[galaxyproject/galaxy] 417d1d: Initial commit to get this rolling, library-securi...
by GitHub
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 417d1d251e7e7c735a8d4aefd53edcec941db1f4
https://github.com/galaxyproject/galaxy/commit/417d1d251e7e7c735a8d4aefd5...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
Log Message:
-----------
Initial commit to get this rolling, library-security does not exist and needs to be created, among others.
Commit: bc870cdf66ecaaf218cd20debdbcc68b20e7f959
https://github.com/galaxyproject/galaxy/commit/bc870cdf66ecaaf218cd20debd...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Update galaxy.ini.sample and config.
Commit: 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4
https://github.com/galaxyproject/galaxy/commit/11829c4f9df12cf8e8e3e7a14d...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/managers/configuration.py
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
Log Message:
-----------
More defaults, these should be consolidated.
Commit: e12c07cacd12fbf4a2fb148242be5bea7c13221e
https://github.com/galaxyproject/galaxy/commit/e12c07cacd12fbf4a2fb148242...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
Log Message:
-----------
Use config.py for defaults used in managers/configuration.
Commit: ed1d19a967989416caebd3588fe6b8b6460764e2
https://github.com/galaxyproject/galaxy/commit/ed1d19a967989416caebd3588f...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-14 (Tue, 14 Mar 2017)
Changed paths:
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Update reports and toolshed app configs as well.
Commit: 72cd0ba00ad05793751105dccf434c9868791b2a
https://github.com/galaxyproject/galaxy/commit/72cd0ba00ad05793751105dccf...
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Adjust link to the new Galaxy HUB site
Commit: b4fda2ccd49fd7b406a5521bce3243ff6ffb7950
https://github.com/galaxyproject/galaxy/commit/b4fda2ccd49fd7b406a5521bce...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-03-17 (Fri, 17 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Merge pull request #16 from bgruening/wf_link
/learn/advanced-workflow/variables-edit
Commit: ea3796152a01aad87f0585bf83ceb661392ba4d4
https://github.com/galaxyproject/galaxy/commit/ea3796152a01aad87f0585bf83...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Replace wiki.galaxyproject.org links in /lib
Commit: 04a32064f1d553c01828092b445175a9c7d8a53d
https://github.com/galaxyproject/galaxy/commit/04a32064f1d553c01828092b44...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/viz/phyloviz.js
M static/maps/mvc/citation/citation-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/viz/phyloviz.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.map
M static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/viz/phyloviz.js
Log Message:
-----------
Update wiki.galaxyproject.org links in client
Commit: a5143ce7a86cb64c81b0ffa36a90742b872cec15
https://github.com/galaxyproject/galaxy/commit/a5143ce7a86cb64c81b0ffa36a...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/data_manager/index.mako
Log Message:
-----------
Convert wiki.galaxyproject.org links in templates
Commit: 29aa00e42129bec564a9f1009547e3b740b29709
https://github.com/galaxyproject/galaxy/commit/29aa00e42129bec564a9f10095...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M CONTRIBUTING.md
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/mvc/collection/base-creator.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/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.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/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A 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/nls/zh/locale.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/package.json
M client/webpack.config.js
A config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/openid_conf.xml.sample
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
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.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/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.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/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/swarm_manager_conf.yml.sample
M config/tool_conf.xml.sample
M config/tool_destinations.yml.sample
R cron/clean_docker_swarm_mode_services.sh
M display_applications/igv/bigwig.xml
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
M doc/source/admin/framework_dependencies.rst
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/reports.md
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grafana.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/performance_tracking.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
M doc/source/admin/useful_scripts.rst
R doc/source/admin/webhooks.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/project/issues.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/containers/__init__.py
A lib/galaxy/containers/docker.py
A lib/galaxy/containers/docker_decorators.py
A lib/galaxy/containers/docker_model.py
A lib/galaxy/containers/docker_swarm.py
A lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/external_service_types.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/filter_failed_collection.xml
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
A lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/zip_collection.xml
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/handlers.py
R lib/galaxy/util/postfork.py
M lib/galaxy/util/submodules.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/batch.py
A lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/mapper.js
M lib/galaxy/web/proxy/js/package.json
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.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
A lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
R openid/google.xml
M run_tests.sh
M scripts/api/README
M scripts/secret_decoder_ring.py
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
A static/maps/mvc/collection/base-creator.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/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-parameters.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/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
A 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/nls/zh/locale.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.interactive_environments.js
M static/scripts/layout/menu.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/grid_base.mako
M templates/show_params.mako
R templates/user/dbkeys.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/galaxy/workflow/display.mako
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api_asserts.py
M test/base/data/test_workflow_pause.ga
M test/base/driver_util.py
M test/base/populators.py
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/qunit/package.json
M test/qunit/test-data/paired-collection-creator.data.js
M test/qunit/tests/ui_tests.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into wiki-to-hub
Commit: 0dd75e6cdd985ec3711987ef8adb3fe6365b8501
https://github.com/galaxyproject/galaxy/commit/0dd75e6cdd985ec3711987ef8a...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
A templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Attempt to rectify bad merge.
Commit: 05e81192bd91559876da1a82b734c7e49e15f43e
https://github.com/galaxyproject/galaxy/commit/05e81192bd91559876da1a82b7...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M test/qunit/tests/form_tests.js
Log Message:
-----------
Update tool form qunit test text.
Commit: 89e692d980965f5a1963818180ccaf62ae2c207f
https://github.com/galaxyproject/galaxy/commit/89e692d980965f5a1963818180...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M config/galaxy.ini.sample
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/workflow/workflow-forms.js
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
Log Message:
-----------
Tweaks for @nsoranzo.
Commit: 5fe7b7208c8668b7d4dd9dc31568c77a0a8c2562
https://github.com/galaxyproject/galaxy/commit/5fe7b7208c8668b7d4dd9dc315...
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Fix support link
Commit: f0740136831623adf8b2c1fe9ed17dbf4327ebc4
https://github.com/galaxyproject/galaxy/commit/f0740136831623adf8b2c1fe9e...
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M config/galaxy.ini.sample
Log Message:
-----------
Small tweaks for data-libraries URLS
Commit: dab18fb2387d737f859637bbd37d9b0ce3ec658c
https://github.com/galaxyproject/galaxy/commit/dab18fb2387d737f859637bbd3...
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-04-28 (Fri, 28 Apr 2017)
Changed paths:
M CITATION
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/viz/phyloviz.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M static/maps/mvc/citation/citation-view.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/viz/phyloviz.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/mvc/citation/citation-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/viz/phyloviz.js
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/user/index.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/tool_shed/base_panels.mako
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge branch 'wiki-to-hub' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
Compare: https://github.com/galaxyproject/galaxy/compare/760160a02cd9...dab18fb2387d
5 years, 9 months