- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 66f57f: Remove external services config file
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66f57f51003a7bfa73e44355d901158c06ca9b87 https://github.com/galaxyproject/galaxy/commit/66f57f51003a7bfa73e44355d901… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R config/external_service_types_conf.xml.sample Log Message: ----------- Remove external services config file Commit: 4fe1b16da89847f99dcbc9b46cac8e088a5cb7f6 https://github.com/galaxyproject/galaxy/commit/4fe1b16da89847f99dcbc9b46cac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove external services from galaxy config Commit: 13dad63cc9d95c43b3dae07c4e0c9bfe4e1fc1a4 https://github.com/galaxyproject/galaxy/commit/13dad63cc9d95c43b3dae07c4e0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/454_life_sciences.xml Log Message: ----------- Remove 454 life science Commit: d3f58fde66bb0a3457e4d3e7b9e8a523f782a187 https://github.com/galaxyproject/galaxy/commit/d3f58fde66bb0a3457e4d3e7b9e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/applied_biosystems_solid.xml Log Message: ----------- Remove biosystems xml Commit: ebab8f235f5b2c0578fae2739daa046fcd39a564 https://github.com/galaxyproject/galaxy/commit/ebab8f235f5b2c0578fae2739daa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/pacific_biosciences_smrt_portal.xml Log Message: ----------- Remove pacific biosciences xml Commit: 223044a91e8595c4ba5e8c809c06f232ffad4dde https://github.com/galaxyproject/galaxy/commit/223044a91e8595c4ba5e8c809c06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/simple_unknown_sequencer.xml Log Message: ----------- Remove default wrapper for unkown sequencer Commit: e57b3b83d0e4cf7ff0d91d98156954962bd9f267 https://github.com/galaxyproject/galaxy/commit/e57b3b83d0e4cf7ff0d91d981569… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Remove sample tracking from config Commit: 5e81fc30cc49512c3911dcfaab61acd13d2f95ad https://github.com/galaxyproject/galaxy/commit/5e81fc30cc49512c3911dcfaab61… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove from config Commit: 65a23a895157f1817349c691369ee9439099a7ed https://github.com/galaxyproject/galaxy/commit/65a23a895157f1817349c691369e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py Log Message: ----------- Remove external services from lib Commit: 697eac0be98e006efdc01ac857f545aa767b809d https://github.com/galaxyproject/galaxy/commit/697eac0be98e006efdc01ac857f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Log Message: ----------- Remove deferred job handler from lib Commit: 7ea7493775f95c1f462e44fd713e92eb819bdd82 https://github.com/galaxyproject/galaxy/commit/7ea7493775f95c1f462e44fd713e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Remove request types caller from context manager Commit: 10f4d8e9ee16244ac67bebee9fe2c01c5c6c626e https://github.com/galaxyproject/galaxy/commit/10f4d8e9ee16244ac67bebee9fe2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py Log Message: ----------- Remove sample tracking from lib Commit: e8f96a43f6acf668f6c4115c7b8d7b330835ae0e https://github.com/galaxyproject/galaxy/commit/e8f96a43f6acf668f6c4115c7b8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused name_autocomplete_data from admin controller Commit: 9444686dbd9f01dfcc6c7a2b2ad0ca1d9d89b595 https://github.com/galaxyproject/galaxy/commit/9444686dbd9f01dfcc6c7a2b2ad0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Remove request details parsing to client in root Commit: 7a2be3b625f8217519f07877687124570206ffed https://github.com/galaxyproject/galaxy/commit/7a2be3b625f8217519f078776871… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Remove request parsing to masthead mako Commit: b523ed1262530d35e2ff955da63360c6e7965c8c https://github.com/galaxyproject/galaxy/commit/b523ed1262530d35e2ff955da633… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 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 Log Message: ----------- Remove external services templates Commit: 7eb9501b430b72bcb6b3c493a0c3678a4133dbbc https://github.com/galaxyproject/galaxy/commit/7eb9501b430b72bcb6b3c493a0c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Remove external service handler from security handler Commit: 3e5ce939dec42dd60e238d136f530a7e2613c588 https://github.com/galaxyproject/galaxy/commit/3e5ce939dec42dd60e238d136f53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove edit template controller Commit: 1443b76c307870968eb3c1401bb8690bcb14111b https://github.com/galaxyproject/galaxy/commit/1443b76c307870968eb3c1401bb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove edit template info controller Commit: 728a64cfa85427e48c18fb4301abbb0d5b27ede9 https://github.com/galaxyproject/galaxy/commit/728a64cfa85427e48c18fb4301ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove add template controller Commit: ae6bee39bb49d9dcda46fe0916030665b5ff52f4 https://github.com/galaxyproject/galaxy/commit/ae6bee39bb49d9dcda46fe091603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove delete template controller Commit: b7d802f4088251d1755815120b5206785a4f848f https://github.com/galaxyproject/galaxy/commit/b7d802f4088251d1755815120b52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove widget helper Commit: 98dc0ce5aeeff87cc14880026435a6d87008b192 https://github.com/galaxyproject/galaxy/commit/98dc0ce5aeeff87cc14880026435… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove empty field helper Commit: 08940a3a5169c9709dc4aafcd54922373e8bfa02 https://github.com/galaxyproject/galaxy/commit/08940a3a5169c9709dc4aafcd549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove widget populator for previous refresh on change handler Commit: 70b094650f84a30a04f880ac94b423566d100514 https://github.com/galaxyproject/galaxy/commit/70b094650f84a30a04f880ac94b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove item retrieval helper Commit: 0051d425917d2fef4f17106adacb12ddf0911b12 https://github.com/galaxyproject/galaxy/commit/0051d425917d2fef4f17106adacb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove select field build helper Commit: 3f1dda688376dcfd8e9a09abc275e089fa7d5e2f https://github.com/galaxyproject/galaxy/commit/3f1dda688376dcfd8e9a09abc275… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove form filter helper Commit: bbaea8b67cb9cd8ed2ab66120bbef92574629803 https://github.com/galaxyproject/galaxy/commit/bbaea8b67cb9cd8ed2ab66120bbe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove unused form elements from shared controller endpoint Commit: ed1b4e1f432b86bc212478cccfe64daa12d1d6fe https://github.com/galaxyproject/galaxy/commit/ed1b4e1f432b86bc212478cccfe6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Clean up import section in shared controller Commit: 3e8efaf0a83e08d9457f33be61c0d6b648a682dc https://github.com/galaxyproject/galaxy/commit/3e8efaf0a83e08d9457f33be61c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove requests from user keys Commit: fa516635f38f004724bcf6e89ec2b909bab57ad1 https://github.com/galaxyproject/galaxy/commit/fa516635f38f004724bcf6e89ec2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove model handlers for tables associated with sample tracking Commit: 5e4b76c422cba4421c39d19e6883c3372bd5b250 https://github.com/galaxyproject/galaxy/commit/5e4b76c422cba4421c39d19e6883… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused form types Commit: 7c2fab59ee027594cd7a2ee22b5face3a1ac7e09 https://github.com/galaxyproject/galaxy/commit/7c2fab59ee027594cd7a2ee22b5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused imports, align comments Commit: 7abb1890594cb411780925bbeae782b19c222e74 https://github.com/galaxyproject/galaxy/commit/7abb1890594cb411780925bbeae7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove mapping classes for external services Commit: f305ab724eb4101f7c0a744131d764c39f6c9d52 https://github.com/galaxyproject/galaxy/commit/f305ab724eb4101f7c0a744131d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Remove external service from mapping Commit: 26163538f314fa32d789ada6df91ecdec475e0f3 https://github.com/galaxyproject/galaxy/commit/26163538f314fa32d789ada6df91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M .gitignore M Makefile M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/mvc/history/job-states-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/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js R client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/graph_tests.js R client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js R client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js R client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js R client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js R client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/list-item.less M client/gulpfile.js M client/karma.config.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.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/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.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/actions/upload_common.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/util/image_util.py R lib/galaxy/util/multi_byte.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M scripts/db_shell.py R static/GruntFile.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js R static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/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/pair-collection-creator.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tool/tool-form-base.js A static/scripts/packed M static/scripts/viz/trackster.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/bibtex.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_tool_form.py M test/unit/dataset_collections/test_matching.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into remove_sample_tracking Commit: dad11b8ef6d7f4e332dff616f6092a759c5aa924 https://github.com/galaxyproject/galaxy/commit/dad11b8ef6d7f4e332dff616f609… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: R config/external_service_types_conf.xml.sample M config/galaxy.ini.sample R external_service_types/454_life_sciences.xml R external_service_types/applied_biosystems_solid.xml R external_service_types/pacific_biosciences_smrt_portal.xml R external_service_types/simple_unknown_sequencer.xml M lib/galaxy/app.py M lib/galaxy/config.py R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/root.py 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 M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #5103 from guerler/remove_sample_tracking Remove sample tracking backend support, preserve data tables Compare: https://github.com/galaxyproject/galaxy/compare/fc18b504be91...dad11b8ef6d7

