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tool_shed package

Subpackages

• tool_shed.dependencies package
  • Subpackages
    • tool_shed.dependencies.repository package
      • Submodules
      • tool_shed.dependencies.repository.relation_builder module
    • tool_shed.dependencies.tool package
      • Submodules
      • tool_shed.dependencies.tool.tag_attribute_handler module
  • Submodules
  • tool_shed.dependencies.attribute_handlers module
    • RepositoryDependencyAttributeHandler
      • RepositoryDependencyAttributeHandler.__init__()
      • RepositoryDependencyAttributeHandler.check_tag_attributes()
      • RepositoryDependencyAttributeHandler.handle_complex_dependency_elem()
      • RepositoryDependencyAttributeHandler.handle_elem()
      • RepositoryDependencyAttributeHandler.handle_sub_elem()
      • RepositoryDependencyAttributeHandler.handle_tag_attributes()
    • ToolDependencyAttributeHandler
      • ToolDependencyAttributeHandler.__init__()
      • ToolDependencyAttributeHandler.handle_tag_attributes()
• tool_shed.galaxy_install package
  • Subpackages
    • tool_shed.galaxy_install.grids package
      • Submodules
      • tool_shed.galaxy_install.grids.admin_toolshed_grids module
    • tool_shed.galaxy_install.utility_containers package
  • Submodules
  • tool_shed.galaxy_install.dependency_display module
• tool_shed.grids package
  • Submodules
  • tool_shed.grids.admin_grids module
    • UserGrid
      • UserGrid.UserLoginColumn
      • UserGrid.UserNameColumn
      • UserGrid.GroupsColumn
      • UserGrid.RolesColumn
      • UserGrid.ExternalColumn
      • UserGrid.LastLoginColumn
      • UserGrid.StatusColumn
      • UserGrid.EmailColumn
      • UserGrid.title
      • UserGrid.model_class
      • UserGrid.default_sort_key
      • UserGrid.columns
      • UserGrid.global_actions
      • UserGrid.operations
      • UserGrid.standard_filters
      • UserGrid.use_paging
      • UserGrid.get_current_item()
    • RoleGrid
      • RoleGrid.NameColumn
      • RoleGrid.DescriptionColumn
      • RoleGrid.TypeColumn
      • RoleGrid.StatusColumn
      • RoleGrid.GroupsColumn
      • RoleGrid.RepositoriesColumn
      • RoleGrid.UsersColumn
      • RoleGrid.title
      • RoleGrid.model_class
      • RoleGrid.default_sort_key
      • RoleGrid.columns
      • RoleGrid.global_actions
      • RoleGrid.operations
      • RoleGrid.standard_filters
      • RoleGrid.use_paging
      • RoleGrid.apply_query_filter()
    • GroupGrid
      • GroupGrid.NameColumn
      • GroupGrid.StatusColumn
      • GroupGrid.RolesColumn
      • GroupGrid.UsersColumn
      • GroupGrid.title
      • GroupGrid.model_class
      • GroupGrid.default_sort_key
      • GroupGrid.columns
      • GroupGrid.global_actions
      • GroupGrid.operations
      • GroupGrid.standard_filters
      • GroupGrid.use_paging
    • ManageCategoryGrid
      • ManageCategoryGrid.columns
      • ManageCategoryGrid.global_actions
    • AdminRepositoryGrid
      • AdminRepositoryGrid.DeletedColumn
      • AdminRepositoryGrid.columns
      • AdminRepositoryGrid.operations
      • AdminRepositoryGrid.build_initial_query()
    • RepositoryMetadataGrid
      • RepositoryMetadataGrid.IdColumn
      • RepositoryMetadataGrid.NameColumn
      • RepositoryMetadataGrid.OwnerColumn
      • RepositoryMetadataGrid.RevisionColumn
      • RepositoryMetadataGrid.ToolsColumn
      • RepositoryMetadataGrid.DatatypesColumn
      • RepositoryMetadataGrid.WorkflowsColumn
      • RepositoryMetadataGrid.DeletedColumn
      • RepositoryMetadataGrid.DeprecatedColumn
      • RepositoryMetadataGrid.MaliciousColumn
      • RepositoryMetadataGrid.title
      • RepositoryMetadataGrid.model_class
      • RepositoryMetadataGrid.default_sort_key
      • RepositoryMetadataGrid.use_hide_message
      • RepositoryMetadataGrid.columns
      • RepositoryMetadataGrid.operations
      • RepositoryMetadataGrid.build_initial_query()
  • tool_shed.grids.repository_grid_filter_manager module
