Update app.py

app.py

@@ -1,100 +1,19 @@
 import gradio as gr
-from Bio import Entrez
-from transformers import pipeline
-import os  # For environment variables and file paths
-
+import os
+from components import pubmed_search
+from components import model_utils
+import time
 # ---------------------------- Configuration ----------------------------
-ENTREZ_EMAIL = os.environ.get("ENTREZ_EMAIL", "[email protected]")  # Use environment variable, default fallback
-
-HUGGINGFACE_API_TOKEN = os.environ.get("HUGGINGFACE_API_TOKEN", "HUGGINGFACE_API_TOKEN") # Use environment variable, default fallback
-SUMMARIZATION_MODEL = "facebook/bart-large-cnn"
+ENTREZ_EMAIL = os.environ.get("ENTREZ_EMAIL", "ENTREZ_EMAIL")
+HUGGINGFACE_API_TOKEN = os.environ.get("HUGGINGFACE_API_TOKEN", "HUGGINGFACE_API_TOKEN")
 
 # ---------------------------- Global Variables ----------------------------
-summarizer = None
-initialization_status = "Initializing..."  # Track initialization state
-
-# ---------------------------- Helper Functions ----------------------------
-
-def log_error(message: str):
-    """Logs an error message to the console and a file (if possible)."""
-    print(f"ERROR: {message}")
-    try:
-        with open("error_log.txt", "a") as f:
-            f.write(f"{message}\n")
-    except:
-        print("Couldn't write to error log file.")  #If logging fails, still print to console
-
-# ---------------------------- Tool Functions ----------------------------
-
-def search_pubmed(query: str) -> list:
-    """Searches PubMed and returns a list of article IDs."""
-    try:
-        Entrez.email = ENTREZ_EMAIL
-        handle = Entrez.esearch(db="pubmed", term=query, retmax="5")
-        record = Entrez.read(handle)
-        handle.close()
-        return record["IdList"]
-    except Exception as e:
-        log_error(f"PubMed search error: {e}")
-        return [f"Error during PubMed search: {e}"]
-
-def fetch_abstract(article_id: str) -> str:
-    """Fetches the abstract for a given PubMed article ID."""
-    try:
-        Entrez.email = ENTREZ_EMAIL
-        handle = Entrez.efetch(db="pubmed", id=article_id, rettype="abstract", retmode="text")
-        abstract = handle.read()
-        handle.close()
-        return abstract
-    except Exception as e:
-        log_error(f"Error fetching abstract for {article_id}: {e}")
-        return f"Error fetching abstract for {article_id}: {e}"
-
-# ---------------------------- Agent Function ----------------------------
-
-def medai_agent(query: str) -> str:
-    """Orchestrates the medical literature review and summarization."""
-    article_ids = search_pubmed(query)
-
-    if isinstance(article_ids, list) and article_ids:
-        results = []
-        for article_id in article_ids:
-            abstract = fetch_abstract(article_id)
-            if "Error" not in abstract:
-                results.append(f"<div class='article'>\n"
-                               f"  <h3 class='article-id'>Article ID: {article_id}</h3>\n"
-                               f"  <p class='abstract'><strong>Abstract:</strong> {abstract}</p>\n"
-                               f"</div>\n")
-            else:
-                results.append(f"<div class='article error'>\n"
-                               f"  <h3 class='article-id'>Article ID: {article_id}</h3>\n"
-                               f"  <p class='error-message'>Error processing article: {abstract}</p>\n"
-                               f"</div>\n")
-        return "\n".join(results)
-    else:
-        return f"No articles found or error occurred: {article_ids}"
-
-# ---------------------------- Initialization and Setup ----------------------------
-
-def setup():
-    """Initializes the summarization model."""
-    global summarizer, initialization_status
-    initialization_status = "Initializing..."
-    try:
-        initialization_status = "Model is running. The user is now set to search and obtain abstract articles."
-        return initialization_status
-    except Exception as e:
-        initialization_status = f"Initialization error: {e}"
-        log_error(initialization_status)
-        return initialization_status
 
 # ---------------------------- Gradio Interface ----------------------------
 
 def launch_gradio():
     """Launches the Gradio interface."""
-    global initialization_status
 
-    # CSS to style the article output
     css = """
     .article {
       border: 1px solid #ddd;
@@ -118,14 +37,15 @@ def launch_gradio():
     """
 
     with gr.Blocks(css=css) as iface:
-        gr.Markdown("# MedAI: Medical Literature Review and Abstract Finder")
-        status_display = gr.Textbox(value=initialization_status, interactive=False)
+        gr.Markdown("# MedAI: Medical Literature Review")
+        gr.Markdown("Enter a medical query to retrieve abstracts from PubMed.")
+
         query_input = gr.Textbox(lines=3, placeholder="Enter your medical query (e.g., 'new treatments for diabetes')...")
         submit_button = gr.Button("Submit")
         output_results = gr.HTML()  # Use HTML for formatted output
 
-        submit_button.click(medai_agent, inputs=query_input, outputs=output_results)
-        status_display.value = setup()
+        # Get data
+        submit_button.click(pubmed_search.medai_agent, inputs=query_input, outputs=output_results)
 
     iface.launch()