pbcommand Tool Contract¶

Tool Contract Models

class pbcommand.models.ToolContractTask(task_id, name, description, version, is_distributed, input_types, output_types, options, nproc, resources)[source]¶

Bases: object

Core metadata for a commandline task

Parameters:	task_id (str) – Global id to reference your tool in a pipeline name – Display name of your description – Short description of your tool version – semantic style version string is_distributed – If the task will be run locally or not is_distributed – bool input_types – list[FileType] output_types – options – list of PacBioOption instances nproc – resources –

TASK_TYPE_ID = 'pbsmrtpipe.task_types.standard'¶

to_dict()[source]¶

class pbcommand.models.ToolDriver(driver_exe, env=None, serialization='json')[source]¶

Bases: object

Parameters:	driver_exe – Path to the driver env – path to env to be sourced before it’s run?
Returns:

to_dict()[source]¶

class pbcommand.models.InputFileType(file_type_id, label, display_name, description)[source]¶

Bases: pbcommand.models.tool_contract._IOFileType

to_dict()[source]¶

class pbcommand.models.OutputFileType(file_type_id, label, display_name, description, default_name)[source]¶

Bases: pbcommand.models.tool_contract._IOFileType

to_dict()[source]¶

exception pbcommand.models.MalformedToolContractError[source]¶

Bases: exceptions.ValueError

exception pbcommand.models.MalformedResolvedToolContractError[source]¶

Bases: exceptions.ValueError

class pbcommand.models.ToolContract(task, driver, schema_version='2.0.0')[source]¶

Bases: object

Parameters:	task (ToolContractTask | ScatterToolContractTask | GatherToolContractTask) – driver (ToolDriver) –
Returns:

WRITER_SCHEMA_VERSION = '2.0.0'¶

to_dict()[source]¶

class pbcommand.models.ScatterToolContractTask(task_id, name, description, version, is_distributed, input_types, output_types, tool_options, nproc, resources, chunk_keys, max_nchunks)[source]¶

Bases: pbcommand.models.tool_contract.ToolContractTask

Scatter tasks have a special output signature of [FileTypes.CHUNK]

The chunk keys are the expected to be written to the chunk.json file

TASK_TYPE_ID = 'pbsmrtpipe.task_types.scattered'¶

to_dict()[source]¶

class pbcommand.models.GatherToolContractTask(task_id, name, description, version, is_distributed, input_types, output_types, options, nproc, resources)[source]¶

Bases: pbcommand.models.tool_contract.ToolContractTask

Gather tasks have special input type [FileTypes.CHUNK]

Core metadata for a commandline task

Parameters:	task_id (str) – Global id to reference your tool in a pipeline name – Display name of your description – Short description of your tool version – semantic style version string is_distributed – If the task will be run locally or not is_distributed – bool input_types – list[FileType] output_types – options – list of PacBioOption instances nproc – resources –

TASK_TYPE_ID = 'pbsmrtpipe.task_types.gathered'¶