    • RepositoryGridFilterManager
      • RepositoryGridFilterManager.filters
      • RepositoryGridFilterManager.get_grid_title()
      • RepositoryGridFilterManager.get_filter()
      • RepositoryGridFilterManager.is_valid_filter()
      • RepositoryGridFilterManager.set_filter()
  • tool_shed.grids.repository_grids module
    • CategoryGrid
      • CategoryGrid.NameColumn
      • CategoryGrid.DescriptionColumn
      • CategoryGrid.RepositoriesColumn
      • CategoryGrid.title
      • CategoryGrid.model_class
      • CategoryGrid.template
      • CategoryGrid.default_sort_key
      • CategoryGrid.columns
      • CategoryGrid.num_rows_per_page
    • RepositoryGrid
      • RepositoryGrid.NameColumn
      • RepositoryGrid.TypeColumn
      • RepositoryGrid.HeadsColumn
      • RepositoryGrid.MetadataRevisionColumn
      • RepositoryGrid.LatestInstallableRevisionColumn
      • RepositoryGrid.TipRevisionColumn
      • RepositoryGrid.DescriptionColumn
      • RepositoryGrid.CategoryColumn
      • RepositoryGrid.RepositoryCategoryColumn
      • RepositoryGrid.UserColumn
      • RepositoryGrid.EmailColumn
      • RepositoryGrid.EmailAlertsColumn
      • RepositoryGrid.DeprecatedColumn
      • RepositoryGrid.title
      • RepositoryGrid.model_class
      • RepositoryGrid.default_sort_key
      • RepositoryGrid.use_hide_message
      • RepositoryGrid.columns
      • RepositoryGrid.default_filter
      • RepositoryGrid.num_rows_per_page
      • RepositoryGrid.use_paging
      • RepositoryGrid.allow_fetching_all_results
      • RepositoryGrid.build_initial_query()
    • DockerImageGrid
      • DockerImageGrid.columns
      • DockerImageGrid.operations
      • DockerImageGrid.show_item_checkboxes
    • EmailAlertsRepositoryGrid
      • EmailAlertsRepositoryGrid.columns
      • EmailAlertsRepositoryGrid.operations
      • EmailAlertsRepositoryGrid.global_actions
    • MatchedRepositoryGrid
      • MatchedRepositoryGrid.NameColumn
      • MatchedRepositoryGrid.DescriptionColumn
      • MatchedRepositoryGrid.RevisionColumn
      • MatchedRepositoryGrid.UserColumn
      • MatchedRepositoryGrid.title
      • MatchedRepositoryGrid.model_class
      • MatchedRepositoryGrid.default_sort_key
      • MatchedRepositoryGrid.use_hide_message
      • MatchedRepositoryGrid.columns
      • MatchedRepositoryGrid.operations
      • MatchedRepositoryGrid.num_rows_per_page
      • MatchedRepositoryGrid.use_paging
      • MatchedRepositoryGrid.build_initial_query()
    • InstallMatchedRepositoryGrid
      • InstallMatchedRepositoryGrid.columns
    • MyWritableRepositoriesGrid
      • MyWritableRepositoriesGrid.title
      • MyWritableRepositoriesGrid.columns
      • MyWritableRepositoriesGrid.build_initial_query()
    • RepositoriesByUserGrid
      • RepositoriesByUserGrid.title
      • RepositoriesByUserGrid.columns
      • RepositoriesByUserGrid.default_filter
      • RepositoriesByUserGrid.build_initial_query()
    • RepositoriesInCategoryGrid
      • RepositoriesInCategoryGrid.title
      • RepositoriesInCategoryGrid.columns
      • RepositoriesInCategoryGrid.build_initial_query()
    • RepositoriesIOwnGrid
      • RepositoriesIOwnGrid.title
      • RepositoriesIOwnGrid.columns
      • RepositoriesIOwnGrid.build_initial_query()
    • RepositoriesICanAdministerGrid
      • RepositoriesICanAdministerGrid.title
      • RepositoriesICanAdministerGrid.columns
      • RepositoriesICanAdministerGrid.build_initial_query()
    • RepositoriesMissingToolTestComponentsGrid
      • RepositoriesMissingToolTestComponentsGrid.title
      • RepositoriesMissingToolTestComponentsGrid.columns
      • RepositoriesMissingToolTestComponentsGrid.build_initial_query()
    • MyWritableRepositoriesMissingToolTestComponentsGrid
      • MyWritableRepositoriesMissingToolTestComponentsGrid.title
      • MyWritableRepositoriesMissingToolTestComponentsGrid.columns
      • MyWritableRepositoriesMissingToolTestComponentsGrid.build_initial_query()
    • DeprecatedRepositoriesIOwnGrid
