.map A static/maps/mvc/tool/tools-template.js.map A static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map R static/maps/mvc/tools/tools.js.map A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js R static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (2 of 3) Commit: cc6c15f3b102afd22c3a9f1c7d1a5d92daad03bc https://github.com/galaxyproject/galaxy/commit/cc6c15f3b102afd22c3a9f1c7d1a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-form.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/mvc/annotation.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools-form-base.js.map M static/maps/mvc/tool/tools-form-workflow.js.map M static/maps/mvc/tool/tools-form.js.map M static/maps/mvc/tool/tools-jobs.js.map M static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/annotation.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-form.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (change refs - 3 of 3) Commit: 2956b12e9b292e42dfd2e2309b5c7d29b5b0d48b https://github.com/galaxyproject/galaxy/commit/2956b12e9b292e42dfd2e2309b5c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-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/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/citation/citation-model.js.map M 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static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.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-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: correct tool menu template loading in requirejs/galaxy.panels.mako by using require.config.map; normalize galaxy_config.root and Galaxy.options.root to Galaxy.root across the templates and js Commit: b8870bfedc008d378481bd6740f31ff516271c16 https://github.com/galaxyproject/galaxy/commit/b8870bfedc008d378481bd6740f3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M static/maps/mvc/tool/tools.js.map A static/maps/mvc/tools.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/mvc/tool/tools.js A static/scripts/mvc/tools.js M static/scripts/viz/trackster/tracks.js M static/style/blue/trackster.css M templates/admin/reload_tool.mako M templates/show_params.mako M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh M tools/data_source/upload.py Log Message: ----------- (merge dev) Commit: bb089dfa424cefc64e65f1dd2aab5fe8fe1dad16 https://github.com/galaxyproject/galaxy/commit/bb089dfa424cefc64e65f1dd2aab… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M static/maps/galaxy-app-base.js.map M test/qunit/test-common.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Tests, qunit: fix import of underscore from libs, fix galaxy-app-base to not require config but have it passed in Commit: 474a454958398bc3e70d16f7eaab5805aa89cf19 https://github.com/galaxyproject/galaxy/commit/474a454958398bc3e70d16f7eaab… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/history/hda-model.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Tests, qunit: galaxy_config.root->Galaxy.root, correct locations and shims of underscore and backbone in qunit tests Commit: 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static/style/blue/galaxy.frame.masthead.css M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/casperjs/api-history-permission-tests.js Log Message: ----------- Webpack: polyfill object.assign for phantomjs; remove galaxy.frame.masthead.css in favor of adding styles locally; change css load order to prevent 'ui-button' name collision between base and jquery-ui Commit: d1d2f8388a4bc077275f535e41841158076a56de https://github.com/galaxyproject/galaxy/commit/d1d2f8388a4bc077275f535e4184… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/query-string-parsing.js M client/webpack.config.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M static/scripts/utils/query-string-parsing.js M templates/js-app.mako Log Message: ----------- Webpack: allow extending options from template call, add /login as app entry point for login app (still allowing user/login), add root/welcome and /login to allowed paths when require_login, fix None type error for redirect when visiting user/login directly, fix rendering of masthead, add query string to object util, correct job_id loading from index Commit: 5eb9b206e798522fff1a9332e5d1a58c83528523 https://github.com/galaxyproject/galaxy/commit/5eb9b206e798522fff1a9332e5d1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A client/galaxy/scripts/apps/login.js A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: properly add login app to the repo Commit: 17ec1b08fbc88c4960b94fbd19252c40e8a4e579 https://github.com/galaxyproject/galaxy/commit/17ec1b08fbc88c4960b94fbd1925… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: add masthead div to galaxy.panels.mako as a target for replacement and becauseiamgoingcrazyfromtheeightdifferentwayswehavetorenderwebpages Commit: 7cd5713dbb3acc82ee7c01f5110d37cb413392c8 https://github.com/galaxyproject/galaxy/commit/7cd5713dbb3acc82ee7c01f5110d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M test/casperjs/spaceghost.js Log Message: ----------- Webpack: simplify query routes in analysis, remove duplicate js in display.mako and tabular_chunked.mako, change order of requirejs import; testing, casperjs: quiet requirejs scripterrors when navigating away from pages Commit: 9c5d4cfc0e95966f8a41e8dedf83ea4b4793868e 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client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M config/datatypes_conf.xml.