May 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 384be8: Cleanup of E203 primarily, and some other misc for...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 384be8c66116dda9e979128ff2fdb60216c70a40 https://github.com/galaxyproject/galaxy/commit/384be8c66116dda9e979128ff2fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/drmaa.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/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/inflection.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.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/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_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/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py Log Message: ----------- Cleanup of E203 primarily, and some other misc formatting encountered during it. Commit: aba34eecda840d6f468dfe8ec3031ccf0353dce3 https://github.com/galaxyproject/galaxy/commit/aba34eecda840d6f468dfe8ec303… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.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/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.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/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/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/data/__init__.py M lib/galaxy/tools/data_manager/manager.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/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/test.py M lib/galaxy/tools/util/maf_utilities.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/framework/base.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.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/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.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/requests_common.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/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/upload.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_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 Log Message: ----------- Update to 'new' except style. Commit: ec9423f0867e548a326e5c2fe2dc9d80f2f98f44 https://github.com/galaxyproject/galaxy/commit/ec9423f0867e548a326e5c2fe2dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- dos2unix of molecules datatype module. Commit: 665809f25cb0d841062621a09eabf4bb9d4efcee https://github.com/galaxyproject/galaxy/commit/665809f25cb0d841062621a09eab… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: 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/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.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/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/roles.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/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/commands.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/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/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/framework/base.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.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/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/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_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 Log Message: ----------- Merge pull request #2364 from dannon/fix_comma_usage Cleanup of E203 primarily, and some other misc formatting encountered… Compare: https://github.com/galaxyproject/galaxy/compare/a5f6195c3d4f...665809f25cb0

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[galaxyproject/galaxy] 996933: Revise form data visitor
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99693306e6c41aa011c559e98b137c67c92f0255 https://github.com/galaxyproject/galaxy/commit/99693306e6c41aa011c559e98b13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.html Log Message: ----------- Revise form data visitor Commit: a5f6195c3d4f9a08bbf0b26b2d9225e55da0fbad https://github.com/galaxyproject/galaxy/commit/a5f6195c3d4f9a08bbf0b26b2d92… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.html Log Message: ----------- Merge branch 'revise_visit_000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0c78c2726f71...a5f6195c3d4f

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[galaxyproject/galaxy] 2390da: Fix for slurm's complete_terminal_job where if una...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 2390da54aec143358767e7977cffc70d040b04b5 https://github.com/galaxyproject/galaxy/commit/2390da54aec143358767e7977cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. Commit: cc86096c83b5835e40e034611ad64bf3827e5c6d https://github.com/galaxyproject/galaxy/commit/cc86096c83b5835e40e034611ad6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2362 from dannon/slurm_complete_job_fix [16.04] Fix for slurm's complete_terminal_job where if unable to inspect the … Compare: https://github.com/galaxyproject/galaxy/compare/38209bbbac70...cc86096c83b5

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[galaxyproject/galaxy] 661e00: fix problems in bootstrap_history probably due to ...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 661e008f1d0bda5f9c0de18a46fe018286c8ae79 https://github.com/galaxyproject/galaxy/commit/661e008f1d0bda5f9c0de18a46fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- fix problems in bootstrap_history probably due to refactoring should work out of the box now, also minor rewording Commit: 70c65f6bd26207de001d01f7827255d5368ca18d https://github.com/galaxyproject/galaxy/commit/70c65f6bd26207de001d01f78272… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- remove prints Commit: 0c78c2726f719811b1d2be94fd9ea87664fbecbc https://github.com/galaxyproject/galaxy/commit/0c78c2726f719811b1d2be94fd9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2366 from martenson/fix-bootstrapping Fix release notes generator Compare: https://github.com/galaxyproject/galaxy/compare/ddc2412e60d4...0c78c2726f71

