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| 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 |