Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 54d4c266bd7c724256f44f0057021d0da2dba3b6
https://github.com/galaxyproject/galaxy/commit/54d4c266bd7c724256f44f005702…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-09-10 (Thu, 10 Sep 2015)
Changed paths:
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_file_browser_dev.xml
M tools/genomespace/genomespace_file_browser_prod.xml
M tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Have GenomeSpace tools report the GS tool name (for their internal metrics). Default is "Galaxy", but can be overridden by setting "GENOMESPACE_TOOLNAME" environment variable.
Commit: b79555264e6f1d7b042bd5650efeed1483252095
https://github.com/galaxyproject/galaxy/commit/b79555264e6f1d7b042bd5650efe…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-09-10 (Thu, 10 Sep 2015)
Changed paths:
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_file_browser_dev.xml
M tools/genomespace/genomespace_file_browser_prod.xml
M tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
Log Message:
-----------
Merge pull request #711 from blankenberg/genomespace_toolname
Have GenomeSpace tools report the GS tool name
Compare: https://github.com/galaxyproject/galaxy/compare/e6a603decec5...b79555264e6f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: af2f93b23609b367d15619471a18e3e6fd0c90e8
https://github.com/galaxyproject/galaxy/commit/af2f93b23609b367d15619471a18…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
Log Message:
-----------
flake8 contrib/ .
Commit: df808d0c1e8c46e45adebaafbd30e0a8a1cf9b55
https://github.com/galaxyproject/galaxy/commit/df808d0c1e8c46e45adebaafbd30…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.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/utility_containers/__init__.py
M lib/tool_shed/grids/repository_grid_filter_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/repository_types/util.py
M lib/tool_shed/scripts/api/add_repository_registry_entry.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/api/create_categories.py
M lib/tool_shed/scripts/api/create_users.py
M lib/tool_shed/scripts/api/export.py
M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
M lib/tool_shed/scripts/api/import_capsule.py
M lib/tool_shed/scripts/api/remove_repository_registry_entry.py
M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/container_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
flake8 lib/tool_shed/ .
Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
Commit: b1b710925a4c54f3081fc4b79963085e0c362d42
https://github.com/galaxyproject/galaxy/commit/b1b710925a4c54f3081fc4b79963…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-09-10 (Thu, 10 Sep 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.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/utility_containers/__init__.py
M lib/tool_shed/grids/repository_grid_filter_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/repository_types/util.py
M lib/tool_shed/scripts/api/add_repository_registry_entry.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/api/create_categories.py
M lib/tool_shed/scripts/api/create_users.py
M lib/tool_shed/scripts/api/export.py
M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
M lib/tool_shed/scripts/api/import_capsule.py
M lib/tool_shed/scripts/api/remove_repository_registry_entry.py
M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/container_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
Merge pull request #708 from nsoranzo/flake8_fixes
flake8 contrib/ and lib/tool_shed/ .
Compare: https://github.com/galaxyproject/galaxy/compare/5d79823a2d67...b1b710925a4c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9a376d1ae0a5bdad632b5ad0f280cddddbd2d54d
https://github.com/galaxyproject/galaxy/commit/9a376d1ae0a5bdad632b5ad0f280…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-18 (Tue, 18 Aug 2015)
Changed paths:
M config/galaxy.ini.sample
M templates/webapps/galaxy/tool_form.mako
Log Message:
-----------
Remove tool form downgrade option
Commit: 6c805ccb988a47b2958e9bcaf7c56faed13c1fd0
https://github.com/galaxyproject/galaxy/commit/6c805ccb988a47b2958e9bcaf7c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
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-view.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M lib/galaxy/managers/base.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/util/jstree.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/tool_shed/capsule/capsule_manager.py
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/reports_webapp/run_stats.js
M static/style/blue/base.css
M test/qunit/tests/upload_dialog_tests.js
