class DrugnameMetamapExtractor(object):
def __init__(self, rawTextFileName, intermediateXMLFileName):
self.preprocess = Preprocessor(rawTextFileName,
intermediateXMLFileName)
self.Text = self.preprocess.rawText()
def findEntity(self):
# the server installed on your machine
mm = MetaMap.get_instance('/work/tkakar/public_mm/bin/metamap14')
#sample_Text = '/work/tkakar/FDAfirstNarrative.txt'
rawText = self.Text
#sents= self.Text
concepts, error = mm.extract_concepts([rawText],
word_sense_disambiguation=True)
offset_list = []
drugs_list = []
drug_offset_pair = ()
for concept in concepts:
c = concept.semtypes
c = c.replace("[", "")
c = c.replace("]", "")
semTypes = c.strip().split(",")
#print semTypes, type(semTypes)
for semType in semTypes:
if semType in ['phsu', 'orch']:
token = concept.trigger.strip().split("-")[0]
token = token.replace("[", "")
#print concept.pos_info, "pos_info"
offset = self.preprocess.offsetParse(concept.pos_info, ';')
#print offset , "offset" , len(offset)
for item in offset:
#print item ,item[1]
item[1] = item[0] + item[1]
#print ("offsetMetamap" , item )
if item not in offset_list:
offset_list.append(item)
drugs_list.append(token)
drugs_list = [drug.replace('"', "") for drug in drugs_list]
#print len(drugs_list)
elementList = []
for drug, offset in zip(drugs_list, offset_list):
#print drug, type(drug), type(offset), [offset]
elementList.append(
DrugnameElement(drug, [offset], "DrugnameMetamapExtractor",
"DRUGNAME"))
#print len(elementList)
return elementList
def __init__(self, rawTextFileName, intermediateXMLFileName):
preprocess = Preprocessor(rawTextFileName, intermediateXMLFileName)
self.Text = preprocess.rawText()
