Update app.py

app.py

@@ -217,28 +217,19 @@ def cleanup_file(file_path: str) -> None:
             logger.warning(f"Failed to clean up {file_path}: {cleanup_error}")
 
 def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
-    query_fasta = None  # Predefine to avoid scoping issues
+    query_fasta = None
     try:
-        # Input validation
         if len(sequence.strip()) < 100:
             return False, "Sequence too short (<100 bp).", None, None
-
-        # Setup file paths
         query_id = f"QUERY_{uuid.uuid4().hex[:8]}"
         query_fasta = os.path.join(QUERY_OUTPUT_DIR, f"{query_id}.fa")
         aligned_with_query = os.path.join(QUERY_OUTPUT_DIR, f"{query_id}_aligned.fa")
         output_prefix = os.path.join(QUERY_OUTPUT_DIR, f"{query_id}_placed_tree")
-
-        # Check reference files
         if not os.path.exists(ALIGNMENT_PATH) or not os.path.exists(TREE_PATH):
             cleanup_file(query_fasta)
             return False, "Reference alignment or tree not found.", None, None
-
-        # Write query FASTA
         query_record = SeqRecord(Seq(sequence.upper()), id=query_id, description="")
         SeqIO.write([query_record], query_fasta, "fasta")
-
-        # Run MAFFT
         with open(aligned_with_query, "w") as output_file:
             result = subprocess.run(
                 [mafft_cmd, "--add", query_fasta, "--reorder", ALIGNMENT_PATH],
@@ -251,8 +242,6 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
         if not os.path.exists(aligned_with_query) or os.path.getsize(aligned_with_query) == 0:
             cleanup_file(query_fasta)
             return False, "MAFFT alignment failed.", None, None
-
-        # Run IQ-TREE
         result = subprocess.run(
             [iqtree_cmd, "-s", aligned_with_query, "-g", TREE_PATH, "-m", "GTR+G", "-pre", output_prefix, "-redo"],
             capture_output=True,
@@ -264,16 +253,14 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
         if not os.path.exists(treefile):
             cleanup_file(query_fasta)
             return False, "IQ-TREE placement failed.", aligned_with_query, None
-
-        # Success
         success_msg = f"Placement completed!\nQuery ID: {query_id}\nAlignment: {os.path.basename(aligned_with_query)}\nTree: {os.path.basename(treefile)}"
         cleanup_file(query_fasta)
         return True, success_msg, aligned_with_query, treefile
-
     except Exception as main_error:
         logger.error(f"Phylogenetic placement failed: {main_error}", exc_info=True)
         cleanup_file(query_fasta)
         return False, f"Error: {str(main_error)}", None, None
+
 def analyze_sequence_for_tree(sequence: str, matching_percentage: float):
     try:
         logger.debug("Starting tree analysis...")
@@ -453,11 +440,12 @@ async def run_pipeline_from_file(fasta_file_obj, similarity_score, build_ml_tree
         result = run_pipeline(dna_input, similarity_score, build_ml_tree)
         cleanup_file(temp_file_path)
         return result
-    except Exception as main_error:  # Renamed from 'e'
+    except Exception as main_error:
         logger.error(f"Pipeline from file error: {main_error}", exc_info=True)
         cleanup_file(temp_file_path)
         error_msg = f"❌ Error: {str(main_error)}"
         return error_msg, "", "", "", "", None, None, None, None, error_msg, error_msg, None, None
+
 class AnalysisRequest(BaseModel):
     sequence: str
     similarity_score: float = 95.0
@@ -537,7 +525,7 @@ async def analyze_sequence(request: AnalysisRequest):
             success=False, error_message=str(e)
         )
 
