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from Bio import Entrez
import xml.etree.ElementTree as ET
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="xml")
records = handle.read()
handle.close()
recs = records.decode("utf-8")
f = open("articles.xml", "w")
f.write(recs)
f.close()
return "articles.xml"
def fetch_xml(xml_file):
tree = ET.parse(xml_file)
root = tree.getroot()
articles = {}
# Iterate over each article and extract title, authors, and DOI
for article in root.findall('PubmedArticle'):
# Extract the article title
title = article.find('.//ArticleTitle').text if article.find('.//ArticleTitle') is not None else "No title"
# Extract the authors
authors = []
for author in article.findall('.//Author'):
last_name = author.find('LastName').text if author.find('LastName') is not None else ""
fore_name = author.find('ForeName').text if author.find('ForeName') is not None else ""
authors.append(f"{fore_name} {last_name}".strip())
# Extract the DOI
doi = None
for elocation_id in article.findall('.//ELocationID'):
if elocation_id.get('EIdType') == 'doi':
doi = elocation_id.text
break
pub_date = article.find('.//PubDate')
if pub_date is not None:
year = pub_date.find('Year').text if pub_date.find('Year') is not None else ""
month = pub_date.find('Month').text if pub_date.find('Month') is not None else ""
day = pub_date.find('Day').text if pub_date.find('Day') is not None else ""
publication_date = f"{year}-{month}-{day}".strip("-")
else:
publication_date = "No publication date"
articles.update({doi: {"Title": title, "Authors": authors, "PubDate": publication_date}})
return articles
def respond_to_query(query,address,max_results=10):
pubmed_ids = search_pubmed(query, max_results,address)
pubmed_details = fetch_pubmed_details(pubmed_ids,address)
articles = fetch_xml(pubmed_details)
final_res = ""
for doi in articles:
auths = [f"- <kbd> {author} </kbd>" for author in articles[doi]["Authors"]] if len(articles[doi]["Authors"]) > 0 else ["- <kbd> No authors listed </kbd>",""]
authorrs = '\n'.join(auths)
res = f"**Title**: {articles[doi]['Title']}\n**Publication date**: {articles[doi]['PubDate']}\n<details>\n\t<summary><b>Authors</b></summary>\n\n{authorrs}\n\n</details>\n\n**DOI**: [{doi}🔗](https://doi.org/{doi}) \n\n-----------------------\n"
final_res+=res
return final_res
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