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000
Commit: 104bdcd7c8e8e5557b166d47c9dcdfdadf22cdf6
https://github.com/galaxyproject/galaxy/commit/104bdcd7c8e8e5557b166d47c9dc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-button-check.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M static/maps/mvc/ui/ui-button-check.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/scripts/mvc/ui/ui-button-check.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-options.js
Log Message:
-----------
Minor code cleanup for ui elements
Commit: 5d8ad4249fc6198846bf8cdceabf3fb91acc2973
https://github.com/galaxyproject/galaxy/commit/5d8ad4249fc6198846bf8cdceabf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M static/maps/mvc/ui/ui-color-picker.js.map
M static/scripts/mvc/ui/ui-color-picker.js
Log Message:
-----------
Remove unnecessary condition
Commit: 09445359a4dbcedb2d996dd4c46469f462ca6809
https://github.com/galaxyproject/galaxy/commit/09445359a4dbcedb2d996dd4c464…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M lib/galaxy/model/__init__.py
M scripts/cleanup_datasets/cleanup_datasets.py
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M test/qunit/tests/upload_dialog_tests.js
M test/unit/test_galaxy_mapping.py
R tool-data/fastx_clipper_sequences.txt
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000
Commit: 9a44d780145b6a7b30b40b1a7e61b7df5e526dbc
https://github.com/galaxyproject/galaxy/commit/9a44d780145b6a7b30b40b1a7e61…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-24 (Mon, 24 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/util/common_util.py
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
M templates/base.mako
M templates/spark_base.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_removal_000
Commit: 11e6c9949e2bb58874eedb81d9066c1f460fa34a
https://github.com/galaxyproject/galaxy/commit/11e6c9949e2bb58874eedb81d906…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M templates/base.mako
Log Message:
-----------
Make sure global Galaxy object exists
Commit: aebf0c7fea2f276f68b77d27408c45e330aa629b
https://github.com/galaxyproject/galaxy/commit/aebf0c7fea2f276f68b77d27408c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-31 (Mon, 31 Aug 2015)
Changed paths:
M client/galaxy/scripts/galaxy.panels.js
M static/maps/galaxy.panels.js.map
M templates/base.mako
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Add modified index handling
Commit: 8cf76bd27e30a7b35ad3c7867fdc43bd44a4b661
https://github.com/galaxyproject/galaxy/commit/8cf76bd27e30a7b35ad3c7867fdc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-01 (Tue, 01 Sep 2015)
Changed paths:
M client/galaxy/scripts/galaxy.panels.js
M static/maps/galaxy.panels.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/galaxy.panels.js
M static/scripts/utils/uploadbox.js
M templates/base.mako
Log Message:
-----------
Note root in Galaxy object
Commit: b1949c5805730d2f4ce53759dd5636449a0b08f5
https://github.com/galaxyproject/galaxy/commit/b1949c5805730d2f4ce53759dd56…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-02 (Wed, 02 Sep 2015)
Changed paths:
A client/galaxy/scripts/mvc/app/app-panel-center.js
A client/galaxy/scripts/mvc/app/app-panel-history.js
A client/galaxy/scripts/mvc/app/app-panel-tool.js
A client/galaxy/scripts/mvc/app/app-view.js
A static/maps/mvc/app/app-panel-center.js.map
A static/maps/mvc/app/app-panel-history.js.map
A static/maps/mvc/app/app-panel-tool.js.map
A static/maps/mvc/app/app-view.js.map
A static/scripts/mvc/app/app-panel-center.js
A static/scripts/mvc/app/app-panel-history.js
A static/scripts/mvc/app/app-panel-tool.js
A static/scripts/mvc/app/app-view.js
M templates/base.mako
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Add script files, continue ui replication
Commit: 8444838a3eda2b2e361c32e165cb65ad3a198cc5
https://github.com/galaxyproject/galaxy/commit/8444838a3eda2b2e361c32e165cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-02 (Wed, 02 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-history.js
M client/galaxy/scripts/mvc/app/app-panel-tool.js
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-panel-history.js.map
M static/maps/mvc/app/app-panel-tool.js.map
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-panel-history.js
M static/scripts/mvc/app/app-panel-tool.js
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Fix panel handlers
Commit: 8d8df1ab5d741758a195eaa34b75b49c1339a948
https://github.com/galaxyproject/galaxy/commit/8d8df1ab5d741758a195eaa34b75…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-history.js
M client/galaxy/scripts/mvc/app/app-panel-tool.js
M client/galaxy/scripts/mvc/app/app-view.js