-@app.post("/analyze-file")
+@app.post("/analyze-file", response_model=AnalysisResponse)
 async def analyze_file(
     file: UploadFile = File(...),
     similarity_score: float = Form(95.0),
@@ -550,11 +538,7 @@ async def analyze_file(
             temp_file.write(content)
             temp_file_path = temp_file.name
         result = await run_pipeline_from_file(temp_file_path, similarity_score, build_ml_tree)
-        if temp_file_path and os.path.exists(temp_file_path):
-            try:
-                os.unlink(temp_file_path)
-            except Exception as cleanup_error:
-                logger.warning(f"Failed to clean up {temp_file_path}: {cleanup_error}")
+        cleanup_file(temp_file_path)
         return AnalysisResponse(
             boundary_output=result[0] or "",
             keras_output=result[1] or "",
@@ -565,20 +549,16 @@ async def analyze_file(
             report_html_path=result[12],
             success=True
         )
-    except Exception as main_error:  # Renamed from 'e'
+    except Exception as main_error:
         logger.error(f"Analyze-file error: {main_error}", exc_info=True)
-        if temp_file_path and os.path.exists(temp_file_path):
-            try:
-                os.unlink(temp_file_path)
-            except Exception as cleanup_error:
-                logger.warning(f"Failed to clean up {temp_file_path}: {cleanup_error}")
+        cleanup_file(temp_file_path)
         return AnalysisResponse(
             boundary_output="", keras_output="", ml_tree_output="",
             tree_analysis_output="", summary_output="",
             tree_html_path=None, report_html_path=None,
             success=False, error_message=str(main_error)
         )
-                
+
 @app.get("/download/{file_type}/{query_id}")
 async def download_file(file_type: str, query_id: str):
     try:
@@ -779,21 +759,48 @@ def create_gradio_interface():
             outputs=gr.Textbox(label="Error"),
             title="🧬 Gene Analysis Pipeline (Error Mode)"
         )
+
 # --- Application Startup ---
 def run_application():
     try:
         main_gradio_app = create_gradio_interface()
         main_gradio_app = gr.mount_gradio_app(app, main_gradio_app, path="/gradio")
-        # ... (logging and uvicorn.run)
+        logger.info("🧬 Gene Analysis Pipeline Starting...")
+        logger.info("=" * 50)
+        logger.info("🔍 Checking system components...")
+        logger.info(f"🤖 Boundary Model: {'✅ Loaded' if boundary_model else '❌ Missing'}")
+        logger.info(f"🧠 Keras Model: {'✅ Loaded' if keras_model else '❌ Missing'}")
+        logger.info(f"🌳 Tree Analyzer: {'✅ Loaded' if analyzer else '❌ Missing'}")
+        mafft_available, iqtree_available, _, _ = check_tool_availability()
+        logger.info(f"🧬 MAFFT: {'✅ Available' if mafft_available else '❌ Missing'}")
+        logger.info(f"🌲 IQ-TREE: {'✅ Available' if iqtree_available else '❌ Missing'}")
+        logger.info("=" * 50)
+        logger.info("🚀 Starting Gene Analysis Pipeline...")
+        logger.warning("⚠️ Running without request queuing. Concurrent requests may block.")
+        logger.info("📊 FastAPI docs available at: http://localhost:7860/docs")
+        logger.info("🧬 Gradio interface available at: http://localhost:7860/gradio")
+        uvicorn.run(
+            app,
+            host="0.0.0.0",
+            port=7860,
+            log_level="info",
+            access_log=True
+        )
     except Exception as main_error:
         logger.error(f"Application startup failed: {main_error}", exc_info=True)
         try:
             logger.info("🔄 Falling back to Gradio-only mode...")
             fallback_gradio_app = create_gradio_interface()
-            # ... (launch fallback)
+            logger.info("🧬 Gradio interface available at: http://localhost:7860")
+            fallback_gradio_app.launch(
+                server_name="0.0.0.0",
+                server_port=7860,
+                prevent_thread_lock=True
+            )
         except Exception as fallback_error:
             logger.error(f"Fallback failed: {fallback_error}", exc_info=True)
             print("❌ Application failed to start. Check logs for details.")
+
 if __name__ == "__main__":
     print("🧬 Gene Analysis Pipeline Starting...")
     print("=" * 50)