Merge branch 'main' of https://gitlab.psi.ch/5505/dima

src/hdf5_ops.py

 import sys
 import os
-root_dir = os.path.abspath(os.curdir)
-sys.path.append(root_dir)
+
+try:
+    thisFilePath = os.path.abspath(__file__)
+except NameError:
+    print("Error: __file__ is not available. Ensure the script is being run from a file.")
+    print("[Notice] Path to DIMA package may not be resolved properly.")
+    thisFilePath = os.getcwd()  # Use current directory or specify a default
+
+dimaPath = os.path.normpath(os.path.join(thisFilePath, "..",'..'))  # Move up to project root
+
+if dimaPath not in sys.path:  # Avoid duplicate entries
+    sys.path.append(dimaPath)
+
 
 import h5py
 import pandas as pd
@@ -12,7 +23,6 @@ import src.hdf5_writer as hdf5_lib
 import logging
 import datetime
 
-import os
 import h5py
 
 import yaml
@@ -640,17 +650,20 @@ def read_mtable_as_dataframe(filename):
     return output_dataframe
 
 if __name__ == "__main__":
-    if len(sys.argv) < 4:
-        print("Usage: python hdf5_ops.py serialize <path/to/target_file.hdf5> <format=json|yaml>")
+    if len(sys.argv) < 5:
+        print("Usage: python hdf5_ops.py serialize <path/to/target_file.hdf5> <folder_depth : int = 2> <format=json|yaml>")
         sys.exit(1)
 
     if sys.argv[1] == 'serialize':
         input_hdf5_file = sys.argv[2]
-        file_format = sys.argv[3]
+        folder_depth = int(sys.argv[3])
+        file_format = sys.argv[4]
 
         try:
             # Call the serialize_metadata function and capture the output path
-            path_to_file = serialize_metadata(input_hdf5_file, output_format=file_format)
+            path_to_file = serialize_metadata(input_hdf5_file,
+                                              folder_depth = folder_depth,
+                                               output_format=file_format)
             print(f"Metadata serialized to {path_to_file}")
         except Exception as e:
             print(f"An error occurred during serialization: {e}")