- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0207b0: Specify TagAssociation class when copying a tag
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0207b0186ac7c3d61004718ff7b91c3ea0c52165 https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Specify TagAssociation class when copying a tag This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags. Commit: b978acbe62053596e5c2ae736c848a62dc936591 https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Revert "Remove downloading workflows through controller" This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa. This is used when downloading workflows with the save icom from "pages". Commit: 3b523260551d15241de5dce3d1023790dcfd2250 https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d102… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #4988 from jmchilton/revert_export_to_file [17.09] Revert export to file Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6 https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags [17.05][BUG] Specify TagAssociation class when copying a tag Commit: 1a412bfb1b0497d9e3e2b8f9c348d7aa0f2478d6 https://github.com/galaxyproject/galaxy/commit/1a412bfb1b0497d9e3e2b8f9c348… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: c83a8260fd627955f559ca86c76586566e4b51d0 https://github.com/galaxyproject/galaxy/commit/c83a8260fd627955f559ca86c765… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d2a56959cd02...c83a8260fd62

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[galaxyproject/galaxy] 0207b0: Specify TagAssociation class when copying a tag
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0207b0186ac7c3d61004718ff7b91c3ea0c52165 https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Specify TagAssociation class when copying a tag This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags. Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6 https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags [17.05][BUG] Specify TagAssociation class when copying a tag Commit: 1a412bfb1b0497d9e3e2b8f9c348d7aa0f2478d6 https://github.com/galaxyproject/galaxy/commit/1a412bfb1b0497d9e3e2b8f9c348… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/3b523260551d...1a412bfb1b04

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[galaxyproject/galaxy] 0207b0: Specify TagAssociation class when copying a tag
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 0207b0186ac7c3d61004718ff7b91c3ea0c52165 https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Specify TagAssociation class when copying a tag This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags. Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6 https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags [17.05][BUG] Specify TagAssociation class when copying a tag Compare: https://github.com/galaxyproject/galaxy/compare/6915007f8548...e5587dcb6489

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[galaxyproject/galaxy] 3097fd: Remove library makos
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3097fd46f5e7abe5c3675e390048099dc8a8c80f https://github.com/galaxyproject/galaxy/commit/3097fd46f5e7abe5c3675e390048… Author: guerler <aysam.guerler(a)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/9ff9f4b3219d308d84193e682487… Author: guerler <aysam.guerler(a)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/fe5983aafca1fae0b60ed1683879… Author: guerler <aysam.guerler(a)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/a7a5141ef15c3f913b040ecd7f27… Author: guerler <aysam.guerler(a)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/db3bb5ff433296df4b6265512dba… Author: guerler <aysam.guerler(a)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/b88cbaef7eef341c94e1bb9c4f17… Author: guerler <aysam.guerler(a)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/ab432bf895887a4533d72eda5874… Author: guerler <aysam.guerler(a)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/e7ec08b28e7dca28f5a068f73d79… Author: guerler <aysam.guerler(a)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/c7ca7a6a09bfd5a5022eb3768837… Author: guerler <aysam.guerler(a)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/b1ccba39dcebb888a5daf3ed2d41… Author: guerler <aysam.guerler(a)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/72ba00eed23564a8631af7f6a144… Author: guerler <aysam.guerler(a)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/345cbf62472873cb1fca5d997a0f… Author: guerler <aysam.guerler(a)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/30e0be57f9e7ddae163526e89324… Author: guerler <aysam.guerler(a)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/0ea7720bde2898a0ce5b4924ad4d… Author: guerler <aysam.guerler(a)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/b17eea8566320d55f2de337bc097… Author: guerler <aysam.guerler(a)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/6c96130591e1051c8d4f1045cc5f… Author: guerler <aysam.guerler(a)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/927ff6501a45d75d9ac4b2f4d83a… Author: guerler <aysam.guerler(a)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/ebd6ee5040544531ea85545c4579… Author: guerler <aysam.guerler(a)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 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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 https://github.com/galaxyproject/galaxy/commit/6650e94085b4a491b2994d50d648… Author: guerler <aysam.guerler(a)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/5758f79fe157b3ee05e4f0f6f608… Author: guerler <aysam.guerler(a)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/890197c16c736d2250e498976330… Author: guerler <aysam.guerler(a)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/d0a80fa273d3542f37782b2faa9d… Author: guerler <aysam.guerler(a)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/dd0649c680e2a0975f97bba33371… Author: guerler <aysam.guerler(a)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 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static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/library/library-util.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M 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/ff7b29c49c33e0383293e0712b7d… Author: guerler <aysam.guerler(a)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/29944cffc289011392531fb4dfa1… Author: guerler <aysam.guerler(a)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/063aec3c05a9bf15110f30483f60… Author: guerler <aysam.guerler(a)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/fc9059a4dd521a1742e1c1df0d26… Author: John Chilton <jmchilton(a)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/15852fcbf8b6938bcd34237957a7… Author: Martin Cech <marten(a)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/d2a56959cd0212d5062a6fe727c4… Author: Martin Cech <marten(a)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

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[galaxyproject/galaxy] 048199: Kill off processes when stopping the local job run...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0481993d541c83eca91f87e9ca14f6440a2dcc8c https://github.com/galaxyproject/galaxy/commit/0481993d541c83eca91f87e9ca14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/local.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Kill off processes when stopping the local job runner. Prevent Galaxy parent process space from hanging on to these processes at shutdown and non quiting properly. Commit: 7d8dd639577db6b1d49e63d3353bcbfb0cc0d00a https://github.com/galaxyproject/galaxy/commit/7d8dd639577db6b1d49e63d3353b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/local.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #4962 from jmchilton/job_cleanup_local Kill off processes when stopping the local job runner. Compare: https://github.com/galaxyproject/galaxy/compare/e78efe16f432...7d8dd639577d

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[galaxyproject/galaxy] b978ac: Revert "Remove downloading workflows through contr...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: b978acbe62053596e5c2ae736c848a62dc936591 https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Revert "Remove downloading workflows through controller" This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa. This is used when downloading workflows with the save icom from "pages". Commit: 3b523260551d15241de5dce3d1023790dcfd2250 https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d102… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #4988 from jmchilton/revert_export_to_file [17.09] Revert export to file Compare: https://github.com/galaxyproject/galaxy/compare/577d57a69ce0...3b523260551d

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[galaxyproject/galaxy] b7e05a: otherwise it will overwrite linking source file
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7e05a012cb8dd3bf90f31f5c5a7df44587e97c0 https://github.com/galaxyproject/galaxy/commit/b7e05a012cb8dd3bf90f31f5c5a7… Author: Ignacio Eguinoa <igegu(a)psb.ugent.be> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- otherwise it will overwrite linking source file Commit: 19e5478cb8ffbd9d97db663bb1d04e52bed721a0 https://github.com/galaxyproject/galaxy/commit/19e5478cb8ffbd9d97db663bb1d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4911 from jmchilton/backport_4858 [17.09] Backport #4858 Commit: e3be7c31d59b69571bcee04599bdac6693426b89 https://github.com/galaxyproject/galaxy/commit/e3be7c31d59b69571bcee04599bd… Author: Wolfgang Maier <wolfgang.maier(a)biologie.uni-freiburg.de> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- fix broken link in 17.09 announcement Commit: 222ece4eabb6d080c6b8a0e327f8cf617b8a194f https://github.com/galaxyproject/galaxy/commit/222ece4eabb6d080c6b8a0e327f8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4927 from wm75/patch-2 fix broken link in 17.09 announcement Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3 https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377 https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Encode file content with utf-8 There shouldn't be any disadvantages over doing this only for specific elements. This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378. I have tested this with unicode strings in the name and info fields. Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3 https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Open files in text-mode (thx @nsoranzo) Commit: 6915007f85482648999768eecb9920da57b42e59 https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759 https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4987 from mvdbeek/history_import_bug [17.09][Bug] Encode file content with utf-8 Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0 https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: e78efe16f4325a8abb7701fc62b5969ef89781db https://github.com/galaxyproject/galaxy/commit/e78efe16f4325a8abb7701fc62b5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a18835b5169c...e78efe16f432

