Spaces:
Running
Running
File size: 1,965 Bytes
6a0f953 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 |
from Bio import Entrez
def remove_blankets(ls):
for i in range(len(ls)):
if i<len(ls):
if ls[i]=="" or ls[i]==" ":
ls.remove(ls[i])
else:
pass
else:
pass
def search_pubmed(query, max_results, address):
Entrez.email = address # Replace with your email
handle = Entrez.esearch(db="pubmed", term=query, retmax=max_results)
record = Entrez.read(handle)
handle.close()
return record["IdList"]
def fetch_pubmed_details(pubmed_ids, address):
Entrez.email = address # Replace with your email
handle = Entrez.efetch(db="pubmed", id=pubmed_ids, rettype="medline", retmode="text")
records = handle.read()
handle.close()
return records
def respond_to_query(query,address,max_results=10):
# Perform the PubMed search
pubmed_ids = search_pubmed(query, max_results,address)
# Fetch details for the retrieved PubMed IDs
pubmed_details = fetch_pubmed_details(pubmed_ids,address)
pubmed_split=pubmed_details.split("\n")
str_container=[]
counter=-1
for i in pubmed_split:
str_container.append({})
counter+=1
if i.startswith("TI"):
str_container[counter].update({"Title (sometimes not complete)": i.replace('TI - ', '')})
if i.startswith("AU - "):
str_container[counter].update({"Author": i.replace('AU - ', '')})
if i.startswith("PHST") and i.endswith("[pubmed]"):
str_container[counter].update({"Published on PubMed on": i.replace('PHST- ', '').replace('[pubmed]','')})
if i.endswith("[doi]") and i.startswith("AID - "):
str_container[counter].update({"doi": f"https://doi.org/{i[6:len(i)-5]}\n"})
results=[]
for j in str_container:
ls=[f"{key}: {j[key]}\n" for key in list(j.keys())]
results.append("".join(ls))
remove_blankets(results)
defstr="".join(results)
return defstr |