Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6879507fef3f6b6697f3e8364953b1fc4c9f1361 https://github.com/galaxyproject/galaxy/commit/6879507fef3f6b6697f3e8364953b... Author: guerler aysam.guerler@gmail.com Date: 2017-11-11 (Sat, 11 Nov 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/history/options-menu.js

Log Message: ----------- Add js history form view

Commit: f776229db4b9f81868df35b1e76cf5d605a5b0d4 https://github.com/galaxyproject/galaxy/commit/f776229db4b9f81868df35b1e76cf... Author: guerler aysam.guerler@gmail.com Date: 2017-11-11 (Sat, 11 Nov 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.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 history import

Commit: 3e4058f098446ffddefb4b426233fa00fd4307ff https://github.com/galaxyproject/galaxy/commit/3e4058f098446ffddefb4b426233f... Author: guerler aysam.guerler@gmail.com Date: 2017-11-12 (Sun, 12 Nov 2017)

Changed paths: M client/galaxy/style/less/ui.less 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/style/blue/base.css

Log Message: ----------- Fix styling, fix data submission for history endpoint

Commit: 358dee22ca45e88fbf727fb773616b1f90473540 https://github.com/galaxyproject/galaxy/commit/358dee22ca45e88fbf727fb773616... Author: guerler aysam.guerler@gmail.com Date: 2017-11-12 (Sun, 12 Nov 2017)

Changed paths: M static/scripts/bundled/analysis.bundled.js.map

Log Message: ----------- Use global vars

Commit: 2a122157c540e412b8d37540205b88801e6a0746 https://github.com/galaxyproject/galaxy/commit/2a122157c540e412b8d37540205b8... Author: guerler aysam.guerler@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)

Changed paths: A client/galaxy/scripts/mvc/history/history-import.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/history/history-import.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 A static/scripts/mvc/history/history-import.js

Log Message: ----------- Augment existing api endpoint, redirect post

Commit: 0c615411c9a063ddfaeb6b2e2bfba1b783a1543f https://github.com/galaxyproject/galaxy/commit/0c615411c9a063ddfaeb6b2e2bfba... Author: guerler aysam.guerler@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py

Log Message: ----------- Consolidate endpoints

Commit: 4fd3021330f9d1ec4061807fe739933140f63e91 https://github.com/galaxyproject/galaxy/commit/4fd3021330f9d1ec4061807fe7399... Author: guerler aysam.guerler@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)

Changed paths: M client/galaxy/scripts/mvc/history/history-import.js M static/maps/mvc/history/history-import.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/history/history-import.js

Log Message: ----------- Remove debug helper

Commit: cf66742b4c1ab6d2c5bef8b5064679b5e7963b0a https://github.com/galaxyproject/galaxy/commit/cf66742b4c1ab6d2c5bef8b506467... Author: guerler aysam.guerler@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)

Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/utils/ajax-queue.js M config/galaxy.ini.sample M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/hash_util.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/hg_util.py M run_tests.sh M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/utils/ajax-queue.js R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M test/base/populators.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.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/unit/jobs/test_runner_local.py

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: b96398027e648d8c1c42180c162fbae3c73e31f5 https://github.com/galaxyproject/galaxy/commit/b96398027e648d8c1c42180c162fb... Author: guerler aysam.guerler@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py

Log Message: ----------- Consistent strings

Commit: 8f7dee460e7f90fa945cb6a1ff31c7aa81a4505b https://github.com/galaxyproject/galaxy/commit/8f7dee460e7f90fa945cb6a1ff31c... Author: guerler aysam.guerler@gmail.com Date: 2017-11-22 (Wed, 22 Nov 2017)

Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py A lib/galaxy/util/script.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.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/biostar.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tag.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/app.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.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_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M run_tests.sh M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako R templates/search/index.mako M templates/show_params.mako M templates/user/register.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.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_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.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/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: 2623bf369cae8b658118defad6fbf0dc825c2b73 https://github.com/galaxyproject/galaxy/commit/2623bf369cae8b658118defad6fbf... Author: guerler aysam.guerler@gmail.com Date: 2017-11-22 (Wed, 22 Nov 2017)

Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/style/less/base.less M client/gulpfile.js A client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/panel.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js A static/scripts/libs/vue.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: cb044bd45263341aede9866f219600a2caddfe55 https://github.com/galaxyproject/galaxy/commit/cb044bd45263341aede9866f21960... Author: guerler aysam.guerler@gmail.com Date: 2017-11-22 (Wed, 22 Nov 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/library.bundled.js M static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map

Log Message: ----------- Transform history import to vue component

Commit: 4cf8ad218467b310652b7c2e37190cf56ca68820 https://github.com/galaxyproject/galaxy/commit/4cf8ad218467b310652b7c2e37190... Author: guerler aysam.guerler@gmail.com Date: 2017-11-22 (Wed, 22 Nov 2017)

Changed paths: R client/galaxy/scripts/mvc/history/history-import.js R static/maps/mvc/history/history-import.js.map

Log Message: ----------- Remove former backbone view for history imports

Commit: 4ecf7a05b4d8bd6c20b8f73920c1e36436918c61 https://github.com/galaxyproject/galaxy/commit/4ecf7a05b4d8bd6c20b8f73920c1e... Author: guerler aysam.guerler@gmail.com Date: 2017-11-22 (Wed, 22 Nov 2017)