      • DeprecatedRepositoriesIOwnGrid.title
      • DeprecatedRepositoriesIOwnGrid.columns
      • DeprecatedRepositoriesIOwnGrid.build_initial_query()
    • RepositoriesWithInvalidToolsGrid
      • RepositoriesWithInvalidToolsGrid.InvalidToolConfigColumn
      • RepositoriesWithInvalidToolsGrid.title
      • RepositoriesWithInvalidToolsGrid.columns
      • RepositoriesWithInvalidToolsGrid.build_initial_query()
    • MyWritableRepositoriesWithInvalidToolsGrid
      • MyWritableRepositoriesWithInvalidToolsGrid.title
      • MyWritableRepositoriesWithInvalidToolsGrid.columns
      • MyWritableRepositoriesWithInvalidToolsGrid.build_initial_query()
    • RepositoryMetadataGrid
      • RepositoryMetadataGrid.RepositoryNameColumn
      • RepositoryMetadataGrid.RepositoryTypeColumn
      • RepositoryMetadataGrid.RepositoryOwnerColumn
      • RepositoryMetadataGrid.ChangesetRevisionColumn
      • RepositoryMetadataGrid.MaliciousColumn
      • RepositoryMetadataGrid.DownloadableColumn
      • RepositoryMetadataGrid.HasRepositoryDependenciesColumn
      • RepositoryMetadataGrid.IncludesDatatypesColumn
      • RepositoryMetadataGrid.IncludesToolsColumn
      • RepositoryMetadataGrid.IncludesToolDependenciesColumn
      • RepositoryMetadataGrid.IncludesWorkflowsColumn
      • RepositoryMetadataGrid.title
      • RepositoryMetadataGrid.model_class
      • RepositoryMetadataGrid.default_sort_key
      • RepositoryMetadataGrid.columns
      • RepositoryMetadataGrid.default_filter
      • RepositoryMetadataGrid.num_rows_per_page
      • RepositoryMetadataGrid.use_paging
      • RepositoryMetadataGrid.allow_fetching_all_results
      • RepositoryMetadataGrid.build_initial_query()
    • RepositoryDependenciesGrid
      • RepositoryDependenciesGrid.RequiredRepositoryColumn
      • RepositoryDependenciesGrid.title
      • RepositoryDependenciesGrid.default_sort_key
      • RepositoryDependenciesGrid.columns
      • RepositoryDependenciesGrid.build_initial_query()
    • DatatypesGrid
      • DatatypesGrid.DatatypesColumn
      • DatatypesGrid.title
      • DatatypesGrid.default_sort_key
      • DatatypesGrid.columns
      • DatatypesGrid.build_initial_query()
    • ToolDependenciesGrid
      • ToolDependenciesGrid.ToolDependencyColumn
      • ToolDependenciesGrid.title
      • ToolDependenciesGrid.default_sort_key
      • ToolDependenciesGrid.columns
      • ToolDependenciesGrid.build_initial_query()
    • ToolsGrid
      • ToolsGrid.ToolsColumn
      • ToolsGrid.title
      • ToolsGrid.default_sort_key
      • ToolsGrid.columns
      • ToolsGrid.build_initial_query()
    • ValidCategoryGrid
      • ValidCategoryGrid.RepositoriesColumn
      • ValidCategoryGrid.title
      • ValidCategoryGrid.model_class
      • ValidCategoryGrid.template
      • ValidCategoryGrid.default_sort_key
      • ValidCategoryGrid.columns
      • ValidCategoryGrid.num_rows_per_page
    • ValidRepositoryGrid
      • ValidRepositoryGrid.CategoryColumn
      • ValidRepositoryGrid.RepositoryCategoryColumn
      • ValidRepositoryGrid.InstallableRevisionColumn
      • ValidRepositoryGrid.title
      • ValidRepositoryGrid.columns
      • ValidRepositoryGrid.build_initial_query()
  • 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
    • GroupManager
      • GroupManager.__init__()
      • GroupManager.get()
      • GroupManager.create()
      • GroupManager.update()
      • GroupManager.delete()
      • GroupManager.list()
  • tool_shed.managers.repositories module
    • RepoManager
      • RepoManager.__init__()
      • RepoManager.get()
      • RepoManager.list_by_owner()
      • RepoManager.create()
      • RepoManager.update()
      • RepoManager.delete()
• tool_shed.metadata package
  • Submodules
  • tool_shed.metadata.metadata_generator module
    • MetadataGenerator
      • MetadataGenerator.__init__()
      • MetadataGenerator.generate_environment_dependency_metadata()
      • MetadataGenerator.generate_guid_for_object()
