Fix import statement in pipelines.data_integration.py

pipelines/data_integration.py

@@ -25,7 +25,7 @@ from itertools import chain
 try:
     from dima.src import hdf5_writer as hdf5_lib
     from dima.utils import g5505_utils as utils
-    from dima.instruments.readers import filereader_registry
+    from dima.instruments import filereader_registry
 except ModuleNotFoundError:
     print(':)')
     import src.hdf5_writer as hdf5_lib
@@ -181,6 +181,7 @@ def copy_subtree_and_create_hdf5(src, dst, select_dir_keywords, select_file_keyw
 
     
     logging.info("Creating HDF5 file at: %s", dst)
+    #hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path_new(dst, path_to_files_dict, select_dir_keywords, root_metadata_dict)
     hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path(dst, path_to_files_dict, select_dir_keywords, root_metadata_dict)
     logging.info("Completed creation of HDF5 file %s at: %s", hdf5_path, dst)
 
@@ -238,6 +239,7 @@ def run_pipeline(path_to_config_yamlFile, log_dir='logs/'):
         # Collection mode processing if specified
         if 'collection' in config_dict.get('integration_mode', 'single_experiment'):
             path_to_filenames_dict = {path_to_rawdata_folder: [os.path.basename(path) for path in output_filename_path]} if output_filename_path else {}
+            #hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path_new(path_to_rawdata_folder, path_to_filenames_dict, [], root_metadata_dict)
             hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path(path_to_rawdata_folder, path_to_filenames_dict, [], root_metadata_dict)
             output_filename_path.append(hdf5_path)
     else: