Create pubmedScraper.py

pubmedScraper.py

@@ -0,0 +1,55 @@
+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