Handle trait class generation

Tools/td2owl/td2owl.py

@@ -15,6 +15,30 @@ from pathlib import Path, PurePosixPath
 
 co = Namespace("http://www.cropontology.org/rdf/")
 
+trait_classes={}
+def get_trait_class(output_graph, a_row):
+
+    co_prefix=a_row.get('Trait ID').split(":")[0]
+
+    if a_row.get('Trait class') not in trait_classes:
+        trait_class_id=co_prefix+":900000"+str(len(trait_classes))
+        trait_class_URI = "http://www.cropontology.org/rdf/"+trait_class_id
+        trait_classes[a_row.get('Trait class')]=trait_class_URI
+        add_triple(output_graph, URIRef(trait_class_URI), RDF.type, co.TraitClass )
+        add_triple(output_graph, URIRef(trait_class_URI), co.hasId, Literal(trait_class_id) )
+        add_triple(output_graph, URIRef(trait_class_URI), co.hasName, Literal(a_row.get('Trait class')) )
+
+    return trait_classes[a_row.get('Trait class')]
+
+# dict is of the form: label:id
+#def add_trait_class_triples(output_graph, a_dict):
+#    for a_key in a_dict:
+#        trait_class_URI="http://www.cropontology.org/rdf/" + a_dict[a_key]
+#        add_triple(output_graph, trait_class_URI, RDF.type, co.TraitClass )
+#        add_triple(output_graph, trait_class_URI, co.hasId, Literal(a_dict[a_key]) )
+#        add_triple(output_graph, trait_class_URI, co.hasName, Literal(a_key) )
+
+
 def add_triple(output_graph, s, p, o):
     if o:
         output_graph.add((s, p, o))
@@ -75,7 +99,8 @@ def load_csv2graph(csv_file) -> Graph():
         add_triple(output_graph,URIRef(traitURI), co.hasTraitId, to_literal(row, 'Trait ID'))
         add_triple(output_graph,URIRef(traitURI), RDF.type, co.Trait)
         add_triple(output_graph,URIRef(traitURI), co.hasName, to_literal_lang(row, 'Trait name'))
-        add_triple(output_graph,URIRef(traitURI), co.hasTraitClass, to_literal(row, 'Trait class'))
+        #add_triple(output_graph,URIRef(traitURI), co.hasTraitClass, to_literal(row, 'Trait class'))
+        add_triple(output_graph, URIRef(get_trait_class(output_graph, row)) , co.hasTrait, URIRef(traitURI))
         add_triple(output_graph,URIRef(traitURI), co.hasDescription, to_literal_lang(row, 'Trait description'))
         for tsyn in row['Trait synonyms'].split(','):
             add_triple(output_graph,URIRef(traitURI), co.hasSynonym, Literal(tsyn))
@@ -115,6 +140,9 @@ def load_csv2graph(csv_file) -> Graph():
         add_triple(output_graph,URIRef(scaleURI), co.hasCategory9, Literal(row['Category 9']))
         add_triple(output_graph,URIRef(scaleURI), co.hasCategory10, Literal(row['Category 10']))
 
+    # add trait classes to the graph
+    #add_trait_class_triples(output_graph, trait_classes)
+
     return output_graph
 
 def read_graph_and_write_to_file(file_name):