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modularXml2Csv.py
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modularXml2Csv.py
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class clinical:
def find_nctid(self,root):
x=root.find('id_info')
temp=x.find('nct_id').text
return temp
def get_status(self,root):
temp=root.find('overall_status').text
return temp
def start_date(self,root):
if(root.findall('start_date')):
temp=root.find('start_date').text
return temp
else:
s='N/A'
return s
def completion_date(self,root):
if(root.findall('completion_date')):
temp=root.find('completion_date').text
return temp
else:
s='N/A'
return s
def condition(self,root):
t2=[]
if(root.findall('completion_date')):
for x in root.findall('condition'):
y=x.text
t2.append(y)
listToStr = ','.join(map(str, t2))
temp=listToStr
return temp
else:
s='N/A'
return s
def studydesign(self,root):
study=[]
if(root.findall('study_design_info')):
#z=root.findall('study_design_info')
for content in root.find('study_design_info').iter():
if(content.tag!='study_design_info'):
study.append(content.text)
temp = ','.join(map(str, study))
return temp
else:
s='N/A'
return s
def eligibility(self,root):
study=[]
if(root.findall('eligibility')):
#z=root.findall('study_design_info')
for content in root.find('eligibility').iter():
if content.tag =="gender":
study.append('gender:{}'.format(content.text))
if content.tag =="minimum_age":
study.append('Min Age:{}'.format(content.text))
if content.tag =="maximum_age":
study.append('Max Age:{}'.format(content.text))
if content.tag =="sampling_method":
study.append('sampling_method:{}'.format(content.text))
temp = ','.join(map(str, study))
#print(st)
return temp
else:
s='N/A'
return s
def has_expanded_access(self,root):
if(root.findall("has_expanded_access")):
temp=root.find('has_expanded_access').text
return temp
else:
s='N/A'
return s
def enrollment(self,root):
if(root.findall("enrollment")):
temp=root.find("enrollment").text
return temp
else:
s='N/A'
return s
import xml.etree.ElementTree as ET
import csv
import glob
testdata = open('combined2.csv', 'w')
csvwriter = csv.writer(testdata)
csvwriter.writerow(["nct_id","overall_status","start_date",
"completion_date","condition","Study design info","eligibility","has_expanded_access","enrollment"])
#search_result
data_folder="search_result"
obj=clinical()
for filename in glob.iglob(data_folder+"/*.xml"):
tree = ET.parse(filename)
root = tree.getroot()
t=[]
t.append(obj.find_nctid(root))
t.append(obj.get_status(root))
t.append(obj.start_date(root))
t.append(obj.completion_date(root))
t.append(obj.condition(root))
t.append(obj.studydesign(root))
t.append(obj.eligibility(root))
t.append(obj.has_expanded_access(root))
t.append(obj.enrollment(root))
print(t)
csvwriter.writerow(t)