--- a/COBRAxy/src/exportMetabolicModel.py	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/src/exportMetabolicModel.py	Sun Oct 26 19:27:41 2025 +0000
@@ -1,117 +1,123 @@
-"""
-Convert a tabular (CSV/TSV/Tabular) description of a COBRA model into a COBRA file.
-
-Supported output formats: SBML, JSON, MATLAB (.mat), YAML.
-The script logs to a user-provided file for easier debugging in Galaxy.
-"""
-
-import os
-import cobra
-import argparse
-from typing import List
-import logging
-import utils.model_utils as modelUtils
-
-ARGS : argparse.Namespace
-def process_args(args: List[str] = None) -> argparse.Namespace:
-    """
-    Parse command-line arguments for the CSV-to-COBRA conversion tool.
-
-    Returns:
-        argparse.Namespace: Parsed arguments.
-    """
-    parser = argparse.ArgumentParser(
-    usage="%(prog)s [options]",
-    description="Convert a tabular/CSV file to a COBRA model"
-    )
-
-
-    parser.add_argument("--out_log", type=str, required=True,
-    help="Output log file")
-
-
-    parser.add_argument("--input", type=str, required=True,
-    help="Input tabular file (CSV/TSV)")
-
-
-    parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
-    help="Model format (SBML, JSON, MATLAB, YAML)")
-
-
-    parser.add_argument("--output", type=str, required=True,
-    help="Output model file path")
-
-    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
-    help="Tool directory (passed from Galaxy as $__tool_directory__)")
-
-
-    return parser.parse_args(args)
-
-
-###############################- ENTRY POINT -################################
-
-def main(args: List[str] = None) -> None:
-    """
-    Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
-    and save it in the requested format.
-
-    Returns:
-        None
-    """
-    global ARGS
-    ARGS = process_args(args)
-
-    # configure logging to the requested log file (overwrite each run)
-    logging.basicConfig(filename=ARGS.out_log,
-                        level=logging.DEBUG,
-                        format='%(asctime)s %(levelname)s: %(message)s',
-                        filemode='w')
-
-    logging.info('Starting fromCSVtoCOBRA tool')
-    logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)
-
-    try:
-        # Basic sanity checks
-        if not os.path.exists(ARGS.input):
-            logging.error('Input file not found: %s', ARGS.input)
-
-        out_dir = os.path.dirname(os.path.abspath(ARGS.output))
-        
-        if out_dir and not os.path.isdir(out_dir):
-            try:
-                os.makedirs(out_dir, exist_ok=True)
-                logging.info('Created missing output directory: %s', out_dir)
-            except Exception as e:
-                logging.exception('Cannot create output directory: %s', out_dir)
-
-        model = modelUtils.build_cobra_model_from_csv(ARGS.input)
-        
-        
-        logging.info('Created model with name: %s (ID: %s)', model.name, model.id)
-
-        # Save model in requested format - Galaxy handles the filename
-        if ARGS.format == "sbml":
-            cobra.io.write_sbml_model(model, ARGS.output)
-        elif ARGS.format == "json":
-            cobra.io.save_json_model(model, ARGS.output)
-        elif ARGS.format == "mat":
-            cobra.io.save_matlab_model(model, ARGS.output)
-        elif ARGS.format == "yaml":
-            cobra.io.save_yaml_model(model, ARGS.output)
-        else:
-            logging.error('Unknown format requested: %s', ARGS.format)
-            raise ValueError(f"Unknown format: {ARGS.format}")
-
-
-        logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
-        print(f"Model created successfully in {ARGS.format.upper()} format")
-
-    except Exception as e:
-        # Log full traceback to the out_log so Galaxy users/admins can see what happened
-        logging.exception('Unhandled exception in fromCSVtoCOBRA')
-        print(f"ERROR: {str(e)}")
-        raise
-
-
-if __name__ == '__main__':
-    main()
+"""
+Convert a tabular (CSV/TSV/Tabular) description of a COBRA model into a COBRA file.
