Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c47516a1cb3f1e66fb24fcd78e078fd04d77f9a6 https://github.com/galaxyproject/galaxy/commit/c47516a1cb3f1e66fb24fcd78e078... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-08 (Mon, 08 Jan 2018)
Changed paths: A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/mvc/history/options-menu.js A lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py 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/mvc/history/options-menu.js R templates/webapps/galaxy/history/display_structured.mako
Log Message: ----------- Remove show history structure mako
Commit: 9c8fb8f9d97ba0d5ab6eaec74ea62706483a9148 https://github.com/galaxyproject/galaxy/commit/9c8fb8f9d97ba0d5ab6eaec74ea62... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M lib/galaxy/util/create_history_template.py M static/scripts/bundled/analysis.bundled.js
Log Message: ----------- Update the styling
Commit: c1ec73aa58467d255dd3aa8ca43bb20721b5f4e3 https://github.com/galaxyproject/galaxy/commit/c1ec73aa58467d255dd3aa8ca43bb... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/nls/zh/locale.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/production.md M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/model/migrate/check.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M scripts/db_shell.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/nls/zh/locale.js M test/api/test_workflows.py
Log Message: ----------- Merging with dev
Commit: e9755e111ac6f3e3d8412d539ecd91fb6a98cc31 https://github.com/galaxyproject/galaxy/commit/e9755e111ac6f3e3d8412d539ecd9... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message: ----------- Remove extra spacings around the braces
Commit: 5d5260260b3f44cbc9aac5018f41166006380c12 https://github.com/galaxyproject/galaxy/commit/5d5260260b3f44cbc9aac5018f411... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue
Log Message: ----------- Remove unused variables
Commit: 30a3ebee184de55755141b5baa1f495b2cf2b2ec https://github.com/galaxyproject/galaxy/commit/30a3ebee184de55755141b5baa1f4... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/HistoryView.vue 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/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js
Log Message: ----------- Update structure to replace history/view mako file
Commit: 394ae3340c52d632d2cc58929448352eae42dbdb https://github.com/galaxyproject/galaxy/commit/394ae3340c52d632d2cc589294483... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py 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
Log Message: ----------- Add view feature for a history in the list of histories
Commit: 92c7900356842fce23504bca607d4712b8adc8c8 https://github.com/galaxyproject/galaxy/commit/92c7900356842fce23504bca607d4... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths: R templates/webapps/galaxy/history/view.mako
Log Message: ----------- Remove history/view.mako file
Commit: 2e8ce77fc099481ec29bc5f65390640260073ec3 https://github.com/galaxyproject/galaxy/commit/2e8ce77fc099481ec29bc5f653906... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py M lib/galaxy/tools/__init__.py M scripts/common_startup.sh
Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into history_structure
Commit: 523bccdef829e03cbe84144d7139c5a9b163ba1b https://github.com/galaxyproject/galaxy/commit/523bccdef829e03cbe84144d7139c... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M lib/galaxy/util/create_history_template.py
Log Message: ----------- Update the dataset url
Commit: f2b0a3936e33081999103023f52397ecef492512 https://github.com/galaxyproject/galaxy/commit/f2b0a3936e33081999103023f5239... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/history/options-menu.js
Log Message: ----------- Update styling
Commit: dab7248c4e2bc6975052136a28f614321574dc78 https://github.com/galaxyproject/galaxy/commit/dab7248c4e2bc6975052136a28f61... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue
Log Message: ----------- Remove console.log statement from vue
Commit: 99f744f8353b37fd4d0a43b2ed9fe1493846c844 https://github.com/galaxyproject/galaxy/commit/99f744f8353b37fd4d0a43b2ed9fe... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M client/galaxy/scripts/components/HistoryView.vue M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/library/library-dataset-view.js
Log Message: ----------- Update json structure and add static files
Commit: 29695ecf52ba1ce1ea07d2e1158e1f7fe5432678 https://github.com/galaxyproject/galaxy/commit/29695ecf52ba1ce1ea07d2e1158e1... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message: ----------- Fix build fail issues
Commit: e619faefe405fe30c1d2a06b4d337e275f06ee5f https://github.com/galaxyproject/galaxy/commit/e619faefe405fe30c1d2a06b4d337... Author: anuprulez anup.rulez@gmail.com Date: 2018-01-17 (Wed, 17 Jan 2018)
Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message: ----------- Fix scripts
Commit: 3f8b38f4cb90e26cb13533a44c41e3756af68db0 https://github.com/galaxyproject/galaxy/commit/3f8b38f4cb90e26cb13533a44c41e... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-28 (Sun, 28 Jan 2018)