Changed paths: M .gitignore M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.complexify.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R static/maps/libs/jquery/jquery.mousewheel.js.map R static/maps/libs/jquery/jquery.rating.js.map R static/maps/libs/jquery/jquery.wymeditor.js.map R static/maps/libs/jquery/jstorage.js.map R static/maps/libs/jquery/jstree.js.map R static/maps/libs/jquery/select2.js.map R static/maps/libs/raven.js.map R static/maps/libs/require.js.map R static/maps/libs/showdown.js.map R static/maps/libs/toastr.js.map R static/maps/libs/underscore.js.map R static/maps/mvc/annotation.js.map R static/maps/mvc/base-mvc.js.map R static/maps/mvc/base/controlled-fetch-collection.js.map R static/maps/mvc/collection/base-creator.js.map R static/maps/mvc/collection/collection-li-edit.js.map R static/maps/mvc/collection/collection-li.js.map R static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-view-edit.js.map R static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/collection/list-collection-creator.js.map R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-item-li.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/lazy/lazy-limited.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/library/library-util.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/page/page-list.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R static/maps/mvc/toolshed/sheds-list-view.js.map R static/maps/mvc/toolshed/toolshed-model.js.map R static/maps/mvc/toolshed/util.js.map R static/maps/mvc/toolshed/workflows-view.js.map R static/maps/mvc/tours.js.map R static/maps/mvc/ui/error-modal.js.map R static/maps/mvc/ui/icon-button.js.map R static/maps/mvc/ui/popup-menu.js.map R static/maps/mvc/ui/ui-buttons.js.map R static/maps/mvc/ui/ui-color-picker.js.map R static/maps/mvc/ui/ui-drilldown.js.map R static/maps/mvc/ui/ui-frames.js.map R static/maps/mvc/ui/ui-list.js.map R static/maps/mvc/ui/ui-misc.js.map R static/maps/mvc/ui/ui-modal.js.map R static/maps/mvc/ui/ui-options.js.map R static/maps/mvc/ui/ui-popover.js.map R static/maps/mvc/ui/ui-portlet.js.map R static/maps/mvc/ui/ui-select-content.js.map R static/maps/mvc/ui/ui-select-default.js.map R static/maps/mvc/ui/ui-select-ftp.js.map R static/maps/mvc/ui/ui-select-genomespace.js.map R static/maps/mvc/ui/ui-select-library.js.map R static/maps/mvc/ui/ui-select.js.map R static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-extension.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-model.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js 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/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M 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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/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-import.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M 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static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M 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/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: 78508e200ab1ce2b6a665e0076eebabd1db4a14f https://github.com/galaxyproject/galaxy/commit/78508e200ab1ce2b6a665e0076eeb... Author: guerler aysam.guerler@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py R static/maps/galaxy.library.js.map R static/maps/layout/panel.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/citations.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/library.bundled.js.map R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js R static/scripts/bundled/workflow.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tag.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: f58ef136168999c3dc86468b3cf9d1220b4cf59a https://github.com/galaxyproject/galaxy/commit/f58ef136168999c3dc86468b3cf9d... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml

Log Message: ----------- Fix import by url for history archive import tool

Commit: 3c3b47e8ef2b5b2c4072f3e9d92dd6dadd72646e https://github.com/galaxyproject/galaxy/commit/3c3b47e8ef2b5b2c4072f3e9d92dd... Author: guerler aysam.guerler@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: A client/galaxy/scripts/components/history-import.vue M static/scripts/bundled/analysis.bundled.js

Log Message: ----------- Restore history vue component

Commit: 1785f6314d0e3fc2d2b189839f6e031448781dca https://github.com/galaxyproject/galaxy/commit/1785f6314d0e3fc2d2b189839f6e0... Author: guerler aysam.guerler@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M client/galaxy/scripts/components/history-import.vue M static/scripts/bundled/analysis.bundled.js

Log Message: ----------- Fix inline, remove unused message div

Commit: fa661bf7b0a905310188562204adac3afec9fb63 https://github.com/galaxyproject/galaxy/commit/fa661bf7b0a905310188562204ada... Author: guerler aysam.guerler@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/qunit/test.js M client/karma.config.js M client/package.json M config/workflow_schedulers_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/commit_util.py R manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main A scripts/get_uwsgi_args.py R scripts/manage_tools.py M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py

Log Message: ----------- Merge branch 'dev' into replace_history_import

Commit: 9800013ec2cd7433db329ad9db9114e57af37e07 https://github.com/galaxyproject/galaxy/commit/9800013ec2cd7433db329ad9db911... Author: guerler aysam.guerler@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py

Log Message: ----------- Switch to transparent readmode for history tarfiles

Commit: 081cbc4bb0cdbe202cf24b394beba4eb50125d0f https://github.com/galaxyproject/galaxy/commit/081cbc4bb0cdbe202cf24b394beba... Author: guerler aysam.guerler@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)

Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml

Log Message: ----------- Add quotes

Commit: 75a6d434ee00b51d66ea5bf40b0ddd19601d35e3 https://github.com/galaxyproject/galaxy/commit/75a6d434ee00b51d66ea5bf40b0dd... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-11-29 (Wed, 29 Nov 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/history-import.vue M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css

Log Message: ----------- Merge pull request #4993 from guerler/replace_history_import

Replace history import form

Compare: https://github.com/galaxyproject/galaxy/compare/8d7f344140d7...75a6d434ee00