Owl api5 manipulation

amor/build.gradle

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2014 Alessio Capitanelli.
+ * Copyright (C) 2017 Luca Buoncompagni.
  *
  * Licensed under the Apache License, Version 2.0 (the "License"); you may not
  * use this file except in compliance with the License. You may obtain a copy of
@@ -30,10 +30,11 @@ repositories {
 
 dependencies {
 
-    //compile group: 'org.openrdf.sesame', name: 'sesame-model', version: '2.7.0'
+    //runtime group: 'org.openrdf.sesame', name: 'sesame-model', version: '2.7.14'
 
-    compile group: 'com.github.galigator.openllet', name: 'openllet-owlapi', version: '2.5.1'
-    compile group: 'net.sourceforge.owlapi', name: 'owlapi-distribution', version: '5.0.2'
+    //compile group: 'net.sourceforge.owlapi', name: 'org.semanticweb.hermit', version: '1.3.8.510'
 
+    compile group: 'com.github.galigator.openllet', name: 'openllet-owlapi', version: '2.5.1'
+    compile group: 'net.sourceforge.owlapi', name: 'owlapi-distribution', version: '5.0.5'
 }
 

amor/src/main/java/it/emarolab/amor/examples/Benchmarks.java

@@ -105,7 +105,5 @@ public static void main(String[] args) {
 //
 //
 
-
-        // todo: cheep track of changes in queries and benchmarks in the 'files/benchmarks' directory
     }
 }

amor/src/main/java/it/emarolab/amor/examples/BufferingTest.java

@@ -1,102 +1,101 @@
 package it.emarolab.amor.examples;
 
-import org.semanticweb.owlapi.model.OWLLiteral;
-
 import it.emarolab.amor.owlInterface.OWLReferences;
 import it.emarolab.amor.owlInterface.OWLReferencesInterface.OWLReferencesContainer;
+import org.semanticweb.owlapi.model.OWLLiteral;
 
