November 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c0a3e6: Update imports for galaxy.util.path moves
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0a3e6c12a32f0e2fc1c657493a9a2ad3e515b03 https://github.com/galaxyproject/galaxy/commit/c0a3e6c12a32f0e2fc1c657493a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Update imports for galaxy.util.path moves Commit: ae720d6f4cea03268e8303454088c89c4849cf41 https://github.com/galaxyproject/galaxy/commit/ae720d6f4cea03268e8303454088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Log a more useful error message when tool loading fails due to IOError/OSError or a nonexistent tool config. Commit: f8e59b922a8bad9f1ca0b6b62eae6707144e4456 https://github.com/galaxyproject/galaxy/commit/f8e59b922a8bad9f1ca0b6b62eae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Improve util.listify documentation and allow it to accept tuples Commit: f5ee540df102526219f8347bbcb7217fbb704b11 https://github.com/galaxyproject/galaxy/commit/f5ee540df102526219f8347bbcb7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: A lib/galaxy/util/script.py M scripts/manage_tool_dependencies.py Log Message: ----------- To avoid duplication, move common utilities used by external scripts to galaxy.util.script. Update one such script to use the new module. Commit: eed12ad15c9bd3f5ba9122826e5f6be0e8a4e615 https://github.com/galaxyproject/galaxy/commit/eed12ad15c9bd3f5ba9122826e5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Docstring fixes Commit: fb78cb6be3fa6e7debb6ac4e5e528322571afd03 https://github.com/galaxyproject/galaxy/commit/fb78cb6be3fa6e7debb6ac4e5e52… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py A lib/galaxy/util/script.py M lib/tool_shed/capsule/capsule_manager.py M scripts/manage_tool_dependencies.py Log Message: ----------- Merge pull request #4994 from natefoo/non-mule-changes Changes made while working on uWSGI mules that don't belong in the mules PR Compare: https://github.com/galaxyproject/galaxy/compare/95c297c5560c...fb78cb6be3fa

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[galaxyproject/infrastructure-playbook] f54bfe: Redirect training.galaxyproject.org ->
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f54bfe05fd383af1439e84f31c4afcc27752b231 https://github.com/galaxyproject/infrastructure-playbook/commit/f54bfe05fd3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- Redirect training.galaxyproject.org -> galaxyproject.github.io/training-material with the $request_uri appended (previously all pages redirected to the training root).

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[galaxyproject/galaxy] 538d63: Remove unused galaxy-side set_tool_version code
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 538d63a8c6b9d5ad138ba377808c8f32e4fae5c9 https://github.com/galaxyproject/galaxy/commit/538d63a8c6b9d5ad138ba377808c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Remove unused galaxy-side set_tool_version code This is all unnecessary or handled by the tool lineage. Commit: 95c297c5560c50f1cb9992c630193c3d06392ba9 https://github.com/galaxyproject/galaxy/commit/95c297c5560c50f1cb9992c63019… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/tool_version_manager.py M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Merge pull request #4986 from mvdbeek/remove_galaxy_set_tool_versions Remove unused galaxy-side set_tool_version code Compare: https://github.com/galaxyproject/galaxy/compare/9d9c323f735f...95c297c5560c

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[galaxyproject/galaxy] 80ba1c: Fix allow-register option in auth module
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80ba1c07bf614f8d116249ed904f61cd43bbaa35 https://github.com/galaxyproject/galaxy/commit/80ba1c07bf614f8d116249ed904f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- Fix allow-register option in auth module config/auth_conf.xml.sample specifies that the possible values are True, False and Challenge. Broken in commit b3174efa8e2996dc8e05e85d563e546cc66e2848 . Also remove _get_bool(d, k, o) function in favour of the more explicit `string_as_bool(d.get(k, o))` . Commit: 9d9c323f735faca44d70eee817f87f17146b9ec6 https://github.com/galaxyproject/galaxy/commit/9d9c323f735faca44d70eee817f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- Merge pull request #4989 from nsoranzo/fix_allow-register Fix allow-register option in auth module Compare: https://github.com/galaxyproject/galaxy/compare/148e91f5b711...9d9c323f735f

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[galaxyproject/galaxy] aa640f: Fix tox envlist to contain all envs that should pa...
by GitHub 13 Nov '17

13 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa640f493d3fc7f709607c7c4777f9957b2f6ff9 https://github.com/galaxyproject/galaxy/commit/aa640f493d3fc7f709607c7c4777… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Fix tox envlist to contain all envs that should pass Now simply running: ``` $ tox ``` is the equivalent of running all the Travis jobs that are not in the `allow_failures` list. Also: - remove py33-lint env - sort envs alphabetically Commit: 148e91f5b71121a203a82c33bf20a34102ec4277 https://github.com/galaxyproject/galaxy/commit/148e91f5b71121a203a82c33bf20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4992 from nsoranzo/fix_tox_envlist Fix tox envlist to contain all envs that should pass Compare: https://github.com/galaxyproject/galaxy/compare/c83a8260fd62...148e91f5b711

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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/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 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 client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.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/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.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/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.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/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/levenshtein.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M 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 M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py M static/maps/admin.toolshed.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.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/generic-nav-view.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/modal.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/layout/router.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/collection/base-creator.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/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-error.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/dataset/states.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/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map 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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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/8422feb46bf57e1a248ccbb62e1b… 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 whoosh from directory creation method Commit: 4b30e84a657a544543eae92319c298c9b02d82cf https://github.com/galaxyproject/galaxy/commit/4b30e84a657a544543eae92319c2… Author: guerler <aysam.guerler(a)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/991ee7d471a2ed0e39ff391ba103… Author: guerler <aysam.guerler(a)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/c9ab13fb411bab8a5e0021087f4c… Author: guerler <aysam.guerler(a)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/ed4b0042572a47f505f1496047bb… Author: guerler <aysam.guerler(a)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/7e372c908ef37fd8054ff2001844… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/galaxy.interactive_environments.js M 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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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