Java tutorial
//The MIT License // // Copyright (c) 2004 Mindswap Research Group, University of Maryland, College Park // // Permission is hereby granted, free of charge, to any person obtaining a copy // of this software and associated documentation files (the "Software"), to // deal in the Software without restriction, including without limitation the // rights to use, copy, modify, merge, publish, distribute, sublicense, and/or // sell copies of the Software, and to permit persons to whom the Software is // furnished to do so, subject to the following conditions: // // The above copyright notice and this permission notice shall be included in // all copies or substantial portions of the Software. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS // IN THE SOFTWARE. package org.mindswap.swoop.renderer.entity; import java.awt.Component; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.io.PrintWriter; import java.io.StringWriter; import java.io.Writer; import java.net.URI; import java.net.URL; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JScrollPane; import org.apache.commons.lang.StringEscapeUtils; import org.mindswap.pellet.debug.owlapi.Reasoner; import org.mindswap.pellet.debug.utils.Timer; import org.mindswap.swoop.Swoop; import org.mindswap.swoop.SwoopDisplayPanel; import org.mindswap.swoop.SwoopModel; import org.mindswap.swoop.TermsDisplay; import org.mindswap.swoop.debugging.RepairFrame; import org.mindswap.swoop.popup.PopupAddAnnotation; import org.mindswap.swoop.popup.PopupAddClass; import org.mindswap.swoop.popup.PopupAddIndividual; import org.mindswap.swoop.popup.PopupAddProperty; import org.mindswap.swoop.popup.PopupAddRule; import org.mindswap.swoop.popup.PopupAddValue; import org.mindswap.swoop.reasoner.PelletReasoner; import org.mindswap.swoop.reasoner.SwoopReasoner; import org.mindswap.swoop.renderer.BaseEntityRenderer; import org.mindswap.swoop.renderer.SwoopEditableRenderer; import org.mindswap.swoop.renderer.SwoopEntityRenderer; import org.mindswap.swoop.renderer.SwoopRenderingVisitor; import org.mindswap.swoop.utils.RuleValue; import org.mindswap.swoop.utils.RulesExpressivity; import org.mindswap.swoop.utils.SetUtils; import org.mindswap.swoop.utils.XPointers; import org.mindswap.swoop.utils.change.BooleanElementChange; import org.mindswap.swoop.utils.change.EnumElementChange; import org.mindswap.swoop.utils.external.ExternalRuleSubmitter; import org.mindswap.swoop.utils.owlapi.CorrectedRDFRenderer; import org.mindswap.swoop.utils.owlapi.OWLDescriptionFinder; import org.mindswap.swoop.utils.owlapi.OWLOntBuilder; import org.mindswap.swoop.utils.ui.SwoopIcons; import org.semanticweb.owl.io.RendererException; import org.semanticweb.owl.io.vocabulary.OWLVocabularyAdapter; import org.semanticweb.owl.model.OWLAnd; import org.semanticweb.owl.model.OWLAnnotationInstance; import org.semanticweb.owl.model.OWLAnnotationProperty; import org.semanticweb.owl.model.OWLClass; import org.semanticweb.owl.model.OWLClassAxiom; import org.semanticweb.owl.model.OWLDataFactory; import org.semanticweb.owl.model.OWLDataProperty; import org.semanticweb.owl.model.OWLDataRange; import org.semanticweb.owl.model.OWLDataType; import org.semanticweb.owl.model.OWLDataValue; import org.semanticweb.owl.model.OWLDescription; import org.semanticweb.owl.model.OWLDifferentIndividualsAxiom; import org.semanticweb.owl.model.OWLDisjointClassesAxiom; import org.semanticweb.owl.model.OWLEntity; import org.semanticweb.owl.model.OWLEnumeration; import org.semanticweb.owl.model.OWLEquivalentClassesAxiom; import org.semanticweb.owl.model.OWLEquivalentPropertiesAxiom; import org.semanticweb.owl.model.OWLException; import org.semanticweb.owl.model.OWLIndividual; import org.semanticweb.owl.model.OWLIndividualAxiom; import org.semanticweb.owl.model.OWLIndividualTypeAssertion; import org.semanticweb.owl.model.OWLNamedObject; import org.semanticweb.owl.model.OWLNot; import org.semanticweb.owl.model.OWLObject; import org.semanticweb.owl.model.OWLObjectProperty; import