Merge pull request #1160 from hkir-dev/issue_1157

Extract subset "annotate-with-source" support

Author: jamesaoverton

CHANGELOG.md

@@ -8,10 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Fixed
-
+- '--annotate-with-source true' does not work with extract --method subset [#1160]
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
 
-
 ## [1.9.5] - 2023-09-20
 
 ### Added
@@ -381,6 +380,7 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1160]: https://github.com/ontodev/robot/pull/1160
 [#1148]: https://github.com/ontodev/robot/pull/1148
 [#1135]: https://github.com/ontodev/robot/pull/1135
 [#1119]: https://github.com/ontodev/robot/pull/1119

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

@@ -189,20 +189,7 @@ public static OWLOntology extract(
     }
     // Maybe annotate entities with rdfs:isDefinedBy
     if (OptionsHelper.optionIsTrue(options, "annotate-with-source")) {
-      Set<OWLAnnotationAxiom> sourceAxioms = new HashSet<>();
-      for (OWLEntity entity : OntologyHelper.getEntities(outputOntology)) {
-        // Check if rdfs:isDefinedBy already exists
-        Set<OWLAnnotationValue> existingValues =
-            OntologyHelper.getAnnotationValues(outputOntology, isDefinedBy, entity.getIRI());
-        if (existingValues == null || existingValues.size() == 0) {
-          // If not, add it
-          OWLAnnotationAxiom def = getIsDefinedBy(entity, sourceMap);
-          if (def != null) {
-            sourceAxioms.add(def);
-          }
-        }
-      }
-      manager.addAxioms(outputOntology, sourceAxioms);
+      annotateWithSource(sourceMap, outputOntology, manager);
     }
 
     // Determine what to do based on intermediates
@@ -219,6 +206,31 @@ public static OWLOntology extract(
     }
   }
 
+  /**
+   * Annotates entities of the outputOntology with rdfs:isDefinedBy.
+   *
+   * @param sourceMap map of term IRI to source IRI, or null.
+   * @param outputOntology output ontology.
+   * @param manager OWL ontology manager.
+   */
+  private static void annotateWithSource(
+      Map<IRI, IRI> sourceMap, OWLOntology outputOntology, OWLOntologyManager manager) {
+    Set<OWLAnnotationAxiom> sourceAxioms = new HashSet<>();
+    for (OWLEntity entity : OntologyHelper.getEntities(outputOntology)) {
+      // Check if rdfs:isDefinedBy already exists
+      Set<OWLAnnotationValue> existingValues =
+          OntologyHelper.getAnnotationValues(outputOntology, isDefinedBy, entity.getIRI());
+      if (existingValues == null || existingValues.size() == 0) {
+        // If not, add it
+        OWLAnnotationAxiom def = getIsDefinedBy(entity, sourceMap);
+        if (def != null) {
+          sourceAxioms.add(def);
+        }
+      }
+    }
+    manager.addAxioms(outputOntology, sourceAxioms);
+  }
+
   /**
    * Extracts a materialized sub-ontology from the given ontology that only contains the given terms
    * and the relations between them. The input ontology is not changed.
@@ -249,6 +261,11 @@ public static OWLOntology extractSubset(
     copyPropertyAnnotations(inputOntology, filteredOnt);
     ReduceOperation.reduce(filteredOnt, new org.semanticweb.elk.owlapi.ElkReasonerFactory());
 
+    // Maybe annotate entities with rdfs:isDefinedBy
+    if (OptionsHelper.optionIsTrue(options, "annotate-with-source")) {
+      annotateWithSource(sourceMap, filteredOnt, OWLManager.createOWLOntologyManager());
+    }
+
     return filteredOnt;
   }