From e2fec03d4ae968dd42585d9e191c5a508029f40b Mon Sep 17 00:00:00 2001
From: Florez Ospina Juan Felipe <juan.florez-ospina@psi.ch>
Date: Tue, 29 Oct 2024 07:56:43 +0100
Subject: [PATCH] Included cli commands update and serialize to simplify
 running metadata revision pipeline.

---
 pipelines/metadata_revision.py | 18 ++++++++++++------
 src/hdf5_ops.py                | 19 ++++++++++++++++++-
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/pipelines/metadata_revision.py b/pipelines/metadata_revision.py
index 49e23ab..f7e8a94 100644
--- a/pipelines/metadata_revision.py
+++ b/pipelines/metadata_revision.py
@@ -1,5 +1,9 @@
 import sys
 import os
+
+# Add the parent directory to the system path
+sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+
 import h5py
 import yaml
 import src.hdf5_ops as hdf5_ops
@@ -153,12 +157,14 @@ def count(hdf5_obj,yml_dict):
         print('additions',count_additions, 'deletions', count_delections)
 
 if __name__ == "__main__":
-    if len(sys.argv) != 4:
-        print("Usage: python metadata_revision.py update <path/to/review_file.hdf5> <path/to/review_file.yaml>")
-        sys.exit(1)
 
-    if sys.argv[2] == 'update':
-        input_hdf5_file = sys.argv[3]
-        yaml_review_file = sys.argv[4]
+    if len(sys.argv) < 4:
+        print("Usage: python metadata_revision.py update <path/to/target_file.hdf5> <path/to/metadata_review_file.yaml>")
+        sys.exit(1)   
+
+
+    if sys.argv[1] == 'update':
+        input_hdf5_file = sys.argv[2]
+        yaml_review_file = sys.argv[3]
         update_hdf5_file_with_review(input_hdf5_file, yaml_review_file)
     #run(sys.argv[2])
diff --git a/src/hdf5_ops.py b/src/hdf5_ops.py
index f0e82fb..134d788 100644
--- a/src/hdf5_ops.py
+++ b/src/hdf5_ops.py
@@ -388,7 +388,7 @@ class HDF5DataOpsManager():
         # Parse value into HDF5 admissible type
         for key in dataset_dict['attributes'].keys():
             value = dataset_dict['attributes'][key] 
-            if isinstance(key, dict):
+            if isinstance(value, dict):
                 dataset_dict['attributes'][key] = utils.convert_attrdict_to_np_structured_array(value)
 
         if not group_name in self.file_obj:
@@ -573,5 +573,22 @@ def get_groups_at_a_level(file: h5py.File, level: str):
     return groups
 
 
+if __name__ == "__main__":
+    if len(sys.argv) < 4:
+        print("Usage: python hdf5_ops.py serialize <path/to/target_file.hdf5> <format=json|yaml>")
+        sys.exit(1)
 
+    if sys.argv[1] == 'serialize':
+        input_hdf5_file = sys.argv[2]
+        file_format = sys.argv[3]
+
+        try:
+            # Call the serialize_metadata function and capture the output path
+            path_to_file = serialize_metadata(input_hdf5_file, output_format=file_format)
+            print(f"Metadata serialized to {path_to_file}")
+        except Exception as e:
+            print(f"An error occurred during serialization: {e}")
+            sys.exit(1)
+
+    #run(sys.argv[2])