org.semanticweb.owl.model.OWLObjectPropertyInstance; import org.semanticweb.owl.model.OWLObjectPropertyRangeAxiom; import org.semanticweb.owl.model.OWLOntology; import org.semanticweb.owl.model.OWLOr; import org.semanticweb.owl.model.OWLProperty; import org.semanticweb.owl.model.OWLPropertyDomainAxiom; import org.semanticweb.owl.model.OWLRestriction; import org.semanticweb.owl.model.OWLSameIndividualsAxiom; import org.semanticweb.owl.model.OWLSubClassAxiom; import org.semanticweb.owl.model.OWLSubPropertyAxiom; import org.semanticweb.owl.model.change.AddAnnotationInstance; import org.semanticweb.owl.model.change.AddClassAxiom; import org.semanticweb.owl.model.change.AddDataPropertyInstance; import org.semanticweb.owl.model.change.AddDataPropertyRange; import org.semanticweb.owl.model.change.AddDomain; import org.semanticweb.owl.model.change.AddEntity; import org.semanticweb.owl.model.change.AddEnumeration; import org.semanticweb.owl.model.change.AddEquivalentClass; import org.semanticweb.owl.model.change.AddIndividualAxiom; import org.semanticweb.owl.model.change.AddIndividualClass; import org.semanticweb.owl.model.change.AddInverse; import org.semanticweb.owl.model.change.AddObjectPropertyInstance; import org.semanticweb.owl.model.change.AddObjectPropertyRange; import org.semanticweb.owl.model.change.AddPropertyAxiom; import org.semanticweb.owl.model.change.AddSuperClass; import org.semanticweb.owl.model.change.AddSuperProperty; import org.semanticweb.owl.model.change.ChangeVisitor; import org.semanticweb.owl.model.change.OntologyChange; import org.semanticweb.owl.model.change.RemoveAnnotationInstance; import org.semanticweb.owl.model.change.RemoveClassAxiom; import org.semanticweb.owl.model.change.RemoveDataPropertyInstance; import org.semanticweb.owl.model.change.RemoveDataPropertyRange; import org.semanticweb.owl.model.change.RemoveDomain; import org.semanticweb.owl.model.change.RemoveEntity; import org.semanticweb.owl.model.change.RemoveEnumeration; import org.semanticweb.owl.model.change.RemoveEquivalentClass; import org.semanticweb.owl.model.change.RemoveIndividualAxiom; import org.semanticweb.owl.model.change.RemoveIndividualClass; import org.semanticweb.owl.model.change.RemoveInverse; import org.semanticweb.owl.model.change.RemoveObjectPropertyInstance; import org.semanticweb.owl.model.change.RemoveObjectPropertyRange; import org.semanticweb.owl.model.change.RemovePropertyAxiom; import org.semanticweb.owl.model.change.RemoveSuperClass; import org.semanticweb.owl.model.change.RemoveSuperProperty; import org.semanticweb.owl.model.change.SetFunctional; import org.semanticweb.owl.model.change.SetInverseFunctional; import org.semanticweb.owl.model.change.SetSymmetric; import org.semanticweb.owl.model.change.SetTransitive; import org.semanticweb.owl.model.helper.OntologyHelper; import org.semanticweb.owl.rules.OWLRule; import org.semanticweb.owl.rules.OWLRuleAtom; import org.semanticweb.owl.rules.OWLRuleClassAtom; import org.semanticweb.owl.rules.OWLRuleDataPropertyAtom; import org.semanticweb.owl.rules.OWLRuleObjectPropertyAtom; /** * @author Aditya Kalyanpur, Evren Sirin */ public class ConciseFormatEntityRenderer extends BaseEntityRenderer implements SwoopEditableRenderer, SwoopEntityRenderer { List changes = null; public Map OWLDescHash = new HashMap(); OWLEntity displayedEntity; String[] depictions = { "http://www.mindswap.org/~glapizco/technical.owl#depiction", "http://xmlns.com/foaf/0.1/depiction" }; String HR = "</tr><tr></tr><tr bgcolor=\"#FFF68F\">"; boolean imported = false; Map sortLevelMap; // params used for black box sos derivation boolean sosBlackBox = false; int axiomLimit = 40; // two maps for entities HashMap usageMap = new HashMap(); HashMap axiomMap = new HashMap(); // one map for axioms HashMap signatureMap = new HashMap(); private long parseTime = 0; private long netTime = 0; private int mupsCount = 0; public ConciseFormatEntityRenderer() { } public String getContentType() { return "text/html"; } public String getName() { return "Concise Format"; } public SwoopRenderingVisitor createVisitor() { return new ConciseFormatVisitor(this, swoopModel); } protected void renderEntity() throws OWLException { print("<html><body style='color: black; background-color: white;'>"); print("<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); super.renderEntity(); print("</FONT>"); print("</body></html>"); } // silly hack to remove artifact in display when show_divisions is ON private String postProcess(String rendStr) { if (swoopModel.getShowDivisions()) { String remove = "<tr bgcolor=\"#FFF68F\">"; if (rendStr.lastIndexOf(remove) > rendStr.lastIndexOf("<b>")) { rendStr = rendStr.substring(0, rendStr.lastIndexOf(remove)); } } return rendStr; } /* Well dodgy coding */ protected void renderAnnotationContent(Object o) throws OWLException { if (o instanceof URI) { print(escape(o)); } else if (o instanceof OWLIndividual) { print(escape(((OWLIndividual) o).getURI())); } else { String content = o.toString(); if (o instanceof OWLDataValue) { OWLDataValue dv = (OWLDataValue) o; /* Only show it if it's not string */ URI dvdt = dv.getURI(); String dvlang = dv.getLang(); if (dvdt != null) { print("(Datatype " + escape(dvdt) + ") "); } else { if (dvlang != null && !dvlang.equals("")) { print("(" + escape(dvlang) + ") "); } } content = dv.getValue().toString(); } // print(escape(dv.getValue())); // } else { // This is such a hack - Ron // if (content.indexOf("html")>=0 && content.indexOf("body")>=0) { // content = content.replaceAll("<", "<"); // content = content.replaceAll(">", ">"); // content = content.replaceAll("&", "&"); // // // remove <html><body> outer tags because it's being rendered inside a new html doc anyway // // int spos = content.indexOf("<body>")+6; // int epos = content.indexOf("</body>"); // content = content.substring(spos, epos); // if (content.trim().indexOf("<p")>=0) { // content = content.substring(content.indexOf(">")+1, content.length()); // } // content += " (**Stripped HTML tags**)"; // } // // System.out.println(content); print(" : " + escape(content)); } } /** * Return an ontology change which deletes OWL Annotation Instances * @param subj - subject of the annotation * @param prop - OWL Annotation property used * @param content - content of the annotation * @return */ private OntologyChange isDeleted(OWLObject subj, OWLAnnotationProperty prop, Object content) { OntologyChange deleted = null; Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof RemoveAnnotationInstance) { RemoveAnnotationInstance change = (RemoveAnnotationInstance) oc; if (change.getSubject().equals(subj) && change.getProperty().equals(prop) && change.getContent().equals(content)) deleted = oc; } } return deleted; } protected boolean renderAnnotations(OWLObject obj) throws OWLException { boolean printed = false; if (!obj.getAnnotations(reasoner.getOntology()).isEmpty()) { printed = true; println(); String annTitle = " <b>Annotations</b>:"; if (editorEnabled) annTitle += addTitle("A-ANN"); println(annTitle); for (Iterator it = obj.getAnnotations(reasoner.getOntology()).iterator(); it.hasNext();) { OWLAnnotationInstance oai = (OWLAnnotationInstance) it.next(); if (editorEnabled) { OntologyChange deleted = isDeleted(obj, oai.getProperty(), oai.getContent()); if (deleted != null) { print("<font color=\"red\"><strike>"); print(" " + escape(shortForm(oai.getProperty().getURI())) + " "); renderAnnotationContent(oai.getContent()); print("</strike></font>"); addUndo(deleted, "Delete", annTitle); } else { print(" " + escape(shortForm(oai.getProperty().getURI())) + " "); renderAnnotationContent(oai.getContent()); addDelete(oai, "A-ANN"); } } else { print(" " + escape(shortForm(oai.getProperty().getURI())) + " "); renderAnnotationContent(oai.getContent()); } println(); /* Do we need to do this??? */ visitor.reset(); oai.accept(visitor); // if (it.hasNext()) { // println(); // } } } // print temporarily added changes if (editorEnabled) { Set added = this.getAddedAnnotations(obj); if (added.size() > 0) { // print title if not printed already String annTitle = " <b>Annotations</b>:"; annTitle += addTitle("A-ANN"); if (!printed) { println(annTitle); printed = true; } // print added changes in green (and add undo links) for (Iterator iter = added.iterator(); iter.hasNext();) { AddAnnotationInstance change = (AddAnnotationInstance) iter.next(); print("<font color=\"green\">"); print(" " + escape(shortForm(change.getProperty().getURI())) + " "); renderAnnotationContent(change.getContent()); print("</font>"); this.addUndo(change, "Add", annTitle); println(); } } } return printed; } private boolean isExplicit(OWLObject subj, String code, OWLObject obj) throws OWLException { return this.isExplicit(subj, code, obj, null); } /** * Given a subject (OWL entity) and an object (OWL entity) and a type of relation * checks if the relation is explicitly defined in the ontology or not * If not, it is either inferred by the reasoner or imported and hence is * displayed in italics * @param subj - subject of the relationship * @param code - type of relationship * @param obj - object of the relationship * @param value - value only specified for ind-prop-value assertions * @return * @throws OWLException */ private boolean isExplicit(OWLObject subj, String code, OWLObject obj, Object value) throws OWLException { OWLOntology ontology = reasoner.getOntology(); OWLDataFactory factory = ontology.getOWLDataFactory(); if (code.equals("C-INT")) { if (subj instanceof OWLClass) { OWLClass cla = (OWLClass) subj; Iterator iter = cla.getEquivalentClasses(ontology).iterator(); while (iter.hasNext()) { Object equ = iter.next(); if (equ instanceof OWLAnd) { OWLAnd inter = (OWLAnd) equ; if (inter.getOperands().contains(obj)) return true; } } return false; } } else if (code.equals("C-UNI")) { if (subj instanceof OWLClass) { OWLClass cla = (OWLClass) subj; Iterator iter = cla.getEquivalentClasses(ontology).iterator(); while (iter.hasNext()) { Object equ = iter.next(); if (equ instanceof OWLOr) { OWLOr union = (OWLOr) equ; if (union.getOperands().contains(obj)) return true; } } return false; } } else if (code.equals("I-ONE")) { if (subj instanceof OWLClass && obj instanceof OWLIndividual) { OWLClass cla = (OWLClass) subj; Iterator iter = cla.getEnumerations(ontology).iterator(); while (iter.hasNext()) { OWLEnumeration enumer = (OWLEnumeration) iter.next(); for (Iterator iter2 = enumer.getIndividuals().iterator(); iter2.hasNext();) { OWLIndividual ind = (OWLIndividual) iter2.next(); if (ind.equals(obj)) return true; } } } return false; } else if (code.equals("C-DIS")) { Iterator iter = ontology.getClassAxioms().iterator(); while (iter.hasNext()) { OWLClassAxiom axiom = (OWLClassAxiom) iter.next(); if (axiom instanceof OWLDisjointClassesAxiom) { OWLDisjointClassesAxiom disjAxiom = (OWLDisjointClassesAxiom) axiom; if (disjAxiom.getDisjointClasses().contains(subj) && disjAxiom.getDisjointClasses().contains(obj)) return true; } } return false; } else if (code.equals("C-SUB")) { boolean asserted = false; if (subj instanceof OWLClass) asserted = ((OWLClass) subj).getSuperClasses(ontology).contains(obj); OWLSubClassAxiom subClassAxiom = factory.getOWLSubClassAxiom((OWLDescription) subj, (OWLDescription) obj); if (!asserted) asserted = (ontology.getClassAxioms().contains(subClassAxiom)); return asserted; } else if (code.equals("C-SUP")) { boolean asserted = false; if (obj instanceof OWLClass) asserted = ((OWLClass) obj).getSuperClasses(ontology).contains(subj); OWLSubClassAxiom subClassAxiom = factory.getOWLSubClassAxiom((OWLDescription) obj, (OWLDescription) subj); if (!asserted) asserted = (ontology.getClassAxioms().contains(subClassAxiom)); return asserted; } else if (code.equals("C-EQU")) { if (subj instanceof OWLClass) return ((OWLClass) subj).getEquivalentClasses(reasoner.getOntologies()).contains(obj); if (obj instanceof OWLClass) return ((OWLClass) obj).getEquivalentClasses(reasoner.getOntologies()).contains(subj); else { Set set = new HashSet(); set.add(subj); set.add(obj); OWLEquivalentClassesAxiom eqClassAxiom = factory.getOWLEquivalentClassesAxiom(set); return (ontology.getClassAxioms().contains(eqClassAxiom)); } } else if (code.equals("C-NOT")) { if (subj instanceof OWLClass) return OWLDescriptionFinder.getComplements((OWLClass) subj, reasoner.getOntologies()).contains(obj); if (obj instanceof OWLClass) return OWLDescriptionFinder.getComplements((OWLClass) obj, reasoner.getOntologies()).contains(subj); } else if (code.equals("P-DOM")) { if ((subj instanceof OWLClass) && (obj instanceof OWLProperty)) { OWLClass cla = (OWLClass) subj; OWLProperty prop = (OWLProperty) obj; return (prop.getDomains(ontology).contains(cla)); //return (getPropertiesWithDomain(cla, false).contains(prop)); } } else if (code.equals("P-INV")) { if ((subj instanceof OWLProperty) && (obj instanceof OWLProperty)) { OWLProperty p1 = (OWLProperty) subj; OWLProperty p2 = (OWLProperty) obj; return (((OWLObjectProperty) p1).getInverses(ontology).contains(p2)); //return (getPropertiesWithDomain(cla, false).contains(prop)); } } else if (code.equals("C-HASDOM")) { if ((obj instanceof OWLClass) && (subj instanceof OWLProperty)) { OWLClass cla = (OWLClass) obj; OWLProperty prop = (OWLProperty) subj; return (prop.getDomains(ontology).contains(cla)); } } else if (code.equals("P-RAN")) { if ((subj instanceof OWLClass) && (obj instanceof OWLProperty)) { OWLClass cla = (OWLClass) subj; OWLProperty prop = (OWLProperty) obj; return (prop.getRanges(ontology).contains(cla)); //return (getPropertiesWithRange(cla, false).contains(prop)); } } else if (code.equals("C-HASRAN")) { if ((obj instanceof OWLClass) && (subj instanceof OWLProperty)) { OWLClass cla = (OWLClass) obj; OWLProperty prop = (OWLProperty) subj; return (prop.getRanges(ontology).contains(cla)); } } else if (code.equals("C-TYP")) { OWLIndividual ind = (OWLIndividual) subj; OWLDescription desc = (OWLDescription) obj; if (desc instanceof OWLClass) return ind.getTypes(ontology).contains(desc); else return true; } else if (code.equals("I-INS")) { OWLIndividual ind = (OWLIndividual) obj; OWLClass c = (OWLClass) subj; return ind.getTypes(ontology).contains(c); } else if (code.equals("I-SAM")) { // get individual axioms for the ontology for (Iterator iter = ontology.getIndividualAxioms().iterator(); iter.hasNext();) { OWLIndividualAxiom indAxiom = (OWLIndividualAxiom) iter.next(); // get the set of individuals participating in each axiom Set inds = indAxiom.getIndividuals(); if (!(indAxiom instanceof OWLSameIndividualsAxiom)) continue; if (inds.contains(subj) && inds.contains(obj)) return true; } return false; } else if (code.equals("I-DIF")) { // get individual axioms for the ontology for (Iterator iter = ontology.getIndividualAxioms().iterator(); iter.hasNext();) { OWLIndividualAxiom indAxiom = (OWLIndividualAxiom) iter.next(); // get the set of individuals participating in each axiom Set inds = indAxiom.getIndividuals(); if (!(indAxiom instanceof OWLDifferentIndividualsAxiom)) continue; if (inds.contains(subj) && inds.contains(obj)) return true; } return false; } else if (code.equals("P-INSD")) { OWLIndividual ind = (OWLIndividual) subj; OWLDataProperty prop = (OWLDataProperty) obj; Set allValues = (Set) ind.getDataPropertyValues(ontology).get(prop); OWLDataValue val = (OWLDataValue) value; // Evren: if the values are defined in another ontology then allValues will be null if (allValues != null) { for (Iterator iter = allValues.iterator(); iter.hasNext();) { OWLDataValue v = (OWLDataValue) iter.next(); if (v.equals(val)) return true; } } return false; } else if (code.equals("P-INSO")) { OWLIndividual ind = (OWLIndividual) subj; OWLObjectProperty prop = (OWLObjectProperty) obj; OWLIndividual val = (OWLIndividual) value; Set allValues = (Set) ind.getObjectPropertyValues(ontology).get(prop); return (allValues != null) && allValues.contains(val); } return true; } /** * Check if a property attribute removal change is currently in