Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71db6b461da3d3b2e3c6880c9d2bf90bcd44098e https://github.com/galaxyproject/galaxy/commit/71db6b461da3d3b2e3c6880c9d2bf... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Fix lint
Fix
Commit: c72aca479729ddee6a8bf8e19431b41e98d39d89 https://github.com/galaxyproject/galaxy/commit/c72aca479729ddee6a8bf8e19431b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.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: ----------- Revise admin groups endpoint
Commit: 097cae67956b972cd609f1155890d122c5bb3742 https://github.com/galaxyproject/galaxy/commit/097cae67956b972cd609f1155890d... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: 9822dede69c95796c24e87a1c60cd845788095d1 https://github.com/galaxyproject/galaxy/commit/9822dede69c95796c24e87a1c60cd... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map
Log Message: ----------- Add client route
Commit: 1bf2d1782fca4c79708261ca98cabe92822e86cb https://github.com/galaxyproject/galaxy/commit/1bf2d1782fca4c79708261ca98cab... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.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: ----------- Use client side formbuilder for rename group form
Commit: 7a58fd113d32659c9ea6e0c4fdb830d5c1ca7a72 https://github.com/galaxyproject/galaxy/commit/7a58fd113d32659c9ea6e0c4fdb83... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove self directed operation
Commit: b2d54b377c6c78f016ccb730178afd3f7a70c0b3 https://github.com/galaxyproject/galaxy/commit/b2d54b377c6c78f016ccb730178af... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Add async support for group deleting
Commit: afdfbf69ff8d1636c661c5758f52c636f9160220 https://github.com/galaxyproject/galaxy/commit/afdfbf69ff8d1636c661c5758f52c... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Add async support for undeleting groups
Commit: 96557cd136730033c3a4b84e506b3cc5831d06af https://github.com/galaxyproject/galaxy/commit/96557cd136730033c3a4b84e506b3... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Add async support for purging groups
Commit: 037b7fa75754ae90917d0ee25b1565c9ab29cd03 https://github.com/galaxyproject/galaxy/commit/037b7fa75754ae90917d0ee25b156... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove exposure of async operation handlers, align naming
Commit: 3840c6d61735fa674239be19a10af04d0d3647f9 https://github.com/galaxyproject/galaxy/commit/3840c6d61735fa674239be19a10af... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Fix purge handler for groups
Commit: 1e83a48c4635ba05576cdb8e42bbdf8f971b825a https://github.com/galaxyproject/galaxy/commit/1e83a48c4635ba05576cdb8e42bbd... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove exposure of user related operations
Commit: 1795247bd849e3d7d1c034416d27d5c1672039e8 https://github.com/galaxyproject/galaxy/commit/1795247bd849e3d7d1c034416d27d... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove new line
Commit: e805db6896352042aa5eb8482febbd75af46b008 https://github.com/galaxyproject/galaxy/commit/e805db6896352042aa5eb8482febb... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.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: ----------- Use client to build create groups form
Commit: 5605f390fe36c8ab562d049b105db7164b8097c1 https://github.com/galaxyproject/galaxy/commit/5605f390fe36c8ab562d049b105db... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.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: ----------- Build manage users and roles for groups with client form builder
Commit: c827bb0a867e2fcdf89417bb7ea912641e49cf8a https://github.com/galaxyproject/galaxy/commit/c827bb0a867e2fcdf89417bb7ea91... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M lib/tool_shed/util/admin_util.py R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
Log Message: ----------- Move unused mako templates to toolshed, adjust paths
Commit: dbad2556d05dead2ac0991a7897d95f1eda16087 https://github.com/galaxyproject/galaxy/commit/dbad2556d05dead2ac0991a7897d9... Author: guerler aysam.guerler@gmail.com Date: 2017-08-08 (Tue, 08 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map
Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: c57c36b51465b1bfaefcf486b9814c32f7f92840 https://github.com/galaxyproject/galaxy/commit/c57c36b51465b1bfaefcf486b9814... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Remove over indent
Commit: 4a77956dc8756300825c3744ccfa3a4646be5775 https://github.com/galaxyproject/galaxy/commit/4a77956dc8756300825c3744ccfa3... Author: guerler aysam.guerler@gmail.com Date: 2017-08-09 (Wed, 09 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: b38ccbc10547ded7e3afec262a5819bd3d44613f https://github.com/galaxyproject/galaxy/commit/b38ccbc10547ded7e3afec262a581... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py
Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups
Commit: ad2f39c1e6475c65fcb1e300201c035701640f10 https://github.com/galaxyproject/galaxy/commit/ad2f39c1e6475c65fcb1e300201c0... Author: guerler aysam.guerler@gmail.com Date: 2017-08-10 (Thu, 10 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Fix lint
Commit: eccdc8c248fabef6bc5a988cdb1889c1aa32ca7a https://github.com/galaxyproject/galaxy/commit/eccdc8c248fabef6bc5a988cdb188... Author: guerler aysam.guerler@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message: ----------- Removed unreached message line
Commit: fd5f42dc17009cfdfbfc08583549ba608efb166a https://github.com/galaxyproject/galaxy/commit/fd5f42dc17009cfdfbfc08583549b... Author: guerler aysam.guerler@gmail.com Date: 2017-08-14 (Mon, 14 Aug 2017)
Changed paths: M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml
Log Message: ----------- Merge branch 'dev' into admin_grid_groups
Commit: e72948cb743e50b50a21bf7f778792ba36ec38bd https://github.com/galaxyproject/galaxy/commit/e72948cb743e50b50a21bf7f77879... Author: guerler aysam.guerler@gmail.com Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js
Log Message: ----------- Merge branch 'dev' into admin_grid_groups
Commit: 4bddd617fe5df41efcebacdda7a6bb1d280ac2ce https://github.com/galaxyproject/galaxy/commit/4bddd617fe5df41efcebacdda7a6b... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-15 (Tue, 15 Aug 2017)
Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.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/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
Log Message: ----------- Merge pull request #4405 from guerler/admin_grid_groups
Admin grid groups revision
Compare: https://github.com/galaxyproject/galaxy/compare/462b7def5d9b...4bddd617fe5d