def map_concept(self, concept):
r = Concepts()
db_cursor.execute(self._MAP_QUERY % concept.code)
for (code,) in db_cursor.fetchall():
c = self.terminology2.get(code)
if c: r.add(c)
return r
def map_concepts(self, concepts):
r = Concepts()
for concept in concepts:
db_cursor.execute("SELECT DISTINCT CUI FROM MRCONSO WHERE AUI IN %s" % concept._sql_uis)
for (code,) in db_cursor.fetchall():
concept = self.terminology2.get(code) # get() because it might be a suppressed concept
if concept: r.add(concept)
return r
def map_concepts(self, concepts):
r = Concepts()
for concept in concepts:
db_cursor.execute(self._MAP_QUERY, (str(concept.code),))
for (code,) in db_cursor.fetchall():
concept = self.terminology2.get(code) # get() because it might be a suppressed concept
if concept: r.add(concept)
return r
def map_concepts(self, concepts):
r = Concepts()
for concept in concepts:
try:
code = concept.english_code
if self.reversed and (code in _ICD10_CHAPTER_MAPPING_REVERSE): code = _ICD10_CHAPTER_MAPPING_REVERSE[code]
elif not(self.reversed) and (code in _ICD10_CHAPTER_MAPPING ): code = _ICD10_CHAPTER_MAPPING [code]
elif "-" in code:
if self.reversed:
if code.endswith(".9"): code = code[:-2]
else: code += ".9"
c = self.terminology2[code]
r.add(c)
except ValueError: pass
return r
def first_levels(self): source = tuple(UMLS_SRC["V-%s" % self._original_terminology_name] >> UMLS_CUI)[0] sources_in_self = source >> UMLS_AUI >> self if sources_in_self: return list(sources_in_self) roots = Concepts(source.children) >> UMLS_AUI >> self return list(root for root in roots if not root.parents)
def map_concepts(self, concepts, cumulated_concepts = None):
r = Concepts()
cumulated_concepts = cumulated_concepts or set(concepts)
concepts_partially_matched = Concepts(concepts)
for concept in tuple(concepts_partially_matched):
r2 = None
if self._umls_mapping: r2 = self._umls_mapping.map_concept(concept)
if r2:
r.update(r2)
concepts_partially_matched.discard(concept)
else:
db_cursor.execute(self._MAP_QUERY % concept._sql_uis)
for (code,) in db_cursor.fetchall():
c = self.terminology2.get(code)
if c:
r.add(c)
concepts_partially_matched.discard(concept)
if concepts_partially_matched:
concepts = Concepts(sum([self._get_concept_parents(concept) for concept in concepts_partially_matched], []))
concepts = concepts - cumulated_concepts
if concepts:
cumulated_concepts.update(concepts)
r.update(self.map_concepts(concepts, cumulated_concepts))
return r
def map_concepts(self, concepts, cumulated_concepts = None):
r = Concepts()
cumulated_concepts = cumulated_concepts or set(concepts)
concepts_partially_matched = Concepts(concepts)
for concept in tuple(concepts_partially_matched):
corresponding_concepts = self.terminology2._concepts_from_cui(concept.code)
if corresponding_concepts:
for c in corresponding_concepts: r.add(c)
concepts_partially_matched.discard(concept)
if concepts_partially_matched:
concepts = Concepts(sum([self._get_concept_parents(concept) for concept in concepts_partially_matched], []))
concepts = concepts - cumulated_concepts
if concepts:
cumulated_concepts.update(concepts)
r.update(self.map_concepts(concepts, cumulated_concepts))
return r
def map_concepts(self, concepts): return Concepts([self.terminology2[ui] for concept in concepts for ui in concept._uis])