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[galaxyproject/usegalaxy-playbook] 6ca912: Update Test
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6ca9126f93d03bf7eb9255394e3e80a9668027f1 https://github.com/galaxyproject/usegalaxy-playbook/commit/6ca9126f93d03bf7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: eea8722ea758a976f5de601b9b52d0767c65e49f https://github.com/galaxyproject/usegalaxy-playbook/commit/eea8722ea758a976… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4ae2fa71f5d7...…

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[galaxyproject/galaxy] 06e950: Allow get_history calls with create=False when eva...
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06e9509d3868c885d41d94e455d7245f4af10156 https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Allow get_history calls with create=False when evaluation workflows. No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history. Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2 https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Do not attempt to visit parameters of invalid conditionals Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8 https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Check for key/value errors only when testing conditional cases Commit: 75f84bfc476ea94c22a38097d20f694265fcded6 https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test cases to cover version changes Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Remove unnecessary name setting for non-group parameters Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116 https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix comments Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix workflow editor output attributes. Commit: 5dc2254417667216dab982a4bc375a85d3b55316 https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4997 from jmchilton/allow_create_false_in_work_context [17.09] Allow get_history calls with create=False when evaluation workflows. Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8 https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #5022 from dannon/workflow_editor_fix_backport [17.09] Fix workflow editor output attributes. Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add ICM datatype for glimmer Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- copy paste mistake... Commit: f60a75c285830bff963bd31120f3420e9815dbe2 https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f3… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- extraneous %s Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0 https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #5048 from erasche/fix-ufr-6206 Remove extraneous %s in condor logging Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38 https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e388… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Bug fix - expose proper element_identifier in tool action template expansions. (#5049) xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3… Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't read too much Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Closes https://github.com/galaxyproject/galaxy/issues/2645. Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ``` Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix metadata setting for Otu datatypes I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard. Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes [BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade [BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation [BUG][17.09] Fix metadata setting for Otu datatypes Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446 https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix exception in admin panel TypeError: Non-hexadecimal digit found File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories return self.repository_installation_grid(trans, **kwd) File "galaxy/web/framework/helpers/grids.py", line 85, in __call__ query = self.build_initial_query(trans, **kwargs) File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id)) File "galaxy/web/security/__init__.py", line 107, in decode_id return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!")) File "encodings/hex_codec.py", line 42, in hex_decode output = binascii.a2b_hex(input) This is due to `tool_shed_repository_ids` being a json dump of a list in certain consitions (noticed this after installing a new repository). Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt [17.09] Add ICM datatype for glimmer Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix [17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045 [17.09] Backport #5045 Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03 https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #5010 from guerler/fix_pages_workflows [17.09] Do not visit child inputs of invalid conditionals Commit: a82d325d18375797ce8ab53366320f3c9a772ab7 https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab5336632… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Merge pull request #5079 from mvdbeek/admin_panel_exception_fix [17.09] Fix exception in admin panel Commit: 4dd05fc942988367cd5dd83695321063733f080e https://github.com/galaxyproject/galaxy/commit/4dd05fc942988367cd5dd8369532… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/work/context.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.09' into dev Commit: fc18b504be91a9f2eeb2ae74d136674ba70df1f6 https://github.com/galaxyproject/galaxy/commit/fc18b504be91a9f2eeb2ae74d136… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/work/context.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5108 from mvdbeek/merge_forward_17_09 Merge forward 17 09 Compare: https://github.com/galaxyproject/galaxy/compare/e48f0bf319d0...fc18b504be91

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[galaxyproject/galaxy] 48aca7: Update to flake8-import-order 0.16
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48aca7dce8608a7288b4613757f9085fad242785 https://github.com/galaxyproject/galaxy/commit/48aca7dce8608a7288b4613757f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M cron/build_chrom_db.py M lib/galaxy/actions/library.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/execute.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/microbes/harvest_bacteria.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/integration_util.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_local_job_cancellation.py M test/integration/test_workflow_handler_configuration.py M test/integration/test_workflow_scheduling_options.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Update to flake8-import-order 0.16 Commit: e48f0bf319d09c460bd62572f10ce3d7c6b6a168 https://github.com/galaxyproject/galaxy/commit/e48f0bf319d09c460bd62572f10c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M cron/build_chrom_db.py M lib/galaxy/actions/library.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/execute.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/microbes/harvest_bacteria.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/integration_util.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_local_job_cancellation.py M test/integration/test_workflow_handler_configuration.py M test/integration/test_workflow_scheduling_options.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #5110 from nsoranzo/flake8-import-order Update to flake8-import-order 0.16 Compare: https://github.com/galaxyproject/galaxy/compare/dcd7e7809e14...e48f0bf319d0

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[galaxyproject/galaxy] b3271a: Optimize history collection response.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3271a42cb174af5c86bd4e6c32bdcb8cf0c6cab https://github.com/galaxyproject/galaxy/commit/b3271a42cb174af5c86bd4e6c32b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Optimize history collection response. Introduce a new collection view type (between view="collection" and view="element") called "element-reference" that fetches the element structure of a collection and enough information to resolve references for leaf datasets but doesn't include details that aren't used in rendering the structure of the collection in the GUI. Prevents transmitting metadata, dataset name (since element identifier is used), info, peek, dbkey, etc.... Backbone and the rest of the infrastructure seems to just work and fills in all remaining details when datasets are actually expanded by users. Optimization mentioned in #3795 - mitigates the issue (hopefully to large degree - but doesn't fix it). Commit: 09c0d2384dbd047a96910f5e6e2daa375b1baf88 https://github.com/galaxyproject/galaxy/commit/09c0d2384dbd047a96910f5e6e2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Limit the number of elements the UX renders/fetches for collections. Fixes #3795 - more or less. Commit: 4b4a6e5a1c0d248ec32f07157ff6ecc3e7364ef3 https://github.com/galaxyproject/galaxy/commit/4b4a6e5a1c0d248ec32f07157ff6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Instrumentable paging... Commit: 485f64ee38bfeb31601817cac06028c7d043481c https://github.com/galaxyproject/galaxy/commit/485f64ee38bfeb31601817cac060… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Selenium testing for pagination of the history panel. Commit: 2a165c9afce58a8428bbdffaa0a5887e57285272 https://github.com/galaxyproject/galaxy/commit/2a165c9afce58a8428bbdffaa0a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js Log Message: ----------- Refactor subtitle of collection display. Commit: 98e5d932f980c0e60f72d6d7184fea145deef3a9 https://github.com/galaxyproject/galaxy/commit/98e5d932f980c0e60f72d6d7184f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Synchronize logic/code for displaying short collection descriptions. Commit: 37705885db99ed3ae104787730e1d8b04a6f81f4 https://github.com/galaxyproject/galaxy/commit/37705885db99ed3ae104787730e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-content-model.js M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Warn the user if not all collection elements are rendered. With test case. Commit: 345ee9aa9d6dfc6407657786c080accc1f5bad8c https://github.com/galaxyproject/galaxy/commit/345ee9aa9d6dfc6407657786c080… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Make new Selenium pagination test as flakey - doesn't work consistently on Jenkins. Commit: 94a5cc141dabce5e95044517550a80b2d60e44f6 https://github.com/galaxyproject/galaxy/commit/94a5cc141dabce5e95044517550a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Repack client. Commit: dcd7e7809e144885652a386b3eb14fc59e20deb2 https://github.com/galaxyproject/galaxy/commit/dcd7e7809e144885652a386b3eb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Merge pull request #5091 from jmchilton/open_large_collections Render arbitrarily large collections in the UI. Compare: https://github.com/galaxyproject/galaxy/compare/f70e6f5627bc...dcd7e7809e14