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[galaxyproject/galaxy] b6a0a1: Tolerate IOError in tool and data table watcher
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3 https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. Commit: 6915007f85482648999768eecb9920da57b42e59 https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0 https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/a0b4a2de5379...577d57a69ce0

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[galaxyproject/galaxy] cb01f3: Create the $GALAXY_MEMORY_MB tool job environment ...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb01f3dd332c4ff1b6a5e1ffff53a3758b8ac15e https://github.com/galaxyproject/galaxy/commit/cb01f3dd332c4ff1b6a5e1ffff53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: 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/xsd/galaxy.xsd Log Message: ----------- Create the $GALAXY_MEMORY_MB tool job environment variable and attempt to set it automatically under Slurm. Commit: 49c0c406e5f386307c20b190844a25fd41974a73 https://github.com/galaxyproject/galaxy/commit/49c0c406e5f386307c20b190844a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- When setting $GALAXY_MEMORY_MB, redirect stderr to memory_statement.log in the job directory. Also, use -1 as the default for the final test to see if $GALAXY_MEMORY_MB is a positive integer. This allows an admin to differentiate between a legit case where we don't set $GALAXY_MEMORY_MB (currently any DRM other than Slurm) and where the command ran but returned nothing on stdout. Commit: a18835b5169cbc281daa7de9dbfd655ab96f17f4 https://github.com/galaxyproject/galaxy/commit/a18835b5169cbc281daa7de9dbfd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: 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/xsd/galaxy.xsd Log Message: ----------- Merge pull request #4958 from natefoo/memory-env-var Create the $GALAXY_MEMORY_MB tool job environment variable Compare: https://github.com/galaxyproject/galaxy/compare/0799e511c41d...a18835b5169c

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[galaxyproject/galaxy] 79e96e: Run `hg clone` in a subprocess instead of using Me...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79e96e610dfb4dc6ce53ec39fe294ddde1600651 https://github.com/galaxyproject/galaxy/commit/79e96e610dfb4dc6ce53ec39fe29… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Run `hg clone` in a subprocess instead of using Mercurial API Using the API is discouraged by upstream, see: https://www.mercurial-scm.org/wiki/MercurialApi Moreover, the old code randomly causes the following error when installing big ToolShed repositories (e.g. any qiime tool) through the admin UI: tool_shed.util.hg_util DEBUG 2017-11-03 17:36:45,950 Error cloning repository: signal only works in main thread This error occurs when Galaxy runs under Paste and also when it runs under uWSGI with multiple threads per process. Commit: 0799e511c41d8a739dc5e137e70848c079da92ea https://github.com/galaxyproject/galaxy/commit/0799e511c41d8a739dc5e137e708… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #4979 from nsoranzo/hg_clone Run `hg clone` in a subprocess instead of using Mercurial API Compare: https://github.com/galaxyproject/galaxy/compare/87ebf9c54ae6...0799e511c41d

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[galaxyproject/galaxy] 231ce4: Encode file content with utf-8
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377 https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Encode file content with utf-8 There shouldn't be any disadvantages over doing this only for specific elements. This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378. I have tested this with unicode strings in the name and info fields. Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3 https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Open files in text-mode (thx @nsoranzo) Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759 https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4987 from mvdbeek/history_import_bug [17.09][Bug] Encode file content with utf-8 Compare: https://github.com/galaxyproject/galaxy/compare/222ece4eabb6...a0b4a2de5379

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[galaxyproject/galaxy] 6d5b7c: Install numpy before bx-python in case you are ins...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d5b7c0ebc588c12f55ada87b2b900b66e8c8114 https://github.com/galaxyproject/galaxy/commit/6d5b7c0ebc588c12f55ada87b2b9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Install numpy before bx-python in case you are installing from sdists. Commit: 8079dd5fc03bb034e99bdf995eaf6f1e7bc32050 https://github.com/galaxyproject/galaxy/commit/8079dd5fc03bb034e99bdf995eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add comment about numpy order in requirements. As requested by @nsoranzo. Commit: 87ebf9c54ae62948dfa22b8c8bc8b7ca3b5e31d1 https://github.com/galaxyproject/galaxy/commit/87ebf9c54ae62948dfa22b8c8bc8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4982 from natefoo/source-requirements Install numpy before bx-python in case you are installing from sdists Compare: https://github.com/galaxyproject/galaxy/compare/a2c164a53ad9...87ebf9c54ae6