 public class BufferingTest {
 
-	// ontology configurations
-	public static final String OWLREFERENCES_NAME = "refName";
-	public static final String ONTOLOGY_FILE_PATH = "files/ontologies/ontology_manipulation.owl";
-	public static final String ONTOLOGY_IRI_PATH = "http://www.semanticweb.org/luca-buoncompagni/aMor/examples";
-	public static final Boolean BUFFERING_REASONER = true; // if true you must to update manually the reasoner. Otherwise it synchronizes itself any time is needed
-	public static final Boolean BUFFERING_OWLMANIPULATOR = true; // if true you must to apply changes manually. Otherwise their are applied as soon as possible.
-
-	// ontological entities name
-	public static final Integer INITIAL_CNT = 3;
-	public static final String CNT_IND = "Counter"; // this is an individual with cares about the new ID to assign to X_IND
-	public static final String CNT_DATAPROP = "hasMaxCount";
-	public static final String X1_IND = "Ind1"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
-	public static final String X2_IND = "Ind2"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
-	public static final String X3_IND = "Ind3"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
-	public static final String X_DATAPROP = "hasId";
-		
-	public static void main(String[] args) {
-		// 1) let create new ontology with default reasoner (Pellet) and start GUI result visualisation
-		OWLReferences ontoRef = OWLReferencesContainer.newOWLReferencesCreated( OWLREFERENCES_NAME, ONTOLOGY_FILE_PATH, ONTOLOGY_IRI_PATH, BUFFERING_REASONER);
-		ontoRef.setOWLManipulatorBuffering( BUFFERING_OWLMANIPULATOR); // if not specified, default value=false {@link OWLManipulator#DEFAULT_CHANGE_BUFFERING}
-		
-		// 2) add base ontological entities
-		ontoRef.addIndividual( CNT_IND);
-		ontoRef.addDataPropertyB2Individual( CNT_IND, CNT_DATAPROP, INITIAL_CNT);
-		ontoRef.addIndividual( X1_IND);
-		ontoRef.addIndividual( X2_IND);
-		ontoRef.addIndividual( X3_IND);
-		applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
-		
-		// 3) get the starting cnt
-		Integer javaCnt = 0;
-		OWLLiteral ontoCnt = ontoRef.getOnlyDataPropertyB2Individual( CNT_IND, CNT_DATAPROP);
-		if( ontoCnt != null)
-			javaCnt = Integer.valueOf( ontoCnt.getLiteral());
-		
-		// 4) assign a new id for couple of times and apply owl manipulator changes (if flag is true)
-		assignIncrementalId( ontoRef, X1_IND, javaCnt); 			// id1 = INITIAL_CNT, 		cnt = INITIAL_CNT + 1;
-		assignIncrementalId( ontoRef, X2_IND, javaCnt);				// id2 = INITIAL_CNT, 		cnt = INITIAL_CNT + 1;
-		javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);	// id3 = INITIAL_CNT,	 	cnt = INITIAL_CNT + 1;
-		applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
-		
-		// 5) do something similar to (3) for testing purposes
-		assignIncrementalId( ontoRef, X1_IND, javaCnt);				// id1 = INITIAL_CNT + 1, 	cnt = INITIAL_CNT + 2;
-		assignIncrementalId( ontoRef, X2_IND, javaCnt);				// id2 = INITIAL_CNT + 1, 	cnt = INITIAL_CNT + 2;
-		javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);	// id3 = INITIAL_CNT + 1, 	cnt = INITIAL_CNT + 2;
-		applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
-		
-		// 6) do something similar to (3) for testing purposes
-		assignIncrementalId( ontoRef, X1_IND, javaCnt);				// id1 = INITIAL_CNT + 2, 	cnt = INITIAL_CNT + 3;
-		assignIncrementalId( ontoRef, X2_IND, javaCnt);				// id2 = INITIAL_CNT + 2, 	cnt = INITIAL_CNT + 3;
-		javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);	// id3 = INITIAL_CNT + 2, 	cnt = INITIAL_CNT + 3;
-		applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
-		
-		// 7) reason (if it is buffer)
-		reason( ontoRef);
-		
-		// 8) show results
-		ontoRef.printOntologyOnConsole();
-		
-		System.err.println( ontoRef.getIndividualB2Thing());
-		
-		ontoRef.saveOntology();
-		
-	}
-	
-	// procedure to assign a new id to X_IND and update the counter to point to an ID not assigned to any individuals
-	private static Integer assignIncrementalId( OWLReferences ontoRef, String ind, Integer cnt){
-		// get the actual value of the counter
-		OWLLiteral ontoCnt = ontoRef.getOWLLiteral( cnt);
-		OWLLiteral newOntoCount = ontoRef.getOWLLiteral( cnt + 1);
-		// get the actual value of the id
-		OWLLiteral ontoId = ontoRef.getOnlyDataPropertyB2Individual( ind,	X_DATAPROP);
-		// update the new id to the individual by overwriting the old value
-		ontoRef.replaceDataProperty( ontoRef.getOWLIndividual( ind), ontoRef.getOWLDataProperty( X_DATAPROP),	ontoId, ontoCnt);
-		// get the actual cnt
-		OWLLiteral oldCnt = ontoRef.getOnlyDataPropertyB2Individual( CNT_IND, CNT_DATAPROP);
-		// update the counter individual by overwriting the old value
-		ontoRef.replaceDataProperty( ontoRef.getOWLIndividual( CNT_IND), ontoRef.getOWLDataProperty( CNT_DATAPROP),	oldCnt, newOntoCount);
-		return cnt + 1;
-	}
-	
-	// apply changes w.r.t. to buggering flag
-	private static void applyChanges( OWLReferences ontoRef){
-		if( BUFFERING_OWLMANIPULATOR) 
-			ontoRef.applyOWLManipulatorChanges();
-	}
-	
-	// update the state of the reasoner w.r.t. buffering flag
-	private static void reason( OWLReferences ontoRef){
-		if( BUFFERING_REASONER)
-			ontoRef.synchronizeReasoner();
-	}
+    // ontology configurations
+    public static final String OWLREFERENCES_NAME = "refName";
+    public static final String ONTOLOGY_FILE_PATH = "files/ontologies/ontology_manipulation.owl";
+    public static final String ONTOLOGY_IRI_PATH = "http://www.semanticweb.org/luca-buoncompagni/aMor/examples";