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[galaxyproject/galaxy] 051a31: Fix some datatype issues
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 051a3173fcffb0fe682bc5c0d692b77855c37a53 https://github.com/galaxyproject/galaxy/commit/051a3173fcffb0fe682bc5c0d692… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix some datatype issues - dmnd had a wrong class name - biom1, cool and postgresql shouldn't have `subclass="true"` - extension should be lowercase - add missing file_ext attribute to various datatype classes Commit: 743d5a37e8d4e35313fa872f4afe6ea616cfa36c https://github.com/galaxyproject/galaxy/commit/743d5a37e8d4e35313fa872f4afe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix append_to_sniff_order() `isinstance()` was leaving out e.g. the BigWig datatype because BigBed, which was added first, is a subclass of BigWig. Instead, add a datatype only if it is not already in `sniff_order`, it has a `sniff()` method and was not defined with `subclass="true"`. Commit: 0e0acb5200720cddaaff32bddf71c65f6cfe777e https://github.com/galaxyproject/galaxy/commit/0e0acb5200720cddaaff32bddf71… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/image_util.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Remove is_multi_byte from upload.py Also, when sniffing binary files, sniff images together with the other formats and respect sniff order. Also remove `is_multi_byte` from: - `stream_to_open_named_file()` - `stream_to_file()` Remove the now unused `get_image_ext()` and `Binary.is_sniffable_binary()` and all the calls to `Binary.register_sniffable_binary_format()`. Commit: fea6ddeeca7ccf89f1cacf9bcf49bfa18d16ad83 https://github.com/galaxyproject/galaxy/commit/fea6ddeeca7ccf89f1cacf9bcf49… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py R lib/galaxy/util/multi_byte.py Log Message: ----------- Remove last remnants of is_multi_byte, drop wchartype dependency Commit: f70e6f5627bc1f1e9398b9e88d398292d8e08998 https://github.com/galaxyproject/galaxy/commit/f70e6f5627bc1f1e9398b9e88d39… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample 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/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/image_util.py R lib/galaxy/util/multi_byte.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5088 from nsoranzo/remove_wchartype_dep Remove wchartype dependency and is_multi_byte [2/2] Compare: https://github.com/galaxyproject/galaxy/compare/1b4d8e5b9a51...f70e6f5627bc

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[galaxyproject/usegalaxy-playbook] 4ae2fa: Disable HTTP/2 =( because it seems to be causing u...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4ae2fa71f5d7307db4dc9dce0840a47462d135fe https://github.com/galaxyproject/usegalaxy-playbook/commit/4ae2fa71f5d7307d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M env/main/templates/nginx/usegalaxy.j2 M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Disable HTTP/2 =( because it seems to be causing upload failures: 2017/11/30 14:23:27 [alert] 11002#0: *16 epoll_ctl(1, 25) failed (17: File exists), client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:23:27 [alert] 11002#0: *16 header already sent, client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:25:34 [alert] 11002#0: *16 epoll_ctl(1, 25) failed (17: File exists), client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:25:34 [alert] 11002#0: *16 header already sent, client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:25:39 [alert] 11002#0: *16 epoll_ctl(1, 25) failed (17: File exists), client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:25:39 [alert] 11002#0: *16 header already sent, client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list" 2017/11/30 14:25:54 [alert] 11002#0: *16 aborted uploading file "1.bed" to "/galaxy-repl/test/upload/0025242369", dest file removed, client: 128.118.201.137, server: test.galaxyproject.org, request: "POST /_upload HTTP/2.0", host: "test.galaxyproject.org", referrer: "https://test.galaxyproject.org/histories/list"

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[galaxyproject/galaxy] 58b976: Fixup modal_tests.js
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58b9767d179cd7e877f6cc8e637f1859d8dd5138 https://github.com/galaxyproject/galaxy/commit/58b9767d179cd7e877f6cc8e637f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/tests/modal_tests.js M client/karma.config.js Log Message: ----------- Fixup modal_tests.js Disable jQuery FX instead of mocking time - mocking time with sinon seems to not be working :(. Tests are conceptually cleaner this way IMO anyway. Commit: 2983a04e999193c1a250b1d6aaf9ed67a40536fa https://github.com/galaxyproject/galaxy/commit/2983a04e999193c1a250b1d6aaf9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js M client/karma.config.js Log Message: ----------- Re-enable form qunit tests. Commit: 2f2ee90c6c103f39db716aaabb38297f0e53d540 https://github.com/galaxyproject/galaxy/commit/2f2ee90c6c103f39db716aaabb38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/karma.config.js Log Message: ----------- Re-enable masthead tests. Commit: f0dc1e4f7a5a36bd1a01bbc938e27db97301663f https://github.com/galaxyproject/galaxy/commit/f0dc1e4f7a5a36bd1a01bbc938e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: R client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js R client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/graph_tests.js R client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js R client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js R client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js R client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js R client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/utils_tests.js M client/karma.config.js Log Message: ----------- Rename qunit test files for consistency. Commit: 364e4518a833a77b977b8b48392e86e8833fe091 https://github.com/galaxyproject/galaxy/commit/364e4518a833a77b977b8b48392e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/test.js Log Message: ----------- In qunit single pack mode - enumerate the files to figure out the problems. Commit: 4270a7b0e39e36a8177dc596b839355eac115035 https://github.com/galaxyproject/galaxy/commit/4270a7b0e39e36a8177dc596b839… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js Log Message: ----------- Fix a missing server.restore in a test case. Commit: 395a6c3a5f5f2c1ed24b17b7b6f6753625d3e4b7 https://github.com/galaxyproject/galaxy/commit/395a6c3a5f5f2c1ed24b17b7b6f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Switch qunit testing to producing a single webpack bundle. I think a lot of the remaining issues stem from attempting to load multiple bundles in the same web browser window - repeatedly loading jQuery, select2, etc.... This variant is much closer to running all the tests in a seemingly more flexible order and I've never seen a select2 problem this way. Commit: 930ac1ab796a7d4414d6c573c752d9dcc07f4de2 https://github.com/galaxyproject/galaxy/commit/930ac1ab796a7d4414d6c573c752… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/graph_tests.js M client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job_dag_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Convert qunit tests to ES6. ... and make client-format them. Commit: 4769a98ea0db663b33465de48485f69965e39da8 https://github.com/galaxyproject/galaxy/commit/4769a98ea0db663b33465de48485… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js Log Message: ----------- Comment out the one failing qunit test. Commit: 1b4d8e5b9a518a9116168added511a099ac1acf4 https://github.com/galaxyproject/galaxy/commit/1b4d8e5b9a518a9116168added51… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js R client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/graph_tests.js R client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js R client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js R client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js R client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js R client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/karma.config.js M client/package.json Log Message: ----------- Merge pull request #5074 from jmchilton/qunit_fixes More QUnit Fixes and Enhancements Compare: https://github.com/galaxyproject/galaxy/compare/1385cf4f83ac...1b4d8e5b9a51

