weaver.processes.builtin.collection_processor
Retrieves relevant data or files resolved from a collection reference using its metadata, queries and desired outputs.
Module Contents
- weaver.processes.builtin.collection_processor.process_collection(collection_input: weaver.typedefs.JobValueCollection, input_definition: weaver.typedefs.ProcessInputOutputItem, output_dir: weaver.typedefs.Path, logger: weaver.utils.LoggerHandler = LOGGER) List[weaver.typedefs.CWL_IO_FileValue][source]
Processor of a Collection.
This function is intended to be employed either as a standalone Builtin Process (for validating resolution) or as an intermediate Collection resolution when submitted as input for another Process execution.
- Parameters:
collection_input – Collection Input parameters with minimally the URI to the collection used as reference. Can contain additional filtering or hint format parameters.
input_definition – Process input definition that indicates the target types, formats and schema to retrieve from the collection.
output_dir – Directory to write the output (provided by the CWL definition).
logger – Optional logger handler to employ.
- Returns:
Resolved data references.
- weaver.processes.builtin.collection_processor.parse_collection_parameters(parameters: Dict[str, weaver.typedefs.JSON]) Dict[str, weaver.typedefs.JSON][source]
Applies any relevant conversions of known parameters between allowed request format and expected utilities.