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[galaxyproject/galaxy] b6a0a1: Tolerate IOError in tool and data table watcher
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3 https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. Commit: 6915007f85482648999768eecb9920da57b42e59 https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher Compare: https://github.com/galaxyproject/galaxy/compare/7688b057e604...6915007f8548

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[galaxyproject/galaxy] 84c925: Bumping pysam to 0.12 *core*, without customizatio...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84c92590635358a0c0798dfc8aa8ae6d2b37660e https://github.com/galaxyproject/galaxy/commit/84c92590635358a0c0798dfc8aa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: 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/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Bumping pysam to 0.12 *core*, without customization Commit: dadb3680f59e4646a53589d572d25df06d3850ed https://github.com/galaxyproject/galaxy/commit/dadb3680f59e4646a53589d572d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: 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 Log Message: ----------- Separate non-stdlib pysam from other imports. Commit: ee120745afa1e30a58287591fa9fe5776c83abfa https://github.com/galaxyproject/galaxy/commit/ee120745afa1e30a58287591fa9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Explicitly pin pysam to 0.12.0.1 Commit: c04cf6b228ec44ae1ec97820947954551cc1a33a https://github.com/galaxyproject/galaxy/commit/c04cf6b228ec44ae1ec978209479… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index. 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test/unit/jobs/test_job_wrapper.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_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_security_helper.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_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joiner.xml M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into pysam012 Commit: 5581d270e7b921419f89d70ccda5c9d3eabe417b https://github.com/galaxyproject/galaxy/commit/5581d270e7b921419f89d70ccda5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- All the way to 0.13 for pysam. Commit: a2c164a53ad99a0815cd3dbcc0b0b44605d4cfc2 https://github.com/galaxyproject/galaxy/commit/a2c164a53ad99a0815cd3dbcc0b0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: 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/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #4497 from dannon/pysam012 Bumping pysam to 0.13 *core*, without customization Compare: https://github.com/galaxyproject/galaxy/compare/7722fbaaad29...a2c164a53ad9

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[galaxyproject/galaxy] 4f9275: Include path in job script integrity errors
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f92759c4930bbaac79dbede0ac7a19b6a6d8580 https://github.com/galaxyproject/galaxy/commit/4f92759c4930bbaac79dbede0ac7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Include path in job script integrity errors Commit: 7722fbaaad29443325c8de8ac66f46375fc717af https://github.com/galaxyproject/galaxy/commit/7722fbaaad29443325c8de8ac66f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #4991 from nsoranzo/path_in_job_script_integrity_errors Include path in job script integrity errors Compare: https://github.com/galaxyproject/galaxy/compare/c7ef71dfc9df...7722fbaaad29

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[galaxyproject/galaxy] 493c3e: Fix initialization of named ajax queue
by GitHub 12 Nov '17

12 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 493c3e6475094628b2b35f752b065b469ee5130b https://github.com/galaxyproject/galaxy/commit/493c3e6475094628b2b35f752b06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js 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 Log Message: ----------- Fix initialization of named ajax queue Commit: c7ef71dfc9dff5f6650b3ddeeb88ab9734c76076 https://github.com/galaxyproject/galaxy/commit/c7ef71dfc9dff5f6650b3ddeeb88… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js 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 Log Message: ----------- Merge pull request #4985 from dannon/fix-named-ajax-queue Fix initialization of named ajax queue Compare: https://github.com/galaxyproject/galaxy/compare/7857b152cd10...c7ef71dfc9df

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[galaxyproject/usegalaxy-playbook] 31fa1e: Upgrade du novo to 2.0.9
by GitHub 10 Nov '17

10 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 31fa1e38d70bb7f77c64a2b2c6bb841189ac7ea1 https://github.com/galaxyproject/usegalaxy-playbook/commit/31fa1e38d70bb7f7… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgrade du novo to 2.0.9

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[galaxyproject/galaxy] 875fb3: Add @flakey test annotation and "skip" them if the...
by GitHub 10 Nov '17