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[galaxyproject/galaxy] d76d92: API, sharable: serialize users_shared_with
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d76d92d3a0c8a053f17b7bdb9f988c4ab9be322a https://github.com/galaxyproject/galaxy/commit/d76d92d3a0c8a053f17b7bdb9f98… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, sharable: serialize users_shared_with - Changes sharable serializers so that, when requested with `keys=users_shared_with`, they return a list of encoded user ids for each user that the item has been shared with - Adds tests in test_HistoryManager Commit: dc1924bcdf780949df2614f6c721b48780da9d16 https://github.com/galaxyproject/galaxy/commit/dc1924bcdf780949df2614f6c721… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Testing: fixes galaxy_mock set_datatypes_registry - Add the datatypes_registry to the mock app using an empty registry Commit: 7ffa8aac676cf4f2ea8051a0ddd4056135935752 https://github.com/galaxyproject/galaxy/commit/7ffa8aac676cf4f2ea8051a0ddd4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, sharable: deserialize users_shared_with - Adds a deserializer for users_shared_with. PUT a list of user ids to update who an item is shared with. - Invalid users are skipped, bad ids error - (Only affects histories ATM) - Tests added to test_HistoryManager Commit: 133d8c65556ef1e709500dcce8707914cf2293a8 https://github.com/galaxyproject/galaxy/commit/133d8c65556ef1e709500dcce870… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.sharing-api Commit: 4baa3377ed7809278d224ee1af90577e1dbd7627 https://github.com/galaxyproject/galaxy/commit/4baa3377ed7809278d224ee1af90… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Tests: load_datatypes in galaxy_mock Commit: e2f34f7a25d3c6ee081dfa7126b15f2585803df9 https://github.com/galaxyproject/galaxy/commit/e2f34f7a25d3c6ee081dfa7126b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: skip users_shared_with for non-owner - If the requesting user is not the owner, don't return users_shared_with even when requested - add tests Commit: ddc2412e60d4a651e629262ff8e74b00a5838bcf https://github.com/galaxyproject/galaxy/commit/ddc2412e60d4a651e629262ff8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #2340 from carlfeberhard/history.sharing-api History/Sharable model user sharing API Compare: https://github.com/galaxyproject/galaxy/compare/a0291c61426c...ddc2412e60d4

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[galaxyproject/galaxy] 45ba2b: API, history: add DCE count to HDCA serializer
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45ba2b4e101c7e73494fa6237bc27f6b34f44210 https://github.com/galaxyproject/galaxy/commit/45ba2b4e101c7e73494fa6237bc2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- API, history: add DCE count to HDCA serializer Commit: a16ba6c615558ddcd8847e236575f155638a7064 https://github.com/galaxyproject/galaxy/commit/a16ba6c615558ddcd8847e236575… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Commit: f9afb7bcdca49add9d0112e4b46e61c423665202 https://github.com/galaxyproject/galaxy/commit/f9afb7bcdca49add9d0112e4b46e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI & API, history: return element_count by default - Adds element_count to summary serialization for hdcas through history/{:id}/contents - Implements a HistoryContents fetch method to decorate the hdcas after loading if necessary Commit: 8ce93d7fed04163ae524c829bac12f54068e3ee0 https://github.com/galaxyproject/galaxy/commit/8ce93d7fed04163ae524c829bac1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Commit: 3aaccdac7b626f58303602dd9cf4728c9b0c7796 https://github.com/galaxyproject/galaxy/commit/3aaccdac7b626f58303602dd9cf4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: get element_counts after history load - Waits 2s after history contents loading and fetches element_count for all dataset collections in the history - Removes element_count as a default summary field for HDCAs Commit: ab60901cdc678bd57dd11caaa8ba49b557a439ff https://github.com/galaxyproject/galaxy/commit/ab60901cdc678bd57dd11caaa8ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile 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 Log Message: ----------- (merge conflicts) Commit: a0291c61426cda865e0a2535fc7fa0a8acccaaf9 https://github.com/galaxyproject/galaxy/commit/a0291c61426cda865e0a2535fc7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- Merge branch 'show-dce-count' into dev Compare: https://github.com/galaxyproject/galaxy/compare/28acca5276b5...a0291c61426c

