Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64a1e514587ea4d2d9fa870ebb9230212dbec244 https://github.com/galaxyproject/galaxy/commit/64a1e514587ea4d2d9fa870ebb923... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.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/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Adds tags to library dataset items, and allows users to specify that tags should be generated from filenames

Commit: dcdbfd64d1e94c200c023e1d3b51a8a96c60ca1a https://github.com/galaxyproject/galaxy/commit/dcdbfd64d1e94c200c023e1d3b51a... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/web/base/controller.py

Log Message: ----------- According to John, this is not actually deprecated

Commit: ce7e10cf07ca0061a168bd637cd8ca5a0b88bec5 https://github.com/galaxyproject/galaxy/commit/ce7e10cf07ca0061a168bd637cd8c... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- shows tags in library views

Commit: 14a0de0c21e40a88ab9b917db28c5a6365ebc7c9 https://github.com/galaxyproject/galaxy/commit/14a0de0c21e40a88ab9b917db28c5... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- copies tags on library items to history (and to copies of library items, though I don’t think anything called this)

Commit: 72e9e69467125afd9cff9e086c3b153c1f20a289 https://github.com/galaxyproject/galaxy/commit/72e9e69467125afd9cff9e086c3b1... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/model/migrate/versions/0135_add_library_tags.py

Log Message: ----------- Removes unused import

Commit: 3b0c25f73b542022c706787b4cb910a6365c1c75 https://github.com/galaxyproject/galaxy/commit/3b0c25f73b542022c706787b4cb91... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/model/__init__.py

Log Message: ----------- Fixes style violation # comment not #comment

Commit: efd6d053bcae0c9eeede93dc17e0069302646967 https://github.com/galaxyproject/galaxy/commit/efd6d053bcae0c9eeede93dc17e00... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- fixes import order to comply with flake8

Commit: 5add359cde29a9e6ccc7b94b6b9420522e6d5fea https://github.com/galaxyproject/galaxy/commit/5add359cde29a9e6ccc7b94b6b942... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- need to construct this field to avoid a conditional check failure

Commit: 33900e5bc913b494611373a9bd926643e760be95 https://github.com/galaxyproject/galaxy/commit/33900e5bc913b494611373a9bd926... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py

Log Message: ----------- Rather than trying to find every path into this Function, assume no tagging if dataset does not Have a tag_using_filenames property

Commit: dd2224e92ddab51deaf646b04a23ec3112815733 https://github.com/galaxyproject/galaxy/commit/dd2224e92ddab51deaf646b04a23e... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py

Log Message: ----------- updates doc to include tag_using_filenames

Commit: 73012c942e77d5fe7993ddbd67559c51c2832813 https://github.com/galaxyproject/galaxy/commit/73012c942e77d5fe7993ddbd67559... Author: Brad Langhorst langhorst@neb.com Date: 2017-07-05 (Wed, 05 Jul 2017)

Changed paths: M lib/galaxy/tools/parameters/grouping.py

Log Message: ----------- Allow passing in tag_using_filenames via grouping

Commit: cb7b34f320a82cb8e4efe96e72f4165f72e1930c https://github.com/galaxyproject/galaxy/commit/cb7b34f320a82cb8e4efe96e72f41... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-07-06 (Thu, 06 Jul 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- Swap two more spots initializing TagManagers to new session instead of app

Commit: 7b423e19c92868a6a3e7abee2a4ad6e92a03aad8 https://github.com/galaxyproject/galaxy/commit/7b423e19c92868a6a3e7abee2a4ad... Author: Brad Langhorst langhorst@neb.com Date: 2017-08-07 (Mon, 07 Aug 2017)

Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py

Log Message: ----------- Merge pull request #1 from dannon/library_tags

Swap two more spots initializing TagManagers to new session

Commit: 06c70d34e2c218b826d813d3dd4e52d077ab94d4 https://github.com/galaxyproject/galaxy/commit/06c70d34e2c218b826d813d3dd4e5... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js

Log Message: ----------- make client

Commit: cff21d350dc71b1e7b088985eeeb3f27b0fec1d0 https://github.com/galaxyproject/galaxy/commit/cff21d350dc71b1e7b088985eeeb3... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/package-lock.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/webhooks/demo/search/static/script.js M config/tool_conf.xml.main M config/tool_shed.ini.sample A config/user_preferences_extra_conf.yml.sample M doc/source/admin/special_topics/grt.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/proteomics.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/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/collections.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 M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/metadata/metadata_generator.py A lib/tool_shed/util/admin_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py M scripts/runtime_stats.py M static/maps/galaxy.js.map M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/data.js.map A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-model.js.map A static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/page/page-list.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.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 M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/data.js A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/page/page-list.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako R templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako R templates/webapps/galaxy/visualization/list.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py A test/functional/tools/identifier_source.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py A test/unit/test_remote_shell.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M tox.ini

Log Message: ----------- Merge branch 'dev' into library_tags

Commit: fd0ce1284a9663fab95558fd38ad9477c98d8311 https://github.com/galaxyproject/galaxy/commit/fd0ce1284a9663fab95558fd38ad9... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map

Log Message: ----------- make client again...

Commit: d52ac533daa8bcfef209f66f8c4e3020d93c09df https://github.com/galaxyproject/galaxy/commit/d52ac533daa8bcfef209f66f8c4e3... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M lib/galaxy/model/migrate/versions/0135_add_library_tags.py

Log Message: ----------- fix indentation

Commit: 429771820200acd1a0d0b12c85a39ab7fe530195 https://github.com/galaxyproject/galaxy/commit/429771820200acd1a0d0b12c85a39... Author: Martin Cech marten@bx.psu.edu Date: 2017-08-09 (Wed, 09 Aug 2017)

Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/managers/tags.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/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/library_common.py 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.map 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/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js

Log Message: ----------- Merge pull request #4262 from bwlang/library_tags

Library tags

Compare: https://github.com/galaxyproject/galaxy/compare/2e53858a2973...429771820200