R client/galaxy/scripts/mvc/ui/ui-button-check.js
R client/galaxy/scripts/mvc/ui/ui-button-menu.js
A client/galaxy/scripts/mvc/ui/ui-buttons.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-default.js
M static/maps/mvc/app/app-panel-history.js.map
M static/maps/mvc/app/app-panel-tool.js.map
M static/maps/mvc/app/app-view.js.map
R static/maps/mvc/ui/ui-button-check.js.map
R static/maps/mvc/ui/ui-button-menu.js.map
A static/maps/mvc/ui/ui-buttons.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-default.js.map
M static/scripts/mvc/app/app-panel-history.js
M static/scripts/mvc/app/app-panel-tool.js
M static/scripts/mvc/app/app-view.js
R static/scripts/mvc/ui/ui-button-check.js
R static/scripts/mvc/ui/ui-button-menu.js
A static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Revise/unify buttons, cleanup default ui element code, add panel button
Commit: c7bb8873ca46a67993ad5cb25a85bc81bb780777
https://github.com/galaxyproject/galaxy/commit/c7bb8873ca46a67993ad5cb25a85…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-history.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/app/app-panel-history.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/mvc/app/app-panel-history.js
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Add buttons to panel history builder, apply coding conventions
Commit: d546d08c86fc506edb7912adefe723c60e0738fb
https://github.com/galaxyproject/galaxy/commit/d546d08c86fc506edb7912adefe7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-history.js
M static/maps/mvc/app/app-panel-history.js.map
M static/scripts/mvc/app/app-panel-history.js
Log Message:
-----------
Minor fix
Commit: 910f95188c3ea5fffc36e80aa5f8d689e4450ddf
https://github.com/galaxyproject/galaxy/commit/910f95188c3ea5fffc36e80aa5f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-tool.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/app/app-panel-tool.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/app/app-panel-tool.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Fix tool panel handling
Commit: ad6fdc3dc226af9238b4e366ddc3f246db1e5a87
https://github.com/galaxyproject/galaxy/commit/ad6fdc3dc226af9238b4e366ddc3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-panel-history.js
M client/galaxy/scripts/mvc/app/app-panel-tool.js
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-panel-history.js.map
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-panel-history.js
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Add history panel specific css style
Commit: b99b8f2853c49f432eb6e400c734ef087ce36af2
https://github.com/galaxyproject/galaxy/commit/b99b8f2853c49f432eb6e400c734…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Remove unnecessary div
Commit: df52c62f4d662cd73587cd8450c33f86799ff79e
https://github.com/galaxyproject/galaxy/commit/df52c62f4d662cd73587cd8450c3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Reinsert message divs
Commit: 521677623fae73e07aa98f67c6a65c1913885150
https://github.com/galaxyproject/galaxy/commit/521677623fae73e07aa98f67c6a6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/tools/tools-form.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/reports.less
M config/tool_data_table_conf.xml.sample
A doc/source/api/quickstart.rst
M doc/source/api_doc.rst
A doc/source/dev/faq.rst
A doc/source/dev/index.rst
M doc/source/index.rst
A doc/source/releases/15.07.rst
M doc/source/releases/15.07_announce.rst
A doc/source/releases/15.10_announce.rst
M doc/source/releases/index.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/shed_util_common.py
M scripts/bootstrap_history.py
A scripts/bootstrap_history_announce_template.rst
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/tools/tools-form.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/tools/tools-form.js
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/reports/job_info.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/system.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
M test/base/asserts/__init__.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/qunit/README.txt
M test/qunit/package.json
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
M test/tool_shed/functional/test_1085_repository_dependency_handling.py
M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_1130_datatype_converters.py
M test/tool_shed/functional/test_1140_tool_help_images.py
M test/tool_shed/functional/test_1150_prior_installation_required.py
M test/tool_shed/functional/test_1160_circular_prior_installation_required.py
M test/tool_shed/functional/test_1170_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