      • MetadataGenerator.generate_metadata_for_changeset_revision()
      • MetadataGenerator.generate_package_dependency_metadata()
      • MetadataGenerator.generate_repository_dependency_metadata()
      • MetadataGenerator.generate_tool_metadata()
      • MetadataGenerator.generate_tool_dependency_metadata()
      • MetadataGenerator.get_invalid_file_tups()
      • MetadataGenerator.get_metadata_dict()
      • MetadataGenerator.get_relative_path_to_repository_file()
      • MetadataGenerator.get_sample_files_from_disk()
      • MetadataGenerator.handle_repository_elem()
      • MetadataGenerator.set_changeset_revision()
      • MetadataGenerator.set_relative_install_dir()
      • MetadataGenerator.set_repository()
      • MetadataGenerator.set_repository_clone_url()
      • MetadataGenerator.set_repository_files_dir()
      • MetadataGenerator.update_repository_dependencies_metadata()
  • tool_shed.metadata.repository_metadata_manager module
    • RepositoryMetadataManager
      • RepositoryMetadataManager.__init__()
      • RepositoryMetadataManager.add_tool_versions()
      • RepositoryMetadataManager.build_repository_ids_select_field()
      • RepositoryMetadataManager.clean_repository_metadata()
      • RepositoryMetadataManager.compare_changeset_revisions()
      • RepositoryMetadataManager.compare_data_manager()
      • RepositoryMetadataManager.compare_datatypes()
      • RepositoryMetadataManager.compare_readme_files()
      • RepositoryMetadataManager.compare_repository_dependencies()
      • RepositoryMetadataManager.compare_tool_dependencies()
      • RepositoryMetadataManager.compare_workflows()
      • RepositoryMetadataManager.create_or_update_repository_metadata()
      • RepositoryMetadataManager.different_revision_defines_tip_only_repository_dependency()
      • RepositoryMetadataManager.get_parent_id()
      • RepositoryMetadataManager.get_query_for_setting_metadata_on_repositories()
      • RepositoryMetadataManager.new_datatypes_metadata_required()
      • RepositoryMetadataManager.new_metadata_required_for_utilities()
      • RepositoryMetadataManager.new_readme_files_metadata_required()
      • RepositoryMetadataManager.new_repository_dependency_metadata_required()
      • RepositoryMetadataManager.new_tool_metadata_required()
      • RepositoryMetadataManager.new_tool_dependency_metadata_required()
      • RepositoryMetadataManager.new_workflow_metadata_required()
      • RepositoryMetadataManager.reset_all_metadata_on_repository_in_tool_shed()
      • RepositoryMetadataManager.reset_all_tool_versions()
      • RepositoryMetadataManager.reset_metadata_on_selected_repositories()
      • RepositoryMetadataManager.set_repository()
      • RepositoryMetadataManager.set_repository_metadata()
      • RepositoryMetadataManager.set_repository_metadata_due_to_new_tip()
• tool_shed.repository_types package
  • Submodules
  • tool_shed.repository_types.metadata module
    • Metadata
      • Metadata.__init__()
      • Metadata.get_changesets_for_setting_metadata()
      • Metadata.is_valid_for_type()
    • TipOnly
      • TipOnly.__init__()
      • TipOnly.get_changesets_for_setting_metadata()
  • tool_shed.repository_types.registry module
    • Registry
      • Registry.__init__()
      • Registry.get_class_by_label()
  • tool_shed.repository_types.repository_suite_definition module
    • RepositorySuiteDefinition
      • RepositorySuiteDefinition.__init__()
      • RepositorySuiteDefinition.is_valid_for_type()
  • tool_shed.repository_types.tool_dependency_definition module
    • ToolDependencyDefinition
      • ToolDependencyDefinition.__init__()
      • ToolDependencyDefinition.is_valid_for_type()
  • tool_shed.repository_types.unrestricted module
    • Unrestricted
      • Unrestricted.__init__()
      • Unrestricted.is_valid_for_type()
  • tool_shed.repository_types.util module
    • build_repository_type_select_field()
    • generate_message_for_repository_type_change()
• tool_shed.test package