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[galaxyproject/galaxy] ca2eb5: Simple tool test for citations.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca2eb5b2a5a3b4e9a026806dc5f228fcce681379 https://github.com/galaxyproject/galaxy/commit/ca2eb5b2a5a3b4e9a026806dc5f2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M test/functional/tools/bibtex.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Simple tool test for citations. Commit: b3d06f481a5fa6c649cb1ea6709038041566b9c5 https://github.com/galaxyproject/galaxy/commit/b3d06f481a5fa6c649cb1ea67090… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M client/galaxy/scripts/components/citations.vue Log Message: ----------- Restore classes on citation switching buttons. Commit: 95c0ff6bf9ae19374eb660731e42370157c366c6 https://github.com/galaxyproject/galaxy/commit/95c0ff6bf9ae19374eb660731e42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js Log Message: ----------- Repack client. Commit: 05ddc50c1a7b0989e100e7ca817a96bad3d68ad7 https://github.com/galaxyproject/galaxy/commit/05ddc50c1a7b0989e100e7ca817a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Make test more robust - citations take a while to fetch from doi. Commit: bb7d06f59ed20fcbef7ad36d06a1ec138fac7e96 https://github.com/galaxyproject/galaxy/commit/bb7d06f59ed20fcbef7ad36d06a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-25 (Sat, 25 Nov 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Pre-fetch citations in new test so available quickly at render time. Commit: d8fe56c670ec78bb00e70d56cf59a895a1b8418b https://github.com/galaxyproject/galaxy/commit/d8fe56c670ec78bb00e70d56cf59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Modify citations test to clarify some bugs. Commit: 1385cf4f83ac508b997ca0cd2a3e893c69b84408 https://github.com/galaxyproject/galaxy/commit/1385cf4f83ac508b997ca0cd2a3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/components/Citations.vue M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M test/functional/tools/bibtex.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/citations' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5124c5610900...1385cf4f83ac

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[galaxyproject/galaxy] cd91e8: Fix trackster link to custom builds view
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd91e8d85cb98b4bbdb35c569c1a3047933439a8 https://github.com/galaxyproject/galaxy/commit/cd91e8d85cb98b4bbdb35c569c1a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/viz/trackster.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/viz/trackster.js Log Message: ----------- Fix trackster link to custom builds view Commit: 5124c561090013f84d78232218a325199215fa41 https://github.com/galaxyproject/galaxy/commit/5124c561090013f84d78232218a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/viz/trackster.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/viz/trackster.js Log Message: ----------- Merge branch 'fix_trackster_link' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0c97e1158ea5...5124c5610900

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[galaxyproject/galaxy] 78df0e: Refactor populators for easier nested collection c...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78df0e2cc5c1118184a64fb8ea122844cca1d402 https://github.com/galaxyproject/galaxy/commit/78df0e2cc5c1118184a64fb8ea12… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_dataset_collections.py M test/base/populators.py Log Message: ----------- Refactor populators for easier nested collection creation. Commit: d0e9a80c58d08eadafb966ce9736dd595ec2dc82 https://github.com/galaxyproject/galaxy/commit/d0e9a80c58d08eadafb966ce9736… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_history_multi_view.py M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- More GUI tests for collections. Commit: 1c3d49b07a3b790cc4b7d418415d223c05956584 https://github.com/galaxyproject/galaxy/commit/1c3d49b07a3b790cc4b7d418415d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Refactor client collections - collapse List and Paired models. They don't have different functionality - they shouldn't be different. Commit: adef3a6a59fcc5395350519f146e010c9409a04c https://github.com/galaxyproject/galaxy/commit/adef3a6a59fcc5395350519f146e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Refactor client collections - rename List -> Flat at lowest level models. It represents both lists and paireds now. Commit: e70a7748565897832e20119735f5bcd38e56a15c https://github.com/galaxyproject/galaxy/commit/e70a7748565897832e20119735f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Refactor client collections - collapse nested paireds model into nested lists. Commit: ba111325437473995dfd6dc5b82378d6ca8f32cd https://github.com/galaxyproject/galaxy/commit/ba111325437473995dfd6dc5b823… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Refactor client collections - rename listoflists model to nested model. Commit: a5513a4868ca5229348189d1b0ff4a4801ef0863 https://github.com/galaxyproject/galaxy/commit/a5513a4868ca5229348189d1b0ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Refactor client collections - eliminate class distinction between history bound nested collections. Commit: 0c1e6e46b20222912f35380d7f45aeeb0aa75778 https://github.com/galaxyproject/galaxy/commit/0c1e6e46b20222912f35380d7f45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Refactor client collections - eliminate class distinction between flat view edit collections. Commit: 1535a0f01803c19d8db7f4035832ae1109bcbefe https://github.com/galaxyproject/galaxy/commit/1535a0f01803c19d8db7f4035832… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Refactor client collections - renamed list collection edit to flat. Since it represents boths lists and paireds now. Commit: 957ff9d0269b55a16095d3f94679d8e464df9dfc https://github.com/galaxyproject/galaxy/commit/957ff9d0269b55a16095d3f94679… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - eliminate class distinction between flat view collections. Commit: dd13193fc40ade2203503a926c4dd479936a91e0 https://github.com/galaxyproject/galaxy/commit/dd13193fc40ade2203503a926c4d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - renamed list collection to flat. Commit: b9bd5287d08f1a7a4b252af21a20e8115f216dec https://github.com/galaxyproject/galaxy/commit/b9bd5287d08f1a7a4b252af21a20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - eliminate ListOfPairsCollectionView. Just use ListOfListsCollectionView. Commit: 897ff7e54ef6935a190de4974c7004d089477db3 https://github.com/galaxyproject/galaxy/commit/897ff7e54ef6935a190de4974c70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Refactor client collections - eliminate class distinction between nested view edit collections. Commit: fdfa725a8b70d2182acfb3c971f34fd12bdded98 https://github.com/galaxyproject/galaxy/commit/fdfa725a8b70d2182acfb3c971f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - rename nested collection views. Both edit and RO variants - to reflect new generality. Commit: 5a7eea6a810c15ca7175e7de86b136b355063007 https://github.com/galaxyproject/galaxy/commit/5a7eea6a810c15ca7175e7de86b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Refactor client collections - rename NestedPairCollectionViewEdit ... to NestedCollectionElementViewEdit since it isn't just used for paired collection contents and hasn't been for some time. Commit: bcf0fb11e98a58224a33fabf1024b99f30262b89 https://github.com/galaxyproject/galaxy/commit/bcf0fb11e98a58224a33fabf1024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Refactor client collections - eliminate incorrect comments. Commit: 1afd6e136f73db6116c6126412a80c80d35d1ea0 https://github.com/galaxyproject/galaxy/commit/1afd6e136f73db6116c6126412a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Refactor client collections - eliminate Flat vs Nested dataset collection. Just dispatch on collection type to determine collection contents. Commit: 200cf96c2dda2ca5a353e78fcf54a3f1a024fcdc https://github.com/galaxyproject/galaxy/commit/200cf96c2dda2ca5a353e78fcf54… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - eliminate FlatCollectionView & FlatCollectionViewEdit. These just did the same thing as CollectionView and CollectionViewEdit. Commit: 4db301a9ab36852bd066d82bfe91f182343ec5fb https://github.com/galaxyproject/galaxy/commit/4db301a9ab36852bd066d82bfe91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Refactor client collections - eliminate NestedCollectionView and NestedCollectionViewEdit. They are just CollectionViews now. Commit: a3cc810e93018744607fc6120d43f71ebaa52d0e https://github.com/galaxyproject/galaxy/commit/a3cc810e93018744607fc6120d43… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Refactor client collections - eliminated another class without a distinction. Commit: ef81006c451e6e59bf23d8c9cc1c7714fae97505 https://github.com/galaxyproject/galaxy/commit/ef81006c451e6e59bf23d8c9cc1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Refactor client collections - eliminate all history bound collection distinctions. Commit: eb735357e7b7f37b9601ef21f9c71a910c019a11 https://github.com/galaxyproject/galaxy/commit/eb735357e7b7f37b9601ef21f9c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Refactor client collections - eliminate unneeded subclass of CollectionView. Commit: 4defaa2188993450e0aa044e7316121d664c89b7 https://github.com/galaxyproject/galaxy/commit/4defaa2188993450e0aa044e7316… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/hdca-model.js Log Message: ----------- Reformat client. Commit: c6bc1538be4d06aa3c7df84066ffc3e33548ab22 https://github.com/galaxyproject/galaxy/commit/c6bc1538be4d06aa3c7df84066ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Mark one of the new history collection tests as @flakey. Reason noted in PR. Commit: 307d33ada15f1afe49d784df14d9fbcaf7178db1 https://github.com/galaxyproject/galaxy/commit/307d33ada15f1afe49d784df14d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M static/scripts/bundled/analysis.bundled.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/pair-collection-creator.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Repack. Commit: 0c97e1158ea51128c9a0277aeccebb2a397a2f16 https://github.com/galaxyproject/galaxy/commit/0c97e1158ea51128c9a0277aecce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/scripts/bundled/analysis.bundled.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/pair-collection-creator.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M test/api/test_dataset_collections.py M test/base/populators.py M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_history_multi_view.py M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Merge pull request #5038 from jmchilton/unwind_collection_client Render arbitrarily nested lists in the UI Compare: https://github.com/galaxyproject/galaxy/compare/5e17e44db533...0c97e1158ea5