+
+Supported output formats: SBML, JSON, MATLAB (.mat), YAML.
+The script logs to a user-provided file for easier debugging in Galaxy.
+"""
+
+import os
+import cobra
+import argparse
+from typing import List
+import logging
+
+try:
+    from .utils import model_utils as modelUtils
+    from .utils import general_utils as utils
+except:
+    import utils.model_utils as modelUtils
+    import utils.general_utils as utils
+
+ARGS : argparse.Namespace
+def process_args(args: List[str] = None) -> argparse.Namespace:
+    """
+    Parse command-line arguments for the CSV-to-COBRA conversion tool.
+
+    Returns:
+        argparse.Namespace: Parsed arguments.
+    """
+    parser = argparse.ArgumentParser(
+    usage="%(prog)s [options]",
+    description="Convert a tabular/CSV file to a COBRA model"
+    )
+
+
+    parser.add_argument("--out_log", type=str, required=True,
+    help="Output log file")
+
+
+    parser.add_argument("--input", type=str, required=True,
+    help="Input tabular file (CSV/TSV)")
+
+
+    parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
+    help="Model format (SBML, JSON, MATLAB, YAML)")
+
+
+    parser.add_argument("--output", type=str, required=True,
+    help="Output model file path")
+
+    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(os.path.abspath(__file__)),
+    help="Tool directory (default: auto-detected package location)")
+
+
+    return parser.parse_args(args)
+
+
+###############################- ENTRY POINT -################################
+
+def main(args: List[str] = None) -> None:
+    """
+    Entry point: parse arguments, build the COBRA model from a CSV/TSV file,
+    and save it in the requested format.
+
+    Returns:
+        None
+    """
+    global ARGS
+    ARGS = process_args(args)
+
+    # configure logging to the requested log file (overwrite each run)
+    logging.basicConfig(filename=ARGS.out_log,
+                        level=logging.DEBUG,
+                        format='%(asctime)s %(levelname)s: %(message)s',
+                        filemode='w')
+
+    logging.info('Starting fromCSVtoCOBRA tool')
+    logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)
+
+    try:
+        # Basic sanity checks
+        if not os.path.exists(ARGS.input):
+            logging.error('Input file not found: %s', ARGS.input)
+
+        out_dir = os.path.dirname(os.path.abspath(ARGS.output))
+        
+        if out_dir and not os.path.isdir(out_dir):
+            try:
+                os.makedirs(out_dir, exist_ok=True)
+                logging.info('Created missing output directory: %s', out_dir)
+            except Exception as e:
+                logging.exception('Cannot create output directory: %s', out_dir)
+
+        model = modelUtils.build_cobra_model_from_csv(ARGS.input)
+        
+        
+        logging.info('Created model with name: %s (ID: %s)', model.name, model.id)
+
+        # Save model in requested format - Galaxy handles the filename
+        if ARGS.format == "sbml":
+            cobra.io.write_sbml_model(model, ARGS.output)
+        elif ARGS.format == "json":
+            cobra.io.save_json_model(model, ARGS.output)
+        elif ARGS.format == "mat":
+            cobra.io.save_matlab_model(model, ARGS.output)
+        elif ARGS.format == "yaml":
+            cobra.io.save_yaml_model(model, ARGS.output)
+        else:
+            logging.error('Unknown format requested: %s', ARGS.format)
+            raise ValueError(f"Unknown format: {ARGS.format}")
+
+
+        logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
+        print(f"Model created successfully in {ARGS.format.upper()} format")
+
+    except Exception as e:
+        # Log full traceback to the out_log so Galaxy users/admins can see what happened
+        logging.exception('Unhandled exception in fromCSVtoCOBRA')
+        print(f"ERROR: {str(e)}")
+        raise
+
+
+if __name__ == '__main__':
+    main()