Update app.py

app.py

@@ -14,7 +14,7 @@ import os
 import plotly.graph_objects as go
 import networkx as nx
 
-# --- IMPORTANT: set_page_config MUST be the very first Streamlit command ---
+# --- IMPORTANT: st.set_page_config MUST be the very first Streamlit command ---
 st.set_page_config(page_title="Pharma Research Expert Platform", layout="wide")
 
 # Setup logging
@@ -30,7 +30,9 @@ API_ENDPOINTS = {
     "who_drugs": "https://health-products.canada.ca/api/drug/product",
     "fda_drug_approval": "https://api.fda.gov/drug/label.json",
     "faers_adverse_events": "https://api.fda.gov/drug/event.json",
+    # PharmGKB endpoints expect a PharmGKB accession (e.g., PA1234)
     "pharmgkb_variant_clinical_annotations": "https://api.pharmgkb.org/v1/data/variant/{}/clinicalAnnotations",
+    "pharmgkb_gene": "https://api.pharmgkb.org/v1/data/gene/{}",  # expects PharmGKB accession
     "pharmgkb_gene_variants": "https://api.pharmgkb.org/v1/data/gene/{}/variants",
     "bioportal_search": "https://data.bioontology.org/search",
     "dailymed": "https://dailymed.nlm.nih.gov/dailymed/services/v2/spls.json",
@@ -60,10 +62,7 @@ from openai import OpenAI
 client = OpenAI(api_key=OPENAI_API_KEY)
 
 def generate_content(prompt: str) -> str:
-    """
-    Generates content using GPT‑4 via the new OpenAI SDK.
-    Uses the chat completions endpoint.
-    """
+    """Generate content using GPT-4 via the new OpenAI SDK."""
     try:
         completion = client.chat.completions.create(
             model="gpt-4",
@@ -169,18 +168,34 @@ def _get_pharmgkb_clinical_annotations(variant_id: str) -> Optional[Dict]:
     st.write(f"No clinical annotations found for variant {variant_id}.")
     return None
 
-def _get_pharmgkb_variants_for_gene(gene_symbol: str) -> Optional[List[str]]:
-    """Retrieves variant IDs for a gene from PharmGKB."""
-    gene_search_endpoint = "https://api.pharmgkb.org/v1/data/gene"
-    params = {"name": gene_symbol}
-    gene_data = _query_api(gene_search_endpoint, params)
-    if gene_data and gene_data.get("data") and len(gene_data["data"]) > 0:
-        gene_id = gene_data["data"][0]["id"]
-        variants_endpoint = API_ENDPOINTS["pharmgkb_gene_variants"].format(gene_id)
-        variants_data = _query_api(variants_endpoint)
-        if variants_data and variants_data.get("data"):
-            return [variant["id"] for variant in variants_data["data"]]
-    st.warning(f"No variants found for gene {gene_symbol}.")
+def _get_pharmgkb_variants_for_gene(pharmgkb_gene_id: str) -> Optional[List[str]]:
+    """
+    Retrieves variant IDs for a gene using the PharmGKB accession.
+    The input must start with "PA". If not, a warning is issued.
+    """
+    if not pharmgkb_gene_id.startswith("PA"):
+        st.warning("Please provide a valid PharmGKB accession ID for the gene (e.g., PA1234).")
+        return None
+    endpoint = API_ENDPOINTS["pharmgkb_gene_variants"].format(pharmgkb_gene_id)
+    data = _query_api(endpoint)
+    if data and data.get("data"):
+        return [variant["id"] for variant in data["data"]]
+    st.warning(f"No variants found for PharmGKB gene {pharmgkb_gene_id}.")
+    return None
+
+def get_pharmgkb_gene_data(pharmgkb_gene_id: str) -> Optional[Dict]:
+    """
+    Retrieves PharmGKB gene data using a PharmGKB accession.
+    If the gene identifier does not start with "PA", a warning is issued.
+    """
+    if not pharmgkb_gene_id.startswith("PA"):
+        st.warning("Please enter a valid PharmGKB gene accession ID (e.g., PA1234).")
+        return None
+    endpoint = API_ENDPOINTS["pharmgkb_gene"].format(pharmgkb_gene_id)
+    data = _query_api(endpoint)
+    if data and data.get("data"):
+        return data["data"][0]
+    st.write(f"No data found for PharmGKB gene {pharmgkb_gene_id}.")
     return None
 
