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

notebooks/demo_h5_file_2_obis_props_mapping.py

@@ -1,9 +1,21 @@
-import src.openbis_lib as openbis_lib
-import 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')
@@ -20,7 +32,8 @@ 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_hdf5_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)    

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)    

notebooks/example_workflow_metadata_annotation.ipynb

@@ -23,11 +23,29 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Imports successful!\n"
+     ]
+    }
+   ],
    "source": [
-    "import src.metadata_review_lib as metadata_annotation\n",
-    "import src.hdf5_vis as hdf5_vis\n",
-    "import os"
+    "import os\n",
+    "from nbutils import add_project_path_to_sys_path\n",
+    "\n",
+    "\n",
+    "# Add project root to sys.path\n",
+    "add_project_path_to_sys_path()\n",
+    "\n",
+    "try:\n",
+    "    import src.hdf5_ops as hdf5_ops\n",
+    "    import pipelines.metadata_revision as metadata_revision\n",
+    "    print(\"Imports successful!\")\n",
+    "except ImportError as e:\n",
+    "    print(f\"Import error: {e}\")"
    ]
   },
   {
@@ -46,7 +64,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hdf5_file_path = \"output_files/kinetic_flowtube_study_2023-06-29_LuciaI.h5\""
+    "hdf5_file_path = \"../output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.h5\""
    ]
   },
   {
@@ -62,11 +80,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The YAML file representation output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.json of the HDF5 file output_files/collection_kinetic_flowtube_study_LuciaI_2022-01-31_2023-06-29/kinetic_flowtube_study_LuciaI_2023-06-29.h5 was created successfully.\n"
+     ]
+    }
+   ],
    "source": [
-    "yaml_file_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(hdf5_file_path)\n",
+    "yaml_file_path = hdf5_ops.serialize_metadata(hdf5_file_path,output_format='json')\n",
     "\n",
     "if os.path.exists(yaml_file_path):\n",
     "    print(f'The YAML file representation {yaml_file_path} of the HDF5 file {hdf5_file_path} was created successfully.')"
@@ -118,7 +144,7 @@
    "outputs": [],
    "source": [
     "\n",
-    "metadata_annotation.update_hdf5_file_with_review(hdf5_file_path,yaml_file_path)"
+    "metadata_revision.update_hdf5_file_with_review(hdf5_file_path,yaml_file_path)"
    ]
   }
  ],