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[galaxyproject/galaxy] 3c0ffb: Separate dev and production builds.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c0ffb0ce9e5cf0939abf7abed5f664e7b0b80b7 https://github.com/galaxyproject/galaxy/commit/3c0ffb0ce9e5cf0939abf7abed5f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M Makefile M client/gulpfile.js M client/package.json M client/webpack.config.js Log Message: ----------- Separate dev and production builds. Commit: 8a91ba848e8dab85fdf3d10716d3f7286ebc0823 https://github.com/galaxyproject/galaxy/commit/8a91ba848e8dab85fdf3d10716d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: R static/maps/galaxy.library.js.map R static/maps/layout/panel.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/citations.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/user/user_api_keys.js.map Log Message: ----------- Strip maps left behind previously. Commit: 5e2c73801143e0cf1735bfcd15ac7746967cc0dd https://github.com/galaxyproject/galaxy/commit/5e2c73801143e0cf1735bfcd15ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Reapply accidentally dropped -p flag on default webpack invocation. Commit: 35f08be9c828046b62c3e6889244ff12f647c7c6 https://github.com/galaxyproject/galaxy/commit/35f08be9c828046b62c3e6889244… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Slight refactoring in package.json to standardize with 'dev' being the common, default option and 'production' being the non-default (logic being a build system should be the thing remembering extra options over the default) Commit: 06af0175cba55d64aef3bdc0f812a41cfd2dceb5 https://github.com/galaxyproject/galaxy/commit/06af0175cba55d64aef3bdc0f812… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/package.json Log Message: ----------- Drop production-watch package script. Commit: 97b9eed8afef5433163859fd216d3d40c67671aa https://github.com/galaxyproject/galaxy/commit/97b9eed8afef5433163859fd216d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M .gitignore R static/scripts/bundled/admin.bundled.js.map R static/scripts/bundled/adminToolshed.bundled.js.map R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/library.bundled.js.map R static/scripts/bundled/libs.bundled.js.map R static/scripts/bundled/login.bundled.js.map R static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/viz.bundled.js.map R static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- More straggler maps (from bundles) Commit: a36542a72b12796b27be3d4c7ed57f35d8533e1a https://github.com/galaxyproject/galaxy/commit/a36542a72b12796b27be3d4c7ed5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/gulpfile.js M client/package.json M client/webpack.config.js Log Message: ----------- Add production + sourcemaps build targets. Not as granular as I want, but SourceMapDevTool has weird interactions with -p Commit: 0417699825174666bc8bb720c313c608bc4d8dbe https://github.com/galaxyproject/galaxy/commit/0417699825174666bc8bb720c313… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/history-import.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/qunit/test.js M client/galaxy/style/less/ui.less M client/karma.config.js M client/package.json M config/datatypes_conf.xml.sample M config/error_report.yml.sample M config/workflow_schedulers_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py R manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main A scripts/get_uwsgi_args.py R scripts/manage_tools.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/layout/menu.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tag.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M test-data/1.fastqsanger M test-data/1.fastqsolexa M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into maps_for_developer_only Commit: 9626350168b6e0551506505979815de4e8d56af8 https://github.com/galaxyproject/galaxy/commit/9626350168b6e055150650597981… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M Makefile R static/GruntFile.js.map Log Message: ----------- Makefile targets, and somehow we had a gruntfile map in the repo from ancient times. Commit: fde9f823d592db70b220e73e24305751c90c7ca7 https://github.com/galaxyproject/galaxy/commit/fde9f823d592db70b220e73e2430… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/README.md Log Message: ----------- Update client README Commit: 1c30a850afe24950343266efa3120cfe0134a314 https://github.com/galaxyproject/galaxy/commit/1c30a850afe24950343266efa312… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M Makefile Log Message: ----------- Add a better client commit warning to the Makefile. Commit: 5e17e44db533cea7be20f5f0a1455219f4de67c1 https://github.com/galaxyproject/galaxy/commit/5e17e44db533cea7be20f5f0a145… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M .gitignore M Makefile M client/README.md M client/gulpfile.js M client/package.json M client/webpack.config.js R static/GruntFile.js.map R static/scripts/bundled/adminToolshed.bundled.js.map Log Message: ----------- Merge pull request #5058 from dannon/maps_for_developer_only Build endpoint separation Compare: https://github.com/galaxyproject/galaxy/compare/893e494c0275...5e17e44db533

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[galaxyproject/galaxy] 893e49: Add packed symlink back pending a deprecation cycl...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 893e494c0275f23d689b01065e4ca98c4bf2266f https://github.com/galaxyproject/galaxy/commit/893e494c0275f23d689b01065e4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: A static/scripts/packed Log Message: ----------- Add packed symlink back pending a deprecation cycle. (#5094)

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[galaxyproject/galaxy]
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/ie Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 566f6b: Update Jupyter IE default image (#5095)
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 566f6ba123e518a8c56a4e4f6171ac730e689b0b https://github.com/galaxyproject/galaxy/commit/566f6ba123e518a8c56a4e4f6171… Author: Enis Afgan <afgane(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter IE default image (#5095)

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[galaxyproject/usegalaxy-playbook] c63497: Update Test and Main to use HTTP/2.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c6349702456fd638e79f94840f1fc463ee182c11 https://github.com/galaxyproject/usegalaxy-playbook/commit/c6349702456fd638… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M env/main/templates/nginx/usegalaxy.j2 M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Update Test and Main to use HTTP/2.

