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
class AERecognitionEventDateExtractor(object):
def __init__(self, rawTextFileName, intermediateXMLFileName):
self.preprocess = Preprocessor(rawTextFileName, intermediateXMLFileName)
self.tokens = self.preprocess.timexTagAndTokenizeText()
# print self.tokens
def findEntity(self):
# print self.tokens
#search for words (e.g. 'AE(s)' or 'Adverse Event(s)')
pattern = r'\bAE(\s|s)'
pattern2 = r'\bevents?\b'
pattern3 = r'<\/?TIMEX2>'
re_pat = re.compile(pattern, re.IGNORECASE)
re_pat2 = re.compile(pattern2, re.IGNORECASE)
re_pat3 = re.compile(pattern3, re.IGNORECASE)
ae_index_list = []
#Go through and check for all adverse event/AE keyworks
for index in range (0, len(self.tokens)):
if (self.tokens[index].lower() == 'Adverse'.lower() and
re_pat2.search(self.tokens[index + 1])) or (re_pat.search(self.tokens[index])):
ae_index_list.append(index)
if ae_index_list == []:
print "There are no instances of keyword 'adverse event/AE'"
return False
#Get the indices for all the found tagged words
time_index_list = [index for index in range(0,len(self.tokens)) if re_pat3.search(self.tokens[index])]
if time_index_list == []:
print "There are no temporal expressions in the text."
return False
#Minimize difference between indices for AE keywork and dates
diff = min(product(ae_index_list, time_index_list), key = lambda t: abs(t[0] - t[1]))
if re_pat3.search(self.tokens[diff[0]]):
timexTuple = (diff[0],self.tokens[diff[0]])
aeTuple = (diff[1],self.tokens[diff[1]])
else:
timexTuple = (diff[1],self.tokens[diff[1]])
aeTuple = (diff[0],self.tokens[diff[0]])
#Figure out of timex tuple is <TIMEX2> or </TIMEX2> and act accordingly
if timexTuple[1].lower() == '<TIMEX2>'.lower():
date = list(itertools.takewhile(lambda x: x.lower() != '</TIMEX2>'.lower(), self.tokens[timexTuple[0] + 1:]))
else:
reversedList = self.tokens[::-1]
date = list(itertools.takewhile(lambda x: x.lower() != '<TIMEX2>'.lower(), reversedList[(len(self.tokens) - timexTuple[0]):]))
date = date[::-1]
count = 0
#the rest is to find the offset
for idx, token in enumerate(self.tokens):
if idx > timexTuple[0]: break
if token.lower() == '<TIMEX2>'.lower() or token.lower() == '</TIMEX2>'.lower():
count += 1
# add one because tokens index starts at 0
loc = timexTuple[0] + 1 - count
print "this is the timexTuple: ", timexTuple[0]
print "this is the loc: ", loc
root = self.preprocess.getRoot()
offsets = []
for x in range(0,len(date)):
elem = root.find(".//*[@globalID='"+str(loc + x)+r"']")
if elem is not None:
offsets.append(elem.attrib['offset'])
print 'AERecognitionEventDateExtractor: ', " ".join(date)
offsetList = self.preprocess.offsetParse(";".join(offsets), delimiter=";")
print " ".join(date), offsetList
#
if not offsetList:
return EventDateElement(" ".join(date),[[]], "AERecognitionEventDateExtractor", 'EVENT_DT')
else:
return EventDateElement(" ".join(date), offsetList, "AERecognitionEventDateExtractor", 'EVENT_DT')