 def scrape_ema_drug_info(drug_name: str) -> Optional[Dict]:
@@ -188,7 +203,9 @@ def scrape_ema_drug_info(drug_name: str) -> Optional[Dict]:
     try:
         search_url = f"https://www.ema.europa.eu/en/search?text={drug_name.replace(' ', '+')}&type=Product"
         headers = {
-            "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/90.0.4430.93 Safari/537.36"
+            "User-Agent": ("Mozilla/5.0 (Windows NT 10.0; Win64; x64) "
+                           "AppleWebKit/537.36 (KHTML, like Gecko) "
+                           "Chrome/90.0.4430.93 Safari/537.36")
         }
         response = requests.get(search_url, headers=headers, timeout=10)
         response.raise_for_status()
@@ -291,10 +308,13 @@ def _create_variant_network(gene: str, variants: List[str], annotations: Dict) -
         x1, y1 = pos[edge[1]]
         edge_x.extend([x0, x1, None])
         edge_y.extend([y0, y1, None])
-    edge_trace = go.Scatter(x=edge_x, y=edge_y,
-                            line=dict(width=0.5, color="#888"),
-                            hoverinfo="none",
-                            mode="lines")
+    edge_trace = go.Scatter(
+        x=edge_x,
+        y=edge_y,
+        line=dict(width=0.5, color="#888"),
+        hoverinfo="none",
+        mode="lines"
+    )
     node_x, node_y, node_text, node_color = [], [], [], []
     for node in G.nodes():
         x, y = pos[node]
@@ -351,7 +371,7 @@ tabs = st.tabs([
 with tabs[0]:
     st.header("AI-Driven Drug Development Strategy")
     target = st.text_input("Target Disease/Pathway:", placeholder="Enter disease mechanism or target")
-    target_gene = st.text_input("Target Gene (for Pharmacogenomics):", placeholder="Enter the gene symbol")
+    target_gene = st.text_input("Target Gene (PharmGKB Accession):", placeholder="Enter PharmGKB accession (e.g., PA1234)")
     strategy = st.selectbox("Development Strategy:", ["First-in-class", "Me-too", "Repurposing", "Biologic"])
     
     if st.button("Generate Development Plan"):
@@ -378,25 +398,27 @@ with tabs[0]:
         # Pharmacogenomic Considerations via PharmGKB
         st.subheader("Pharmacogenomic Considerations")
         if target_gene:
-            variant_ids = _get_pharmgkb_variants_for_gene(target_gene)
-            if variant_ids:
-                annotations = {}
-                for variant_id in variant_ids[:5]:
-                    pgx_data = _get_pharmgkb_clinical_annotations(variant_id)
-                    if pgx_data and pgx_data.get("data"):
-                        # Collect a list of drugs (or object names) from the annotations
-                        annotations[variant_id] = [anno.get("obj2Name", "N/A") for anno in pgx_data["data"]]
-                    else:
-                        annotations[variant_id] = []
-                    st.write(f"### Clinical Annotations for Variant: {variant_id}")
-                    if pgx_data:
-                        st.json(pgx_data)
-                    else:
-                        st.write(f"No annotations for variant {variant_id}.")
+            if not target_gene.startswith("PA"):
+                st.warning("Please provide a valid PharmGKB accession (e.g., PA1234) for the gene.")
             else:
-                st.write("No variants found for the specified gene.")
+                variant_ids = _get_pharmgkb_variants_for_gene(target_gene)
+                if variant_ids:
+                    annotations = {}
+                    for variant_id in variant_ids[:5]:
+                        pgx_data = _get_pharmgkb_clinical_annotations(variant_id)
+                        if pgx_data and pgx_data.get("data"):
+                            annotations[variant_id] = [anno.get("obj2Name", "N/A") for anno in pgx_data["data"]]
+                        else:
+                            annotations[variant_id] = []
+                        st.write(f"### Clinical Annotations for Variant: {variant_id}")
+                        if pgx_data:
+                            st.json(pgx_data)
+                        else:
+                            st.write(f"No annotations for variant {variant_id}.")
+                else:
+                    st.write("No variants found for the specified PharmGKB gene accession.")
         else:
-            st.write("Please enter a target gene for pharmacogenomic data.")
+            st.write("Please enter a PharmGKB accession for the target gene to retrieve pharmacogenomic data.")
 