M test/tool_shed/functional_tests.py
M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
M test/unit/managers/test_DatasetManager.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox_filters.py
M tools/extract/liftOver_wrapper.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000
Commit: a8ffdc523eebe21162e8e29cb6311200d7a2816b
https://github.com/galaxyproject/galaxy/commit/a8ffdc523eebe21162e8e29cb631…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
R client/galaxy/scripts/mvc/app/app-panel-center.js
R client/galaxy/scripts/mvc/app/app-panel-history.js
R client/galaxy/scripts/mvc/app/app-panel-tool.js
M client/galaxy/scripts/mvc/app/app-view.js
R static/maps/mvc/app/app-panel-center.js.map
R static/maps/mvc/app/app-panel-history.js.map
R static/maps/mvc/app/app-panel-tool.js.map
M static/maps/mvc/app/app-view.js.map
R static/scripts/mvc/app/app-panel-center.js
R static/scripts/mvc/app/app-panel-history.js
R static/scripts/mvc/app/app-panel-tool.js
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Group analysis panels
Commit: d0c77f17610c1361de1447840bafae9cea3a575d
https://github.com/galaxyproject/galaxy/commit/d0c77f17610c1361de1447840baf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Revise page building
Commit: 53b84fd17f662ba595d0a72ca79a24d5792ec0f8
https://github.com/galaxyproject/galaxy/commit/53b84fd17f662ba595d0a72ca79a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/style/less/base.less
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
M static/style/blue/base.css
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Style fixes, generalizations
Commit: 92bdf0de2436549546951645a7f1e8d852715e49
https://github.com/galaxyproject/galaxy/commit/92bdf0de2436549546951645a7f1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Remove unused styles
Commit: 3a94f35468622b6819c7f07c2a2f95a85ca03870
https://github.com/galaxyproject/galaxy/commit/3a94f35468622b6819c7f07c2a2f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
R templates/webapps/galaxy/root/tool_menu.mako
Log Message:
-----------
Remove tool menu mako
Commit: b8304e1ab7538b5bcc315f87905d242554b2171a
https://github.com/galaxyproject/galaxy/commit/b8304e1ab7538b5bcc315f87905d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Reinsert active view identifier
Commit: 94e8b312d4548be90f7ae4e899080298f87380f5
https://github.com/galaxyproject/galaxy/commit/94e8b312d4548be90f7ae4e89908…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Reinsert message classes
Commit: 93be500441a5c454168de3c504db341709be7191
https://github.com/galaxyproject/galaxy/commit/93be500441a5c454168de3c504db…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-03 (Thu, 03 Sep 2015)
Changed paths:
A client/galaxy/scripts/mvc/app/app-analysis.js
A static/maps/mvc/app/app-analysis.js.map
A static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Add unified panel script
Commit: 5043dd2b7265e7b489428f2858936cd7edac75d3
https://github.com/galaxyproject/galaxy/commit/5043dd2b7265e7b489428f285893…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/app/app-view.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix panel notifications
Commit: c08aab0bd358a8568841a4b43af2e416dec5a513
https://github.com/galaxyproject/galaxy/commit/c08aab0bd358a8568841a4b43af2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
Log Message:
-----------
Code style fix
Commit: 823fd4ae47ccbf6ed1d19665a7a921d53441833c
https://github.com/galaxyproject/galaxy/commit/823fd4ae47ccbf6ed1d19665a7a9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
A CODE_OF_CONDUCT.md
M README.rst
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/style/less/history.less
M config/auth_conf.xml.sample
M lib/galaxy/auth/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/multi-panel.js
M static/style/blue/base.css
M templates/webapps/galaxy/history/copy.mako
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into ui_revision_000
Conflicts:
static/style/blue/base.css
Commit: 192239f8d7832e24e9cca55f2ec20c6e3f8e4773
https://github.com/galaxyproject/galaxy/commit/192239f8d7832e24e9cca55f2ec2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M static/maps/mvc/ui/ui-color-picker.js.map
Log Message:
-----------
Fix codestyle color picker
Commit: bcf77efb5aa79f20afd4cb1104013892fac97959
https://github.com/galaxyproject/galaxy/commit/bcf77efb5aa79f20afd4cb110401…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Remove fixed message
Commit: 2f08578ff607c67ddcfcf15f299e26ea99008ecb
https://github.com/galaxyproject/galaxy/commit/2f08578ff607c67ddcfcf15f299e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix center panel
