Update handler.py

handler.py

@@ -241,42 +241,48 @@ def download_file(s3_public_url: str, output_fn) -> Path:
 
 def _run_align_script(bo_fn, en_fn, output_dir):
     start = time.time()
+
+    # Execute the alignment script
     cmd = [str(ALIGNER_SCRIPT_PATH), str(bo_fn), str(en_fn), str(output_dir)]
-    output = subprocess.run(
-        cmd,
-        check=True,
-        capture_output=True,
-        text=True,
-        cwd=str(ALIGNER_SCRIPT_DIR),
-    )
-    logging.info(f"Content length of output: {output.stdout} characters")
+    try:
+        output = subprocess.run(
+            cmd,
+            check=True,
+            capture_output=True,
+            text=True,
+            cwd=str(ALIGNER_SCRIPT_DIR),
+        )
+    except subprocess.CalledProcessError as e:
+        logging.error(f"Alignment script failed with error: {e}")
+        return None
 
-    match = re.search(r"\[OUTPUT\] (.*)", output.stdout)
-    if not match:
+    # Extract the output file path
+    try:
+        output_fn = re.search(r"\[OUTPUT\] (.*)", output.stdout).group(1)
+        output_fn = "/" + output_fn.split("//")[-1]  # Correcting the duplicated path
+    except IndexError as e:
+        logging.error(f"Error processing file path: {e}")
+        return None
+    except AttributeError as e:
         logging.error("Failed to find output file path in script output.")
         return None
 
-    output_fn = match.group(1).strip()
-    # Normalize the file path
     output_fn = Path(output_fn)
 
+    # Check if the file exists and read its content
+    if output_fn.exists() and output_fn.is_file():
+        content = output_fn.read_text()
+        if content:
+            logging.info(f"Contents of {output_fn}: {content[:100]}...")  # Log first 100 characters
+        else:
+            logging.warning(f"The file {output_fn} is empty.")
+    else:
+        logging.error(f"The file {output_fn} does not exist.")
+
     end = time.time()
     total_time = round((end - start) / 60, 2)
     logging.info(f"Total time taken for Aligning: {total_time} mins")
 
-    # Read and log the contents of the output file
-    try:
-        if output_fn.exists():
-            content = output_fn.read_text()
-            if content:
-                logging.info(f"First 100 characters of {output_fn}: {content[:100]}...")
-            else:
-                logging.error(f"The file {output_fn} is empty.")
-        else:
-            logging.error(f"The file {output_fn} does not exist.")
-    except Exception as e:
-        logging.error(f"Error reading file {output_fn}: {e}")
-
     return output_fn
 def align(text_pair):