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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 | |