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tool_shed package
Subpackages
- tool_shed.dependencies package
- Subpackages
- Submodules
- tool_shed.dependencies.attribute_handlers module
RepositoryDependencyAttributeHandlerRepositoryDependencyAttributeHandler.__init__()RepositoryDependencyAttributeHandler.transRepositoryDependencyAttributeHandler.appRepositoryDependencyAttributeHandler.check_tag_attributes()RepositoryDependencyAttributeHandler.handle_complex_dependency_elem()RepositoryDependencyAttributeHandler.handle_elem()RepositoryDependencyAttributeHandler.handle_sub_elem()RepositoryDependencyAttributeHandler.handle_tag_attributes()
ToolDependencyAttributeHandler
- tool_shed.galaxy_install package
- tool_shed.grids package
- Submodules
- tool_shed.grids.admin_grids module
UserGridUserGrid.UserLoginColumnUserGrid.UserNameColumnUserGrid.GroupsColumnUserGrid.RolesColumnUserGrid.ExternalColumnUserGrid.LastLoginColumnUserGrid.StatusColumnUserGrid.EmailColumnUserGrid.titleUserGrid.model_classUserGrid.default_sort_keyUserGrid.columnsUserGrid.global_actionsUserGrid.operationsUserGrid.standard_filtersUserGrid.use_pagingUserGrid.get_current_item()
RoleGridRoleGrid.NameColumnRoleGrid.DescriptionColumnRoleGrid.TypeColumnRoleGrid.StatusColumnRoleGrid.GroupsColumnRoleGrid.RepositoriesColumnRoleGrid.UsersColumnRoleGrid.titleRoleGrid.model_classRoleGrid.default_sort_keyRoleGrid.columnsRoleGrid.global_actionsRoleGrid.operationsRoleGrid.standard_filtersRoleGrid.use_pagingRoleGrid.apply_query_filter()
GroupGridManageCategoryGridAdminRepositoryGridRepositoryMetadataGridRepositoryMetadataGrid.IdColumnRepositoryMetadataGrid.NameColumnRepositoryMetadataGrid.OwnerColumnRepositoryMetadataGrid.RevisionColumnRepositoryMetadataGrid.ToolsColumnRepositoryMetadataGrid.DatatypesColumnRepositoryMetadataGrid.WorkflowsColumnRepositoryMetadataGrid.DeletedColumnRepositoryMetadataGrid.DeprecatedColumnRepositoryMetadataGrid.MaliciousColumnRepositoryMetadataGrid.titleRepositoryMetadataGrid.model_classRepositoryMetadataGrid.default_sort_keyRepositoryMetadataGrid.use_hide_messageRepositoryMetadataGrid.columnsRepositoryMetadataGrid.operationsRepositoryMetadataGrid.build_initial_query()
- tool_shed.grids.repository_grid_filter_manager module
- tool_shed.grids.repository_grids module
CategoryGridRepositoryGridRepositoryGrid.NameColumnRepositoryGrid.TypeColumnRepositoryGrid.HeadsColumnRepositoryGrid.MetadataRevisionColumnRepositoryGrid.LatestInstallableRevisionColumnRepositoryGrid.TipRevisionColumnRepositoryGrid.DescriptionColumnRepositoryGrid.CategoryColumnRepositoryGrid.RepositoryCategoryColumnRepositoryGrid.UserColumnRepositoryGrid.EmailColumnRepositoryGrid.EmailAlertsColumnRepositoryGrid.DeprecatedColumnRepositoryGrid.titleRepositoryGrid.model_classRepositoryGrid.default_sort_keyRepositoryGrid.use_hide_messageRepositoryGrid.columnsRepositoryGrid.default_filterRepositoryGrid.num_rows_per_pageRepositoryGrid.use_pagingRepositoryGrid.allow_fetching_all_resultsRepositoryGrid.build_initial_query()
DockerImageGridEmailAlertsRepositoryGridMatchedRepositoryGridMatchedRepositoryGrid.NameColumnMatchedRepositoryGrid.DescriptionColumnMatchedRepositoryGrid.RevisionColumnMatchedRepositoryGrid.UserColumnMatchedRepositoryGrid.titleMatchedRepositoryGrid.model_classMatchedRepositoryGrid.default_sort_keyMatchedRepositoryGrid.use_hide_messageMatchedRepositoryGrid.columnsMatchedRepositoryGrid.operationsMatchedRepositoryGrid.num_rows_per_pageMatchedRepositoryGrid.use_pagingMatchedRepositoryGrid.build_initial_query()
InstallMatchedRepositoryGridMyWritableRepositoriesGridRepositoriesByUserGridRepositoriesInCategoryGridRepositoriesIOwnGridRepositoriesICanAdministerGridRepositoriesMissingToolTestComponentsGridMyWritableRepositoriesMissingToolTestComponentsGridDeprecatedRepositoriesIOwnGridRepositoriesWithInvalidToolsGridMyWritableRepositoriesWithInvalidToolsGridRepositoryMetadataGridRepositoryMetadataGrid.RepositoryNameColumnRepositoryMetadataGrid.RepositoryTypeColumnRepositoryMetadataGrid.RepositoryOwnerColumnRepositoryMetadataGrid.ChangesetRevisionColumnRepositoryMetadataGrid.MaliciousColumnRepositoryMetadataGrid.DownloadableColumnRepositoryMetadataGrid.HasRepositoryDependenciesColumnRepositoryMetadataGrid.IncludesDatatypesColumnRepositoryMetadataGrid.IncludesToolsColumnRepositoryMetadataGrid.IncludesToolDependenciesColumnRepositoryMetadataGrid.IncludesWorkflowsColumnRepositoryMetadataGrid.titleRepositoryMetadataGrid.model_classRepositoryMetadataGrid.default_sort_keyRepositoryMetadataGrid.columnsRepositoryMetadataGrid.default_filterRepositoryMetadataGrid.num_rows_per_pageRepositoryMetadataGrid.use_pagingRepositoryMetadataGrid.allow_fetching_all_resultsRepositoryMetadataGrid.build_initial_query()
