Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8bbc42167d249e2dcb3130e795dd5e0b384df61 https://github.com/galaxyproject/galaxy/commit/f8bbc42167d249e2dcb3130e795dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove sample request links from admin panel Commit: a5fab9f67de730bae6ff85e3a579bbbc1b22edcb https://github.com/galaxyproject/galaxy/commit/a5fab9f67de730bae6ff85e3a579b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Do not serialize if a user has requests Commit: f9e8b4f2ad4cf3d1cb95fce327fda79a2a13e41e https://github.com/galaxyproject/galaxy/commit/f9e8b4f2ad4cf3d1cb95fce327fda... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py Log Message: ----------- Remove controller endpoints for requests and external services Commit: 413a07878e751497ef39340736f2fa8a3a40c803 https://github.com/galaxyproject/galaxy/commit/413a07878e751497ef39340736f2f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako Log Message: ----------- Remove admin makos for requests and external services Commit: 3b4c124cccf1e343cc075741e93acad30577d934 https://github.com/galaxyproject/galaxy/commit/3b4c124cccf1e343cc075741e93ac... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako Log Message: ----------- Remove user makos for requests and external services Commit: 82f5a4cff7da178af841aa9bcd69ec03e90f2c1a https://github.com/galaxyproject/galaxy/commit/82f5a4cff7da178af841aa9bcd69e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A templates/webapps/galaxy/external_services/generic_jquery_grid.mako A templates/webapps/galaxy/external_services/generic_json.mako A templates/webapps/galaxy/external_services/json_common.mako Log Message: ----------- Leave makos used by external service result handlers in for now Commit: 6237eba32ffaef96e273186d13dbc7de32c2bb95 https://github.com/galaxyproject/galaxy/commit/6237eba32ffaef96e273186d13dbc... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/iphone.less A client/galaxy/style/less/theme/plain.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed M lib/galaxy/web/framework/base.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/workflow/modules.py R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.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/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css R static/style/blue/iphone.css M templates/webapps/galaxy/dataset/copy_view.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako M test/api/test_jobs.py M test/functional/tools/sample_datatypes_conf.xml A test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: ecf5031eef6b591f81a5d799955347f194b0df47 https://github.com/galaxyproject/galaxy/commit/ecf5031eef6b591f81a5d79995534... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Remove unused library Commit: c6c7cb855ae579bb1d8a338f526d2231a8ca9c6a https://github.com/galaxyproject/galaxy/commit/c6c7cb855ae579bb1d8a338f526d2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Fix failing test Commit: ce3e2ebf7db681b8611b47c0c29c121c511ebe02 https://github.com/galaxyproject/galaxy/commit/ce3e2ebf7db681b8611b47c0c29c1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/error_report.yml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M doc/source/admin/special_topics/bug_reports.rst A doc/source/dev/finding_and_improving_slow_code.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_to_bai.xml A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/requirements.py A lib/galaxy/tools/deps/resolvers/lmod.py A 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/imp_exp/__init__.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/base/controller.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.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/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/xml_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.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/layout/page.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/options-menu.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-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/editor.mako A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_histories.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml A test/functional/twilltestcase.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.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 A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.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 M test/unit/tools/test_tool_deps.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 9045e3fb4eb3023285fe16a55e06e3610babf89f https://github.com/galaxyproject/galaxy/commit/9045e3fb4eb3023285fe16a55e06e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-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 Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 7ea5f3a3a27f4fbfbd90606405eec0d60db5b106 https://github.com/galaxyproject/galaxy/commit/7ea5f3a3a27f4fbfbd90606405eec... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Remove lab tab from masthead Commit: ebbe5a103920c5581bc2b1332a5552002867abce https://github.com/galaxyproject/galaxy/commit/ebbe5a103920c5581bc2b1332a555... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M create_db.sh M extract_dataset_parts.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webhooks/__init__.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.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-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/user/user-custom-builds.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/mvc/base/controlled-fetch-collection.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-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/user/user-custom-builds.js M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 1494207a0decfdd18c0f951a8480372e06bc53f1 https://github.com/galaxyproject/galaxy/commit/1494207a0decfdd18c0f951a84803... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M client/galaxy/style/less/upload.less M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/dynamic_options.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/base.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_watchers.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/tool_validator.py M static/style/blue/base.css R templates/admin/tool_shed_repository/browse_category.mako R templates/export_base.mako R templates/rss.mako R templates/webapps/galaxy/admin/toolsheds.mako M test/api/test_dataset_collections.py M test/base/driver_util.py M test/base/populators.py A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py A test/integration/tool_sheds_conf.xml M test/selenium_tests/framework.py A test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 81f111c720954fd54d54b7604e7be6fd3e4aeeb9 https://github.com/galaxyproject/galaxy/commit/81f111c720954fd54d54b7604e7be... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/managers/users.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M static/maps/layout/menu.js.map 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/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/history/options-menu.js R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge remote-tracking branch 'erasche/what-i-have' into remove_samples_000 Commit: 291922174cb240c5526eb06fa469974dfcb376fc https://github.com/galaxyproject/galaxy/commit/291922174cb240c5526eb06fa4699... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.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/onload.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/tool_shed/model/__init__.py M static/maps/mvc/history/history-view.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/onload.