Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b18736d82447637d7257f3fd406e1c40a02afed0 https://github.com/galaxyproject/galaxy/commit/b18736d82447637d7257f3fd406e1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating Cytoscape viewer in Viz/Charts, replacing the previous 'basic' folder name to 'viewer' and updating the wrapper.js file Commit: 69b9b575172086376657433ff0a066bf732d4e4d https://github.com/galaxyproject/galaxy/commit/69b9b575172086376657433ff0a06... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding basic options like layout name and curve style for cytoscape graphs Commit: 504f4ac670b3135b9df885d9d884d176dc494768 https://github.com/galaxyproject/galaxy/commit/504f4ac670b3135b9df885d9d884d... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding min and max zoom settings for graphs Commit: b437be2c566c431267d814b7718380969b8bd3b7 https://github.com/galaxyproject/galaxy/commit/b437be2c566c431267d814b771838... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding SIF to JSON converter for Cytoscape viewer Commit: 2275d098eeeaeb115fa69b0d1fa7856f7bfa4d18 https://github.com/galaxyproject/galaxy/commit/2275d098eeeaeb115fa69b0d1fa78... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph resize property for window resize Commit: 56338972b9767b9e0be474d99b8f4ea915e6dd96 https://github.com/galaxyproject/galaxy/commit/56338972b9767b9e0be474d99b8f4... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Extending the sif to json converter to allow single nodes to be plotted Commit: c6bd499d001b667f20bd4caf99612a3d56b200c1 https://github.com/galaxyproject/galaxy/commit/c6bd499d001b667f20bd4caf99612... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding node text and colors for graphs Commit: 2a6391550b2256c18f2671b2260f58746b507db7 https://github.com/galaxyproject/galaxy/commit/2a6391550b2256c18f2671b2260f5... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding directed/undirected attribute for graphs Commit: 9f42821f57c3126826ebc773407ac02084a965ea https://github.com/galaxyproject/galaxy/commit/9f42821f57c3126826ebc773407ac... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Breadth First Search for cytoscape graphs. Tapping any node plays BFS Commit: a2affcc618ae5ec8d0f36e55a0f7ef15de53ef68 https://github.com/galaxyproject/galaxy/commit/a2affcc618ae5ec8d0f36e55a0f7e... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Depth First Search for cytoscape graphs Commit: c658ef3c7efd56986c096dc71a73c06260351ccc https://github.com/galaxyproject/galaxy/commit/c658ef3c7efd56986c096dc71a73c... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-19 (Sun, 19 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Kruskal algorithm for graphs and color choosing scheme for highlighted edges Commit: 0d95b4e2079aa0d442a2e030fe7606c7627bd1e6 https://github.com/galaxyproject/galaxy/commit/0d95b4e2079aa0d442a2e030fe760... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph traversal types Commit: cbc7dd17fcf3bfe9eecdd8a0577a6d63e565f509 https://github.com/galaxyproject/galaxy/commit/cbc7dd17fcf3bfe9eecdd8a0577a6... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing unused if else Commit: 50417de1b4971db4fe42b1c797024081c66deef5 https://github.com/galaxyproject/galaxy/commit/50417de1b4971db4fe42b1c797024... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding A* search algorithm for finding shortest distance between root and destination Commit: 50a51575f1d4f0a7ccc8c476ab0ad7de2ffca3c8 https://github.com/galaxyproject/galaxy/commit/50a51575f1d4f0a7ccc8c476ab0ad... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js 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static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/style/blue/base.css R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py M test/qunit/package.json A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merging with dev Commit: 086dfd71ca4b82a7aeb2421cb2a08e76975639b3 https://github.com/galaxyproject/galaxy/commit/086dfd71ca4b82a7aeb2421cb2a08... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing tabs and updating time out for path animation Commit: 04941d0aea0be51fd169cb332070f6a420b71d0c https://github.com/galaxyproject/galaxy/commit/04941d0aea0be51fd169cb332070f... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing review comments- removing sliders for colors and zoom and adding color pickers, updating values for min and max zoom and replacing logo of the plugin Commit: f1206a8e352b9ef4288aa08bd18ac6b3387c790e https://github.com/galaxyproject/galaxy/commit/f1206a8e352b9ef4288aa08bd18ac... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map Log Message: ----------- Updating library files Commit: 90c534570876c0f76a02458433960d9923a96ec3 https://github.com/galaxyproject/galaxy/commit/90c534570876c0f76a02458433960... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing an issue with JSON data 'elements' attribute Commit: 7964c7d1d0564422131760d1c6a1b9334954ca48 https://github.com/galaxyproject/galaxy/commit/7964c7d1d0564422131760d1c6a1b... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding styles for selected nodes and updating default colors for nodes, edges and higlighted elements Commit: 0809c19c36cf5f73f60928bd11c6a091c96e06b2 https://github.com/galaxyproject/galaxy/commit/0809c19c36cf5f73f60928bd11c6a... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/jobs/__init__.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 static/maps/mvc/collection/base-creator.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/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.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/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merging with dev Commit: cfd8ec776e692fe2706c1bd7cc40dcf1a8c56832 https://github.com/galaxyproject/galaxy/commit/cfd8ec776e692fe2706c1bd7cc40d... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #3817 from bgruening/cytoscape Cytoscape as the Galaxy charts plugin Compare: https://github.com/galaxyproject/galaxy/compare/db09acb02637...cfd8ec776e69