Abstracted a code snippet from def create_hdf5_file_from_filesystem_path(..) as transfer_file_dict_to_hdf5() so that it can be reusable.

src/hdf5_lib.py

@@ -308,7 +308,54 @@ def copy_directory_with_contraints(input_dir_path, output_dir_path, select_dir_k
 
     return path_to_files_dict 
 
+def transfer_file_dict_to_hdf5(h5file, group_name, file_dict):
+    """
+    Transfers data from a file_dict to an HDF5 file.
 
+    Parameters:
+        h5file (h5py.File): HDF5 file object where the data will be written.
+        group_name (str): Name of the HDF5 group where data will be stored.
+        file_dict (dict): Dictionary containing file data to be transferred.
+            Required structure:
+                {
+                    'name': str,
+                    'attributes_dict': dict,
+                    'datasets': [
+                        {
+                            'name': str,
+                            'data': array-like,
+                            'shape': tuple,
+                            'attributes': dict (optional)
+                        },
+                        ...
+                    ]
+                }
+        
+        
+    """
+    if not file_dict:
+        return
+
+    try:
+        # Create group and add their attributes
+        group = h5file[group_name].create_group(name=file_dict['name'])
+        # Add group attributes                                
+        group.attrs.update(file_dict['attributes_dict'])
+        
+        # Add datasets to the just created group
+        for dataset in file_dict['datasets']:
+            dataset_obj = group.create_dataset(
+                name=dataset['name'], 
+                data=dataset['data'],
+                shape=dataset['shape']
+            )
+            
+            # Add dataset's attributes                                
+            attributes = dataset.get('attributes', {})
+            dataset_obj.attrs.update(attributes)
+    except Exception as inst: 
+        print(inst) 
+        logging.error('Failed to transfer data into HDF5: %s', inst)
 
 def create_hdf5_file_from_filesystem_path(output_filename : str, 
                                           input_file_system_path : str, 
@@ -407,28 +454,7 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
                     #file_dict = config_file.select_file_readers(group_id)[file_ext](os.path.join(dirpath,filename))
                     file_dict = ext_to_reader_dict[file_ext](os.path.join(dirpath,filename))
 
-                    if not file_dict:
+                    transfer_file_dict_to_hdf5(h5file, group_name, file_dict)
-                        continue
-
-                    try:
-                        # Create group and add their attributes
-                        h5file[group_name].create_group(name=file_dict['name'])
-                        # Add group attributes                                
-                        h5file[group_name][file_dict['name']].attrs.update(file_dict['attributes_dict'])
-                            
-                        # Add datasets to just created group
-                        for dataset in file_dict['datasets']:
-                            h5file[group_name][file_dict['name']].create_dataset(name  = dataset['name'], 
-                                                data  = dataset['data'],
-                                                #dtype = file_dict['dtype'],
-                                                shape = dataset['shape'])
-                            
-                            # Add dataset's attributes                                
-                            attributes = dataset.get('attributes', {})
-                            h5file[group_name][file_dict['name']][dataset['name']].attrs.update(attributes)
-                    except Exception as inst: 
-                        print(inst) 
-                        logging.error('Fail to transfer %s into HDF5: %s',os.path.join(dirpath,filename),inst)
                     
                 else:
                     source_file_path = os.path.join(dirpath,filename)