switching json attributes edge property to be a list of json strings …

…instead of one big json string
ranking-agent · Aug 7, 2024 · fe1058f · fe1058f
1 parent 4322e8f
commit fe1058f
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Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/reasoner_transpiler/cypher.py b/reasoner_transpiler/cypher.py
@@ -422,17 +422,19 @@ def transform_attributes(result_item, node=False):
     ignore_list = RESERVED_NODE_PROPS if node else EDGE_SOURCE_PROPS + RESERVED_EDGE_PROPS
     ignore_list += ATTRIBUTE_SKIP_LIST
 
-    # an "attributes" attribute in neo4j should be a json list,
+    # an "attributes" attribute in neo4j should be a list of json strings,
     # attempt to start the attributes section of transformed attributes with its contents
-    json_attributes_attribute = result_item.pop('attributes', None)
     json_attributes = []
+    json_attributes_attribute = result_item.pop('attributes', None)
     if json_attributes_attribute:
-        try:
-            json_attributes = json.loads(json_attributes_attribute)
-            if not isinstance(json_attributes, list):
-                print(f'! attributes property was not a list, ignoring: {json_attributes_attribute}')
-        except json.JSONDecodeError as e:
-            print(f'! JSONDecodeError parsing attributes property, it should be a json list, ignoring: {json_attributes_attribute}')
+        if isinstance(json_attributes_attribute, list):
+            try:
+                json_attributes = [json.loads(json_attribute_string)
+                                   for json_attribute_string in json_attributes_attribute]
+            except json.JSONDecodeError:
+                print(f'!!! JSONDecodeError while parsing attributes property, ignoring: {json_attributes_attribute}')
+        else:
+            print(f'!!! the attributes edge property should be a list, ignoring: {json_attributes_attribute}')
     transformed_attributes = {
         'attributes': json_attributes
     }

diff --git a/tests/neo4j_csv/edges.csv b/tests/neo4j_csv/edges.csv
@@ -20,7 +20,7 @@ t2d_associated_with_CASP3,MONDO:0005148,biolink:genetically_associated_with,NCBI
 obesity_ga_CASP3,MONDO:0011122,biolink:genetically_associated_with,NCBIGene:836,"{}"
 metformin_treats_carcinoma,CHEBI:6801,biolink:treats,MONDO:0004993,"{}"
 carcinoma_associated_with_CASP8,MONDO:0004993,biolink:genetically_associated_with,NCBIGene:841,"{}"
-carcinoma_associated_with_BRCA1,NCBIGene:672,biolink:gene_associated_with_condition,MONDO:0004993,"{\"publications\": [\"xxx\"], \"attributes\": \"[{\\\"attribute_type_id\\\": \\\"json_attribute_1\\\", \\\"value\\\": \\\"json_value_1\\\"}, {\\\"attribute_type_id\\\": \\\"json_attribute_2\\\", \\\"value\\\": \\\"json_value_2\\\"}, {\\\"attribute_type_id\\\": \\\"json_attribute_3\\\", \\\"value\\\": \\\"json_value_3\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"nested_json_attribute_1\\\", \\\"value\\\": \\\"nested_json_value_1\\\"}] }]\" }"
+carcinoma_associated_with_BRCA1,NCBIGene:672,biolink:gene_associated_with_condition,MONDO:0004993,"{\"publications\": [\"xxx\"], \"attributes\": [\"{\\\"attribute_type_id\\\": \\\"json_attribute_1\\\", \\\"value\\\": \\\"json_value_1\\\"}\", \"{\\\"attribute_type_id\\\": \\\"json_attribute_2\\\", \\\"value\\\": \\\"json_value_2\\\"}\", \"{\\\"attribute_type_id\\\": \\\"json_attribute_3\\\", \\\"value\\\": \\\"json_value_3\\\", \\\"attributes\\\": [{\\\"attribute_type_id\\\": \\\"nested_json_attribute_1\\\", \\\"value\\\": \\\"nested_json_value_1\\\"}] }\"] }"
 t2d_invalid_predicate_albuminaria,MONDO:0005148,biolink:invalid_predicate,HP:0012592,"{}"
 qualified_edge_single_qualifier,PUBCHEM.COMPOUND:5460341,biolink:affects,NCBIGene:283871,"{\"qualified_predicate\": \"biolink:causes\"}"
 qualified_edge_multiple_qualifier,PUBCHEM.COMPOUND:5460341,biolink:affects,NCBIGene:283871,"{\"qualified_predicate\": \"biolink:causes\",\"object_aspect_qualifier\": \"activity\",\"object_direction_qualifier\": \"decreased\",\"primary_knowledge_source\": \"infores:ctd\"}}"