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/mvc/history/history-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/onload.js A test-data/selenium-test-notebook.ipynb M test/api/test_tools.py A test/api/test_tools_upload.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/populators.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/integration/test_upload_configuration_options.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_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.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/unit/test_security_helper.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/filters/joiner.xml Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 0d5d2aea830a44a7c6d805d5f9fee0eebe69f0ae https://github.com/galaxyproject/galaxy/commit/0d5d2aea830a44a7c6d805d5f9fee... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/package-lock.json M config/error_report.yml.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M run.sh M run_tests.sh M setup.cfg M static/maps/layout/router.js.map M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-view.js.map M 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static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js A static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M templates/sharing_base.mako M templates/show_params.mako M test/api/test_tools_upload.py M test/base/populators.py A test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/qunit/tests/upload_dialog_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.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_library_contents.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 3a06f76254497674c627931a560c7f3d3241d547 https://github.com/galaxyproject/galaxy/commit/3a06f76254497674c627931a560c7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/py3_sources.txt M .gitignore M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M 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static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js R static/scripts/analysis.js R static/scripts/app.js R static/scripts/app/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M 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static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js R static/scripts/libs/showdown.js M static/scripts/libs/toastr.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/citation/citation-model.js M static/scripts/mvc/citation/citation-view.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 static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/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 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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 M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako M test/functional/tools/collection_split_on_column.xml A test/functional/tools/empty_datasets.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js R test/qunit/test-libs/sinon-1.17.3.js A test/qunit/test-libs/sinon-1.17.7.js M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 454e00d9bf4b3ec97f005373a801765ac8ed7483 https://github.com/galaxyproject/galaxy/commit/454e00d9bf4b3ec97f005373a8017... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.complexify.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/underscore.js Log Message: ----------- Repack scripts Commit: a123bee6cf58f1cd9880cccb575b1dcfbccfec9d https://github.com/galaxyproject/galaxy/commit/a123bee6cf58f1cd9880cccb575b1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/slideshow/architecture/galaxy_architecture.md A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-parameters.js.map 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/libs/backbone.js M static/scripts/libs/bibtex.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 7c3fdbe1a5a1c8b59c80ce19434fa0f22ec46f00 https://github.com/galaxyproject/galaxy/commit/7c3fdbe1a5a1c8b59c80ce19434fa... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/managers/groups.py M scripts/cleanup_datasets/pgcleanup.py M static/maps/galaxy.interactive_environments.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js M tools/data_source/data_source.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 08913b6f74d19b33ff6ea68b34664652b780c864 https://github.com/galaxyproject/galaxy/commit/08913b6f74d19b33ff6ea68b34664... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack Commit: df658082ff36c8ea920b8cb952117ecccffbaeae https://github.com/galaxyproject/galaxy/commit/df658082ff36c8ea920b8cb952117... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- remove the mentionof sample tracking from admin page Commit: d11ed538c679b2aec889ed8e64153f7c2c1d4176 https://github.com/galaxyproject/galaxy/commit/d11ed538c679b2aec889ed8e64153... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- tie sample tracking api controllers functionality to config introduce enable_legacy_sample_tracking_api config option that controls that disable by default Commit: 8f6e5eb6f578dd9141b511f1d64aa350ee8f9663 https://github.com/galaxyproject/galaxy/commit/8f6e5eb6f578dd9141b511f1d64aa... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/utils/utils.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.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/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.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/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy_ext/metadata/set_metadata.py M lib/psyco_full.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/utils/utils.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/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/utils/utils.js R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into remove_samples_000 Commit: 52a566eb056f442e12fcdb79e655e183f1727dd8 https://github.com/galaxyproject/galaxy/commit/52a566eb056f442e12fcdb79e655e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/requests.py Log Message: ----------- Remove api dependency on web controller Commit: 8e9a7e86250ab015309e4fe43171918f33374403 https://github.com/galaxyproject/galaxy/commit/8e9a7e86250ab015309e4fe431719... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/requests.py Log Message: ----------- Remove unused import Commit: d3a6af5f71141eb01392788e87f993f21fe2d758 https://github.com/galaxyproject/galaxy/commit/d3a6af5f71141eb01392788e87f99... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add legacy data libraries link Commit: 1e23a6397b2383c7b985a765f65b559b5bb6aa2b https://github.com/galaxyproject/galaxy/commit/1e23a6397b2383c7b985a765f65b5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Fix order in center panel information view Commit: 3dd45099ba5a3a3f4f206553c122994d7746112e https://github.com/galaxyproject/galaxy/commit/3dd45099ba5a3a3f4f206553c1229... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Remove "Lab" from masthead Commit: a1f0895c927e759e30a59dcc1b40a4507eb1e82e https://github.com/galaxyproject/galaxy/commit/a1f0895c927e759e30a59dcc1b40a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/samples.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M static/maps/layout/menu.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bibtex.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.cookie.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/jquery/jquery.mousewheel.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/underscore.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #4526 from guerler/remove_samples_000 Removes Sample request and External services makos/controllers Compare: https://github.com/galaxyproject/galaxy/compare/52b16ecd329d...a1f0895c927e