Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3097fd46f5e7abe5c3675e390048099dc8a8c80f https://github.com/galaxyproject/galaxy/commit/3097fd46f5e7abe5c3675e3900480... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: R templates/admin/library/grid.mako R templates/admin/library/new_library.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 Log Message: ----------- Remove library makos Commit: 9ff9f4b3219d308d84193e682487c1fe5633d59c https://github.com/galaxyproject/galaxy/commit/9ff9f4b3219d308d84193e682487c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-10-31 (Tue, 31 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py Log Message: ----------- Remove functions from controller Commit: fe5983aafca1fae0b60ed16838799b58f4aca11c https://github.com/galaxyproject/galaxy/commit/fe5983aafca1fae0b60ed16838799... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove library common controller Commit: a7a5141ef15c3f913b040ecd7f27c1dcb1a4b878 https://github.com/galaxyproject/galaxy/commit/a7a5141ef15c3f913b040ecd7f27c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Add create folder from controller to api Commit: db3bb5ff433296df4b6265512dba2fc096ab6f03 https://github.com/galaxyproject/galaxy/commit/db3bb5ff433296df4b6265512dba2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Move checks from controller, possible bug found Commit: b88cbaef7eef341c94e1bb9c4f1754293454b870 https://github.com/galaxyproject/galaxy/commit/b88cbaef7eef341c94e1bb9c4f175... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Remove mako related controller options Commit: ab432bf895887a4533d72eda5874aafad1ebb6f1 https://github.com/galaxyproject/galaxy/commit/ab432bf895887a4533d72eda5874a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Move api calls to legacy controller to api endpoint Commit: e7ec08b28e7dca28f5a068f73d7911696fcb3793 https://github.com/galaxyproject/galaxy/commit/e7ec08b28e7dca28f5a068f73d791... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Fix caller Commit: c7ca7a6a09bfd5a5022eb376883726359b415e0a https://github.com/galaxyproject/galaxy/commit/c7ca7a6a09bfd5a5022eb37688372... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Remove unused variables Commit: b1ccba39dcebb888a5daf3ed2d41c5594e3be6f4 https://github.com/galaxyproject/galaxy/commit/b1ccba39dcebb888a5daf3ed2d41c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Remove unused imports Commit: 72ba00eed23564a8631af7f6a144d2fa987f5652 https://github.com/galaxyproject/galaxy/commit/72ba00eed23564a8631af7f6a144d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Remove unused variables Commit: 345cbf62472873cb1fca5d997a0f57280737fc2d https://github.com/galaxyproject/galaxy/commit/345cbf62472873cb1fca5d997a0f5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/style/less/upload.less M config/local_conda_mapping.yml.sample M doc/source/releases/17.09_announce.rst M lib/galaxy/app.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/config_watchers.py M scripts/common_startup.sh M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 30e0be57f9e7ddae163526e89324c8dc72ec740d https://github.com/galaxyproject/galaxy/commit/30e0be57f9e7ddae163526e89324c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: A .ci/tox_envs/flake8/Pipfile A .ci/tox_envs/flake8/requirements.txt A .ci/tox_envs/flake8_imports/Pipfile A .ci/tox_envs/flake8_imports/requirements.txt A .ci/tox_envs/update.sh M Makefile M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/grouping.py R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/bootstrap_history.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M tox.ini Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 0ea7720bde2898a0ce5b4924ad4db65049bc7d01 https://github.com/galaxyproject/galaxy/commit/0ea7720bde2898a0ce5b4924ad4db... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Fix import order Commit: b17eea8566320d55f2de337bc09704b78005b143 https://github.com/galaxyproject/galaxy/commit/b17eea8566320d55f2de337bc0970... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/migrate/check.py M run_tests.sh M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 6c96130591e1051c8d4f1045cc5f119dadc44139 https://github.com/galaxyproject/galaxy/commit/6c96130591e1051c8d4f1045cc5f1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Fix order Commit: 927ff6501a45d75d9ac4b2f4d83aa94179682bf5 https://github.com/galaxyproject/galaxy/commit/927ff6501a45d75d9ac4b2f4d83aa... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: R .ci/tox_envs/flake8/Pipfile R .ci/tox_envs/flake8/requirements.txt R .ci/tox_envs/flake8_imports/Pipfile R .ci/tox_envs/flake8_imports/requirements.txt R .ci/tox_envs/update.sh M Makefile M client/galaxy/scripts/mvc/grid/grid-template.js M config/galaxy.ini.sample M doc/source/project/issues.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/dependencies/dev-requirements.txt R lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/Pipfile A lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock A lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/Pipfile A lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock A lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile A lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock A lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/migrate/check.py A lib/galaxy/util/monitors.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/grid/grid-template.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/grid/grid-template.js M tox.ini Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: ebd6ee5040544531ea85545c45791a15c850b997 https://github.com/galaxyproject/galaxy/commit/ebd6ee5040544531ea85545c45791... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M Makefile M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js 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/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.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-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M 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client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/scripts/viz/viz_views.js M client/gulpfile.js M client/package.json M client/yarn.lock M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako 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M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/group/index.mako M test/qunit/test-app.