Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a373bbbfe506b81fbfd260002124be4d02b8a853 https://github.com/galaxyproject/galaxy/commit/a373bbbfe506b81fbfd260002124b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client-side routes to connect visualization edit controller endpoint with front-end form builder Commit: 3e4b0a247123107a2ffe2e0e1fb8ecd6c19e9ee9 https://github.com/galaxyproject/galaxy/commit/3e4b0a247123107a2ffe2e0e1fb8e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add client input element definition for visualization editing form Commit: ed11e87f9b567307ad12820f55c51d0b23880241 https://github.com/galaxyproject/galaxy/commit/ed11e87f9b567307ad12820f55c51... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add help text to annotation field, remove redundant visualization label from inputs Commit: 279ccd11cd830dbcd298ebc9ec45d4d872d9ab9c https://github.com/galaxyproject/galaxy/commit/279ccd11cd830dbcd298ebc9ec45d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add support to save changed attributes Commit: 1547d1b91e930b438162364db4ae8b7ed6e23a69 https://github.com/galaxyproject/galaxy/commit/1547d1b91e930b438162364db4ae8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/mvc/grid/grid-shared.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/grid/grid-shared.js Log Message: ----------- Add message handling support Commit: 78aa69d456c3bd47531651bc36760e7de98b53e8 https://github.com/galaxyproject/galaxy/commit/78aa69d456c3bd47531651bc36760... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add error handler Commit: 6dec4f79e6492cd9d33f76edd67522c6341fb572 https://github.com/galaxyproject/galaxy/commit/6dec4f79e6492cd9d33f76edd6752... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add text sanitization, remove comments Commit: 1578f92e074298fd9304b79ce1dca298578f8b8b https://github.com/galaxyproject/galaxy/commit/1578f92e074298fd9304b79ce1dca... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Flush visualization with new attributes to database Commit: 43bd4e6abd0a61d69ee91f5fe26b6d36b0d716bb https://github.com/galaxyproject/galaxy/commit/43bd4e6abd0a61d69ee91f5fe26b6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: R templates/webapps/galaxy/visualization/create.mako Log Message: ----------- Remove visualization edit mako Commit: 88f135d0d3b283ba81f911bac410ff9ba7f149d8 https://github.com/galaxyproject/galaxy/commit/88f135d0d3b283ba81f911bac410f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add support to change dbkey for visualizations after creation Commit: 4ee1473bab78dbb02b3c4fb7c96fdb4a40c95089 https://github.com/galaxyproject/galaxy/commit/4ee1473bab78dbb02b3c4fb7c96fd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove trackster specific create form, visualizations are created through the visualization icon in the history Commit: 9ceb4ac2ec42296ea6af126f747fe6cd8abf5d06 https://github.com/galaxyproject/galaxy/commit/9ceb4ac2ec42296ea6af126f747fe... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Revise help text, make visualization dbkey optional since many do not require it Commit: daa973a5d9e47cb9cc92dd8b83823fe8be7f7f52 https://github.com/galaxyproject/galaxy/commit/daa973a5d9e47cb9cc92dd8b83823... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/visualization/genomes.py Log Message: ----------- Improve resilience of backend if genome build is missing Fix Commit: b482ac162b8e04a88afdca9bf56ca6a8a05ee2f0 https://github.com/galaxyproject/galaxy/commit/b482ac162b8e04a88afdca9bf56ca... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CITATION M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.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/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M templates/display_base.mako M templates/display_common.mako M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' into replace_visualization_edit_form Commit: df14b8dd02edb01b122704b89c459a928e698039 https://github.com/galaxyproject/galaxy/commit/df14b8dd02edb01b122704b89c459... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/grid/grid-shared.js M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/mvc/grid/grid-shared.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/grid/grid-shared.js R templates/webapps/galaxy/visualization/create.mako Log Message: ----------- Merge pull request #4682 from guerler/replace_visualization_edit_form Remove visualization edit form mako Compare: https://github.com/galaxyproject/galaxy/compare/0dd7f01008d2...df14b8dd02ed