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[galaxyproject/galaxy] 0ff639: More debugging in workflows API tests.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ff639a29c6179e530c977b358cebf229c76139d https://github.com/galaxyproject/galaxy/commit/0ff639a29c6179e530c977b358ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- More debugging in workflows API tests. Commit: 4e9ee22ebcd5cc358d1b86f60e957846f35765a5 https://github.com/galaxyproject/galaxy/commit/4e9ee22ebcd5cc358d1b86f60e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflow_extraction.py M test/base/populators.py Log Message: ----------- More verbose workflow extraction test cases. Commit: 0e0894bbba8ee1d8b7c6946a5a42695fa6bd0858 https://github.com/galaxyproject/galaxy/commit/0e0894bbba8ee1d8b7c6946a5a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Refactoring history contents API. Commit: 8c1658f61a12b9c1e2efdb04ee3530c1272b0bde https://github.com/galaxyproject/galaxy/commit/8c1658f61a12b9c1e2efdb04ee35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Mixin for uses create and update time. Commit: c076b3b6c5bf5ac9d374d56d42c9a91c352688ce https://github.com/galaxyproject/galaxy/commit/c076b3b6c5bf5ac9d374d56d42c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Refactor workflow testing toward reuse via "populators". Should allow more functionality to be shared between vanilla API tests and integration tests for various workflow scheduling options. Commit: 55aa7bce5540469fad266f1166c9a2e7365030d4 https://github.com/galaxyproject/galaxy/commit/55aa7bce5540469fad266f1166c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_tools.py A test/functional/tools/output_filter_with_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test cases for mapping for outputs with filter statements. Checked through tools-iuc and I couldn't find any tools that use the actual input data parameters in filter statements so I think it is a fairly good approximation to assume that all mapped jobs will either filter or not at least with current execution model. Commit: d5f98f49045bca351e982f17cac9386308089eeb https://github.com/galaxyproject/galaxy/commit/d5f98f49045bca351e982f17cac9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/base/populators.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Formalize workflow invocation and invocation step outputs. Workflow Invocations -------------------- The workflow invocation outputs half of this is relatively straight forward. It is modelled somewhat on job outputs, output datasets and output dataset collections are now tracked for each workflow invocation and exposed via the workflow invocation API. This required adding new tables (linked to WorkflowInvocations and WorkflowOutputs) that track these output associations. Previously one could imagine backtracking this information for simple tool steps via the WorkflowInvocationStep -> Job table, but for steps that have many jobs (i.e. mapping over a collection) or for non-tool steps such information was more difficult to recover (and simply couldn't be recovered from the API at all or even internally without significant knowledge of the underlying workflow). Workflow Invocation Steps ------------------------- Tracking the outputs of WorkflowInvocationSteps was not previously done at all, one would have to follow the Job table as well. A signficant downside to this is that one cannot map over empty collections in a workflow - since no such job would exist. Tracking job outputs for WorkflowInvocationSteps is not a simple matter of just attaching outputs to an existing table because we had no concept of a workflow step tracked - since there could be many WorklfowInvocationSteps corresponding to the same combination of WorkflowInvocation and WorkflowStep. That should feel wrong and that is because it is - when collections were added the possiblity of having many jobs for the same combination of WorkflowInvocation and WorkflowStep was added. I should have split WorkflowInvocationSteps into WorkflowInvocationSteps and WorkflowInvocationStepJobAssociations at that time but didn't. This commit now does it - effectively normalizing the ``workflow_invocation_step`` table by introducing the new ``wo rkflow_invocation_step_job_association`` table. Splitting up the WorkflowInvocationStep table this way allows recovering the mapped over output (e.g. the implicitly created collection from all the jobs) as well the outputs from the individual jobs (by walking WorkflowInvocationStep -> WorkflowInvocationStepJobAssociation -> Job -> JobToOutput*Association). This split up involves failrly substantial changes to the workflow module interface. Any place a list of WorkflowInvocationSteps was assumed, I reworked it to just expect a single WorkflowInvocationStep. I vastly simplified recover_mapping to just use the persisted outputs (this was needed in order to also implment empty collection mapping in workflows). This also fixes a bug (or implements a missing feature) where Subworkflow moudles had no recover_mapping methods - so for instance if a tool that produces dynamic collections appeared anywhere in a workflow after a subworkflow step - that workflow would not complete scheduling properly. Now that we have a way to reference the set of jobs corresponding to a workflow step within an invocation, we can start to track partial scheduling of such steps. This is outlined in https://github.com/galaxyproject/galaxy/issues/3883 and refactoring toward this goal is included here - including adding a state to WorkflowInvocationStep so Galaxy can determine if it has started scheduling this step and an index when scheduling jobs so it can tell how far into a scheduling things have gone as well as augmenting the tool executor to take a maximum number of jobs to execute and allow recovery of existing jobs for collection building purposes. *Applications* These changes will enable: - A simple, consistent API for finding workflow outputs that can be consumed by Planemo for testing workflows. - Mapping over empty collections in workflows. - Re-scheduling workflow invocations that include subworkflow steps. - Partial scheduling within steps requiring a large number of jobs when scheduling workflow invocations. Commit: 64835c1e72eea545269260256c7a238a4e5ea7fe https://github.com/galaxyproject/galaxy/commit/64835c1e72eea545269260256c7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Three new worklfow test cases to verify mapping over workflows is possible. - Simple mapping over an input dataset. - Mapping that produces nested collections. - Mapping over subworkflows. Commit: 0185e04a5beaf951bb20d670d9421d988d70bb29 https://github.com/galaxyproject/galaxy/commit/0185e04a5beaf951bb20d670d942… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test recover_mapping in conjunction with subworkflow executions. Commit: 9e471d3e97a6d6b6893ed243b6a48108076899c4 https://github.com/galaxyproject/galaxy/commit/9e471d3e97a6d6b6893ed243b6a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow mapping over empty collections. If one maps a tool over an empty collection, one should get an empty output collection for each of the tool's outputs. This should have always been a valid operation I think, the code just wasn't quite structured right when the collection work was merged - there were too many places I was assuming the existence of at least one actual output or input that was mapped over to continue going. This reworks all of that and seems to handle empty collections appropriately. Fixes #4025 (not being informing the user of the operation, but actually by allowing the operation - which it should be allowed I think). Commit: 53cba4aa74b0d2543445824a7636f92249baa150 https://github.com/galaxyproject/galaxy/commit/53cba4aa74b0d2543445824a7636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Refactor collection manager into smaller, more focused methods. Stronger assertions to verify arguments are correct. Commit: 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 https://github.com/galaxyproject/galaxy/commit/78babab6455f4cd1c51aed0b1ddf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/__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/execute.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/unit/dataset_collections/test_matching.py Log Message: ----------- Pre-build collections during mapping to be more recoverable. Create mapped over collections ahead of time instead of at the end only if they are valid. - This way if there is a problem that problem can be reported in the state of the mapped collection. - This way datasets can just be hidden instead of displayed and then hidden (fixes #1790). - I think this should improve performance and prevent locks because we no longer have conflicting threads trying to write dataset state. - We populate the collection as we go so we can recover and continue scheduling the mapped step (needed for #3883) Commit: 40fd72a1980bd2df5ea116aae1016c8bad6c3ca1 https://github.com/galaxyproject/galaxy/commit/40fd72a1980bd2df5ea116aae101… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py Log Message: ----------- Allow rescheduling of single workflow steps. Implement maximum_workflow_jobs_per_scheduling_iteration to test this and mitigate memory issues associated with scheduling large workflow steps (maybe). Fixes #3883. Commit: d69962e7f4de38963401a032ada5131e6190b5e5 https://github.com/galaxyproject/galaxy/commit/d69962e7f4de38963401a032ada5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/db_shell.py M test/api/test_history_contents.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement model abstraction for ``ImplicitCollectionJobs``. These aggregate all the jobs contributing to an implicitly created HistoryDatasetCollectionAssociation. - Model enhancements that allow this. - API endpoint for jobs summary of history content (somewhat uniform across HDAs and HDCAs just for consistency). - Test cases. - Rework history contents API a bit to eliminate more costly state summary checks by default. Commit: e82012bde154c456f24743f3b61c0ed9ffc7eca2 https://github.com/galaxyproject/galaxy/commit/e82012bde154c456f24743f3b61c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/execute.py Log Message: ----------- Undo splitting WorkflowInvocationStep... ... this concept of ImplicitCollectionJobs makes more sense for tracking collections of implicitly created jobs. Commit: 0dceb5a553d589324d4a9a97ec5f7629bc379b48 https://github.com/galaxyproject/galaxy/commit/0dceb5a553d589324d4a9a97ec5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M test/api/test_dataset_collections.py Log Message: ----------- Add element count to DatasetCollection objects. There are no places where this count is not set atomically in one thread so this should not have any performance downsides versus the older approach of calculating it on the fly (which was very expensive). Commit: ca09e803aeaf856556433e69bf5a48f8bab60c5d https://github.com/galaxyproject/galaxy/commit/ca09e803aeaf856556433e69bf5a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_tools.py M test/base/populators.py M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Dataset collection state UX test case. Commit: 5a9f0dd11eb0ba0abfed29ae9da1d0a5a5a01360 https://github.com/galaxyproject/galaxy/commit/5a9f0dd11eb0ba0abfed29ae9da1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.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/history-view.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/base.less M client/galaxy/style/less/list-item.less M lib/galaxy/managers/jobs.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add job state tracking to the GUI. - ``populated`` in the API response is gone - it was very expensive on the backend to calculate. - Eliminate GUI "thread" fetching ``element_count`` for collections after the panel is loaded, this value is now available at load time thanks to recent state change optimizations on the backend. - Track job state and implicit collection job states over time in a new "thread". - New different colors of job states, add progress bar for multiple jobs. Commit: e7e659cabcf2a5928ab58e73715c0959c78cc997 https://github.com/galaxyproject/galaxy/commit/e7e659cabcf2a5928ab58e73715c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/style/less/dataset.less Log Message: ----------- Better dataset loading description. Commit: 075d8c1d0ab7dca9c8573fe69a5ef7ec18ab2202 https://github.com/galaxyproject/galaxy/commit/075d8c1d0ab7dca9c8573fe69a5e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py R lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py Log Message: ----------- Rename huge database migration to reflect new PR topic. Commit: 8fa5496ba59e39ce4d16bd7c8da1d92989c7f5da https://github.com/galaxyproject/galaxy/commit/8fa5496ba59e39ce4d16bd7c8da1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Restructure collection state GUI tests to separate flakey tests of running state out. Paste just sometimes randomly hangs when it is not supposed to. Commit: c47d8992ba52e5af8eae635a4ce50cca8a6d02c9 https://github.com/galaxyproject/galaxy/commit/c47d8992ba52e5af8eae635a4ce5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css Log Message: ----------- Repack client. Commit: 9ef4e3bd70d3abe7b36388e9d9e52c609749002d https://github.com/galaxyproject/galaxy/commit/9ef4e3bd70d3abe7b36388e9d9e5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.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/history-view.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/list-item.less M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.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/execute.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M scripts/db_shell.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py M test/unit/dataset_collections/test_matching.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #5013 from jmchilton/workflow_and_collection_state Improved Collection and Workflow State with Applications Compare: https://github.com/galaxyproject/galaxy/compare/711107473fa5...9ef4e3bd70d3