10 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 875fb3641fbc70bc406be2744174e4945f61b99d https://github.com/galaxyproject/galaxy/commit/875fb3641fbc70bc406be2744174… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/base/populators.py M test/selenium_tests/test_jupyter.py Log Message: ----------- Add @flakey test annotation and "skip" them if the fail on Jenkins. Use it to skip the Juypter test that keeps randomly failing builds if there are problems. Commit: 7857b152cd10d9490ac2433ff2905ca1a47ee32c https://github.com/galaxyproject/galaxy/commit/7857b152cd10d9490ac2433ff290… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/base/populators.py M test/selenium_tests/test_jupyter.py Log Message: ----------- Merge pull request #4972 from jmchilton/flakey Add @flakey test annotation and "skip" them if the fail on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/438177d6ed77...7857b152cd10

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[galaxyproject/galaxy] 2f63d8: Capture a bunch of labelled screenshots of Galaxy ...
by GitHub 10 Nov '17

10 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f63d8bd70241e0db725e60734762a785a84da56 https://github.com/galaxyproject/galaxy/commit/2f63d8bd70241e0db725e6073476… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh 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_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 Log Message: ----------- Capture a bunch of labelled screenshots of Galaxy durings tests. During pull requests reviews this allows easy visual inspection of various components to augment the automated testing. Commit: 438177d6ed7754ecd7c82a67a56bc851c6b48165 https://github.com/galaxyproject/galaxy/commit/438177d6ed7754ecd7c82a67a56b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh 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_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 Log Message: ----------- Merge pull request #4971 from jmchilton/selenium_screenshot_suite Capture labelled screenshots of Galaxy during PR CI testing. Compare: https://github.com/galaxyproject/galaxy/compare/84c40e94d0b1...438177d6ed77

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[galaxyproject/galaxy] 50de50: Add CRAM to BAM converter
by GitHub 10 Nov '17

10 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50de5081d6f284c61bd36ae11e467af1b829c9eb https://github.com/galaxyproject/galaxy/commit/50de5081d6f284c61bd36ae11e46… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-06 (Mon, 06 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: ----------- Add CRAM to BAM converter Commit: 84c40e94d0b19747bd2ac0bb151437456ca5ab8f https://github.com/galaxyproject/galaxy/commit/84c40e94d0b19747bd2ac0bb1514… Author: John Chilton <jmchilton(a)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 pull request #4939 from mvdbeek/cram_to_bam Add CRAM to BAM converter Compare: https://github.com/galaxyproject/galaxy/compare/0982dc0f0439...84c40e94d0b1

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[galaxyproject/galaxy] 5df61d: fi xlink to deps
by GitHub 09 Nov '17

09 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5df61d91f3ead709692f36d2dc2ba5f635b6e548 https://github.com/galaxyproject/galaxy/commit/5df61d91f3ead709692f36d2dc2b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M README.rst Log Message: ----------- fi xlink to deps Commit: b0c7d8da23a6fbf7cef58ba9a0ae5a8c5c9731a2 https://github.com/galaxyproject/galaxy/commit/b0c7d8da23a6fbf7cef58ba9a0ae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M README.rst Log Message: ----------- bring readme on par with features Commit: c1421fda32e7c74905a3920681b2abf397f759c1 https://github.com/galaxyproject/galaxy/commit/c1421fda32e7c74905a3920681b2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M README.rst Log Message: ----------- add dot Commit: 0982dc0f043999aa0e12446a475edd4974828347 https://github.com/galaxyproject/galaxy/commit/0982dc0f043999aa0e12446a475e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M README.rst Log Message: ----------- Merge pull request #4968 from martenson/readme readme - bring on par with manage dependencies feature Compare: https://github.com/galaxyproject/galaxy/compare/0a3b5255434a...0982dc0f0439

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[galaxyproject/galaxy] 92519e: Fix up admin panel's run_stats.
by GitHub 09 Nov '17