  • Subpackages
    • tool_shed.test.base package
      • Submodules
      • tool_shed.test.base.common module
      • tool_shed.test.base.test_db_util module
      • tool_shed.test.base.twilltestcase module
    • 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
• tool_shed.tools package
  • Submodules
  • tool_shed.tools.data_table_manager module
    • ToolDataTableManager
    • ShedToolDataTableManager
      • ShedToolDataTableManager.__init__()
      • ShedToolDataTableManager.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
    • ToolValidator
      • ToolValidator.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
    • ToolVersionManager
      • ToolVersionManager.__init__()
      • ToolVersionManager.get_version_lineage_for_tool()
• tool_shed.util package
  • Submodules
  • tool_shed.util.admin_util module
    • Admin
      • Admin.user_list_grid
      • Admin.role_list_grid
      • Admin.group_list_grid
      • Admin.delete_operation
      • Admin.undelete_operation
      • Admin.purge_operation
      • Admin.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()
  • tool_shed.util.basic_util module
    • get_file_type_str()
    • move_file()
    • remove_dir()
    • size_string()
    • stringify()
    • strip_path()
    • to_html_string()
  • tool_shed.util.commit_util module
    • check_archive()
    • check_file_contents_for_email_alerts()
    • check_file_content_for_html_and_images()
    • get_change_lines_in_file_for_tag()
    • get_upload_point()
    • handle_bz2()
    • handle_directory_changes()
    • handle_gzip()
    • uncompress()
  • 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()
    • get_user_by_username()
    • 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
    • generate_repository_dependencies_key_for_repository()
    • get_components_from_key()
  • 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
    • HgWebConfigManager
      • HgWebConfigManager.__init__()
      • HgWebConfigManager.add_entry()
      • HgWebConfigManager.change_entry()
      • HgWebConfigManager.get_entry()
      • HgWebConfigManager.hgweb_config
      • HgWebConfigManager.make_backup()
      • HgWebConfigManager.read_config()
      • HgWebConfigManager.write_config()
  • 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()
  • tool_shed.util.readme_util module
    • build_readme_files_dict()
    • get_readme_files_dict_for_display()
  • tool_shed.util.repository_content_util module
    • upload_tar()
  • 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
    • in_tool_dict()
    • make_same_length()
    • search_ids_names()
    • search_ids_versions()
    • search_names_versions()
    • search_repository_metadata()
  • tool_shed.util.shed_index module
    • build_index()
    • get_repos()
    • debug_handler()
    • load_one_dir()
  • tool_shed.util.shed_util_common module
    • can_eliminate_repository_dependency()
    • clean_dependency_relationships()
    • count_repositories_in_category()
    • generate_tool_guid()
    • get_categories()
    • get_category()
    • get_category_by_name()
    • get_ctx_rev()
    • get_next_prior_import_or_install_required_dict_entry()
    • get_repository_categories()
    • get_repository_file_contents()
    • get_repository_type_from_tool_shed()
    • get_tool_dependency_definition_metadata_from_tool_shed()
    • get_tool_panel_config_tool_path_install_dir()
    • get_tool_path_by_shed_tool_conf_filename()
    • get_user()
    • handle_email_alerts()
    • have_shed_tool_conf_for_install()
    • is_path_within_dependency_dir()
    • is_path_within_repo()
    • open_repository_files_folder()
    • set_image_paths()
    • tool_shed_is_this_tool_shed()
  • tool_shed.util.tool_dependency_util module
  • tool_shed.util.tool_util module
    • copy_sample_file()
    • copy_sample_files()
    • generate_message_for_invalid_tools()
    • new_state()
  • tool_shed.util.web_util module
    • escape()
  • tool_shed.util.xml_util module
