switching to use the categories init parameter of kgxnode and a const…

…ant instead of hardcoding node category

Common/node_types.py

@@ -25,6 +25,7 @@
 GENE_FAMILY = 'biolink:GeneFamily'
 GENOMIC_ENTITY = 'biolink:GenomicEntity'
 FOOD = 'biolink:Food'
+MACROMOLECULAR_COMPLEX = 'biolink:MacromolecularComplex'
 
 # The root of all biolink_model entities
 ROOT_ENTITY = NAMED_THING
@@ -55,7 +56,8 @@
     GENETIC_CONDITION,
     UNSPECIFIED,
     GENE_FAMILY,
-    FOOD
+    FOOD,
+    MACROMOLECULAR_COMPLEX
 ]
 
 # The following are used by edges:

parsers/Reactome/src/loadReactome.py

@@ -9,6 +9,7 @@
 from Common.loader_interface import SourceDataLoader
 from Common.kgxmodel import kgxnode, kgxedge
 from Common.neo4j_tools import Neo4jTools
+from Common.node_types import MACROMOLECULAR_COMPLEX, NAMED_THING
 from Common.prefixes import REACTOME, NCBITAXON, GTOPDB, UNIPROTKB, CHEBI, KEGG_COMPOUND, KEGG_GLYCAN, PUBCHEM_COMPOUND, NCBIGENE, CLINVAR
 from Common.utils import GetData
 
@@ -340,13 +341,18 @@ def process_node_from_neo4j(self, reference_entity_mapping, node_identity, node:
 
         node_properties = {}
         if any(x == 'Complex' for x in node_labels):
-            node_properties['category'] = ['biolink:MacromolecularComplex']
+            node_categories = [NAMED_THING, MACROMOLECULAR_COMPLEX]
+        else:
+            node_categories = [NAMED_THING]
         if 'definition' in node.keys():
             node_properties['definition'] = node['definition']
         if 'url' in node.keys():
             node_properties['url'] = node['url']
         node_name = node['displayName'] if 'displayName' in node else ''
-        node_to_write = kgxnode(node_id, name=node_name, nodeprops=node_properties)
+        node_to_write = kgxnode(node_id,
+                                name=node_name,
+                                categories=node_categories,
+                                nodeprops=node_properties)
         self.output_file_writer.write_kgx_node(node_to_write)
         return node_id