Cache the result of the search for deprecation annotation.

Since checking whether a given entity is deprecated requires iterating
over all the annotations on said entity, and we might have to check the
same entity many times (the entity can be referenced from many different
axioms), we cache the result of that check.

Author: gouttegd

src/main/java/org/incenp/obofoundry/odk/CheckCommand.java

@@ -19,8 +19,10 @@
 package org.incenp.obofoundry.odk;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import org.apache.commons.cli.CommandLine;
@@ -44,6 +46,7 @@ public class CheckCommand extends BasePlugin {
     private static final Logger logger = LoggerFactory.getLogger(CheckCommand.class);
 
     private Set<String> basePrefixes = new HashSet<>();
+    private Map<OWLEntity, Boolean> cache = new HashMap<>();
 
     public CheckCommand() {
         super("check", "perform some checks on an ontology", "robot check --checks [CHECK,...]");
@@ -58,6 +61,7 @@ public void performOperation(CommandState state, CommandLine line) throws Except
         for ( String prefix : CommandLineHelper.getOptionalValues(line, "base-iri") ) {
             basePrefixes.add(getIRI(prefix, "base-iri").toString());
         }
+        cache.clear();
 
         int failed = 0;
         for ( String check : line.getOptionValues("checks") ) {
@@ -128,13 +132,20 @@ private boolean checkDeprecatedReferences(OWLOntology ontology) {
     }
 
     private boolean isDeprecated(OWLOntology ontology, OWLEntity entity) {
+        Boolean cached = cache.get(entity);
+        if ( cached != null ) {
+            return cached;
+        }
+
         for ( OWLOntology ont : ontology.getImportsClosure() ) {
             for ( OWLAnnotationAssertionAxiom ax : ont.getAnnotationAssertionAxioms(entity.getIRI()) ) {
                 if ( ax.isDeprecatedIRIAssertion() ) {
+                    cache.put(entity, true);
                     return true;
                 }
             }
         }
+        cache.put(entity, false);
         return false;
     }