[galaxy-commits] [galaxyproject/galaxy] a0cd5b: [WIP] Separate upload modal and default upload vie...

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0cd5b7410c0136c874649bdc41f5c7e6a369e46 https://github.com/galaxyproject/galaxy/commit/a0cd5b7410c0136c874649bdc41f5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js A client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-button.js.map A static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-button.js A static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Separate upload modal and default upload view, insert tabs Commit: 85fc57696f0f92014780134ade8a1482dd61dca6 https://github.com/galaxyproject/galaxy/commit/85fc57696f0f92014780134ade8a1... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Reinserting button panel Commit: f42981810af88c46da482cba940b3c580ee3b193 https://github.com/galaxyproject/galaxy/commit/f42981810af88c46da482cba940b3... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Fix button states Commit: f36f7854568462bc9615fa7edd45425c49708410 https://github.com/galaxyproject/galaxy/commit/f36f7854568462bc9615fa7edd454... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view-default.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Adjust styles Commit: ad661147e82e72641e5709dd3a131017d0227e13 https://github.com/galaxyproject/galaxy/commit/ad661147e82e72641e5709dd3a131... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Style adjustments Commit: 3678c111a6547cbcebc48101a39afa42601a481d https://github.com/galaxyproject/galaxy/commit/3678c111a6547cbcebc48101a39af... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- Prepare composite tab Commit: 04eadf4bfcec7b1848ad4c2e6d84607b40c4eb16 https://github.com/galaxyproject/galaxy/commit/04eadf4bfcec7b1848ad4c2e6d846... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix uploadbox trigger for local upload Commit: dbc1bd50b425522cfc4cb22369e9efa59c5d3357 https://github.com/galaxyproject/galaxy/commit/dbc1bd50b425522cfc4cb22369e9e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Code style adjustments for uploadbox code Commit: 51dca28794f68ec07647854373d94b33aed19e6e https://github.com/galaxyproject/galaxy/commit/51dca28794f68ec07647854373d94... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Continue API integration Commit: 64a7b9e197d1c029a8846a5cbd1485972ddcab6f https://github.com/galaxyproject/galaxy/commit/64a7b9e197d1c029a8846a5cbd148... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Add composite datatype details to datatypes api response Commit: a022738cf2f70555f1f8dc67026e87200e5e87a3 https://github.com/galaxyproject/galaxy/commit/a022738cf2f70555f1f8dc67026e8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Move uploadbox variables to local scope Commit: 3c6a43148ab571a950b0009c1cdb43c6186841f0 https://github.com/galaxyproject/galaxy/commit/3c6a43148ab571a950b0009c1cdb4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Parse composite file details to front-end, hide in regular upload view Commit: 486bbb0bf5d7a866a7205aab03d8b63279f3b3de https://github.com/galaxyproject/galaxy/commit/486bbb0bf5d7a866a7205aab03d8b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: R client/galaxy/scripts/mvc/upload/upload-row.js R client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Separate regular and composite upload elements into directories Commit: a390f071cc453d7d2895ba6e30ffd025414d63b3 https://github.com/galaxyproject/galaxy/commit/a390f071cc453d7d2895ba6e30ffd... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add separated files, repack Commit: 3c372fce95c90ee1f1d5599155471f8bc16983b2 https://github.com/galaxyproject/galaxy/commit/3c372fce95c90ee1f1d5599155471... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix and adjust styles for composite upload view Commit: 95ed2a2921110686a55afff909b466aa7bb7022b https://github.com/galaxyproject/galaxy/commit/95ed2a2921110686a55afff909b46... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/style/blue/base.css Log Message: ----------- [WIP] Further customizations and adjustments of the upload ui Commit: e5d61f3766588a4b9624a085035d20282bcd67a6 https://github.com/galaxyproject/galaxy/commit/e5d61f3766588a4b9624a085035d2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-panel.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/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-slider.