Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d98c8965eb3433b9dbf26e9aa96a26818f8fc0fb
https://github.com/galaxyproject/galaxy/commit/d98c8965eb3433b9dbf26e9aa96a…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-28 (Thu, 28 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Move metadata-related methods from shed_util_common to metadata_util.
Commit: 03102e5565319b7a38993fae934f7a27337adbd0
https://github.com/galaxyproject/galaxy/commit/03102e5565319b7a38993fae934f…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-28 (Thu, 28 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Correct travis errors and missing imports.
Commit: 64f6a8bc7d09b61e7337e18011a7f852cea5c978
https://github.com/galaxyproject/galaxy/commit/64f6a8bc7d09b61e7337e18011a7…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-05-04 (Wed, 04 May 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/categories.py
Log Message:
-----------
Update method call.
Commit: abb6176a4e1356595d33284a769245e63ece24d0
https://github.com/galaxyproject/galaxy/commit/abb6176a4e1356595d33284a7692…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-04 (Wed, 04 May 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/categories.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0000_basic_repository_features.py
Log Message:
-----------
Fix category/repositories API endpoint. Add test.
Commit: d78fd5f20c75a77b96d0dd9d54c477ad5ca9fe54
https://github.com/galaxyproject/galaxy/commit/d78fd5f20c75a77b96d0dd9d54c4…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-04 (Wed, 04 May 2016)
Changed paths:
M test/shed_functional/functional/test_0000_basic_repository_features.py
Log Message:
-----------
Placate Travis.
Commit: acaedd470be1fbc53ac6f4cf8e6e7c109c9bcb29
https://github.com/galaxyproject/galaxy/commit/acaedd470be1fbc53ac6f4cf8e6e…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
Log Message:
-----------
Refactor out repository-related methods from shed_util_common.
Commit: e1d9ce920d3272614b335002ed7d54d6dba2ffc1
https://github.com/galaxyproject/galaxy/commit/e1d9ce920d3272614b335002ed7d…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
Move more methods from shed_util_common to repository_util.
Commit: 0400c172d6ba7f0fff2bd5a597b814eadf70500a
https://github.com/galaxyproject/galaxy/commit/0400c172d6ba7f0fff2bd5a597b8…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.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/tools/tool_validator.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/admin/tool_shed_repository/repair_repository.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Move a lot more things from shed_util_common to repository_util.
Commit: 26396ffc82762edcaadb76eac31b1bdec675ba40
https://github.com/galaxyproject/galaxy/commit/26396ffc82762edcaadb76eac31b…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
Log Message:
-----------
Fix travis errors.
Commit: 9f9e008d9f63d6fa19255a52122c6cf6e374058c
https://github.com/galaxyproject/galaxy/commit/9f9e008d9f63d6fa19255a52122c…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
Log Message:
-----------
Remove another unused import.
Commit: ac2fb6d745522d68b063226b622f25893052e1df
https://github.com/galaxyproject/galaxy/commit/ac2fb6d745522d68b063226b622f…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-17 (Tue, 17 May 2016)
Changed paths:
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/README.md
M client/bower.json
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/collection/collection-li.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/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.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/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/util/inflection.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.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/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.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/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fastq.py
M lib/tool_shed/capsule/capsule_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/installed_repository_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.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/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.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/hg_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.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
A scripts/api/filter_failed_datasets_from_collection.py
M scripts/bootstrap_history.py
M static/maps/libs/backbone.js.map
M static/maps/libs/bootstrap-tour.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/jquery/jquery.migrate.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/libs/underscore.js.map
M static/maps/mvc/collection/collection-li.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/dataset/dataset-model.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.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/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/utils/metrics-logger.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/libs/backbone.js
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/d3.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/libs/underscore.js
M static/scripts/mvc/collection/collection-li.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/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/utils/metrics-logger.js
M static/style/blue/base.css
M templates/sharing_base.mako
M templates/show_params.mako
A templates/slug_editing_js.mako
M templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/workflow/sharing.mako
A test-data/composite_output_expected_log
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/interface.py
M test/api/workflows_format_2/main.py
M test/functional/tools/composite_output.xml
M test/qunit/test-app.js
M test/qunit/test-common.js
M test/qunit/test-data/fakeserver.js
R test/qunit/test-libs/qunit-1.14.0.css
R test/qunit/test-libs/qunit-1.14.0.js
A test/qunit/test-libs/qunit-1.23.1.css
A test/qunit/test-libs/qunit-1.23.1.js
A test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-1.9.1.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/test_objectstore.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into refactor_suc
Commit: 8eb4f90be0e49b2ceda230a68ff3a888aaad1e9d
https://github.com/galaxyproject/galaxy/commit/8eb4f90be0e49b2ceda230a68ff3…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-17 (Tue, 17 May 2016)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Remove merge conflict aftereffects.