Commit: c948bc70caa9f241c56df0a0e1ff7e542bdabee3
https://github.com/galaxyproject/galaxy/commit/c948bc70caa9f241c56df0a0e1ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
Log Message:
-----------
Remove gap
Commit: 759c2142e744476c7bfa3164c34ac351bfb37fa0
https://github.com/galaxyproject/galaxy/commit/759c2142e744476c7bfa3164c34a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/galaxy.menu.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/app/app-view.js.map
M static/scripts/galaxy.menu.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/app/app-view.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix user object usage
Commit: 359e812f4fbea0e207537b482b7ab601aa5a3d8f
https://github.com/galaxyproject/galaxy/commit/359e812f4fbea0e207537b482b7a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M templates/webapps/galaxy/galaxy.masthead.mako
Log Message:
-----------
Adjust old masthead config
Commit: ac3fc394571da6d33eca6943d58f18aeb5e00814
https://github.com/galaxyproject/galaxy/commit/ac3fc394571da6d33eca6943d58f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M templates/webapps/galaxy/galaxy.masthead.mako
Log Message:
-----------
Fix masthead
Commit: 200c2e640b3665b7c63ce487ccdee044b7c9b054
https://github.com/galaxyproject/galaxy/commit/200c2e640b3665b7c63ce487ccde…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/galaxy.menu.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Fix tabs
Commit: fcbd8b241024ea5a419287759f33b622e94af4fa
https://github.com/galaxyproject/galaxy/commit/fcbd8b241024ea5a419287759f33…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Remove unused user json
Commit: 00806d484b2007aaf0adb1efbf83db49c8dc5ff4
https://github.com/galaxyproject/galaxy/commit/00806d484b2007aaf0adb1efbf83…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Use Galaxy object instead of galaxy_config
Commit: e9009f63936cbef0248ef60638c9de7d6ffb034b
https://github.com/galaxyproject/galaxy/commit/e9009f63936cbef0248ef60638c9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-04 (Fri, 04 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Start adding workflows back into tool panel
Commit: a47a5e89da8ef30b10115a96ade74e2efb6fbf1f
https://github.com/galaxyproject/galaxy/commit/a47a5e89da8ef30b10115a96ade7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-05 (Sat, 05 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix workflow links in tool panel
Commit: cfbe362cb985f873bb7733e92542bf97ee2ec1bc
https://github.com/galaxyproject/galaxy/commit/cfbe362cb985f873bb7733e92542…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-05 (Sat, 05 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Fix links
Commit: af6a51f0046e10aad46045fc513b3ea2af77995b
https://github.com/galaxyproject/galaxy/commit/af6a51f0046e10aad46045fc513b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-05 (Sat, 05 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M static/maps/mvc/tools/tools-form-base.js.map
M static/scripts/mvc/tools/tools-form-base.js
Log Message:
-----------
Fix admin check
Commit: 4971a8f54003f38b427d6ebb3398f88182912174
https://github.com/galaxyproject/galaxy/commit/4971a8f54003f38b427d6ebb3398…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-05 (Sat, 05 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
Log Message:
-----------
Disable iframe for tool form
Commit: 1b86748a97c8eaa96882d370970d99603c967303
https://github.com/galaxyproject/galaxy/commit/1b86748a97c8eaa96882d370970d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-05 (Sat, 05 Sep 2015)
Changed paths:
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Insert bibtex support
Commit: 6f8dd18ede82d35b60f2b8c99e6d8781f9b9d085
https://github.com/galaxyproject/galaxy/commit/6f8dd18ede82d35b60f2b8c99e6d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-07 (Mon, 07 Sep 2015)
Changed paths:
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix style
Commit: f99ff868657161a79e760760b73fba0ad1368c9e
https://github.com/galaxyproject/galaxy/commit/f99ff868657161a79e760760b73f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-07 (Mon, 07 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-view.js
M static/maps/mvc/app/app-view.js.map
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Fix select2 leak
Commit: 514da84b07a78a24767d9f9318c735d52fc77d32
https://github.com/galaxyproject/galaxy/commit/514da84b07a78a24767d9f9318c7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M static/maps/mvc/form/form-view.js.map
M static/scripts/mvc/form/form-view.js
Log Message:
-----------
Fix scrolling
Commit: 4bcc60b04484d7dc54a6bab3ab7c48de27838f9e