RepositoryDependenciesGridDatatypesGridToolDependenciesGridToolsGridValidCategoryGridValidRepositoryGrid
- tool_shed.grids.repository_review_grids module
- tool_shed.grids.util module
build_changeset_revision_select_field()filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components()filter_by_latest_metadata_changeset_revision_that_has_invalid_tools()get_latest_downloadable_repository_metadata()get_latest_downloadable_repository_metadata_if_it_includes_tools()get_latest_repository_metadata()get_latest_repository_metadata_if_it_includes_invalid_tools()
- tool_shed.managers package
- Submodules
- tool_shed.managers.groups module
- tool_shed.managers.repositories module
search()UpdatesRequestcheck_updates()guid_to_repository()index_tool_ids()index_repositories()can_manage_repo()can_update_repo()get_repository_metadata_for_management()get_install_info()get_value_mapper()get_ordered_installable_revisions()get_repository_metadata_dict()readmes()reset_metadata_on_repository()create_repository()to_element_dict()repositories_by_category()to_model()to_detailed_model()upload_tar_and_set_metadata()
- tool_shed.metadata package
- Submodules
- tool_shed.metadata.metadata_generator module
- tool_shed.metadata.repository_metadata_manager module
ToolShedMetadataGeneratorToolShedMetadataGenerator.__init__()ToolShedMetadataGenerator.appToolShedMetadataGenerator.repositoryToolShedMetadataGenerator.repository_clone_urlToolShedMetadataGenerator.invalid_file_tupsToolShedMetadataGenerator.initial_metadata_dict()ToolShedMetadataGenerator.set_repository()ToolShedMetadataGenerator.handle_repository_elem()
RepositoryMetadataManagerRepositoryMetadataManager.__init__()RepositoryMetadataManager.appRepositoryMetadataManager.build_repository_ids_select_field()RepositoryMetadataManager.compare_changeset_revisions()RepositoryMetadataManager.compare_data_manager()RepositoryMetadataManager.compare_repository_dependencies()RepositoryMetadataManager.compare_tool_dependencies()RepositoryMetadataManager.create_or_update_repository_metadata()RepositoryMetadataManager.different_revision_defines_tip_only_repository_dependency()RepositoryMetadataManager.get_repositories_for_setting_metadata()RepositoryMetadataManager.new_metadata_required_for_utilities()RepositoryMetadataManager.new_repository_dependency_metadata_required()RepositoryMetadataManager.new_data_manager_required()RepositoryMetadataManager.new_tool_metadata_required()RepositoryMetadataManager.new_tool_dependency_metadata_required()RepositoryMetadataManager.reset_all_metadata_on_repository_in_tool_shed()RepositoryMetadataManager.reset_metadata_on_selected_repositories()RepositoryMetadataManager.set_repository()RepositoryMetadataManager.set_repository_metadata()RepositoryMetadataManager.repositoryRepositoryMetadataManager.invalid_file_tupsRepositoryMetadataManager.repository_clone_urlRepositoryMetadataManager.changeset_revisionRepositoryMetadataManager.shed_config_dictRepositoryMetadataManager.metadata_dictRepositoryMetadataManager.relative_install_dirRepositoryMetadataManager.repository_files_dirRepositoryMetadataManager.persistRepositoryMetadataManager.set_repository_metadata_due_to_new_tip()
get_user_by_username()get_repository()get_repository_metadata()get_current_repositories()get_filtered_repositories()
- tool_shed.repository_types package
- Submodules
- tool_shed.repository_types.metadata module
- tool_shed.repository_types.registry module
- tool_shed.repository_types.repository_suite_definition module
- tool_shed.repository_types.tool_dependency_definition module
- tool_shed.repository_types.unrestricted module
- tool_shed.repository_types.util module
- tool_shed.test package
- Subpackages
- tool_shed.test.base package
- tool_shed.test.functional package
- Submodules