Commit: 964779373e82b4096ffd4fe34acf9b9ce7161400
https://github.com/galaxyproject/galaxy/commit/964779373e82b4096ffd4fe34acf…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-17 (Tue, 17 May 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Fix another incorrectly resolved merge conflict.
Commit: 9ee0d880db830c6a59ed9e9efffc2fce9aaf90c6
https://github.com/galaxyproject/galaxy/commit/9ee0d880db830c6a59ed9e9efffc…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-05-17 (Tue, 17 May 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Fix missing import and unused import.
Commit: 172a4778c3a5fb54f8eec91a071b8f0a43bd2c3a
https://github.com/galaxyproject/galaxy/commit/172a4778c3a5fb54f8eec91a071b…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M test/shed_functional/functional/test_1000_install_basic_repository.py
Log Message:
-----------
Create categories in the right order.
Commit: c0b5a2840bc954b199bb4cf0db4dafc81116df46
https://github.com/galaxyproject/galaxy/commit/c0b5a2840bc954b199bb4cf0db4d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.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/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_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/grids/repository_grids.py
M lib/tool_shed/grids/util.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/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/admin/tool_shed_repository/repair_repository.mako
M templates/webapps/tool_shed/repository/common.mako
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0000_basic_repository_features.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
Log Message:
-----------
Merge pull request #2269 from davebx/refactor_suc
Move specific methods from shed_util_common.py to specific_util.py
Compare: https://github.com/galaxyproject/galaxy/compare/e2f219335532...c0b5a2840bc9
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: edca79a0cf4d0e6afceb0f3b3894b6b3a169bd53
https://github.com/galaxyproject/galaxy/commit/edca79a0cf4d0e6afceb0f3b3894…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-06-06 (Mon, 06 Jun 2016)
Changed paths:
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Do not encode dict items that start with 'metadata_' in return value of api/tools/create.
Resolves #2423, #2137, and https://github.com/galaxyproject/tools-iuc/pull/770. However, this whole act of encoding by key.endswith('_id') is very messy.
Commit: 42739c88c80d10742add92f2e3978ed65a295188
https://github.com/galaxyproject/galaxy/commit/42739c88c80d10742add92f2e397…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
A test-data/biom1_metadata_test.txt
A test-data/input_taxonomy.biom1
A test/functional/tools/metadata_biom1.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add test for failing handling of BIOM1 metadata.
Commit: 10a3f23de2f8d728780b7c1615e7d4c9afeaeeb2
https://github.com/galaxyproject/galaxy/commit/10a3f23de2f8d728780b7c1615e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
A test-data/biom1_metadata_test.txt
A test-data/input_taxonomy.biom1
A test/functional/tools/metadata_biom1.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #2459 from blankenberg/metadata-id-fix
[16.04] Do not encode dict items that start with 'metadata_' in return value of api/tools/create.
Compare: https://github.com/galaxyproject/galaxy/compare/37a491599257...10a3f23de2f8
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 21ef339f9467246cdcfef53ea3d363ba767db795
https://github.com/galaxyproject/infrastructure-playbook/commit/21ef339f946…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M common_roles
M roles/galaxyprojectdotorg.nginx/README.md
M roles/galaxyprojectdotorg.nginx/defaults/main.yml
M roles/galaxyprojectdotorg.nginx/handlers/main.yml
M roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info
M roles/galaxyprojectdotorg.nginx/meta/main.yml
M roles/galaxyprojectdotorg.nginx/tasks/apt.yml
R roles/galaxyprojectdotorg.nginx/tasks/epel.yml
M roles/galaxyprojectdotorg.nginx/tasks/main.yml
A roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml
A roles/galaxyprojectdotorg.nginx/tasks/yum.yml
A roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2
A roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2
A roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2
A roles/galaxyprojectdotorg.nginx/vars/pkgin.yml
Log Message:
-----------
Update nginx and common roles
Commit: c72d9b100b10740a4028a9a672085a0dbf395c63
https://github.com/galaxyproject/infrastructure-playbook/commit/c72d9b100b1…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M galaxyenv/host_vars/orval.galaxyproject.org.yml
A galaxyenv/templates/nginx/bioarchive.j2
A galaxyenv/templates/nginx/depot.j2
A galaxyenv/templates/nginx/images.j2
A galaxyenv/templates/nginx/orval.j2
A galaxyenv/templates/nginx/sample-data.j2
A galaxyenv/templates/nginx/screencast.j2
A galaxyenv/templates/nginx/snpeff-data.j2
Log Message:
-----------
Orval nginx stuff
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6b30c2af50…