def test_read_umls_types(self):
meta_path = 'tests/fixtures/umls_META'
concept_details = {}
umls_utils.read_umls_concepts(meta_path, concept_details)
umls_utils.read_umls_types(meta_path, concept_details)
for expected_concept in self.expected_concepts:
concept = concept_details[expected_concept['concept_id']]
assert concept['types'] == expected_concept['types']
def test_read_umls_definitions(self):
meta_path = 'tests/fixtures/umls_META'
concept_details = {}
umls_utils.read_umls_concepts(meta_path, concept_details)
umls_utils.read_umls_definitions(meta_path, concept_details)
for expected_concept in self.expected_concepts:
concept = concept_details[expected_concept['concept_id']]
if 'definition' in expected_concept:
assert concept['definition'] == expected_concept['definition']
def test_read_umls_concepts(self):
meta_path = 'tests/fixtures/umls_META'
concept_details = {}
umls_utils.read_umls_concepts(meta_path, concept_details)
assert len(self.expected_concepts) == len(concept_details)
for expected_concept in self.expected_concepts:
assert expected_concept['concept_id'] in concept_details
concept = concept_details[expected_concept['concept_id']]
if 'canonical_name' in expected_concept:
assert concept['canonical_name'] == expected_concept[
'canonical_name']
assert concept['aliases'] == expected_concept['aliases']
def main(meta_path: str, output_path: str, source: str = None):
concept_details = {} # dictionary of concept_id -> {
# 'concept_id': str,
# 'canonical_name': str
# 'aliases': List[str]
# 'types': List[str]
# 'definition': str
# }
print('Reading concepts ... ')
umls_utils.read_umls_concepts(meta_path, concept_details, source)
print('Reading types ... ')
umls_utils.read_umls_types(meta_path, concept_details)
print('Reading definitions ... ')
umls_utils.read_umls_definitions(meta_path, concept_details)
without_canonical_name_count = 0
without_aliases_count = 0
with_one_alias_count = 0
with_more_than_one_alias_count = 0
without_type_count = 0
with_one_type_count = 0
with_more_than_one_type_count = 0
without_definition_count = 0
with_definition_pref_source_count = 0
with_definition_other_sources_count = 0
for concept in concept_details.values():
without_canonical_name_count += 1 if 'canonical_name' not in concept else 0
without_aliases_count += 1 if len(concept['aliases']) == 0 else 0
with_one_alias_count += 1 if len(concept['aliases']) == 1 else 0
with_more_than_one_alias_count += 1 if len(concept['aliases']) > 1 else 0
without_type_count += 1 if len(concept['types']) == 0 else 0
with_one_type_count += 1 if len(concept['types']) == 1 else 0
with_more_than_one_type_count += 1 if len(concept['types']) >= 1 else 0
without_definition_count += 1 if 'definition' not in concept else 0
with_definition_pref_source_count += 1 if concept.get('is_from_preferred_source') == 'Y' else 0
with_definition_other_sources_count += 1 if concept.get('is_from_preferred_source') == 'N' else 0
print(f'Number of concepts: {len(concept_details)}')
print(f'Number of concepts without canonical name (one of the aliases will be used instead): '
f'{without_canonical_name_count}')
print(f'Number of concepts with no aliases: {without_aliases_count}')
print(f'Number of concepts with 1 alias: {with_one_alias_count}')
print(f'Number of concepts with > 1 alias: {with_more_than_one_alias_count}')
print(f'Number of concepts with no type: {without_type_count}')
print(f'Number of concepts with 1 type: {with_one_type_count}')
print(f'Number of concepts with > 1 type: {with_more_than_one_type_count}')
print(f'Number of concepts with no definition: {without_definition_count}')
print(f'Number of concepts with definition from preferred sources: {with_definition_pref_source_count}')
print(f'Number of concepts with definition from other sources: {with_definition_other_sources_count}')
print('Deleting unused fields and choosing a canonical name from aliases ... ')
for concept in concept_details.values():
# Some concepts have many duplicate aliases. Here we remove them.
concept["aliases"] = list(set(concept["aliases"]))
# if a concept doesn't have a canonical name, use the first alias instead
if 'canonical_name' not in concept:
aliases = concept['aliases']
concept['canonical_name'] = aliases[0]
del aliases[0]
# deleting `is_from_preferred_source`
if 'is_from_preferred_source' in concept:
del concept['is_from_preferred_source']
print('Exporting to the a jsonl file {} ...'.format(output_path))
with open(output_path, 'w') as fout:
for value in concept_details.values():
fout.write(json.dumps(value) + "\n")
print('DONE.')