+    public static final Boolean BUFFERING_REASONER = true; // if true you must to update manually the reasoner. Otherwise it synchronizes itself any time is needed
+    public static final Boolean BUFFERING_OWLMANIPULATOR = true; // if true you must to apply changes manually. Otherwise their are applied as soon as possible.
+
+    // ontological entities name
+    public static final Integer INITIAL_CNT = 3;
+    public static final String CNT_IND = "Counter"; // this is an individual with cares about the new ID to assign to X_IND
+    public static final String CNT_DATAPROP = "hasMaxCount";
+    public static final String X1_IND = "Ind1"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
+    public static final String X2_IND = "Ind2"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
+    public static final String X3_IND = "Ind3"; // this is an individual which must have a unique (in the ontology w.r.t. CNT_IND) identifier
+    public static final String X_DATAPROP = "hasId";
+
+    public static void main(String[] args) {
+        // 1) let create new ontology with default reasoner (Pellet) and start GUI result visualisation
+        OWLReferences ontoRef = OWLReferencesContainer.newOWLReferencesCreated( OWLREFERENCES_NAME, ONTOLOGY_FILE_PATH, ONTOLOGY_IRI_PATH, BUFFERING_REASONER);
+        ontoRef.setOWLManipulatorBuffering( BUFFERING_OWLMANIPULATOR); // if not specified, default value=false {@link OWLManipulator#DEFAULT_CHANGE_BUFFERING}
+
+        // 2) add base ontological entities
+        ontoRef.addIndividual( CNT_IND);
+        ontoRef.addDataPropertyB2Individual( CNT_IND, CNT_DATAPROP, INITIAL_CNT);
+        ontoRef.addIndividual( X1_IND);
+        ontoRef.addIndividual( X2_IND);
+        ontoRef.addIndividual( X3_IND);
+        applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
+
+        // 3) get the starting cnt
+        Integer javaCnt = 0;
+        OWLLiteral ontoCnt = ontoRef.getOnlyDataPropertyB2Individual( CNT_IND, CNT_DATAPROP);
+        if( ontoCnt != null)
+            javaCnt = Integer.valueOf( ontoCnt.getLiteral());
+
+        // 4) assign a new id for couple of times and apply owl manipulator changes (if flag is true)
+        assignIncrementalId( ontoRef, X1_IND, javaCnt);              // id1 = INITIAL_CNT,         cnt = INITIAL_CNT + 1;
+        assignIncrementalId( ontoRef, X2_IND, javaCnt);              // id2 = INITIAL_CNT,         cnt = INITIAL_CNT + 1;
+        javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);    // id3 = INITIAL_CNT,         cnt = INITIAL_CNT + 1;
+        applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
+
+        // 5) do something similar to (3) for testing purposes
+        assignIncrementalId( ontoRef, X1_IND, javaCnt);              // id1 = INITIAL_CNT + 1,     cnt = INITIAL_CNT + 2;
+        assignIncrementalId( ontoRef, X2_IND, javaCnt);              // id2 = INITIAL_CNT + 1,     cnt = INITIAL_CNT + 2;
+        javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);    // id3 = INITIAL_CNT + 1,     cnt = INITIAL_CNT + 2;
+        applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
+
+        // 6) do something similar to (3) for testing purposes
+        assignIncrementalId( ontoRef, X1_IND, javaCnt);                // id1 = INITIAL_CNT + 2,     cnt = INITIAL_CNT + 3;
+        assignIncrementalId( ontoRef, X2_IND, javaCnt);                // id2 = INITIAL_CNT + 2,     cnt = INITIAL_CNT + 3;
+        javaCnt = assignIncrementalId( ontoRef, X3_IND, javaCnt);    // id3 = INITIAL_CNT + 2,     cnt = INITIAL_CNT + 3;
+        applyChanges( ontoRef); // this considers BUFFERING_MANIPULATOR flag
+
+        // 7) reason (if it is buffer)
+        reason( ontoRef);
+
+        // 8) show results
+        ontoRef.printOntologyOnConsole();
+
+        System.err.println( ontoRef.getIndividualB2Thing());
+
+        ontoRef.saveOntology();
+
+    }
+
+    // procedure to assign a new id to X_IND and update the counter to point to an ID not assigned to any individuals
+    private static Integer assignIncrementalId( OWLReferences ontoRef, String ind, Integer cnt){
+        // get the actual value of the counter
+        OWLLiteral ontoCnt = ontoRef.getOWLLiteral( cnt);
+        OWLLiteral newOntoCount = ontoRef.getOWLLiteral( cnt + 1);
+        // get the actual value of the id
+        OWLLiteral ontoId = ontoRef.getOnlyDataPropertyB2Individual( ind,    X_DATAPROP);
+        // update the new id to the individual by overwriting the old value
+        ontoRef.replaceDataProperty( ontoRef.getOWLIndividual( ind), ontoRef.getOWLDataProperty( X_DATAPROP),    ontoId, ontoCnt);
+        // get the actual cnt
+        OWLLiteral oldCnt = ontoRef.getOnlyDataPropertyB2Individual( CNT_IND, CNT_DATAPROP);
+        // update the counter individual by overwriting the old value
+        ontoRef.replaceDataProperty( ontoRef.getOWLIndividual( CNT_IND), ontoRef.getOWLDataProperty( CNT_DATAPROP),    oldCnt, newOntoCount);
+        return cnt + 1;
+    }
+
+    // apply changes w.r.t. to buggering flag
+    private static void applyChanges( OWLReferences ontoRef){
+        if( BUFFERING_OWLMANIPULATOR)
+            ontoRef.applyOWLManipulatorChanges();
+    }
+
+    // update the state of the reasoner w.r.t. buffering flag
+    private static void reason( OWLReferences ontoRef){
+        if( BUFFERING_REASONER)
+            ontoRef.synchronizeReasoner();
+    }
 }