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 6650e94085b4a491b2994d50d6485e649bc171ae 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Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-04 (Sat, 04 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools_upload.py Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 5758f79fe157b3ee05e4f0f6f608269fadfd5dd0 https://github.com/galaxyproject/galaxy/commit/5758f79fe157b3ee05e4f0f6f6082... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-04 (Sat, 04 Nov 2017) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Remove info statement for legacy data library interface Commit: 890197c16c736d2250e49897633077a48aa9f37f https://github.com/galaxyproject/galaxy/commit/890197c16c736d2250e4989763307... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Remove explicit controller name parsing for api Commit: d0a80fa273d3542f37782b2faa9d01763e1a185e https://github.com/galaxyproject/galaxy/commit/d0a80fa273d3542f37782b2faa9d0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove unused whoosh indexing config options Commit: dd0649c680e2a0975f97bba3337145adc0eaad8b https://github.com/galaxyproject/galaxy/commit/dd0649c680e2a0975f97bba333714... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove from galaxy.ini Commit: e1b167bc076f83e1551e7e107da7e764b9215a20 https://github.com/galaxyproject/galaxy/commit/e1b167bc076f83e1551e7e107da7e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/trackster.less M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M run_tests.sh M static/maps/galaxy.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/metrics-logger.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/mvc/collection/collection-view.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/metrics-logger.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/trackster.css M test/api/test_dataset_collections.py M test/base/populators.py M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py M test/selenium_tests/test_published_histories_grid.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 8422feb46bf57e1a248ccbb62e1b59bf8bf1f119 https://github.com/galaxyproject/galaxy/commit/8422feb46bf57e1a248ccbb62e1b5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove whoosh from directory creation method Commit: 4b30e84a657a544543eae92319c298c9b02d82cf https://github.com/galaxyproject/galaxy/commit/4b30e84a657a544543eae92319c29... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Remove other unused library config options Commit: 991ee7d471a2ed0e39ff391ba103bdcf52e1ad87 https://github.com/galaxyproject/galaxy/commit/991ee7d471a2ed0e39ff391ba103b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-07 (Tue, 07 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: c9ab13fb411bab8a5e0021087f4c1bb6d4981315 https://github.com/galaxyproject/galaxy/commit/c9ab13fb411bab8a5e0021087f4c1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: R database/info.txt A lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Move shared actions to separate file Commit: ed4b0042572a47f505f1496047bbcfc84bae4aa6 https://github.com/galaxyproject/galaxy/commit/ed4b0042572a47f505f1496047bbc... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Fix import order, remove unused libraries Commit: 7e372c908ef37fd8054ff200184421b7f65b4170 https://github.com/galaxyproject/galaxy/commit/7e372c908ef37fd8054ff20018442... 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static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/ja/locale.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/search-input.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/localization.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako M test/api/test_history_contents.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: ff7b29c49c33e0383293e0712b7dd2c52d79ae47 https://github.com/galaxyproject/galaxy/commit/ff7b29c49c33e0383293e0712b7dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Use underscores for private functions consistently Commit: 29944cffc289011392531fb4dfa1157b9c7b3d63 https://github.com/galaxyproject/galaxy/commit/29944cffc289011392531fb4dfa11... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml Log Message: ----------- Merge branch 'dev' into remove_old_library Commit: 063aec3c05a9bf15110f30483f60b184e256da8b https://github.com/galaxyproject/galaxy/commit/063aec3c05a9bf15110f30483f60b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/actions/library.py Log Message: ----------- Fix comment Commit: fc9059a4dd521a1742e1c1df0d26ec7bf313640b https://github.com/galaxyproject/galaxy/commit/fc9059a4dd521a1742e1c1df0d26e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: A database/info.txt Log Message: ----------- Restore database/info.txt. It was problematically removed with a recent PR and is causing Travis breakages - Galaxy assumes this directory exists. Commit: 15852fcbf8b6938bcd34237957a7b5934dd01444 https://github.com/galaxyproject/galaxy/commit/15852fcbf8b6938bcd34237957a7b... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/utils/ajax-queue.js M doc/source/releases/17.09_announce.rst 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/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/tool_shed/util/hg_util.py M run_tests.sh M static/maps/utils/ajax-queue.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 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 remove_old_library Commit: d2a56959cd0212d5062a6fe727c4ba014d68e711 https://github.com/galaxyproject/galaxy/commit/d2a56959cd0212d5062a6fe727c4b... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M config/galaxy.ini.sample A lib/galaxy/actions/library.py M lib/galaxy/config.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 static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map 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 Log Message: ----------- Merge pull request #4908 from guerler/remove_old_library Remove legacy library interface Compare: https://github.com/galaxyproject/galaxy/compare/7d8dd639577d...d2a56959cd02