def convert(self, umls_concept):
"""Performs an extra pass through the bad_mhs rules"""
tentative_conversion = Converter.convert(self, umls_concept)
new_conversion = []
for mh in tentative_conversion.utterance:
mh_ls = mh.term.lower().strip()
if mh_ls not in self.bad_mhs:
new_conversion.append(mh)
else:
# Exclusions first, to deal with 'carcinoma'
exclusions = self.bad_mhs[mh_ls][1]
inclusions = self.bad_mhs[mh_ls][0]
exclusion_triggered = False
for e in exclusions:
if e in umls_concept.concept_name:
exclusion_triggered = True
break
if inclusions == INCLUDE_EVERYTHING:
if not exclusion_triggered:
new_conversion.append(mh)
continue
for i in inclusions:
if i in umls_concept.concept_name:
if not exclusion_triggered:
new_conversion.append(mh)
continue
return Expression(new_conversion)
def convert(self, umls_concept):
"""Performs an extra pass through the bad_mhs rules"""
tentative_conversion=Converter.convert(self, umls_concept)
new_conversion=[]
for mh in tentative_conversion.utterance:
mh_ls=mh.term.lower().strip()
if mh_ls not in self.bad_mhs:
new_conversion.append(mh)
else:
# Exclusions first, to deal with 'carcinoma'
exclusions=self.bad_mhs[mh_ls][1]
inclusions=self.bad_mhs[mh_ls][0]
exclusion_triggered=False
for e in exclusions:
if e in umls_concept.concept_name:
exclusion_triggered=True
break
if inclusions==INCLUDE_EVERYTHING:
if not exclusion_triggered:
new_conversion.append(mh)
continue
for i in inclusions:
if i in umls_concept.concept_name:
if not exclusion_triggered:
new_conversion.append(mh)
continue
return Expression(new_conversion)
def setUp(self):
#logging.basicConfig(level=logging.DEBUG,
# format='%(asctime)s %(levelname)s %(message)s')
# Most of the functionality is really tested under test_converter
self.my_tree = Tree(None, file_mode="c") # Creates an empty tree
self.my_tree._tree['hairitis'] = TreeNode('hairitis', 'MH',
set(['A12.23.45']))
self.my_tree._tree['hairiatic cancer'] = TreeNode(
'hairiatic cancer', 'MH', set(['A12.23.54.65', 'B01.23']))
self.my_tree._tree['hareitosis'] = TreeNode('hareitosis', 'SH',
set(['B02.34']))
self.empty_rules = ConverterData({}, {}, {}, {}, {})
self.ruleless_converter = RankedConverter(
Converter(self.my_tree, self.empty_rules))
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 __init__(self, tree, rule_data=None, skip_unknown_concepts=True):
Converter.__init__(self, tree, rule_data, skip_unknown_concepts, set(["a", "i", "g/p", "g/s", "g/c", "o"]))
def __init__(self, tree, rule_data=None, skip_unknown_concepts=True):
Converter.__init__(self, tree, rule_data, skip_unknown_concepts,
set(['a', 'i', 'g/p', 'g/s', 'g/c', 'o']))
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))