- tool_shed.test.functional.test_0000_basic_repository_features module
- tool_shed.test.functional.test_0010_repository_with_tool_dependencies module
- tool_shed.test.functional.test_0020_basic_repository_dependencies module
- tool_shed.test.functional.test_0030_repository_dependency_revisions module
- tool_shed.test.functional.test_0040_repository_circular_dependencies module
- tool_shed.test.functional.test_0050_circular_dependencies_4_levels module
- tool_shed.test.functional.test_0070_invalid_tool module
- tool_shed.test.functional.test_0080_advanced_circular_dependencies module
- tool_shed.test.functional.test_0090_tool_search module
- tool_shed.test.functional.test_0100_complex_repository_dependencies module
- tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies module
- tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners module
- tool_shed.test.functional.test_0130_datatype_converters module
- tool_shed.test.functional.test_0140_tool_help_images module
- tool_shed.test.functional.test_0150_prior_installation_required module
- tool_shed.test.functional.test_0160_circular_prior_installation_required module
- tool_shed.test.functional.test_0170_complex_prior_installation_required module
- tool_shed.test.functional.test_0300_reset_all_metadata module
- tool_shed.test.functional.test_0310_hg_api_features module
- tool_shed.test.functional.test_0400_repository_component_reviews module
- tool_shed.test.functional.test_0410_repository_component_review_access_control module
- tool_shed.test.functional.test_0420_citable_urls_for_repositories module
- tool_shed.test.functional.test_0430_browse_utilities module
- tool_shed.test.functional.test_0440_deleting_dependency_definitions module
- tool_shed.test.functional.test_0460_upload_to_repository module
- tool_shed.test.functional.test_0470_tool_dependency_repository_type module
- tool_shed.test.functional.test_0480_tool_dependency_xml_verification module
- tool_shed.test.functional.test_0530_repository_admin_feature module
- tool_shed.test.functional.test_0540_get_all_metadata_from_api module
- tool_shed.test.functional.test_0550_metadata_updated_dependencies module
- tool_shed.test.functional.test_1000_install_basic_repository module
- tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies module
- tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies module
- tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions module
- tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies module
- tool_shed.test.functional.test_1050_circular_dependencies_4_levels module
- tool_shed.test.functional.test_1070_invalid_tool module
- tool_shed.test.functional.test_1080_advanced_circular_dependency_installation module
- tool_shed.test.functional.test_1090_repository_dependency_handling module
- tool_shed.test.functional.test_1100_install_updated_repository_dependencies module
- tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies module
- tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency module
- tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners module
- tool_shed.test.functional.test_1150_datatype_converters module
- tool_shed.test.functional.test_1160_tool_help_images module
- tool_shed.test.functional.test_1170_prior_installation_required module
- tool_shed.test.functional.test_1180_circular_prior_installation_required module
- tool_shed.test.functional.test_1190_complex_prior_installation_required module
- tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository module
- tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies module
- tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies module
- tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions module
- tool_shed.test.functional.test_1300_reset_all_metadata module
- tool_shed.test.functional.test_1410_update_manager module
- tool_shed.test.functional.test_1430_repair_installed_repository module
- tool_shed.test.functional.test_1450_installing_datatypes_sniffers module
- tool_shed.test.functional.test_1460_data_managers module
- tool_shed.test.functional.test_1470_updating_installed_repositories module
- Submodules
- tool_shed.test.functional_tests module
- Subpackages
- tool_shed.tools package
- Submodules
- tool_shed.tools.data_table_manager module