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[galaxyproject/galaxy] d074b2: Standard naming for components. TODO: organizatio...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d074b22f296c8ce76a1c982fa63eab60ed74a1e2 https://github.com/galaxyproject/galaxy/commit/d074b22f296c8ce76a1c982fa63e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Standard naming for components. TODO: organization, and re-add citations (working around case-insensitivity here) Commit: 15053783bf52b914830d9afdf4fa1435ec4d8b28 https://github.com/galaxyproject/galaxy/commit/15053783bf52b914830d9afdf4fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: A client/galaxy/scripts/components/Citations.vue Log Message: ----------- Case insensitive filesystems are a terrible idea. Commit: 79b9795f7df223598ec81661bcb2a914fce7fc1c https://github.com/galaxyproject/galaxy/commit/79b9795f7df223598ec81661bcb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Build client. Commit: 711107473fa5bd0875ae6bc1c74c9e1b4f2e9999 https://github.com/galaxyproject/galaxy/commit/711107473fa5bd0875ae6bc1c74c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5092 from dannon/vue_component_standardized_naming Vue component standardized naming Compare: https://github.com/galaxyproject/galaxy/compare/3e7973940a67...711107473fa5

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[galaxyproject/galaxy] 3c20f3: Attempt to make data manager integration test more...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c20f3285a123a243eed57040da3966800ca2438 https://github.com/galaxyproject/galaxy/commit/3c20f3285a123a243eed57040da3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_data_manager_table_reload.py Log Message: ----------- Attempt to make data manager integration test more robust. Increase the timeout - this test fails on Jenkins every now and then and reports the DM job is still queued. I assume this is because of conda_auto_install setting up the requirements for this data manager and the logs seem consistent with that assumption. I also added data manager json type to the sample so this warning goes away: ``` galaxy.model WARNING 2017-11-30 06:39:59,335 Datatype class not found for extension 'data_manager_json' ``` Commit: 3e7973940a67e30506973070ced00e471b914b31 https://github.com/galaxyproject/galaxy/commit/3e7973940a67e30506973070ced0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_data_manager_table_reload.py Log Message: ----------- Merge pull request #5098 from jmchilton/reload_dm_test_robust Attempt to make data manager integration test more robust. Compare: https://github.com/galaxyproject/galaxy/compare/baba3417d08d...3e7973940a67

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[galaxyproject/galaxy] 7dc5fd: Update Jupyter IE default image
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/ie Home: https://github.com/galaxyproject/galaxy Commit: 7dc5fd9b77c330cc6c9643c7622294a24d78df99 https://github.com/galaxyproject/galaxy/commit/7dc5fd9b77c330cc6c9643c76222… Author: Enis Afgan <afgane(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter IE default image

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[galaxyproject/usegalaxy-playbook] 98aeb5: Install augustus 3.2.3
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98aeb5b7d8689e9fff6e2b2b3793235e0b7d1ab8 https://github.com/galaxyproject/usegalaxy-playbook/commit/98aeb5b7d8689e9f… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Install augustus 3.2.3

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[galaxyproject/usegalaxy-playbook] fa4cbb: Fix test installer access
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa4cbb59187be6d3c6e46ba2e18e6efcab809caf https://github.com/galaxyproject/usegalaxy-playbook/commit/fa4cbb59187be6d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Fix test installer access

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[galaxyproject/galaxy] ef8ed0: support separate dsn for sentry
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef8ed0ec3fce0f2e61cc0accfe1dcdb8dd79f97b https://github.com/galaxyproject/galaxy/commit/ef8ed0ec3fce0f2e61cc0accfe1d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M config/error_report.yml.sample M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- support separate dsn for sentry Commit: c6bf20df682a3dac10d4d6fd480d470ec5c8cbc8 https://github.com/galaxyproject/galaxy/commit/c6bf20df682a3dac10d4d6fd480d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- ok, test cases require this to pass Commit: baba3417d08d282c98418e2e62a7167f458c86bd https://github.com/galaxyproject/galaxy/commit/baba3417d08d282c98418e2e62a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/error_report.yml.sample M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5056 from erasche/sentry-stuff Support separate DSN for job sentry error reports Compare: https://github.com/galaxyproject/galaxy/compare/75a6d434ee00...baba3417d08d

