Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6b650b6b872d50c9b2a57a9d31fed7b6b110d3d https://github.com/galaxyproject/galaxy/commit/e6b650b6b872d50c9b2a57a9d31fe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Pages entrypoint; eliminate require. Commit: 81bfe11fbd3ce51ae3e2d01a16620c58211c6799 https://github.com/galaxyproject/galaxy/commit/81bfe11fbd3ce51ae3e2d01a16620... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js Log Message: ----------- WYM needs this global space, this fixes the loaders in a better way (for us) than the export loaders. Compatibility fix for the ~8 year old wymeditor. We should look into newer options. Commit: 7722a2151ae6f0b1910aaf9670de6efce65c9c5e https://github.com/galaxyproject/galaxy/commit/7722a2151ae6f0b1910aaf9670de6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/phyloviz.mako Log Message: ----------- Convert phyloviz loading to bundle instead of require. Commit: d8bbeae47313eb37a97f8fe301c46f182120e65e https://github.com/galaxyproject/galaxy/commit/d8bbeae47313eb37a97f8fe301c46... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Bundle and use createTabularDatasetChunkedView entrypoint. Commit: 00770e28090125595a0f21332be775f2672af438 https://github.com/galaxyproject/galaxy/commit/00770e28090125595a0f21332be77... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- History multiview bundle/entry. Commit: 5f514d44a551d0a3521cca4345788a8da390191e https://github.com/galaxyproject/galaxy/commit/5f514d44a551d0a3521cca4345788... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view.mako Log Message: ----------- History view and view-edit bundling into extended UI. Refactored some of the bootstrapping. We really need a Galaxy singleton for logging/etc. Commit: fc37c728e9ac7eecc652fe4fe085d1090db60f03 https://github.com/galaxyproject/galaxy/commit/fc37c728e9ac7eecc652fe4fe085d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Temporary-ish fix for logging in extended bundle (add logging to whatever Galaxy object exists on the window) Commit: d795bc229bd3f76ea2b1b5737067b474e5f55b87 https://github.com/galaxyproject/galaxy/commit/d795bc229bd3f76ea2b1b5737067b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Only strap in logging when it's not already there. Commit: 32537e136e5bec6651004c5594dc67ecf51fce35 https://github.com/galaxyproject/galaxy/commit/32537e136e5bec6651004c5594dc6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/dataset/display.mako Log Message: ----------- Use bundles for dataset/display; we really probably want to get rid of dataset/display_by_username_and_slug, because 1) there is no slug, and 2) username isn't used... Commit: 4c54c9dfb99e3b9f7d8f972554fbd022852d836e https://github.com/galaxyproject/galaxy/commit/4c54c9dfb99e3b9f7d8f972554fbd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: f5dad8810fcca9fba5e8965d82555a6a4c4031e4 https://github.com/galaxyproject/galaxy/commit/f5dad8810fcca9fba5e8965d82555... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster globals, argh. Needs more refactoring, but I'd like to get it working again first. Commit: f440586738284dba5ccee86ee9668368a1e45395 https://github.com/galaxyproject/galaxy/commit/f440586738284dba5ccee86ee9668... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix circster loading error> Commit: 7f107e8e8b318db89e9fcbd94cc0c8816086cc28 https://github.com/galaxyproject/galaxy/commit/7f107e8e8b318db89e9fcbd94cc0c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Swap to default d3 for circster. Commit: 4d6ab294339924b3930673e914929ddd6247442d https://github.com/galaxyproject/galaxy/commit/4d6ab294339924b3930673e914929... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix d3 event handling in circster. Commit: 55afdb1b25437dfb033367caf0f50604b6a63137 https://github.com/galaxyproject/galaxy/commit/55afdb1b25437dfb033367caf0f50... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Attach toplevel or global viz stuff to window (force_left_panel, force_right_panel, galaxy_config). Commit: 3543cd31748c3a4906e71dfcf339597d11041b4c https://github.com/galaxyproject/galaxy/commit/3543cd31748c3a4906e71dfcf3395... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Embedded page entrypoints, bundling. Commit: 30f98eac21fc838ab4ba4cf0e007223fce1872c6 https://github.com/galaxyproject/galaxy/commit/30f98eac21fc838ab4ba4cf0e0072... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Formatting in workflow canvas and trackster Commit: 993c0b7341ab2f1515d727b0b3c44b7fbf8e4b75 https://github.com/galaxyproject/galaxy/commit/993c0b7341ab2f1515d727b0b3c44... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- More bundling, always bundling. Commit: e69c047bd8e1df1d6cbb178b3de8488600aa076f https://github.com/galaxyproject/galaxy/commit/e69c047bd8e1df1d6cbb178b3de84... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/display.mako Log Message: ----------- Trackster external display bundling. Commit: b9862425acbed31c905448c76573d266ba7cb28b https://github.com/galaxyproject/galaxy/commit/b9862425acbed31c905448c76573d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/display_common.mako Log Message: ----------- Remove SampleDataset and RequestType references from display_common; this prevents any use of this mako currently. Commit: a3b25a345f02a4dab99e57e93549ea21e3c1a563 https://github.com/galaxyproject/galaxy/commit/a3b25a345f02a4dab99e57e93549e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- More request type cruft; seems to be unused and it'd blow up if tried to use Commit: f02895705d2bd171e3f51a34928e050f4563e87b https://github.com/galaxyproject/galaxy/commit/f02895705d2bd171e3f51a34928e0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Bundle sweepster. Commit: d31868ad32bb237f4f72c4e2b10d75fa69b0913a https://github.com/galaxyproject/galaxy/commit/d31868ad32bb237f4f72c4e2b10d7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M templates/webapps/galaxy/history/display.mako Log Message: ----------- History display mako swapped to use existing bundled javascript. Commit: 2e59e92a0b0f888c709695d130a1643d68ab3492 https://github.com/galaxyproject/galaxy/commit/2e59e92a0b0f888c709695d130a16... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Bundle structure view (still has a bug, but that's not new) Commit: 2d2726456c1377f12faeb5ab389ae1c6bd9b0a54 https://github.com/galaxyproject/galaxy/commit/2d2726456c1377f12faeb5ab389ae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Bundle history structure view. Commit: 560b2e0b963e697c51fbf90fce8446d724d7484c https://github.com/galaxyproject/galaxy/commit/560b2e0b963e697c51fbf90fce844... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Package GalaxyApp in extended bundle for bootstrapping outside the primary entrypoints; TODO: Refactor this to be import-based and keep a singleton Commit: ed274a7ca562ad170d86aa2f21748693c8a54e46 https://github.com/galaxyproject/galaxy/commit/ed274a7ca562ad170d86aa2f21748... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py R openid/yahoo.xml M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/bibtex.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/common/select_template.mako R templates/common/template_common.mako R templates/form.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: a4899ae9b32ea081bac02dbc7e4b93c64ae6c6f6 https://github.com/galaxyproject/galaxy/commit/a4899ae9b32ea081bac02dbc7e4b9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako M templates/webapps/galaxy/base_panels.mako Log Message: ----------- Some bundle import reorg in old-style 'base' templates; we basically always want to load the bundle entrypoints here. Commit: e2e271d81a23d9c8a0db716f3f2d6f3d198f0bb2 https://github.com/galaxyproject/galaxy/commit/e2e271d81a23d9c8a0db716f3f2d6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/legacy/grid_base.mako Log Message: ----------- Use bundle entrypoint for legacy grid_base Commit: 38ecceb4c5ba877658b28cce8523afa5d7bc9b29 https://github.com/galaxyproject/galaxy/commit/38ecceb4c5ba877658b28cce8523a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Expose LegacyGridView via extended application bundle. Commit: 8e650ff29bb98f347439c6e808ea919ea974b5c7 https://github.com/galaxyproject/galaxy/commit/8e650ff29bb98f347439c6e808ea9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Remove unused dependencies from ui-select-library Commit: 90ea47e1dae07ab7a9ddd3f0477c57d552660be5 https://github.com/galaxyproject/galaxy/commit/90ea47e1dae07ab7a9ddd3f0477c5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Slight logic clarification in ui-select-library. Commit: 1b39f2d1311cc86164818bc86524a039ead85a28 https://github.com/galaxyproject/galaxy/commit/1b39f2d1311cc86164818bc86524a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.js Log Message: ----------- Add a temporary