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M 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Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Remove mode icon from row Commit: 6de2953c98cfc4ea32b8f6ae6bb6dc096c747d38 https://github.com/galaxyproject/galaxy/commit/6de2953c98cfc4ea32b8f6ae6bb6d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Add 'hide_separator' attribute to modals Commit: e5503824d1c6f691b58e9d790c1c596151285a5c https://github.com/galaxyproject/galaxy/commit/e5503824d1c6f691b58e9d790c1c5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Rename property to 'title_separator' Commit: bb7f9a8a51b9de8b48b15078de498f3f46515442 https://github.com/galaxyproject/galaxy/commit/bb7f9a8a51b9de8b48b15078de498... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- [WIP] Further adjustments to styles and colors Commit: a9274619afcbf2d114ef07ab7759e457411d8a46 https://github.com/galaxyproject/galaxy/commit/a9274619afcbf2d114ef07ab7759e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/style/blue/base.css Log Message: ----------- Adjust icon styles Commit: 6a8fed5feed54263bac775dda908a046d9244c41 https://github.com/galaxyproject/galaxy/commit/6a8fed5feed54263bac775dda908a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix ftp row label style Commit: 5cdd511b7a528940090c01d4d306ccf153f2fc1f https://github.com/galaxyproject/galaxy/commit/5cdd511b7a528940090c01d4d306c... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M lib/galaxy/managers/taggable.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/web_util.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/iphone.css M static/style/blue/library.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: f83eaa8fe7a39f03c522a5b387961ac9154df9d8 https://github.com/galaxyproject/galaxy/commit/f83eaa8fe7a39f03c522a5b387961... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Uploadbox plugin touchup Commit: 237a3d307d808d5be2e6e4d1a093a646f7d791a7 https://github.com/galaxyproject/galaxy/commit/237a3d307d808d5be2e6e4d1a093a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- More touchup/cleanup for upload views Commit: f753a6159e980df064d794c43b1440dd54a241dd https://github.com/galaxyproject/galaxy/commit/f753a6159e980df064d794c43b144... Author: guerler <aysam.guerler@gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix for settings popup and more code cleanup Commit: ecd38ef6dba00cfdb94365616210690091825651 https://github.com/galaxyproject/galaxy/commit/ecd38ef6dba00cfdb943656162106... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css Log Message: ----------- Enable drag-and-drop, use dropdown instead of select, style fix uploadbox.js Commit: 1f9d5443fb5700fe47e3d57a0687f68db6508952 https://github.com/galaxyproject/galaxy/commit/1f9d5443fb5700fe47e3d57a0687f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/ui.less M static/scripts/mvc/upload/upload-settings.js M static/style/blue/base.css Log Message: ----------- Style margin fixes Commit: ea26355761cd04512d4e392f821e7d63fbfc1b53 https://github.com/galaxyproject/galaxy/commit/ea26355761cd04512d4e392f821e7... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-03 (Mon, 03 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- More cleanup, fix model creation Commit: 13389042883fe657c6b289ba6fb2db7630ffd86e https://github.com/galaxyproject/galaxy/commit/13389042883fe657c6b289ba6fb2d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate file submission from upload queue, augment and generalize send function Commit: cc46b65d16275e8f73cfceb4c1546e795146bf35 https://github.com/galaxyproject/galaxy/commit/cc46b65d16275e8f73cfceb4c1546... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/history.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 42c61535d6abdf5b30a4ad10396a42b4e22eb514 https://github.com/galaxyproject/galaxy/commit/42c61535d6abdf5b30a4ad10396a4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate upload post function, remove some unnecessary functions Commit: d85342d5097e66756900592bda86eb0bf4e5c363 https://github.com/galaxyproject/galaxy/commit/d85342d5097e66756900592bda86e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comment Commit: 8e093847f9a718de63c7ac698adadebdffc076e7 https://github.com/galaxyproject/galaxy/commit/8e093847f9a718de63c7ac698adad... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Enable composite data submission Commit: 8eca23e4b473824d1b75635e057d018d0825d767 https://github.com/galaxyproject/galaxy/commit/8eca23e4b473824d1b75635e057d0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Attach success, error handlers for composite uploads, fixes Commit: 960d9e5634826ea6ef1734f9adba25c3bb72a76b https://github.com/galaxyproject/galaxy/commit/960d9e5634826ea6ef1734f9adba2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix ui behavior for restart, progress and result states Commit: 2d332e9b71b4ff28d228ef57c8bd46b6c8b1d2c4 https://github.com/galaxyproject/galaxy/commit/2d332e9b71b4ff28d228ef57c8bd4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Disable restart button if upload completed Commit: d76efc57523daa5cbb05200a2c6868e2eb9db228 https://github.com/galaxyproject/galaxy/commit/d76efc57523daa5cbb05200a2c686... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Activate paste/fetch feature, improve behavior Commit: b0c7b736d450121528c4518880a2c6f128a4ee7c https://github.com/galaxyproject/galaxy/commit/b0c7b736d450121528c4518880a2c... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add green start button, fix text field Commit: 1f3ee5f64806d41bc4166248370aab443c60c49e https://github.com/galaxyproject/galaxy/commit/1f3ee5f64806d41bc4166248370aa... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Adjust start button location Commit: 3fae23368b85682c99b82a855c8ddf0d28238e7b https://github.com/galaxyproject/galaxy/commit/3fae23368b85682c99b82a855c8dd... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix color to primary/blue Commit: 17b84cb7b4bd67e4b0d9941b77cbed3c60201b43 https://github.com/galaxyproject/galaxy/commit/17b84cb7b4bd67e4b0d9941b77cbe... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Fix paste/fetch field style Commit: 5e4c0bcf64666b4c30fe4519479d0d7e1aee9000 https://github.com/galaxyproject/galaxy/commit/5e4c0bcf64666b4c30fe4519479d0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix start button style Commit: 92526c834049a4b8e16f479521400542eeb503c8 https://github.com/galaxyproject/galaxy/commit/92526c834049a4b8e16f479521400... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix update screen calls Commit: eaff25b6eb89bf1cd563b6a350f119e3a8371bc3 https://github.com/galaxyproject/galaxy/commit/eaff25b6eb89bf1cd563b6a350f11... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_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/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png A static/maps/libs/jquery.sparklines.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/libs/jquery.sparklines.js M static/scripts/mvc/form/form-select-content.js A static/scripts/reports_webapp/run_stats.js A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/page_base.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako A templates/webapps/reports/run_stats.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: client/galaxy/scripts/mvc/upload/upload-view.js static/maps/mvc/upload/upload-view.js.map static/scripts/mvc/upload/upload-view.js static/style/blue/base.css Commit: 4beeeecf4c3dda5ee18c4dc928fb416a7b56de79 https://github.com/galaxyproject/galaxy/commit/4beeeecf4c3dda5ee18c4dc928fb4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/upload-model.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/upload-model.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/upload-model.js Log Message: ----------- Fix file names and description Commit: b3c0725d97a1cf5c4229f60a46a878710c41cab5 https://github.com/galaxyproject/galaxy/commit/b3c0725d97a1cf5c4229f60a46a87... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Continue ftp popup integration Commit: c7ad46099c1118a62936d0f2df4bdb2ff920895e https://github.com/galaxyproject/galaxy/commit/c7ad46099c1118a62936d0f2df4bd... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/utils/utils.js M static/style/blue/base.css Log Message: ----------- Enable ftp file selection for composite uploads Commit: a8def9a910ecae7fe5d3507ce38d235e20810038 https://github.com/galaxyproject/galaxy/commit/a8def9a910ecae7fe5d3507ce38d2... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Style fixes, adjustments for ftp popover table Commit: 80e45d230b1ea5a3bf8a77e573ed8a33a4263f4d https://github.com/galaxyproject/galaxy/commit/80e45d230b1ea5a3bf8a77e573ed8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Add icons to buttons in regular view Commit: ab87393897b2948b306c86c692aaabd748abec31 https://github.com/galaxyproject/galaxy/commit/ab87393897b2948b306c86c692aaa... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Place string split in make_html_table call into try block Commit: 7695fec2fa217a056fa34a1cf78fcb41864549f2 https://github.com/galaxyproject/galaxy/commit/7695fec2fa217a056fa34a1cf78fc... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 4da5f1370f8bad346e1a26b913f8fab0bd567f0d https://github.com/galaxyproject/galaxy/commit/4da5f1370f8bad346e1a26b913f8f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Fix corner cases ie missing datatype details Commit: 82c732752f2c201ed223e46abb533ea262f9fe9e https://github.com/galaxyproject/galaxy/commit/82c732752f2c201ed223e46abb533... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix unload message if queue is running/active Commit: 1686109ae8d6ac615ffdb45d1a0a6e7b5f48c786 https://github.com/galaxyproject/galaxy/commit/1686109ae8d6ac615ffdb45d1a0a6... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix sorting for upper case extension Commit: 71bcb8dc9d4b478c098e8ba2adf63e227eb3f658 https://github.com/galaxyproject/galaxy/commit/71bcb8dc9d4b478c098e8ba2adf63... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: 2bdbe8036f93409a8a2d5b7a9b75c205201bd448 https://github.com/galaxyproject/galaxy/commit/2bdbe8036f93409a8a2d5b7a9b75c... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: b07625b0c03045a4539b5f01a7115324f8905ff0 https://github.com/galaxyproject/galaxy/commit/b07625b0c03045a4539b5f01a7115... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Remove unnecessary if condition in ftp uploader Commit: dd421d00076660ef368757c7871b5fa7c3ab80c9 https://github.com/galaxyproject/galaxy/commit/dd421d00076660ef368757c7871b5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Minor fixes Commit: 304e693fd36fe5a84aeef0b1b1a2e3c909e1eb59 https://github.com/galaxyproject/galaxy/commit/304e693fd36fe5a84aeef0b1b1a2e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow safe switching between histories while queue is running Commit: 704e031f6339f63103e24805369db1c28653fd58 https://github.com/galaxyproject/galaxy/commit/704e031f6339f63103e24805369db... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M doc/source/project/organization.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Commit: 0c3fdd2d637255e61a08f4684f63bd6b097c02eb https://github.com/galaxyproject/galaxy/commit/0c3fdd2d637255e61a08f4684f63b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/utils.js A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add test cases for uploader, add generic Galaxy environment to qunit Commit: ed171e95190e651434927e05f67b5a65f1c84828 https://github.com/galaxyproject/galaxy/commit/ed171e95190e651434927e05f67b5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/reports.less M client/grunt-tasks/scripts.js M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.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/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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/history/history-contents.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-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.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-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.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/history/history-contents.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.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-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/maps/utils/utils.js.map static/scripts/utils/utils.js static/style/blue/base.css Commit: 89801414bbdc18f5db98c32ca462ef92f97f5647 https://github.com/galaxyproject/galaxy/commit/89801414bbdc18f5db98c32ca462e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Enhance FTP visibilty handling Commit: e9e3dd62d2178d391f5ba9f0c677063800b0f3a3 https://github.com/galaxyproject/galaxy/commit/e9e3dd62d2178d391f5ba9f0c6770... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Use list comprehension to build composite_files array Commit: b6e0ba29521bbc382a9fe15493e55b2bbde1bfde https://github.com/galaxyproject/galaxy/commit/b6e0ba29521bbc382a9fe15493e55... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/datatypes/genetics.py M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #605 from guerler/upload_000 Add composite file uploader Compare: https://github.com/galaxyproject/galaxy/compare/bb7795f63c47...b6e0ba29521b