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[galaxyproject/galaxy] 1ba740: Improve composite output tool test.
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ba74094a35b5e59a8404d71300a0355d6aeb9d5 https://github.com/galaxyproject/galaxy/commit/1ba74094a35b5e59a8404d71300a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml Log Message: ----------- Improve composite output tool test. - Rename expected output Log from input Log. This relieves a concern I had that the tests were just working because the inputs and outputs match. - Add another "unregistered" output file to the output directory and add a test for it. This verifies that such files are infact tested. - Add a nested "unregistered" output file to the output directory and add a test for it. This verifies that nested files are tested. Commit: 28acca5276b5a4ceb125bafff5d107f062d04166 https://github.com/galaxyproject/galaxy/commit/28acca5276b5a4ceb125bafff5d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml Log Message: ----------- Merge pull request #2363 from jmchilton/test_composite Improve composite output tool test. Compare: https://github.com/galaxyproject/galaxy/compare/d9c0f4fa4444...28acca5276b5

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[galaxyproject/galaxy] 889ed2: UI & API: fix display of inaccessible datasets
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 889ed2547a2b6a94a5a357792eb69349b63f8232 https://github.com/galaxyproject/galaxy/commit/889ed2547a2b6a94a5a357792eb6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M test/unit/managers/test_HDAManager.py Log Message: ----------- UI & API: fix display of inaccessible datasets - Uses contexts in serializers to restore inaccessible field of hdas - Overrides serialize to return only the inaccessible view of inaccessible hdas (no other keys are returned): 'accessible', 'id', 'name', 'history_id', 'hid', 'history_content_type', 'state', 'deleted', 'visible' - If a DatasetAssociation Backbone Model is inaccessible, considers it to have details preventing the (failing) GET for more details Should be revisited if/when thread local contexts (user/session) are working. Commit: d9c0f4fa4444747bfd08ec021102d5a2b66d3cd3 https://github.com/galaxyproject/galaxy/commit/d9c0f4fa4444747bfd08ec021102… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge branch 'datasets.show-inaccessible' into dev Compare: https://github.com/galaxyproject/galaxy/compare/65c57c5d52bc...d9c0f4fa4444

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[galaxyproject/galaxy] 7ab406: Update to latest galaxy-lib.
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ab4065d670ddc82e9e033db34a5f19c1ec80d9d https://github.com/galaxyproject/galaxy/commit/7ab4065d670ddc82e9e033db34a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Update to latest galaxy-lib. An assortment of tweaks and fixes to tool parsing and cwltool handling used by planemo and down stream CWL fork of Galaxy. Commit: b76889f4cac559d6cc2579272a66955b3195a3b3 https://github.com/galaxyproject/galaxy/commit/b76889f4cac559d6cc2579272a66… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py Log Message: ----------- Spelling fix thanks to @nsoranzo. Commit: 65c57c5d52bc1500b2c9ed8502b7bd2203d13eb2 https://github.com/galaxyproject/galaxy/commit/65c57c5d52bc1500b2c9ed8502b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Merge pull request #2354 from jmchilton/galaxy-lib-update Update to latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/aaff453a9031...65c57c5d52bc

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[galaxyproject/galaxy] cd96a5: Fix an issue about not-lowercasing extensions in l...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd96a504bb83ecf5a4d19675f76e8108df9830fc https://github.com/galaxyproject/galaxy/commit/cd96a504bb83ecf5a4d19675f76e… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix an issue about not-lowercasing extensions in load_display_applications. Refactored in a function the lowercasing because DRY Commit: 5d47c7961d0826e9f5531f14e86d963c63a45eb2 https://github.com/galaxyproject/galaxy/commit/5d47c7961d0826e9f5531f14e86d… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Handle the case where extension is None Commit: aaff453a9031a1a07f2e4eddd8c8342aba71c319 https://github.com/galaxyproject/galaxy/commit/aaff453a9031a1a07f2e4eddd8c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #2361 from remimarenco/registry_uppercase Fix issue with lowercasing in datatypes/registry.py Compare: https://github.com/galaxyproject/galaxy/compare/b5ea024cd17b...aaff453a9031

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