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M cron/build_chrom_db.py M doc/source/admin/interactive_environments.rst M doc/source/project/organization.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.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/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_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 run_tests.sh M static/maps/galaxy-app-base.js.map A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/mvc/app/app-login.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/mvc/app/app-login.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/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js A static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M test/api/helpers.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_tool_loader.py Log Message: ----------- (merge dev) Commit: dba7e6640f816325c853fcc320e97c454a465bae https://github.com/galaxyproject/galaxy/commit/dba7e6640f816325c853fcc320e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/grunt-tasks/templates.js M static/maps/layout/panel.js.map M static/maps/mvc/tool/tools.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/layout/panel.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M templates/base/base_panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Webpack: correct handlebars template generation to return an AMD function - this normalizes import of templates between webpack and require, fix sweepster tools import and templates Commit: 51e098649070435570f9b68bf17ecc005da65bc2 https://github.com/galaxyproject/galaxy/commit/51e098649070435570f9b68bf17e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Webpack: add in the libs bundles, Carl. They're kinda important. Commit: baeaae99059fc94ae2a0dc059cfd448d05bdcbbe https://github.com/galaxyproject/galaxy/commit/baeaae99059fc94ae2a0dc059cfd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: rebuild bundles using webpack 1.12.8 as defined in the package.json Commit: f3f8fef28a55c7b4e6994b08e3125a0d66a36140 https://github.com/galaxyproject/galaxy/commit/f3f8fef28a55c7b4e6994b08e312… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/galaxy.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js M client/grunt-tasks/scripts.js M client/webpack.config.js M lib/galaxy/web/base/controller.py M static/maps/galaxy-app-base.js.map R static/maps/galaxy.menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/galaxy.bundled.js R static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy-app-base.js R static/scripts/galaxy.menu.js M templates/js-app.mako Log Message: ----------- Webpack: move Galaxy object creation from mako to app js, clean up and localize page, panels, and app Commit: b15a4082939be8b533dddf9a6a63efec9be6b817 https://github.com/galaxyproject/galaxy/commit/b15a4082939be8b533dddf9a6a63… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/tools/rgenetics/helper_functions.js R client/galaxy/scripts/tools/rgenetics/timer.js R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js Log Message: ----------- Client: remove duplicate rgenetics directory tools/rgenetics Commit: d921b4243101130d7de5517167eb38fa1aa6b1d3 https://github.com/galaxyproject/galaxy/commit/d921b4243101130d7de5517167eb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.js R static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/app/app-login.js.map R static/maps/mvc/app/app-view.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js Log Message: ----------- Webpack: remove mvc/app Commit: 9f91b82245fc3ba467e8bef7b57bfc58ef02e9f0 https://github.com/galaxyproject/galaxy/commit/9f91b82245fc3ba467e8bef7b57b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/viz/visualization.js A static/incompatible-browser.html R static/maps/libs/IE/IE7.js.map R static/maps/libs/IE/IE8.js.map R static/maps/libs/IE/excanvas.js.map R static/maps/libs/IE/ie7-recalc.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/libs/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Client: remove IE7/8 and excanvas polyfills Commit: e3e9579a812c468fba3f8a64fae7c7455e4b5a9e https://github.com/galaxyproject/galaxy/commit/e3e9579a812c468fba3f8a64fae7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js R client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/galaxy.js R static/maps/galaxy-app-base.js.map A static/maps/galaxy.