09 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92519e5a56ace738b63332c055db8f1dc1cbcf3c https://github.com/galaxyproject/galaxy/commit/92519e5a56ace738b63332c055db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Fix up admin panel's run_stats. Commit: dd1f69ad5cf4e424b40af14a670ec171a28e7681 https://github.com/galaxyproject/galaxy/commit/dd1f69ad5cf4e424b40af14a670e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako Log Message: ----------- D3 imports (note the currentEvent hack needed; babel known issue with binding) Commit: 03a033e3c732a7b23c3a987643d0778ac1c3606e https://github.com/galaxyproject/galaxy/commit/03a033e3c732a7b23c3a987643d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- More cleanup for reports/run_stats Commit: eac8573a3caf327b6d766e1f14dfff76afba1bab https://github.com/galaxyproject/galaxy/commit/eac8573a3caf327b6d766e1f14df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Swap from event.path to event.target.parentElement for compatibility Commit: 0a3b5255434a48fcdb845c4f6bb9350d6a70bcd5 https://github.com/galaxyproject/galaxy/commit/0a3b5255434a48fcdb845c4f6bb9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Merge pull request #4967 from dannon/fix-admin-panel Fix up reports javascript Compare: https://github.com/galaxyproject/galaxy/compare/76d4afe3a600...0a3b5255434a

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[galaxyproject/infrastructure-playbook] ffeeed: Add missing people from common sshkeys
by GitHub 09 Nov '17

09 Nov '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ffeeed5b2e00db66f8b84a9b6034fbd237870498 https://github.com/galaxyproject/infrastructure-playbook/commit/ffeeed5b2e0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M env/common/group_vars/sshservers/vault.yml Log Message: ----------- Add missing people from common sshkeys Commit: 93480aed148c9dd839adeaaf7b7fd9c9d8aa820d https://github.com/galaxyproject/infrastructure-playbook/commit/93480aed148… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M env/galaxy/group_vars/starforgebuilders.yml Log Message: ----------- Stop using removed local_users syntax and note an annoyance with the new inheritance merging. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c6fd1ff76b…

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[galaxyproject/galaxy] 4d2a3c: Test both endpoints for collection creation in his...
by GitHub 09 Nov '17

09 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d2a3c6074252a8268141ccfe6575405658fc3cc https://github.com/galaxyproject/galaxy/commit/4d2a3c6074252a8268141ccfe657… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py Log Message: ----------- Test both endpoints for collection creation in history contents API. Commit: 76d4afe3a6009e23de6e54d16c23d0579f9b0ad1 https://github.com/galaxyproject/galaxy/commit/76d4afe3a6009e23de6e54d16c23… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py Log Message: ----------- Merge pull request #4965 from jmchilton/hdca_creation_api_clarification Test both endpoints for collection creation in history contents API. Compare: https://github.com/galaxyproject/galaxy/compare/8ce7d294901f...76d4afe3a600

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[galaxyproject/galaxy] 372d65: Upgrade prettier, fixes comment formatting and han...
by GitHub 09 Nov '17

09 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 372d65d23936c84b7f28fc03465611a2ca12cf58 https://github.com/galaxyproject/galaxy/commit/372d65d23936c84b7f28fc034656… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/galaxy.interactive_environments.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/modal.js M client/galaxy/scripts/mvc/annotation.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/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/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/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/history-model.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/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-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-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-view.js M client/galaxy/scripts/mvc/tag.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/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.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/visualization.js M client/yarn.lock M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/modal.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/library/library-util.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M 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/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 Log Message: ----------- Upgrade prettier, fixes comment formatting and handles string literals a little better. Commit: 8ce7d294901f8f8b22f0bf180e25b10e35195d39 https://github.com/galaxyproject/galaxy/commit/8ce7d294901f8f8b22f0bf180e25… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/galaxy.interactive_environments.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/modal.js M client/galaxy/scripts/mvc/annotation.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/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/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/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/history-model.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/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-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-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-view.js M client/galaxy/scripts/mvc/tag.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/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.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/visualization.js M client/yarn.lock M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.library.js.map M static/maps/galaxy.pages.js.map M static/maps/i18n.js.map M static/maps/layout/modal.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/library/library-util.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M 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/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 Log Message: ----------- Merge pull request #4964 from dannon/prettier_upgrade_18 Prettier upgrade Compare: https://github.com/galaxyproject/galaxy/compare/963cfd1a3faa...8ce7d294901f

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