Rerun jupyternotebooks to check their functionality after relocating them to notebooks. OpenBis related python scripts still need to be tested.

notebooks/demo_single_sample_update_to_openbis.py

@@ -1,12 +1,22 @@
-import os, sys
-sys.path.append(os.path.abspath('src'))
-
-import src.openbis_lib as openbis_lib
-import src.hdf5_lib as hdf5_lib
-import datetime
 import os
+from nbutils import add_project_path_to_sys_path
+
+
+# Add project root to sys.path
+add_project_path_to_sys_path()
+
+import datetime
 import logging
 
+try:
+    import src.openbis_lib as openbis_lib
+    import src.hdf5_ops as hdf5_ops
+    #import pipelines.metadata_revision as metadata_revision
+    print("Imports successful!")
+except ImportError as e:
+    print(f"Import error: {e}")
+
+
 def main():
 
     #df_h5 = hdf5_lib.read_hdf5_as_dataframe_v2('BeamTimeMetaData.h5')
@@ -23,7 +33,7 @@ def main():
         print(sample.identifier)
     df_openbis = samples.df.copy(deep=True)
     h5_file_path = os.path.join(os.path.curdir,'input_files\\BeamTimeMetaData.h5')
-    df_h5 = hdf5_lib.read_mtable_as_dataframe(h5_file_path)
+    df_h5 = hdf5_ops.read_mtable_as_dataframe(h5_file_path)
 
     # dataframe preprocessing steps
     df_h5, df_openbis = openbis_lib.align_datetime_observation_windows(df_h5, df_openbis)