Merge pull request #927 from hkir-dev/issue924

Fix Issue: SPLIT fails with owl:NamedIndividual #924

CHANGELOG.md

@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix `deprecated_class_reference` [`report`] query [#902]
 - Fix error handling for JSON conversion [#907]
 - Fix handling of property chains when removing/filtering base axioms in [#914]
+- Fix SPLIT unpacking in named individuals in [`template`] [#924]
 
 ### Changed
 - Do not allow malformed IRIs to be returned by `IOHelper` [#882]
@@ -276,6 +277,7 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#924]: https://github.com/ontodev/robot/issues/924
 [#914]: https://github.com/ontodev/robot/pull/914
 [#907]: https://github.com/ontodev/robot/pull/907
 [#902]: https://github.com/ontodev/robot/pull/902

robot-core/src/main/java/org/obolibrary/robot/Template.java

@@ -1881,6 +1881,10 @@ private void addIndividualAxioms(IRI iri, List<String> row) throws Exception {
 
       // Handle annotations
       if (template.startsWith("A") || template.startsWith("LABEL")) {
+        if (split != null) {
+          // Add the split back on for getAnnotations
+          template = template + " SPLIT=" + split;
+        }
         // Add the annotations to the individual
         Set<OWLAnnotation> annotations = getAnnotations(template, value, row, column);
         for (OWLAnnotation annotation : annotations) {

robot-core/src/test/java/org/obolibrary/robot/TemplateTest.java

@@ -8,6 +8,7 @@
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxClassExpressionParser;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.search.EntitySearcher;
 
 /**
  * Tests Template class and class methods.
@@ -156,4 +157,33 @@ public void testParseClass() throws Exception {
         TemplateHelper.tryParse("test", checker, parser, label, 0, 0).asOWLClass();
     assert actualClass.getIRI().toString().equals(expectedClass.getIRI().toString());
   }
+
+  /**
+   * Test named individual with split property.
+   *
+   * @throws Exception if entities cannot be found
+   */
+  @Test
+  public void testNamedIndividualSplit() throws Exception {
+    Map<String, String> options = TemplateOperation.getDefaultOptions();
+    IOHelper ioHelper = new IOHelper();
+    ioHelper.addPrefix("ex", "http://example.com/");
+
+    Map<String, List<List<String>>> tables = new LinkedHashMap<>();
+    String path = "/template-individual-split.csv";
+    tables.put(path, TemplateHelper.readCSV(this.getClass().getResourceAsStream(path)));
+
+    OWLOntology ontology = TemplateOperation.template(null, ioHelper, tables, options);
+
+    assertEquals("Count individuals", 1, ontology.getIndividualsInSignature().size());
+    OWLNamedIndividual namedIndividual = ontology.getIndividualsInSignature().iterator().next();
+    assertEquals(
+        "Count annotation properties", 1, ontology.getAnnotationPropertiesInSignature().size());
+    OWLAnnotationProperty annotationProperty =
+        ontology.getAnnotationPropertiesInSignature().iterator().next();
+    assertEquals(
+        "Count annotation properties of individual",
+        2,
+        EntitySearcher.getAnnotationObjects(namedIndividual, ontology, annotationProperty).size());
+  }
 }

robot-core/src/test/resources/template-individual-split.csv

@@ -0,0 +1,3 @@
+ID,Entity Type,Synonyms
+ID,TYPE,A IAO:0000118 SPLIT=|
+ex:indv_1,owl:NamedIndividual,synonym 1|synonym 2