Resolve merge conflicts

Dockerfile

@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 FROM python:3.10
 
 WORKDIR /app
@@ -9,4 +10,17 @@ RUN pip install -r requirements.txt
 
 RUN python -m spacy download en_core_web_sm
 
+=======
+FROM python:3.10
+
+WORKDIR /app
+
+COPY . /app
+
+RUN apt-get update && apt-get install -y curl
+RUN pip install -r requirements.txt
+
+RUN python -m spacy download en_core_web_sm
+
+>>>>>>> 3c8dbea734b3938b3c2fd1f974ec877199a17aea
 CMD ["python", "app.py"]

app.py

@@ -1,110 +1,51 @@
 import gradio as gr
-from Bio import Entrez
-from transformers import pipeline
-import spacy
-
+import os
+from components import pubmed_search
+from components import model_utils
+import time
 # ---------------------------- Configuration ----------------------------
-ENTREZ_EMAIL = "oluwafemidiakhoa@gmail.com"  # Replace with your email!
-HUGGINGFACE_API_TOKEN = "HUGGINGFACE_API_TOKEN"  # Replace with your Hugging Face API token!
-SUMMARIZATION_MODEL = "facebook/bart-large-cnn"  # Or try "google/pegasus-large"
-SPACY_MODEL = "en_core_web_sm" # Small model for faster processing
-# ---------------------------- Global Variables ----------------------------
-
-summarizer = None  # Initialized in the setup function
-nlp = None # Initialized in the setup function
-
-# ---------------------------- Tool Functions ----------------------------
-
-def search_pubmed(query: str) -> list:
-    """Searches PubMed and returns a list of article IDs."""
-    Entrez.email = ENTREZ_EMAIL
-    try:
-        handle = Entrez.esearch(db="pubmed", term=query, retmax="5")  # Limit to 5 for demonstration
-        record = Entrez.read(handle)
-        handle.close()
-        return record["IdList"]
-    except Exception as e:
-        return [f"Error during PubMed search: {e}"]
-
-def fetch_abstract(article_id: str) -> str:
-    """Fetches the abstract for a given PubMed article ID."""
-    Entrez.email = ENTREZ_EMAIL
-    try:
-        handle = Entrez.efetch(db="pubmed", id=article_id, rettype="abstract", retmode="text")
-        abstract = handle.read()
-        handle.close()
-        return abstract
-    except Exception as e:
-        return f"Error fetching abstract for {article_id}: {e}"
-
-def summarize_abstract(abstract: str) -> str:
-    """Summarizes an abstract using a transformer model."""
-    global summarizer  # Access the global summarizer
-    if summarizer is None:
-        return "Summarizer not initialized. Please reload the interface."
-
-    try:
-        summary = summarizer(abstract, max_length=130, min_length=30, do_sample=False)[0]['summary_text']
-        return summary
-    except Exception as e:
-        return f"Error during summarization: {e}"
-
-def extract_entities(text: str) -> list:
-    """Extracts entities (simplified) using SpaCy."""
-    global nlp
-    try:
-        doc = nlp(text)
-        entities = [(ent.text, ent.label_) for ent in doc.ents]
-        return entities
-    except Exception as e:
-        return [f"Error during entity extraction: {e}"]
+ENTREZ_EMAIL = os.environ.get("ENTREZ_EMAIL", "ENTREZ_EMAIL")
+HUGGINGFACE_API_TOKEN = os.environ.get("HUGGINGFACE_API_TOKEN", "HUGGINGFACE_API_TOKEN")
 
-
-# ---------------------------- Agent Function (Simplified) ----------------------------
-
-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:
-                summary = summarize_abstract(abstract)
-                entities = extract_entities(abstract) #extract_entities(abstract)
-                results.append(f"**Article ID:** {article_id}\n\n**Summary:** {summary}\n\n**Entities:** {entities}\n\n---\n")
-            else:
-                results.append(f"Error processing article {article_id}: {abstract}\n\n---\n")
-        return "\n".join(results)
-    else:
-        return f"No articles found or error occurred: {article_ids}"
+# ---------------------------- Global Variables ----------------------------
 
 # ---------------------------- Gradio Interface ----------------------------
 
-def setup():
-    """Initializes the summarization model and Spacy model."""
-    global summarizer, nlp
-    try:
-        summarizer = pipeline("summarization", model=SUMMARIZATION_MODEL, token=HUGGINGFACE_API_TOKEN)
-        nlp = spacy.load(SPACY_MODEL)
-        return "MedAI Agent initialized successfully!"
-    except Exception as e:
-        return f"Initialization error: {e}"
-
 def launch_gradio():
     """Launches the Gradio interface."""
-    with gr.Blocks() as iface:
-        gr.Markdown("# MedAI: Medical Literature Review and Summarization")
-        status = gr.Textbox(value="Initializing...", interactive=False)
+
+    css = """
+    .article {
+      border: 1px solid #ddd;
+      margin-bottom: 10px;
+      padding: 10px;
+      border-radius: 5px;
+    }
+    .article.error {
+      border-color: #f00;
+    }
+    .article-id {
+      font-size: 1.2em;
+      margin-bottom: 5px;
+    }
+    .abstract {
+      font-style: italic;
+    }
+    .error-message {
+      color: #f00;
+    }
+    """
+
+    with gr.Blocks(css=css) as iface:
+        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.Markdown()
-
-        submit_button.click(medai_agent, inputs=query_input, outputs=output_results)
+        output_results = gr.HTML()  # Use HTML for formatted output
 
-        # Initialization setup
-        status.value = setup()
+        # Get data
+        submit_button.click(pubmed_search.medai_agent, inputs=query_input, outputs=output_results)
 
     iface.launch()
 

requirements.txt

@@ -1,4 +1,12 @@
+<<<<<<< HEAD
 gradio 
 transformers 
 biopython 
-spacy
+spacy
+=======
+gradio
+transformers
+biopython
+spacy
+torch
+>>>>>>> 3c8dbea734b3938b3c2fd1f974ec877199a17aea