 # -----------------------------
 # Tab 2: Clinical Trial Analytics
@@ -412,10 +434,10 @@ with tabs[1]:
                 trial_data = []
                 for study in trials["studies"][:5]:
                     trial_data.append({
-                        "Title": study.get("briefTitle", "N/A"),
-                        "Status": study.get("overallStatus", "N/A"),
-                        "Phase": study.get("phase", "Not Available"),
-                        "Enrollment": study.get("enrollmentCount", "Not Available")
+                        "Title": study.get("protocolSection", {}).get("identificationModule", {}).get("briefTitle", "N/A"),
+                        "Status": study.get("protocolSection", {}).get("statusModule", {}).get("overallStatus", "N/A"),
+                        "Phase": study.get("protocolSection", {}).get("designModule", {}).get("phases", ["Not Available"])[0],
+                        "Enrollment": study.get("protocolSection", {}).get("designModule", {}).get("enrollmentInfo", {}).get("count", "Not Available")
                     })
                 _display_dataframe(trial_data, list(trial_data[0].keys()))
             else:
@@ -452,7 +474,7 @@ with tabs[2]:
     if st.button("Analyze Compound"):
         with st.spinner("Querying PubChem..."):
             smiles = None
-            # Check if the input is a valid SMILES string
+            # If the input is already a valid SMILES, use it; otherwise query PubChem
             if Chem.MolFromSmiles(compound_input):
                 smiles = compound_input
             else:
@@ -493,7 +515,7 @@ with tabs[3]:
             ema_info = scrape_ema_drug_info(drug_name)
             ema_status = ema_info.get("EMA Approval Status") if ema_info else "Not Available"
             
-            # WHO Data from Canada Health Products API (may return 404)
+            # WHO Data from Canada Health Products API (this endpoint may return 404)
             who = _query_api(API_ENDPOINTS["who_drugs"], params={"name": drug_name})
             who_status = "Yes" if who else "No"
             
@@ -543,7 +565,7 @@ with tabs[3]:
                     os.remove(report_file)
 
 # -----------------------------
-# Tab 5: Literature Search (PubMed and BioPortal)
+# Tab 5: Literature Search
 # -----------------------------
 with tabs[4]:
     st.header("Literature Search")
@@ -580,7 +602,7 @@ with tabs[4]:
 with tabs[5]:
     st.header("Comprehensive Dashboard")
     
-    # Placeholder KPI counts (replace with actual aggregated data if available)
+    # Placeholder KPI counts (replace with real aggregated data if available)
     fda_count = 5000       # Example value
     ema_count = 3000       # Example value
     who_count = 1500       # Example value
@@ -619,17 +641,4 @@ with tabs[5]:
         network_fig = _create_variant_network(sample_gene, sample_variants, sample_annotations)
         st.plotly_chart(network_fig, use_container_width=True)
     except Exception as e:
-        st.error(f"Error generating network graph: {e}")
-
-# -----------------------------
-# Sidebar Information
-# -----------------------------
-st.sidebar.header("About")
-st.sidebar.info("""
-**Pharma Research Expert Platform**
-
-An integrated tool for drug discovery, clinical research, and regulatory affairs.
-
-**Developed by:** Your Name  
-**Contact:** [[email protected]](mailto:[email protected])
-""")
+        st.error(f"Error generating network graph: {e}")