Changed paths: M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.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/tours.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.phylip M lib/galaxy/dependencies/conda-environment.txt 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/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.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/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/helpers/__init__.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/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/util/admin_util.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/db_shell.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/user/register.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M tools/data_source/microbial_import_code.py
Log Message: ----------- Merging with dev
Commit: dc3fcadda12a71c0eb8e508b88538ca09741d529 https://github.com/galaxyproject/galaxy/commit/dc3fcadda12a71c0eb8e508b88538... Author: anup kumar anup.rulez@gmail.com Date: 2018-01-28 (Sun, 28 Jan 2018)
Changed paths: M lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message: ----------- Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure
Commit: da23ed2ec60a851b011902acd6498ccddcb03f64 https://github.com/galaxyproject/galaxy/commit/da23ed2ec60a851b011902acd6498... Author: anuprulez anup.rulez@gmail.com Date: 2018-02-06 (Tue, 06 Feb 2018)
Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui/icon-btn.less M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M config/tool_shed.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M 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M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.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/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M 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static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/galaxy_client_app.mako M templates/user/register.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/api/test_tools.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M tools/data_source/microbial_import_code.py M tox.ini
Log Message: ----------- Merge with dev
Commit: 8772dbbb38664edfb6b6d472553ad7e421b35b0b https://github.com/galaxyproject/galaxy/commit/8772dbbb38664edfb6b6d472553ad... Author: anuprulez anup.rulez@gmail.com Date: 2018-02-06 (Tue, 06 Feb 2018)
Log Message: ----------- Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure
Commit: 73db0a5e80fa6cc528ec9170bd443971c001b32c https://github.com/galaxyproject/galaxy/commit/73db0a5e80fa6cc528ec9170bd443... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
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/style/blue/base.css
Log Message: ----------- Move show_structure to first class client route enabling direct nav, linking, etc. Minor cleanup
Commit: 3c0344bf15fe40f662586ac212e34bf5963c3345 https://github.com/galaxyproject/galaxy/commit/3c0344bf15fe40f662586ac212e34... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- Vue formatting via prettier.
Commit: baeb99e54720767066e8a1e96c9f237c2fcce890 https://github.com/galaxyproject/galaxy/commit/baeb99e54720767066e8a1e96c9f2... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue
Log Message: ----------- Use explicit imports instead of relying on bundleEntries. Kill toastr for axios error -- unnecessary.
Commit: 3c25883d5522c9763a16b977343a50a84cc28ddc https://github.com/galaxyproject/galaxy/commit/3c25883d5522c9763a16b977343a5... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- Remove another toastr error -- this sort of thing should be console; reporting http errors in the main UI isn't great UX
Commit: 433472a315ced57e033583ef0569d95e36d13bc3 https://github.com/galaxyproject/galaxy/commit/433472a315ced57e033583ef0569d... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js
Log Message: ----------- refactor history view entrypoint out of extended bundle into history-view; swap HistoryView.vue to use new points. Minor import refactoring/cleanup, too.
Commit: ee3b25c68f7ceb7fb3022d4002362806eabb38c0 https://github.com/galaxyproject/galaxy/commit/ee3b25c68f7ceb7fb3022d4002362... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- V-cloak hides uncompiled templates -- we precompile everything (and intend to, always) so this isn't necessary
Commit: 97fac3983d894df0b6c75a9c2f0ea3b54421a774 https://github.com/galaxyproject/galaxy/commit/97fac3983d894df0b6c75a9c2f0ea... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryView.vue
Log Message: ----------- Slightly better temporary error handling for new vue components.
Commit: 6b72952e953c118234357585cb6d3a50c3df4837 https://github.com/galaxyproject/galaxy/commit/6b72952e953c118234357585cb6d3... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/utils/localization.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/ui.less M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R 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test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_validation.py
Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history_structure
Commit: a847ce20965ecb6418b48616effb049c56568c01 https://github.com/galaxyproject/galaxy/commit/a847ce20965ecb6418b48616effb0... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js A lib/galaxy/util/create_history_template.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako
Log Message: ----------- Merge pull request #5317 from bgruening/history_structure
History structure
Compare: https://github.com/galaxyproject/galaxy/compare/de2bfa2ccacf...a847ce20965e