Index A | B | C | D | E | F | H | I | L | M | N | O | P | R | S | T | U | V | W A app_runner (bfabric_app_runner.specs.app.app_spec.BfabricAppSpec attribute), [1] application_id (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) application_name (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) AppSpec (class in bfabric_app_runner.specs.app.app_spec) AppSpecTemplate (class in bfabric_app_runner.specs.app.app_spec) AppVersion (class in bfabric_app_runner.specs.app.app_version) AppVersionMultiTemplate (class in bfabric_app_runner.specs.app.app_version) AppVersionTemplate (class in bfabric_app_runner.specs.app.app_version) available_versions (bfabric_app_runner.specs.app.app_spec.AppSpec property) B bfabric (bfabric_app_runner.specs.app.app_spec.AppSpec attribute), [1] (bfabric_app_runner.specs.app.app_spec.AppSpecTemplate attribute), [1] bfabric.experimental.workunit_definition module bfabric_app_runner.app_runner.runner module bfabric_app_runner.specs.app.app_spec module bfabric_app_runner.specs.app.app_version module bfabric_app_runner.specs.inputs_spec module bfabric_app_runner.specs.outputs_spec module BfabricAnnotationSpec (in module bfabric_app_runner.specs.inputs.bfabric_annotation_spec) BfabricAppSpec (class in bfabric_app_runner.specs.app.app_spec) C check_checksum (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_spec.BfabricResourceSpec attribute) checksum (bfabric_app_runner.specs.inputs.file_spec.FileSpec attribute) chunks (bfabric_app_runner.app_runner.runner.ChunksFile attribute) ChunksFile (class in bfabric_app_runner.app_runner.runner) collect (bfabric_app_runner.specs.app.commands_spec.CommandsSpec attribute), [1] column (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) command (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandExec attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandShell attribute), [1] commands (bfabric_app_runner.specs.app.app_version.AppVersion attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionMultiTemplate attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionTemplate attribute) container_id (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) container_type (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) content (bfabric_app_runner.specs.inputs.static_file_spec.StaticFileSpec attribute) CopyResourceSpec (class in bfabric_app_runner.specs.outputs_spec) custom_args (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] D data (bfabric_app_runner.specs.inputs.static_yaml_spec.StaticYamlSpec attribute) dataset (bfabric.experimental.workunit_definition.WorkunitExecutionDefinition attribute) dispatch (bfabric_app_runner.specs.app.commands_spec.CommandsSpec attribute), [1] E engine (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] entity (bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec.BfabricOrderFastaSpec attribute) entity_id (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] entity_type (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] entrypoint (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] env (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandExec attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] evaluate() (bfabric_app_runner.specs.app.app_spec.AppSpecTemplate method) (bfabric_app_runner.specs.app.app_version.AppVersionTemplate method) exclude_patterns (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) execution (bfabric.experimental.workunit_definition.WorkunitDefinition attribute) expand_versions() (bfabric_app_runner.specs.app.app_version.AppVersionMultiTemplate method) extract (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) F filename (bfabric_app_runner.specs.inputs.bfabric_dataset_spec.BfabricDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec.BfabricOrderFastaSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_spec.BfabricResourceSpec attribute) (bfabric_app_runner.specs.inputs.file_spec.FileSpec attribute) (bfabric_app_runner.specs.inputs.static_file_spec.StaticFileSpec attribute) (bfabric_app_runner.specs.inputs.static_yaml_spec.StaticYamlSpec attribute) format (bfabric_app_runner.specs.inputs.bfabric_dataset_spec.BfabricDatasetSpec attribute) from_ref() (bfabric.experimental.workunit_definition.WorkunitDefinition class method) from_workunit() (bfabric.experimental.workunit_definition.WorkunitDefinition class method) (bfabric.experimental.workunit_definition.WorkunitExecutionDefinition class method) (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition class method) from_yaml() (bfabric.experimental.workunit_definition.WorkunitDefinition class method) H has_header (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] hostname (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] I id (bfabric_app_runner.specs.inputs.bfabric_dataset_spec.BfabricDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec.BfabricOrderFastaSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_spec.BfabricResourceSpec attribute) IF_EXISTS (bfabric_app_runner.specs.outputs_spec.UpdateExisting attribute) image (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] include_patterns (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) infer_from_directory() (bfabric_app_runner.app_runner.runner.ChunksFile class method) inputs (bfabric_app_runner.specs.inputs_spec.InputsSpec attribute) InputsSpec (class in bfabric_app_runner.specs.inputs_spec) invalid_characters (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] L link (bfabric_app_runner.specs.inputs.file_spec.FileSpec attribute) load_yaml() (bfabric_app_runner.specs.app.app_spec.AppSpec class method) local_extra_deps (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] local_path (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] M mac_address (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] model_config (bfabric.experimental.workunit_definition.WorkunitDefinition attribute) (bfabric.experimental.workunit_definition.WorkunitExecutionDefinition attribute) (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) (bfabric_app_runner.app_runner.runner.ChunksFile attribute) (bfabric_app_runner.specs.app.app_spec.AppSpec attribute) (bfabric_app_runner.specs.app.app_spec.AppSpecTemplate attribute) (bfabric_app_runner.specs.app.app_spec.BfabricAppSpec attribute) (bfabric_app_runner.specs.app.app_version.AppVersion attribute) (bfabric_app_runner.specs.app.app_version.AppVersionMultiTemplate attribute) (bfabric_app_runner.specs.app.app_version.AppVersionTemplate attribute) (bfabric_app_runner.specs.inputs_spec.InputsSpec