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/galaxy-app-base.js A static/scripts/galaxy.js M templates/galaxy_client_app.mako Log Message: ----------- Webpack: pack scripts, move galaxy-app-base.js to galaxy.js Commit: 68da0004709e88ed8a856d39e9fa4e64aa3bc653 https://github.com/galaxyproject/galaxy/commit/68da0004709e88ed8a856d39e9fa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/rgenetics/helper_functions.js R client/galaxy/scripts/rgenetics/timer.js R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js Log Message: ----------- Client, rgenetics: 'Nuke 'em all' - R.Lazarus Commit: f397584538f59d03d9c37d3f9366b455022e97b2 https://github.com/galaxyproject/galaxy/commit/f397584538f59d03d9c37d3f9366… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/galaxy/scripts/polyfills.js M static/maps/polyfills.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/polyfills.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Webpack: add link rel='index' with href to Galaxy.root, rework browser testing to use the same when redirecting to error pages Commit: 002bc6b40a4314fc5f35f6156a73cad91532484d https://github.com/galaxyproject/galaxy/commit/002bc6b40a4314fc5f35f6156a73… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M .gitignore M client/GruntFile.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/charts/templates/charts.mako A config/reports.ini.sample R config/reports_wsgi.ini.sample M config/tool_shed.ini.sample A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/interval.py M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M run_reports.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/sync_reports_config.py M static/maps/layout/masthead.js.map M 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static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py A test/functional/tools/collection_type_source.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/unit/tools/test_actions.py M test/unit/tools/test_parsing.py Log Message: ----------- (merge dev) Commit: cfdbf8c0e71c5cdfa0ae47f6da7cc4553efd8429 https://github.com/galaxyproject/galaxy/commit/cfdbf8c0e71c5cdfa0ae47f6da7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M test/qunit/test-app.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Testing, webpack: correct name of Galaxy module in qunit, properly call require, pass GalaxyApp data Commit: 963d8637e869a214ee0e2c352a8184feb980a40e https://github.com/galaxyproject/galaxy/commit/963d8637e869a214ee0e2c352a81… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: R client/galaxy/scripts/galaxy.tools.js R static/maps/galaxy.tools.js.map R static/maps/galaxy.workflows.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/galaxy.tools.js R static/scripts/galaxy.workflows.js Log Message: ----------- Webpack: remove cruft galaxy.tools.js and (remnants of) galaxy.workflows.js Commit: a3e3bde6a2b5c2fc9433336526ec32badfc8ce9d https://github.com/galaxyproject/galaxy/commit/a3e3bde6a2b5c2fc9433336526ec… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/login.js M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: restore redirect for after login when require_login; remove allowed_paths for require_login: /index, /tool_menu, /masthead, library/browse, history/list, dataset/list Commit: b72035c9fc4136af5f3db464fd5b2a9c5e330cca https://github.com/galaxyproject/galaxy/commit/b72035c9fc4136af5f3db464fd5b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M static/maps/layout/masthead.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Webpack: fix/re-work the pub-sub connection between the quotameter and the history panel so that the meter updates properly when a new dataset is added Commit: f40d4fc178cbf3a3266a56ce0108b87e21bd5be0 https://github.com/galaxyproject/galaxy/commit/f40d4fc178cbf3a3266a56ce0108… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M config/galaxy.ini.sample R templates/webapps/galaxy/root/index.mako Log Message: ----------- Webpack: re-add show_welcome_with_login config option (lost due to merge/gitignore?); remove root/index.mako Commit: 9e8068f3671cdef499ed51aca3869f91e2e5b69d https://github.com/galaxyproject/galaxy/commit/9e8068f3671cdef499ed51aca386… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M README.rst M client/galaxy/scripts/mvc/history/options-menu.js M config/datatypes_conf.xml.sample A config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/migrate/check.py M run_tests.sh M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_workflows.py A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- (merge dev) Commit: 9f8eb465e718d4b643120e8554d119702c264135 https://github.com/galaxyproject/galaxy/commit/9f8eb465e718d4b643120e8554d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A 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static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.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/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1144 from carlfeberhard/webpack Webpack Compare: https://github.com/galaxyproject/galaxy/compare/3e8b58c5aa66...9f8eb465e718

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[galaxyproject/galaxy] f08d51: Use fixed path to sync like in dev.