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[galaxyproject/galaxy] 687950: Add js history form view
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6879507fef3f6b6697f3e8364953b1fc4c9f1361 https://github.com/galaxyproject/galaxy/commit/6879507fef3f6b6697f3e8364953… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Add js history form view Commit: f776229db4b9f81868df35b1e76cf5d605a5b0d4 https://github.com/galaxyproject/galaxy/commit/f776229db4b9f81868df35b1e76c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add history import Commit: 3e4058f098446ffddefb4b426233fa00fd4307ff https://github.com/galaxyproject/galaxy/commit/3e4058f098446ffddefb4b426233… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Fix styling, fix data submission for history endpoint Commit: 358dee22ca45e88fbf727fb773616b1f90473540 https://github.com/galaxyproject/galaxy/commit/358dee22ca45e88fbf727fb77361… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js.map Log Message: ----------- Use global vars Commit: 2a122157c540e412b8d37540205b88801e6a0746 https://github.com/galaxyproject/galaxy/commit/2a122157c540e412b8d37540205b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: A client/galaxy/scripts/mvc/history/history-import.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/history/history-import.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/history/history-import.js Log Message: ----------- Augment existing api endpoint, redirect post Commit: 0c615411c9a063ddfaeb6b2e2bfba1b783a1543f https://github.com/galaxyproject/galaxy/commit/0c615411c9a063ddfaeb6b2e2bfb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Consolidate endpoints Commit: 4fd3021330f9d1ec4061807fe739933140f63e91 https://github.com/galaxyproject/galaxy/commit/4fd3021330f9d1ec4061807fe739… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-import.js M static/maps/mvc/history/history-import.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-import.js Log Message: ----------- Remove debug helper Commit: cf66742b4c1ab6d2c5bef8b5064679b5e7963b0a https://github.com/galaxyproject/galaxy/commit/cf66742b4c1ab6d2c5bef8b50646… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/utils/ajax-queue.js M config/galaxy.ini.sample M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/hash_util.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/hg_util.py M run_tests.sh M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/ajax-queue.js R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M test/base/populators.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: b96398027e648d8c1c42180c162fbae3c73e31f5 https://github.com/galaxyproject/galaxy/commit/b96398027e648d8c1c42180c162f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Consistent strings Commit: 8f7dee460e7f90fa945cb6a1ff31c7aa81a4505b https://github.com/galaxyproject/galaxy/commit/8f7dee460e7f90fa945cb6a1ff31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A 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lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M run_tests.sh M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M 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templates/admin/tool_shed_repository/view_tool_metadata.mako R templates/search/index.mako M templates/show_params.mako M templates/user/register.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 2623bf369cae8b658118defad6fbf0dc825c2b73 https://github.com/galaxyproject/galaxy/commit/2623bf369cae8b658118defad6fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/style/less/base.less M client/gulpfile.js A client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/panel.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js A static/scripts/libs/vue.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: cb044bd45263341aede9866f219600a2caddfe55 https://github.com/galaxyproject/galaxy/commit/cb044bd45263341aede9866f2196… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/library.bundled.js M static/scripts/bundled/library.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Transform history import to vue component Commit: 4cf8ad218467b310652b7c2e37190cf56ca68820 https://github.com/galaxyproject/galaxy/commit/4cf8ad218467b310652b7c2e3719… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: R client/galaxy/scripts/mvc/history/history-import.js R static/maps/mvc/history/history-import.js.map Log Message: ----------- Remove former backbone view for history imports Commit: 4ecf7a05b4d8bd6c20b8f73920c1e36436918c61 https://github.com/galaxyproject/galaxy/commit/4ecf7a05b4d8bd6c20b8f73920c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .gitignore M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.complexify.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R static/maps/libs/jquery/jquery.mousewheel.js.map R static/maps/libs/jquery/jquery.rating.js.map R static/maps/libs/jquery/jquery.wymeditor.js.map R static/maps/libs/jquery/jstorage.js.map R static/maps/libs/jquery/jstree.js.map R static/maps/libs/jquery/select2.js.map R static/maps/libs/raven.js.map R static/maps/libs/require.js.map R static/maps/libs/showdown.js.map R static/maps/libs/toastr.js.map R static/maps/libs/underscore.js.map R static/maps/mvc/annotation.js.map R static/maps/mvc/base-mvc.js.map R static/maps/mvc/base/controlled-fetch-collection.js.map R static/maps/mvc/collection/base-creator.js.map R static/maps/mvc/collection/collection-li-edit.js.map R static/maps/mvc/collection/collection-li.js.map R static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-view-edit.js.map R static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/collection/list-collection-creator.js.map R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-item-li.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/lazy/lazy-limited.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/library/library-util.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/page/page-list.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R static/maps/mvc/toolshed/sheds-list-view.js.map R static/maps/mvc/toolshed/toolshed-model.js.map R static/maps/mvc/toolshed/util.js.map R static/maps/mvc/toolshed/workflows-view.js.map R static/maps/mvc/tours.js.map R static/maps/mvc/ui/error-modal.js.map R static/maps/mvc/ui/icon-button.js.map R static/maps/mvc/ui/popup-menu.js.map R static/maps/mvc/ui/ui-buttons.js.map R static/maps/mvc/ui/ui-color-picker.js.map R static/maps/mvc/ui/ui-drilldown.js.map R static/maps/mvc/ui/ui-frames.js.map R static/maps/mvc/ui/ui-list.js.map R static/maps/mvc/ui/ui-misc.js.map R static/maps/mvc/ui/ui-modal.js.map R static/maps/mvc/ui/ui-options.js.map R static/maps/mvc/ui/ui-popover.js.map R static/maps/mvc/ui/ui-portlet.js.map R static/maps/mvc/ui/ui-select-content.js.map R static/maps/mvc/ui/ui-select-default.js.map R static/maps/mvc/ui/ui-select-ftp.js.map R static/maps/mvc/ui/ui-select-genomespace.js.map R static/maps/mvc/ui/ui-select-library.js.map R static/maps/mvc/ui/ui-select.js.map R static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-extension.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-model.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M 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static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 78508e200ab1ce2b6a665e0076eebabd1db4a14f https://github.com/galaxyproject/galaxy/commit/78508e200ab1ce2b6a665e0076ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M 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test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: f58ef136168999c3dc86468b3cf9d1220b4cf59a https://github.com/galaxyproject/galaxy/commit/f58ef136168999c3dc86468b3cf9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: 3c3b47e8ef2b5b2c4072f3e9d92dd6dadd72646e https://github.com/galaxyproject/galaxy/commit/3c3b47e8ef2b5b2c4072f3e9d92d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A client/galaxy/scripts/components/history-import.vue M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Restore history vue component Commit: 1785f6314d0e3fc2d2b189839f6e031448781dca 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test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 9800013ec2cd7433db329ad9db9114e57af37e07 https://github.com/galaxyproject/galaxy/commit/9800013ec2cd7433db329ad9db91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: 081cbc4bb0cdbe202cf24b394beba4eb50125d0f https://github.com/galaxyproject/galaxy/commit/081cbc4bb0cdbe202cf24b394beb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 75a6d434ee00b51d66ea5bf40b0ddd19601d35e3 https://github.com/galaxyproject/galaxy/commit/75a6d434ee00b51d66ea5bf40b0d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/history-import.vue M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4993 from guerler/replace_history_import Replace history import form Compare: https://github.com/galaxyproject/galaxy/compare/8d7f344140d7...75a6d434ee00

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[galaxyproject/infrastructure-playbook] 84239f: Add status.galaxyproject.org to the inventory
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 84239ffd6793dda8b8ab46bf18a1e0908a637d11 https://github.com/galaxyproject/infrastructure-playbook/commit/84239ffd679… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M common_env/secret_group_vars/sslwebservers.yml A galaxyenv/files/ssl/status.galaxyproject.org_cert.pem A galaxyenv/host_vars/status.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/templates/nginx/status.j2 Log Message: ----------- Add status.galaxyproject.org to the inventory

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