def __init__(self, reader, graph_builder, ranker, eval_parameters,
ranking_cutoff, mesh_tree_filename, distance_matrix_filename,
distance_function, umls_converter_data_filename,
umls_concept_data_filename, output_file):
logging.debug("Setting up a Workflow instance.")
logging.debug("My reader is: %r", reader)
self._reader = reader
logging.debug("My graph builder is: %r", graph_builder)
self._graph_builder = graph_builder
self._ranker = MappedRanker(ranker)
logging.debug("My ranker is: %r", self._ranker)
self._ranking_cutoff = ranking_cutoff
logging.debug("My ranking cutoff is: %r", self._ranking_cutoff)
logging.debug("Creating a Tree instance from %s", mesh_tree_filename)
self._mesh_tree = Tree(mesh_tree_filename)
logging.debug(
"Creating SAVCC distance matrix with %r and distance "
"function %r", distance_matrix_filename, distance_function)
self._matrix = SavccNormalizedMatrix(
open(distance_matrix_filename, "rb"), distance_function)
logging.debug("Filling in the rest of the evaluation parameters.")
self._eval_parameters = eval_parameters
self._eval_parameters.mesh_tree = self._mesh_tree
self._eval_parameters.savcc_matrix = self._matrix
logging.debug("My evaluation parameters are: %r",
self._eval_parameters)
if umls_converter_data_filename is None:
converter_data = None
else:
converter_data = pickle.load(
open(umls_converter_data_filename, "rb"))
self._umls_converter = RankedConverter(
Converter(self._mesh_tree, converter_data))
logging.debug("My converter is: %r", self._umls_converter)
logging.debug("Initializing Concept storage from %s",
umls_concept_data_filename)
if umls_concept_data_filename is None:
Concept.init_storage()
else:
Concept.init_storage(StringDBDict(umls_concept_data_filename))
self._output_file = output_file
logging.debug("My output file is: %r", self._output_file)
return
def create_converter(self, mesh_tree, converter_data):
"""Creates and returns the UMLS converter we'll use - override for easy
customization"""
return RankedConverter(Converter(mesh_tree, converter_data))