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534 https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. Compare: https://github.com/galaxyproject/galaxy/compare/736bf3ce843d...f34d70101910

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[galaxyproject/galaxy] 107de0: Add the missing "amqp_ack_republish_time" param fo...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8 https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Add the missing "amqp_ack_republish_time" param for the Pulsar runner (it's available in the Pulsar client lib). Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603 https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #1234 from natefoo/pulsar-missing-param [15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner Commit: 3e8b58c5aa66da83206230d27aacba1eaa7faa00 https://github.com/galaxyproject/galaxy/commit/3e8b58c5aa66da83206230d27aac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge branch 'release_15.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5675617178b6...3e8b58c5aa66

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[galaxyproject/galaxy] 107de0: Add the missing "amqp_ack_republish_time" param fo...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8 https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Add the missing "amqp_ack_republish_time" param for the Pulsar runner (it's available in the Pulsar client lib). Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603 https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #1234 from natefoo/pulsar-missing-param [15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner Compare: https://github.com/galaxyproject/galaxy/compare/516b079ab97d...736bf3ce843d

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[galaxyproject/galaxy] 1cc57b: Add icons and reorganise history menu
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1cc57b1eb2c295dbd68837c864740b6ff079b83d https://github.com/galaxyproject/galaxy/commit/1cc57b1eb2c295dbd68837c86474… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Add icons and reorganise history menu Commit: 564f12c50ffaed386f57e1fd2d4048840e5f8288 https://github.com/galaxyproject/galaxy/commit/564f12c50ffaed386f57e1fd2d40… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Remove icons Commit: 42b6da87554b78fddd5b592a82d46deb83cada15 https://github.com/galaxyproject/galaxy/commit/42b6da87554b78fddd5b592a82d4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Comment out debugging Commit: 9bd2712c5d9aa260012ffdad267434758bf086c0 https://github.com/galaxyproject/galaxy/commit/9bd2712c5d9aa260012ffdad2674… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Just going to clobber everything Commit: 198cb7c9a1534e7914ca76c4648fd750234ddb9f https://github.com/galaxyproject/galaxy/commit/198cb7c9a1534e7914ca76c4648f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/scripts/libs/jquery/jquery.dynatree.js Log Message: ----------- Fix rebase issue Commit: 5675617178b6d103de88ff907d137974b908761e https://github.com/galaxyproject/galaxy/commit/5675617178b6d103de88ff907d13… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #985 from erasche/nicer-history-menu Add icons and reorganise history menu Compare: https://github.com/galaxyproject/galaxy/compare/4d396a6945b3...5675617178b6

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[galaxyproject/galaxy] 69b8d8: * Make default_indicator configurable
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69b8d83ba2b829621183361694f341bda66a77fe https://github.com/galaxyproject/galaxy/commit/69b8d83ba2b829621183361694f3… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Make default_indicator configurable * Document classes Commit: b87c22c73b9a3f6d31507d268e945a6ae8deef60 https://github.com/galaxyproject/galaxy/commit/b87c22c73b9a3f6d31507d268e94… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: A config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Add sample dependency_resolvers_conf.xml that matches actual default Commit: 56054c6d98519541b896a5145998b02688750bb6 https://github.com/galaxyproject/galaxy/commit/56054c6d98519541b896a5145998… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Fix AvailModuleChecker() invocation and propogate default default_indicator Commit: bd0663f65062d60de810478566604b3ee33b109d https://github.com/galaxyproject/galaxy/commit/bd0663f65062d60de81047856660… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Initialise default_indicator before using __modules Commit: ba3e3da946b699a03ef9cab9095ea294d6df3b69 https://github.com/galaxyproject/galaxy/commit/ba3e3da946b699a03ef9cab9095e… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Add sample config for modules resolver Commit: 6f727962945481b75dd675e70eed78e8b785cb0a https://github.com/galaxyproject/galaxy/commit/6f727962945481b75dd675e70eed… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Update sample config for modules resolver Commit: 4d396a6945b3394cd529849076b1f6c9892962c5 https://github.com/galaxyproject/galaxy/commit/4d396a6945b3394cd529849076b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: A config/dependency_resolvers_conf.xml.sample M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #1221 from pvanheus/env-modules-resolve Add documentation and extra options to Environment Modules resolver Compare: https://github.com/galaxyproject/galaxy/compare/4289cf3ab2f9...4d396a6945b3

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