    • create_and_write_tmp_file()
    • parse_xml()
• tool_shed.utility_containers package
  • FailedTest
    • FailedTest.__init__()
  • InvalidRepositoryDependency
    • InvalidRepositoryDependency.__init__()
  • InvalidToolDependency
    • InvalidToolDependency.__init__()
  • MissingTestComponent
    • MissingTestComponent.__init__()
  • NotTested
    • NotTested.__init__()
  • PassedTest
    • PassedTest.__init__()
  • RepositoryInstallationError
    • RepositoryInstallationError.__init__()
  • RepositorySuccessfulInstallation
    • RepositorySuccessfulInstallation.__init__()
  • ToolDependencyInstallationError
    • ToolDependencyInstallationError.__init__()
  • ToolDependencySuccessfulInstallation
    • ToolDependencySuccessfulInstallation.__init__()
  • ToolShedUtilityContainerManager
    • ToolShedUtilityContainerManager.__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
      • Subpackages
      • Submodules
      • tool_shed.webapp.framework.decorators module
    • tool_shed.webapp.model package
      • now()
      • Base
      • APIKeys
      • User
      • PasswordResetToken
      • Group
      • Role
      • UserGroupAssociation
      • UserRoleAssociation
      • GroupRoleAssociation
      • RepositoryRoleAssociation
      • GalaxySession
      • Repository
      • ItemRatingAssociation
      • RepositoryRatingAssociation
      • Category
      • RepositoryCategoryAssociation
      • Tag
      • RepositoryMetadata
      • sort_by_attr()
      • Subpackages
      • Submodules
      • tool_shed.webapp.model.mapping module
    • tool_shed.webapp.search package
      • Submodules
      • tool_shed.webapp.search.repo_search module
      • tool_shed.webapp.search.tool_search module
    • tool_shed.webapp.security package
      • Action
      • RBACAgent
      • CommunityRBACAgent
      • get_permitted_actions()
    • tool_shed.webapp.util package
      • Submodules
      • tool_shed.webapp.util.ratings_util module
      • tool_shed.webapp.util.shed_statistics module
  • Submodules
  • tool_shed.webapp.app module
    • UniverseApplication
      • UniverseApplication.__init__()
      • UniverseApplication.repository_types_registry
      • UniverseApplication.model
      • UniverseApplication.security_agent
      • UniverseApplication.hgweb_config_manager
      • UniverseApplication.repository_registry
  • tool_shed.webapp.buildapp module
    • CommunityWebApplication
      • CommunityWebApplication.injection_aware
    • add_ui_controllers()
    • app_factory()
    • app_pair()
    • wrap_in_middleware()
  • tool_shed.webapp.config module
    • ToolShedAppConfiguration
      • ToolShedAppConfiguration.default_config_file_name
      • ToolShedAppConfiguration.add_sample_file_to_defaults
      • ToolShedAppConfiguration.__init__()
      • ToolShedAppConfiguration.shed_tool_data_path
      • ToolShedAppConfiguration.check()
      • ToolShedAppConfiguration.object_store_store_by
    • Configuration
  • tool_shed.webapp.fast_app module
    • add_request_id_middleware()
    • initialize_fast_app()
  • tool_shed.webapp.fast_factory module
    • factory()

Submodules

tool_shed.repository_registry module

class tool_shed.repository_registry.Registry(app)

Bases: object

__init__(app)

add_category_entry(category)

add_entry(repository)

edit_category_entry(old_name, new_name)

get_certified_level_one_clause_list()

get_certified_level_one_tuple(repository)

Return True if the latest installable changeset_revision of the received repository is level one certified.

is_level_one_certified(repository_metadata)

is_valid(repository)

load_certified_level_one_repository_and_suite_tuple(repository)

load_repository_and_suite_tuple(repository)

load_repository_and_suite_tuples()

load_viewable_repositories_and_suites_by_category()

remove_category_entry(category)

remove_entry(repository)

property sa_session

unload_certified_level_one_repository_and_suite_tuple(repository)

unload_repository_and_suite_tuple(repository)