def execute(link):
queryDict, objective, linkToHealthy = parser.getPubMedQuery(link)
counter = 0
for query in queryDict:
handle = Entrez.egquery(term=queryDict[query])
record = Entrez.read(handle)
tempQ = queryDict[query]
handle1=Entrez.esearch(db="pubmed", term=tempQ, retmax=retcount, usehistory='y')
results=Entrez.read(handle1)
handle1.close()
env1=results["WebEnv"]
key1=results["QueryKey"]
medlFormat = Entrez.efetch(db="pubmed", rettype="MEDLINE", retmode="text", retmax=retcount, WebEnv=env1, query_key=key1)
record_list = Medline.parse(medlFormat)
count=0
for rec in record_list:
if "AB" in rec:
count = count+1
g = open( query +"_" + rec["PMID"] +".txt", 'w')
g.write("Title: " + rec["TI"]+"\n"+"Abstract: "+rec["AB"])
g.close()
else:
count = count+1
g = open( query + "_" + rec["PMID"] + ".txt", 'w')
g.write("Title: " + rec["TI"])
g.close()
break
count += 1
counter += 1
print counter
import csv
from Bio import Entrez
from Bio import Medline
Entrez.email = "*****@*****.**"
import parser
retcount = 20000
link = "http://phpartners.org/hp2020/adolescent_health.html"
queryDict, objective, linkToHealthy = parser.getPubMedQuery(link)
for query in queryDict:
print query
handle1 = Entrez.esearch(db="pubmed", term=queryDict[query])
results = Entrez.read(handle1)
handle1.close()
env1 = results["WebEnv"]
key1 = results["QueryKey"]
medlFormat = Entrez.efetch(
db="pubmed", rettype="MEDLINE", retmode="text", retmax=retcount, WebEnv=env1, query_key=key1
)
record_list = Medline.parse(medlFormat)
count = 0
for rec in record_list:
if "AB" in rec:
count = count + 1