ToolDataTableManagerShedToolDataTableManagerShedToolDataTableManager.__init__()ShedToolDataTableManager.appShedToolDataTableManager.generate_repository_info_elem()ShedToolDataTableManager.generate_repository_info_elem_from_repository()ShedToolDataTableManager.get_tool_index_sample_files()ShedToolDataTableManager.handle_missing_data_table_entry()ShedToolDataTableManager.handle_sample_tool_data_table_conf_file()ShedToolDataTableManager.get_target_install_dir()ShedToolDataTableManager.install_tool_data_tables()ShedToolDataTableManager.reset_tool_data_tables()
- tool_shed.tools.tool_validator module
ToolValidatorToolValidator.can_use_tool_config_disk_file()ToolValidator.concat_messages()ToolValidator.copy_disk_sample_files_to_dir()ToolValidator.get_latest_tool_config_revision_from_repository_manifest()ToolValidator.get_list_of_copied_sample_files()ToolValidator.handle_sample_files_and_load_tool_from_disk()ToolValidator.handle_sample_files_and_load_tool_from_tmp_config()ToolValidator.load_tool_from_changeset_revision()ToolValidator.load_tool_from_tmp_config()
- tool_shed.tools.tool_version_manager module
- tool_shed.util package
- Submodules
- tool_shed.util.admin_util module
AdminAdmin.user_list_gridAdmin.role_list_gridAdmin.group_list_gridAdmin.delete_operationAdmin.undelete_operationAdmin.purge_operationAdmin.index()Admin.center()Admin.roles()Admin.create_role()Admin.rename_role()Admin.manage_users_and_groups_for_role()Admin.mark_role_deleted()Admin.undelete_role()Admin.purge_role()Admin.groups()Admin.rename_group()Admin.manage_users_and_roles_for_group()Admin.create_group()Admin.mark_group_deleted()Admin.undelete_group()Admin.purge_group()Admin.create_new_user()Admin.reset_user_password()Admin.mark_user_deleted()Admin.undelete_user()Admin.purge_user()Admin.users()Admin.name_autocomplete_data()Admin.manage_roles_and_groups_for_user()
get_user()get_role()get_group()get_role_id()get_group_id()get_current_users()get_current_groups()get_current_roles()get_ldda_by_dataset()get_library_by_folder()get_user_emails_by_prefix()
- tool_shed.util.basic_util module
- tool_shed.util.commit_util module
- tool_shed.util.common_util module
accumulate_tool_dependencies()check_tool_tag_set()generate_clone_url_for_installed_repository()generate_clone_url_for_repository_in_tool_shed()generate_clone_url_from_repo_info_tup()get_repository_dependencies()get_protocol_from_tool_shed_url()get_tool_shed_repository_ids()get_tool_shed_url_from_tool_shed_registry()get_tool_shed_repository_url()handle_galaxy_url()handle_tool_shed_url_protocol()parse_repository_dependency_tuple()remove_port_from_tool_shed_url()remove_protocol_and_port_from_tool_shed_url()remove_protocol_and_user_from_clone_url()remove_protocol_from_tool_shed_url()
- tool_shed.util.container_util module
- tool_shed.util.encoding_util module
- tool_shed.util.hg_util module
add_changeset()archive_repository_revision()clone_repository()commit_changeset()copy_file_from_manifest()create_hgrc_file()get_changectx_for_changeset()get_config_from_disk()get_ctx_file_path_from_manifest()get_file_context_from_ctx()get_named_tmpfile_from_ctx()get_readable_ctx_date()get_repository_heads()get_reversed_changelog_changesets()get_revision_label()get_rev_label_changeset_revision_from_repository_metadata()get_revision_label_from_ctx()get_rev_label_from_changeset_revision()pull_repository()remove_path()reversed_lower_upper_bounded_changelog()reversed_upper_bounded_changelog()update_repository()init_repository()changeset2rev()
- tool_shed.util.hgweb_config module
- tool_shed.util.metadata_util module
get_all_dependencies()get_current_repository_metadata_for_changeset_revision()get_dependencies_for_metadata_revision()get_latest_changeset_revision()get_latest_downloadable_changeset_revision()get_latest_repository_metadata()get_metadata_revisions()get_next_downloadable_changeset_revision()get_previous_metadata_changeset_revision()get_repository_dependency_tups_from_repository_metadata()get_repository_metadata_by_changeset_revision()repository_metadata_by_changeset_revision()get_repository_metadata_by_id()get_repository_metadata_by_repository_id_changeset_revision()get_updated_changeset_revisions()is_downloadable()is_malicious()get_metadata_by_changeset()
