Merge pull request #188 from Knowledge-Graph-Hub/187-build-fails-due-to-keyerror-broad_synonyms

Repair synonym column names in transform

Author: caufieldjh

kg_phenio/transform_utils/phenio/phenio_node_sources.py

@@ -84,28 +84,28 @@
 
     # Extend the class with additional attributes:
     # * subsets
-    # * broad_synonyms
-    # * exact_synonyms
-    # * narrow_synonyms
-    # * related_synonyms
+    # * broad_synonym
+    # * exact_synonym
+    # * narrow_synonym
+    # * related_synonym
     class NodeClass(base_class):
         """Node class with additional attributes for subsets and synonyms."""
 
         subsets: Optional[List[str]] = Field(
             default=None, description="""Subsets the node belongs to, defined by its source""")
-        broad_synonyms: Optional[List[str]] = Field(
+        broad_synonym: Optional[List[str]] = Field(
             default=None,
             description="""Broad synonyms for the node, defined by its source""",
         )
-        exact_synonyms: Optional[List[str]] = Field(
+        exact_synonym: Optional[List[str]] = Field(
             default=None,
             description="""Exact synonyms for the node, defined by its source""",
         )
-        narrow_synonyms: Optional[List[str]] = Field(
+        narrow_synonym: Optional[List[str]] = Field(
             default=None,
             description="""Narrow synonyms for the node, defined by its source""",
         )
-        related_synonyms: Optional[List[str]] = Field(
+        related_synonym: Optional[List[str]] = Field(
             default=None,
             description="""Related synonyms for the node, defined by its source""",
         )
@@ -140,15 +140,15 @@ class NodeClass(base_class):
         node.xref = xrefs
 
     for synonym_type in ["broad", "exact", "narrow", "related"]:
-        if row[f"{synonym_type}_synonyms"]:
-            these_synonyms = (row[f"{synonym_type}_synonyms"]).split("|")
+        if row[f"{synonym_type}_synonym"]:
+            these_synonyms = (row[f"{synonym_type}_synonym"]).split("|")
             if synonym_type == "broad":
-                node.broad_synonyms = these_synonyms
+                node.broad_synonym = these_synonyms
             elif synonym_type == "exact":
-                node.exact_synonyms = these_synonyms
+                node.exact_synonym = these_synonyms
             elif synonym_type == "narrow":
-                node.narrow_synonyms = these_synonyms
+                node.narrow_synonym = these_synonyms
             elif synonym_type == "related":
-                node.related_synonyms = these_synonyms
+                node.related_synonym = these_synonyms
 
     koza_app.write(node)

kg_phenio/transform_utils/phenio/phenio_node_sources.yaml

@@ -17,13 +17,13 @@ columns:
   - 'xref'
   - 'provided_by'
   - 'synonym'
-  - 'broad_synonyms'
+  - 'broad_synonym'
   - 'deprecated'
-  - 'exact_synonyms'
+  - 'exact_synonym'
   - 'iri'
-  - 'narrow_synonyms'
+  - 'narrow_synonym'
   - 'same_as'
-  - 'related_synonyms'
+  - 'related_synonym'
   - 'subsets'
 
 node_properties:
@@ -38,9 +38,9 @@ node_properties:
   - 'iri'
   - 'same_as'
   - 'subsets'
-  - 'broad_synonyms'
-  - 'exact_synonyms'
-  - 'narrow_synonyms'
-  - 'related_synonyms'
+  - 'broad_synonym'
+  - 'exact_synonym'
+  - 'narrow_synonym'
+  - 'related_synonym'
 
 transform_mode: 'flat'