amor/src/main/java/it/emarolab/amor/examples/OWLRefDebuggingExample.java

@@ -8,35 +8,35 @@
 
 public class OWLRefDebuggingExample {
 
-	public static void main(String[] args) {
-		// 1)  you may want to save on file the logs of the system. Set it to default (time-hour base name) or provide a directory path
-		// you can enable and disable logs by changing the flags in the class Logger.LoggerFlag or you may want to set it like:
-		Logger.LoggerFlag.setLogOntologyExporter( true); // [PARAMETER]
-		Logger.setPrintOnFile( FileManager.DEFAULT_command); // [PARAMETER]
-		
-		// 2) let now open the pizza ontology from web with pellet reasoner (default)
-		String ontoRefName = "ontoRef3"; // this must be a unique identifier for all the references you what to create into the system
-		Boolean bufferingReasoner = false; // reasoning is automatically synchronised
-		String pizzaOntologyIri = "http://www.co-ode.org/ontologies/pizza/pizza.owl";
-		String filePath = "http://protege.stanford.edu/ontologies/pizza/pizza.owl";
-		OWLReferences ontoRef = OWLReferencesContainer.newOWLReferenceFromWeb( ontoRefName, filePath, pizzaOntologyIri, bufferingReasoner);
-		
-		// 3) you may want to print the ontology.
-		ontoRef.printOntologyOnConsole();
-		 
-		// 4) [PERAMETER] the system comes with a simple GUI from which it is possible to see the state of the ontology
-		// during run time as well as make some basic changes. Be aware that the GUI is not stable yet!
-		//NOT PORTED TO OWL API 5 JET
- 		Thread t = new Thread( new GuiRunner( ontoRefName));
-		t.start();
-			
-		// 5) be sure to see all logs!
-		Logger.flush();
-		
-		// wait to give the possibility to interact with the GUI
-		try {
-			for( int i = 0; i < 100 ; i++) // about 20 minutes
-				Thread.sleep( 15000);
-		} catch (InterruptedException e) {}
-	}
+    public static void main(String[] args) {
+        // 1)  you may want to save on file the logs of the system. Set it to default (time-hour base name) or provide a directory path
+        // you can enable and disable logs by changing the flags in the class Logger.LoggerFlag or you may want to set it like:
+        Logger.LoggerFlag.setLogOntologyExporter( true); // [PARAMETER]
+        Logger.setPrintOnFile( FileManager.DEFAULT_command); // [PARAMETER]
+
+        // 2) let now open the pizza ontology from web with pellet reasoner (default)
+        String ontoRefName = "ontoRef3"; // this must be a unique identifier for all the references you what to create into the system
+        Boolean bufferingReasoner = false; // reasoning is automatically synchronised
+        String pizzaOntologyIri = "http://www.co-ode.org/ontologies/pizza/pizza.owl";
+        String filePath = "http://protege.stanford.edu/ontologies/pizza/pizza.owl";
+        OWLReferences ontoRef = OWLReferencesContainer.newOWLReferenceFromWeb( ontoRefName, filePath, pizzaOntologyIri, bufferingReasoner);
+
+        // 3) you may want to print the ontology.
+        ontoRef.printOntologyOnConsole();
+
+        // 4) [PERAMETER] the system comes with a simple GUI from which it is possible to see the state of the ontology
+        // during run time as well as make some basic changes. Be aware that the GUI is not stable yet!
+        //NOT PORTED TO OWL API 5 JET
+         Thread t = new Thread( new GuiRunner( ontoRefName));
+        t.start();
+
+        // 5) be sure to see all logs!
+        Logger.flush();
+
+        // wait to give the possibility to interact with the GUI
+        try {
+            for( int i = 0; i < 100 ; i++) // about 20 minutes
+                Thread.sleep( 15000);
+        } catch (InterruptedException e) {}
+    }
 }