- tool_shed.util.readme_util module
- tool_shed.util.repository_content_util module
- tool_shed.util.repository_util module
change_repository_name_in_hgrc_file()create_or_update_tool_shed_repository()create_repo_info_dict()create_repository_admin_role()create_repository()extract_components_from_tuple()generate_sharable_link_for_repository_in_tool_shed()generate_tool_shed_repository_install_dir()get_absolute_path_to_file_in_repository()get_ids_of_tool_shed_repositories_being_installed()get_installed_repository()get_installed_tool_shed_repository()get_prior_import_or_install_required_dict()get_repo_info_dict()get_repo_info_tuple_contents()get_repositories_by_category()get_repository_admin_role_name()get_repository_and_repository_dependencies_from_repo_info_dict()get_repository_by_id()get_repository_by_name()get_repository_by_name_and_owner()get_repository_dependency_types()get_repository_for_dependency_relationship()get_repository_ids_requiring_prior_import_or_install()get_repository_in_tool_shed()get_repository_owner()get_repository_owner_from_clone_url()get_repository_query()get_role_by_id()get_tool_shed_from_clone_url()get_tool_shed_repository_by_id()get_tool_shed_status_for_installed_repository()handle_role_associations()is_tool_shed_client()repository_was_previously_installed()set_repository_attributes()update_repository()validate_repository_name()
- tool_shed.util.review_util module
- tool_shed.util.search_util module
- tool_shed.util.shed_index module
- tool_shed.util.shed_util_common module
- tool_shed.util.tool_dependency_util module
- tool_shed.util.tool_util module
- tool_shed.util.web_util module
- tool_shed.util.xml_util module
- tool_shed.utility_containers package
FailedTestInvalidRepositoryDependencyInvalidToolDependencyMissingTestComponentNotTestedPassedTestRepositoryInstallationErrorRepositorySuccessfulInstallationToolDependencyInstallationErrorToolDependencySuccessfulInstallationToolShedUtilityContainerManagerToolShedUtilityContainerManager.__init__()ToolShedUtilityContainerManager.build_invalid_repository_dependencies_root_folder()ToolShedUtilityContainerManager.build_invalid_tool_dependencies_root_folder()ToolShedUtilityContainerManager.build_repository_containers()ToolShedUtilityContainerManager.generate_tool_dependencies_key()
- Submodules
- tool_shed.utility_containers.utility_container_manager module
- tool_shed.webapp package
url_for()expose()- Subpackages
- tool_shed.webapp.api package
BaseShedAPIController- Submodules
- tool_shed.webapp.api.authenticate module
- tool_shed.webapp.api.categories module
- tool_shed.webapp.api.configuration module
- tool_shed.webapp.api.groups module
- tool_shed.webapp.api.repositories module
- tool_shed.webapp.api.repository_revisions module
- tool_shed.webapp.api.tools module
- tool_shed.webapp.api.users module
- tool_shed.webapp.controllers package
- Submodules
- tool_shed.webapp.controllers.admin module
- tool_shed.webapp.controllers.groups module
- tool_shed.webapp.controllers.hg module
- tool_shed.webapp.controllers.repository module
- tool_shed.webapp.controllers.repository_review module
- tool_shed.webapp.controllers.upload module
- tool_shed.webapp.controllers.user module
- tool_shed.webapp.framework package
- tool_shed.webapp.model package
now()BaseAPIKeysUserPasswordResetTokenGroupRoleUserGroupAssociationUserRoleAssociationGroupRoleAssociationRepositoryRoleAssociationGalaxySessionRepositoryItemRatingAssociationRepositoryRatingAssociationCategoryRepositoryCategoryAssociationTagRepositoryMetadatasort_by_attr()- Subpackages
- Submodules
- tool_shed.webapp.model.mapping module
- tool_shed.webapp.search package
- tool_shed.webapp.security package
- tool_shed.webapp.util package
- tool_shed.webapp.api package
- Submodules
- tool_shed.webapp.app module
- tool_shed.webapp.buildapp module
- tool_shed.webapp.config module
ToolShedAppConfigurationToolShedAppConfiguration.default_config_file_nameToolShedAppConfiguration.add_sample_file_to_defaultsToolShedAppConfiguration.__init__()ToolShedAppConfiguration.shed_tool_data_pathToolShedAppConfiguration.check()ToolShedAppConfiguration.object_store_store_byToolShedAppConfiguration.shed_tools_dir
Configuration
- tool_shed.webapp.fast_app module
- tool_shed.webapp.fast_factory module