attribute) (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute) (bfabric_app_runner.specs.outputs_spec.OutputsSpec attribute) (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute) (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute) module bfabric.experimental.workunit_definition bfabric_app_runner.app_runner.runner bfabric_app_runner.specs.app.app_spec bfabric_app_runner.specs.app.app_version bfabric_app_runner.specs.inputs_spec bfabric_app_runner.specs.outputs_spec mounts (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] N name (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] NO (bfabric_app_runner.specs.outputs_spec.UpdateExisting attribute) no_duplicate_versions() (bfabric_app_runner.specs.app.app_spec.AppSpec class method), [1] O output_dataset_file_column (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) output_dataset_filename (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) output_dataset_only (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) outputs (bfabric_app_runner.specs.outputs_spec.OutputsSpec attribute) OutputsSpec (class in bfabric_app_runner.specs.outputs_spec) P prepend_paths (bfabric_app_runner.specs.app.commands_spec.CommandExec attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] process (bfabric_app_runner.specs.app.commands_spec.CommandsSpec attribute), [1] protocol (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] pylock (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] python_version (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] R raw_parameters (bfabric.experimental.workunit_definition.WorkunitExecutionDefinition attribute) read() (bfabric_app_runner.app_runner.runner.ChunksFile class method) read_only (bfabric_app_runner.specs.app.commands_spec.MountOptions attribute), [1] read_yaml() (bfabric_app_runner.specs.inputs_spec.InputsSpec class method) (bfabric_app_runner.specs.outputs_spec.OutputsSpec class method) refresh (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] registration (bfabric.experimental.workunit_definition.WorkunitDefinition attribute) require_entity_id_if_not_workunit() (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec method), [1] required (bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec.BfabricOrderFastaSpec attribute) REQUIRED (bfabric_app_runner.specs.outputs_spec.UpdateExisting attribute) resources (bfabric.experimental.workunit_definition.WorkunitExecutionDefinition attribute) reuse_default_resource (bfabric_app_runner.specs.app.app_version.AppVersion attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionMultiTemplate attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionTemplate attribute) run_app() (in module bfabric_app_runner.app_runner.runner) run_collect() (bfabric_app_runner.app_runner.runner.Runner method) run_dispatch() (bfabric_app_runner.app_runner.runner.Runner method) run_inputs() (bfabric_app_runner.app_runner.runner.Runner method) run_process() (bfabric_app_runner.app_runner.runner.Runner method) Runner (class in bfabric_app_runner.app_runner.runner) S SaveDatasetSpec (class in bfabric_app_runner.specs.outputs_spec) SaveLinkSpec (class in bfabric_app_runner.specs.outputs_spec) separator (bfabric_app_runner.specs.inputs.bfabric_dataset_spec.BfabricDatasetSpec attribute) (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] share_bfabric_config (bfabric_app_runner.specs.app.commands_spec.MountOptions attribute), [1] source (bfabric_app_runner.specs.inputs.file_spec.FileSpec attribute) storage_id (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) storage_output_folder (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) store_entry_path (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] store_folder_path (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] strip_root (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) T to_yaml() (bfabric.experimental.workunit_definition.WorkunitDefinition method) type (bfabric_app_runner.specs.app.commands_spec.CommandDocker attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandExec attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandPythonEnv attribute), [1] (bfabric_app_runner.specs.app.commands_spec.CommandShell attribute), [1] (bfabric_app_runner.specs.inputs.bfabric_dataset_spec.BfabricDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_order_fasta_spec.BfabricOrderFastaSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_archive_spec.BfabricResourceArchiveSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_dataset.BfabricResourceDatasetSpec attribute) (bfabric_app_runner.specs.inputs.bfabric_resource_spec.BfabricResourceSpec attribute) (bfabric_app_runner.specs.inputs.file_spec.FileSpec attribute) (bfabric_app_runner.specs.inputs.static_file_spec.StaticFileSpec attribute) (bfabric_app_runner.specs.inputs.static_yaml_spec.StaticYamlSpec attribute) (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] (bfabric_app_runner.specs.outputs_spec.SaveDatasetSpec attribute), [1] (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] U update_existing (bfabric_app_runner.specs.outputs_spec.CopyResourceSpec attribute), [1] (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] UpdateExisting (class in bfabric_app_runner.specs.outputs_spec) url (bfabric_app_runner.specs.outputs_spec.SaveLinkSpec attribute), [1] user_id (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) V validate_no_link_ssh() (bfabric_app_runner.specs.inputs.file_spec.FileSpec method) version (bfabric_app_runner.specs.app.app_version.AppVersion attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionMultiTemplate attribute), [1] (bfabric_app_runner.specs.app.app_version.AppVersionTemplate attribute) versions (bfabric_app_runner.specs.app.app_spec.AppSpec attribute), [1] (bfabric_app_runner.specs.app.app_spec.AppSpecTemplate attribute), [1] W work_dir_target (bfabric_app_runner.specs.app.commands_spec.MountOptions attribute), [1] workflow_template_step_id (bfabric_app_runner.specs.app.app_spec.BfabricAppSpec attribute), [1] workunit_id (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) workunit_name (bfabric.experimental.workunit_definition.WorkunitRegistrationDefinition attribute) WorkunitDefinition (class in bfabric.experimental.workunit_definition) WorkunitExecutionDefinition (class in bfabric.experimental.workunit_definition) WorkunitRegistrationDefinition (class in bfabric.experimental.workunit_definition) write_yaml() (bfabric_app_runner.specs.inputs_spec.InputsSpec class method) (bfabric_app_runner.specs.outputs_spec.OutputsSpec class method) writeable (bfabric_app_runner.specs.app.commands_spec.MountOptions attribute), [1]