Update app.py

app.py

@@ -30,7 +30,7 @@ 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 endpoints require 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",
@@ -43,7 +43,7 @@ API_ENDPOINTS = {
 # -----------------------------------
 OPENAI_API_KEY = st.secrets.get("OPENAI_API_KEY")
 BIOPORTAL_API_KEY = st.secrets.get("BIOPORTAL_API_KEY")
-PUB_EMAIL = st.secrets.get("PUB_EMAIL")
+PUB_EMAIL = st.secrets.get("PUB_EMAIL")  # Not used in clinical trials anymore.
 OPENFDA_KEY = st.secrets.get("OPENFDA_KEY")
 
 if not PUB_EMAIL:
@@ -62,7 +62,7 @@ from openai import OpenAI
 client = OpenAI(api_key=OPENAI_API_KEY)
 
 def generate_content(prompt: str) -> str:
-    """Generate content using GPT-4 via the new OpenAI SDK."""
+    """Generate content using GPT-4 via the latest OpenAI SDK."""
     try:
         completion = client.chat.completions.create(
             model="gpt-4",
@@ -99,7 +99,7 @@ def _get_pubchem_smiles(drug_name: str) -> Optional[str]:
     """Retrieves a drug's SMILES string from PubChem."""
     url = API_ENDPOINTS["pubchem"].format(drug_name)
     data = _query_api(url)
-    if data and "PC_Compounds" in data and len(data["PC_Compounds"]) > 0:
+    if data and "PC_Compounds" in data and data["PC_Compounds"]:
         for prop in data["PC_Compounds"][0].get("props", []):
             if prop.get("name") == "Canonical SMILES":
                 return prop["value"]["sval"]
@@ -119,23 +119,21 @@ def _draw_molecule(smiles: str) -> Optional[Any]:
         logging.error(f"Molecule drawing error: {e}")
         return None
 
-def _get_clinical_trials(query: str, email: Optional[str] = PUB_EMAIL) -> Optional[Dict]:
-    """Queries clinicaltrials.gov with a search term."""
-    if not email:
-        st.error("PubMed email not configured.")
-        return None
-    if query.upper().startswith("NCT") and query[3:].isdigit():
-        params = {"id": query, "fmt": "json"}
-    else:
-        params = {"term": query, "retmax": 10, "retmode": "json", "email": email}
-    return _query_api(API_ENDPOINTS["clinical_trials"], params)
+def _get_clinical_trials(query: str) -> Optional[Dict]:
+    """Queries clinicaltrials.gov with a search term.
+       Note: the email parameter has been removed as it is not required."""
+    # Try using 'term' and if that fails, try 'query.term'
+    params = {"term": query, "retmax": 10, "retmode": "json"}
+    data = _query_api(API_ENDPOINTS["clinical_trials"], params)
+    if not data:
+        # Fallback to alternative parameter name:
+        params = {"query.term": query, "retmax": 10, "retmode": "json"}
+        data = _query_api(API_ENDPOINTS["clinical_trials"], params)
+    return data
 
-def _get_pubmed(query: str, email: Optional[str] = PUB_EMAIL) -> Optional[Dict]:
+def _get_pubmed(query: str) -> Optional[Dict]:
     """Queries PubMed using E-utilities."""
-    if not email:
-        st.error("PubMed email not configured.")
-        return None
-    params = {"db": "pubmed", "term": query, "retmax": 10, "retmode": "json", "email": email}
+    params = {"db": "pubmed", "term": query, "retmax": 10, "retmode": "json", "email": PUB_EMAIL}
     return _query_api(API_ENDPOINTS["pubmed"], params)
 
 def _get_fda_approval(drug_name: str, api_key: Optional[str] = OPENFDA_KEY) -> Optional[Dict]:
@@ -170,8 +168,8 @@ def _get_pharmgkb_clinical_annotations(variant_id: str) -> Optional[Dict]:
 
 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.
+    Retrieves variant IDs for a gene using its PharmGKB accession.
+    If an invalid accession is provided (not starting with "PA"), 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).")
@@ -184,10 +182,7 @@ def _get_pharmgkb_variants_for_gene(pharmgkb_gene_id: str) -> Optional[List[str]
     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.
-    """
+    """Retrieves PharmGKB gene data using a PharmGKB accession."""
     if not pharmgkb_gene_id.startswith("PA"):
         st.warning("Please enter a valid PharmGKB gene accession ID (e.g., PA1234).")
         return None
@@ -199,7 +194,7 @@ def get_pharmgkb_gene_data(pharmgkb_gene_id: str) -> Optional[Dict]:
     return None
 
 def scrape_ema_drug_info(drug_name: str) -> Optional[Dict]:
-    """Scrapes EMA website for drug information using a browser-like header."""
+    """Scrapes the EMA website for drug information using a browser-like header."""
     try:
         search_url = f"https://www.ema.europa.eu/en/search?text={drug_name.replace(' ', '+')}&type=Product"
         headers = {
@@ -234,7 +229,7 @@ def scrape_ema_drug_info(drug_name: str) -> Optional[Dict]:
         return None
 
 def _get_dailymed_label(drug_name: str) -> Optional[Dict]:
-    """Retrieves DailyMed label info; handles missing 'url' key gracefully."""
+    """Retrieves DailyMed label info; if URL is missing, returns None."""
     try:
         params = {"drug_name": drug_name, "page": 1, "pagesize": 1}
         data = _query_api(API_ENDPOINTS["dailymed"], params)
@@ -474,7 +469,7 @@ with tabs[2]:
     if st.button("Analyze Compound"):
         with st.spinner("Querying PubChem..."):
             smiles = None
-            # If the input is already a valid SMILES, use it; otherwise query PubChem
+            # If the input is already a valid SMILES string, use it; otherwise, query PubChem.
             if Chem.MolFromSmiles(compound_input):
                 smiles = compound_input
             else:
@@ -484,7 +479,7 @@ with tabs[2]:
                 if img:
                     st.image(img, caption="2D Structure")
             else:
-                st.error("Compound structure not found in databases.")
+                st.error("Compound structure not found in databases. Please provide a more specific compound name.")
         
         pubchem_data = _query_api(API_ENDPOINTS["pubchem"].format(compound_input))
         if pubchem_data and pubchem_data.get("PC_Compounds"):
@@ -515,7 +510,7 @@ 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 (this endpoint may return 404)
+            # WHO Data from Health Canada API – fallback if not found
             who = _query_api(API_ENDPOINTS["who_drugs"], params={"name": drug_name})
             who_status = "Yes" if who else "No"
             
@@ -630,7 +625,6 @@ with tabs[5]:
     st.pyplot(fig)
     
     st.subheader("Gene-Variant-Drug Network (Sample)")
-    # Sample network demonstration
     sample_gene = "CYP2C19"
     sample_variants = ["rs4244285", "rs12248560"]
     sample_annotations = {
@@ -641,4 +635,17 @@ 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}")
+        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])
+""")