https://github.com/galaxyproject/galaxy/commit/4bcc60b04484d7dc54a6bab3ab7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Fix stored workflow list
Commit: b62bf77d9612e98c6dbe39af0035e0c7f6b18875
https://github.com/galaxyproject/galaxy/commit/b62bf77d9612e98c6dbe39af0035…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Empty center div before hiding it
Commit: bef379dfea1ec7b130fd20dc9dfce59f009ce6e4
https://github.com/galaxyproject/galaxy/commit/bef379dfea1ec7b130fd20dc9dfc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools.js
M static/maps/mvc/tools.js.map
M static/scripts/mvc/tools.js
Log Message:
-----------
Avoid blank screen when switching between tools
Commit: 5bcc452a3718139f511d2097d18ab5644e0a86c2
https://github.com/galaxyproject/galaxy/commit/5bcc452a3718139f511d2097d18a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/app/app-analysis.js
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Reset scrolling when display is called
Commit: 2b43a271ed5987040731ae63df0fe997b9af28e6
https://github.com/galaxyproject/galaxy/commit/2b43a271ed5987040731ae63df0f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/galaxy.panels.js
A client/galaxy/scripts/mvc/app/app-analysis.js
A client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
R client/galaxy/scripts/mvc/ui/ui-button-check.js
R client/galaxy/scripts/mvc/ui/ui-button-menu.js
A 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-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/base.less
M config/galaxy.ini.sample
M static/maps/galaxy.menu.js.map
M static/maps/galaxy.panels.js.map
A static/maps/mvc/app/app-analysis.js.map
A static/maps/mvc/app/app-view.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/tools/tools-form-base.js.map
R static/maps/mvc/ui/ui-button-check.js.map
R static/maps/mvc/ui/ui-button-menu.js.map
A static/maps/mvc/ui/ui-buttons.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-default.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/scripts/galaxy.menu.js
M static/scripts/galaxy.panels.js
A static/scripts/mvc/app/app-analysis.js
A static/scripts/mvc/app/app-view.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
R static/scripts/mvc/ui/ui-button-check.js
R static/scripts/mvc/ui/ui-button-menu.js
A static/scripts/mvc/ui/ui-buttons.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-default.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M templates/base.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/root/index.mako
R templates/webapps/galaxy/root/tool_menu.mako
M templates/webapps/galaxy/tool_form.mako
Log Message:
-----------
Merge pull request #706 from guerler/ui_revision_000
UI revision (panel rendering, iframes and tool forms)
Compare: https://github.com/galaxyproject/galaxy/compare/8205bade71e1...2b43a271ed59
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d55c47a14cca837ed775ff47a0c41a170c591c67
https://github.com/galaxyproject/galaxy/commit/d55c47a14cca837ed775ff47a0c4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tools/tools-form-workflow.js
Log Message:
-----------
Optional argument id display (in workflow editor PJAs we don't care to see this, for example -- and this has been toggled off here)
Commit: 434caeaf9515cee99e1f5ac4f9610bcc6a5e00cd
https://github.com/galaxyproject/galaxy/commit/434caeaf9515cee99e1f5ac4f961…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
Log Message:
-----------
Minor cleanup.
Commit: e2542d7296adf1e9e5cf15fb7c9bc5f68db05002
https://github.com/galaxyproject/galaxy/commit/e2542d7296adf1e9e5cf15fb7c9b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/tools/tools-form-workflow.js
Log Message:
-----------
Swap argument to pja_arg, being more indicative of how this is used. This also obviates the need for the togglable show_arg.
Commit: ca5717d203cf93e0bc4dcb9bd6febd0d8c73d083
https://github.com/galaxyproject/galaxy/commit/ca5717d203cf93e0bc4dcb9bd6fe…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-09-08 (Tue, 08 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/scripts/mvc/tools/tools-form-workflow.js
Log Message:
-----------
Address the regression in #674, add input name list back to rename PJA helptext.
Commit: 8205bade71e1c4977ff9069bae22662fb5af159f
https://github.com/galaxyproject/galaxy/commit/8205bade71e1c4977ff9069bae22…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-09-09 (Wed, 09 Sep 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/scripts/mvc/tools/tools-form-workflow.js
Log Message:
-----------
Merge pull request #703 from dannon/optional_wf_args
Workflow Editor PJA Argument Display + fix #674
Compare: https://github.com/galaxyproject/galaxy/compare/65f6d83459cd...8205bade71e1