workaround for Galaxy not being accessible at static build time Commit: 4ef30c89f43a8d266fc575fda64c8e8573aa7cbf https://github.com/galaxyproject/galaxy/commit/4ef30c89f43a8d266fc575fda64c8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js Log Message: ----------- Remove unused dependencies from dataset/data.js Commit: 3f1f1727c63c682ff959e5e5ee2f32f92e52fe31 https://github.com/galaxyproject/galaxy/commit/3f1f1727c63c682ff959e5e5ee2f3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Swap reports run_stats to extended bundle entrypoint. Commit: 9290a7e5c3cc7b20dd51a655838a3af234b7b700 https://github.com/galaxyproject/galaxy/commit/9290a7e5c3cc7b20dd51a655838a3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Drop debug statement Commit: ddc5f90907094e5b5ebb5bfc41144c2a168b8acc https://github.com/galaxyproject/galaxy/commit/ddc5f90907094e5b5ebb5bfc41144... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js Log Message: ----------- Merge builds gxy/shed Commit: 759014e15e2a5a383c8f280c18eba4554b3e7a1d https://github.com/galaxyproject/galaxy/commit/759014e15e2a5a383c8f280c18eba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/GruntFile.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js Log Message: ----------- Consolidate to the one grunt task. Commit: db1f00fa3cf8ab65d37af776b72e46b70940ee3f https://github.com/galaxyproject/galaxy/commit/db1f00fa3cf8ab65d37af776b72e4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Format toolshed js Commit: 426884284508f6ca949469cec06755d61631647d https://github.com/galaxyproject/galaxy/commit/426884284508f6ca949469cec0675... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js R client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Lots of incremental toolshed js/ groups refactoring, bundling. Commit: 1159c342280a82a804c2192fdd58e11095108f34 https://github.com/galaxyproject/galaxy/commit/1159c342280a82a804c2192fdd58e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- More incremental es6'ing of toolshed client code. Commit: bfb2d049a1a22c474337ca5a614220f5f7d31f93 https://github.com/galaxyproject/galaxy/commit/bfb2d049a1a22c474337ca5a61422... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Remove unused group-model import. Commit: 17e074068ac7c8fff25334ac555a8ff9984ffa6b https://github.com/galaxyproject/galaxy/commit/17e074068ac7c8fff25334ac555a8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js Log Message: ----------- Toolshed client refactoring, fixing, etc. Commit: d79b5fff559e029a33180ab214699def343aa86b https://github.com/galaxyproject/galaxy/commit/d79b5fff559e029a33180ab214699... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Toolshed groups actually work now. Commit: c0eb0fadd8ebd8773d8be743d41667c16700074e https://github.com/galaxyproject/galaxy/commit/c0eb0fadd8ebd8773d8be743d4166... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/README.md Log Message: ----------- Remove toolshed build info (part of the standard client build now) Commit: c2b709ae1c5d270f8d671b6ff8892b9aa1fc31ba https://github.com/galaxyproject/galaxy/commit/c2b709ae1c5d270f8d671b6ff8892... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Old debug cruft removal in structure.mako Commit: 648d4bd5d34ea81bd55e1239c8aea47d112ba9fe https://github.com/galaxyproject/galaxy/commit/648d4bd5d34ea81bd55e1239c8aea... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js Log Message: ----------- Toolshed artifacts initial commit (hopefully we don't do this much more...) Commit: 20fa0e73f2aace2bc872cd49137f4cc23fa8f5d0 https://github.com/galaxyproject/galaxy/commit/20fa0e73f2aace2bc872cd49137f4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js Log Message: ----------- Build client, including toolshed. Commit: e589f1e8bd5b575aaea7992a8769322d722ffe75 https://github.com/galaxyproject/galaxy/commit/e589f1e8bd5b575aaea7992a87693... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R static/scripts/bundled/adminToolshed.bundled.js R static/scripts/bundled/library.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js Log Message: ----------- Remove old, unused bundles. Commit: 77d77a935fa0b4f4c7476e871189a5fb8ecbe54f https://github.com/galaxyproject/galaxy/commit/77d77a935fa0b4f4c7476e871189a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge branch 'require_elimination' into dev Compare: https://github.com/galaxyproject/galaxy/compare/62a3a5c5968c...77d77a935fa0