the * swoopModel.unCommittedChanges and return the change if found * @param prop - property on which attribute is to be changed * @param code - code for the attribute (functional, inversefunctional..) * @return */ private OntologyChange isDeleted(OWLProperty prop, String code) { // isDeleted function for property-attribues Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof SetFunctional && code.equals("P-FUN")) { SetFunctional change = (SetFunctional) oc; if (change.getProperty().equals(prop) && !change.isFunctional()) return oc; } if (oc instanceof SetInverseFunctional && code.equals("P-IFUN")) { SetInverseFunctional change = (SetInverseFunctional) oc; if (change.getProperty().equals(prop) && !change.isInverseFunctional()) return oc; } if (oc instanceof SetTransitive && code.equals("P-TRA")) { SetTransitive change = (SetTransitive) oc; if (change.getProperty().equals(prop) && !change.isTransitive()) return oc; } if (oc instanceof SetSymmetric && code.equals("P-SYM")) { SetSymmetric change = (SetSymmetric) oc; if (change.getProperty().equals(prop) && !change.isSymmetric()) return oc; } } return null; } /** * Function to check instance' property-value axioms that are deleted * If an ontology change is returned, corresponding axiom is striked out in the HTML renderer * @param prop * @param value * @return */ private OntologyChange isDeleted(OWLProperty prop, OWLObject value) { // isDeleted function for instance' property-value pairs only Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof RemoveDataPropertyInstance && prop instanceof OWLDataProperty) { RemoveDataPropertyInstance rem = (RemoveDataPropertyInstance) oc; if (rem.getSubject().equals((OWLIndividual) displayedEntity) && rem.getProperty().equals((OWLDataProperty) prop) && rem.getObject().equals((OWLDataValue) value)) return oc; } if (oc instanceof RemoveObjectPropertyInstance && prop instanceof OWLObjectProperty) { RemoveObjectPropertyInstance rem = (RemoveObjectPropertyInstance) oc; if (rem.getSubject().equals((OWLIndividual) displayedEntity) && rem.getProperty().equals((OWLObjectProperty) prop) && rem.getObject().equals((OWLIndividual) value)) return oc; } } return null; } /** * Given a subject (OWL entity) and an object (OWL entity) and a relationship code, * check if the relationship axiom is deleted by the user or not * If an ontology change is returned, corresponding axiom is striked out in the HTML renderer * @param subj - subject of the relationship axiom * @param code - relation type code * @param obj - object of the relationship axiom * @return * @throws OWLException */ private OntologyChange isDeleted(OWLObject subj, String code, OWLObject obj) throws OWLException { OntologyChange deleted = null; Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof RemoveDomain) { RemoveDomain rem = (RemoveDomain) oc; if ((code.equals("C-HASDOM")) && (rem.getProperty().equals((OWLProperty) subj)) && (rem.getDomain().equals((OWLDescription) obj))) { deleted = oc; } if ((code.equals("P-DOM")) && (rem.getProperty().equals((OWLProperty) obj)) && (rem.getDomain().equals((OWLDescription) subj))) { deleted = oc; } } else if (oc instanceof RemoveInverse) { RemoveInverse rem = (RemoveInverse) oc; if ((code.equals("P-INV")) && (rem.getProperty().equals((OWLObjectProperty) subj)) && (rem.getInverse().equals((OWLObjectProperty) obj))) { deleted = oc; } // also inverse is deleted if ((code.equals("P-INV")) && (rem.getProperty().equals((OWLObjectProperty) obj)) && (rem.getInverse().equals((OWLObjectProperty) subj))) { deleted = oc; } } else if (oc instanceof RemoveObjectPropertyRange) { RemoveObjectPropertyRange rem = (RemoveObjectPropertyRange) oc; if (subj instanceof OWLObjectProperty) { if ((code.equals("C-HASRAN")) && (rem.getProperty().equals((OWLObjectProperty) subj)) && (rem.getRange().equals((OWLDescription) obj))) { deleted = oc; } } if (obj instanceof OWLObjectProperty) { if ((code.equals("P-RAN")) && (rem.getProperty().equals((OWLObjectProperty) obj)) && (rem.getRange().equals((OWLDescription) subj))) { deleted = oc; } } } else if (oc instanceof RemoveDataPropertyRange) { if (subj instanceof OWLDataProperty && obj instanceof OWLDataRange) { RemoveDataPropertyRange rem = (RemoveDataPropertyRange) oc; if ((code.equals("C-HASRAN")) && (rem.getProperty().equals((OWLDataProperty) subj)) && (rem.getRange().equals((OWLDataRange) obj))) { deleted = oc; } } } else if (oc instanceof RemovePropertyAxiom) { RemovePropertyAxiom rem = (RemovePropertyAxiom) oc; if (rem.getAxiom() instanceof OWLEquivalentPropertiesAxiom) { OWLEquivalentPropertiesAxiom epAxiom = (OWLEquivalentPropertiesAxiom) rem.getAxiom(); if (code.equals("P-EQU") && epAxiom.getProperties().contains((OWLProperty) obj) && epAxiom.getProperties().contains((OWLProperty) subj)) { deleted = oc; } } else if (rem.getAxiom() instanceof OWLSubPropertyAxiom) { OWLSubPropertyAxiom subPAxiom = (OWLSubPropertyAxiom) rem.getAxiom(); if (code.equals("P-SUB") && subPAxiom.getSubProperty().equals((OWLProperty) subj) && subPAxiom.getSuperProperty().equals((OWLProperty) obj)) { deleted = oc; } else if (code.equals("P-SUP") && subPAxiom.getSubProperty().equals((OWLProperty) obj) && subPAxiom.getSuperProperty().equals((OWLProperty) subj)) { deleted = oc; } } } else if (oc instanceof RemoveSuperProperty) { RemoveSuperProperty rem = (RemoveSuperProperty) oc; if (code.equals("P-SUB") && rem.getProperty().equals((OWLProperty) subj) && rem.getSuperProperty().equals((OWLProperty) obj)) { deleted = oc; } else if (code.equals("P-SUP") && rem.getProperty().equals((OWLProperty) obj) && rem.getSuperProperty().equals((OWLProperty) subj)) { deleted = oc; } } else if (oc instanceof RemoveClassAxiom) { RemoveClassAxiom rem = (RemoveClassAxiom) oc; if (rem.getAxiom() instanceof OWLDisjointClassesAxiom) { OWLDisjointClassesAxiom change = (OWLDisjointClassesAxiom) rem.getAxiom(); if ((code.equals("C-DIS")) && (change.getDisjointClasses().contains(subj)) && (change.getDisjointClasses().contains(obj))) { return oc; } } else if (rem.getAxiom() instanceof OWLSubClassAxiom) { OWLSubClassAxiom axiom = (OWLSubClassAxiom) rem.getAxiom(); if (code.equals("C-SUB") && axiom.getSubClass().equals(subj) && axiom.getSuperClass().equals(obj)) return oc; else if (code.equals("C-SUP") && axiom.getSubClass().equals(obj) && axiom.getSuperClass().equals(subj)) return oc; } } else if (oc instanceof RemoveSuperClass) { RemoveSuperClass change = (RemoveSuperClass) oc; if (code.equals("C-SUB") && change.getOWLClass().equals(subj) && change.getDescription().equals(obj)) return oc; else if (code.equals("C-SUP") && change.getOWLClass().equals(obj) && change.getDescription().equals(subj)) return oc; } else if (oc instanceof RemoveEquivalentClass) { RemoveEquivalentClass change = (RemoveEquivalentClass) oc; if (code.equals("C-EQU") && change.getOWLClass().equals(subj) && change.getDescription().equals(obj)) return oc; } else if (oc instanceof BooleanElementChange) { BooleanElementChange change = (BooleanElementChange) oc; if (code.equals("C-INT") && change.getChangeType().equals("Remove") && change.getOWLClass().equals(subj) && change.getType().equals(OWLAnd.class) && change.getOWLDescription().hashCode() == obj.hashCode()) deleted = oc; else if (code.equals("C-UNI") && change.getChangeType().equals("Remove") && change.getOWLClass().equals(subj) && change.getType().equals(OWLOr.class) && change.getOWLDescription().hashCode() == obj.hashCode()) deleted = oc; else if (code.equals("C-NOT") && change.getChangeType().equals("Remove") && change.getOWLClass().equals(subj) && change.getType().equals(OWLNot.class) && change.getOWLDescription().hashCode() == obj.hashCode()) deleted = oc; } else if (oc instanceof AddEquivalentClass) { AddEquivalentClass change = (AddEquivalentClass) oc; if (code.equals("C-INT") && change.getOWLClass().equals(subj) && change.getDescription() instanceof OWLAnd && ((OWLAnd) change.getDescription()).getOperands().contains(obj)) deleted = null; else if (code.equals("C-UNI") && change.getOWLClass().equals(subj) && change.getDescription() instanceof OWLOr && ((OWLOr) change.getDescription()).getOperands().contains(obj)) deleted = null; } else if (oc instanceof EnumElementChange) { EnumElementChange change = (EnumElementChange) oc; if (code.equals("I-ONE") && change.getChangeType().equals("Remove") && change.getOWLClass().equals(subj) && change.getOWLIndividual().hashCode() == obj.hashCode()) deleted = oc; } else if (oc instanceof RemoveIndividualClass) { RemoveIndividualClass change = (RemoveIndividualClass) oc; if (code.equals("I-INS") && change.getDescription().equals(subj) && change.getIndividual().equals(obj)) deleted = oc; else if (code.equals("C-TYP") && change.getDescription().equals(obj) && change.getIndividual().equals(subj)) deleted = oc; } else if (oc instanceof AddEnumeration) { AddEnumeration change = (AddEnumeration) oc; if (code.equals("I-ONE") && change.getOWLClass().equals(subj) && change.getEnumeration().getIndividuals().contains(obj)) deleted = null; } else if (oc instanceof RemoveIndividualAxiom) { RemoveIndividualAxiom rem = (RemoveIndividualAxiom) oc; if (rem.getAxiom() instanceof OWLSameIndividualsAxiom) { OWLSameIndividualsAxiom sameAxiom = (OWLSameIndividualsAxiom) rem.getAxiom(); if (code.equals("I-SAM") && sameAxiom.getIndividuals().contains((OWLIndividual) obj) && sameAxiom.getIndividuals().contains((OWLIndividual) subj)) { deleted = oc; } } if (rem.getAxiom() instanceof OWLDifferentIndividualsAxiom) { OWLDifferentIndividualsAxiom diffAxiom = (OWLDifferentIndividualsAxiom) rem.getAxiom(); if (code.equals("I-DIF") && diffAxiom.getIndividuals().contains((OWLIndividual) obj) && diffAxiom.getIndividuals().contains((OWLIndividual) subj)) { deleted = oc; } } } } return deleted; } /** * Same as getAdded(subj, code) except this one only checks * AddAnnotationInstance changes * @param subj * @return * @throws OWLException */ private Set getAddedAnnotations(OWLObject subj) throws OWLException { Set added = new HashSet(); Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof AddAnnotationInstance) { AddAnnotationInstance change = (AddAnnotationInstance) oc; if (change.getSubject().equals(subj)) added.add(oc); } } return added; } /** * Given a subject (OWL entity) and a code for the axiom type, * match any current uncommitted ontology change involving subject and of type code * and return a map between object of the change and the change itself * Stuff returned is rendered in 'green' in the HTML renderer * @param subj - subject of the axiom change * @param code - type of axiom change * @return * @throws OWLException */ private Map getAdded(OWLObject subj, String code) throws OWLException { Map added = new Hashtable(); Iterator i = changes.iterator(); while (i.hasNext()) { OntologyChange oc = (OntologyChange) i.next(); if (oc instanceof SetFunctional) { SetFunctional change = (SetFunctional) oc; if (code.equals("ATTRIB")) { if (change.isFunctional() && change.getProperty().equals(subj)) { // only for property attributes, add a set of ontology changes as the value in the hashmap Set ocSet = new HashSet(); if (added.containsKey(subj)) ocSet = (HashSet) added.get(subj); ocSet.add(oc); added.put(subj, ocSet); } } } else if (oc instanceof SetInverseFunctional) { SetInverseFunctional change = (SetInverseFunctional) oc; if (code.equals("ATTRIB")) { if (change.isInverseFunctional() && change.getProperty().equals(subj)) { // only for property attributes, add a set of ontology changes as the value in the hashmap Set ocSet = new HashSet(); if (added.containsKey(subj)) ocSet = (HashSet) added.get(subj); ocSet.add(oc); added.put(subj, ocSet); } } } else if (oc instanceof SetTransitive) { SetTransitive change = (SetTransitive) oc; if (code.equals("ATTRIB")) { if (change.isTransitive() && change.getProperty().equals(subj)) { // only for property attributes, add a set of ontology changes as the value in the hashmap Set ocSet = new HashSet(); if (added.containsKey(subj)) ocSet = (HashSet) added.get(subj); ocSet.add(oc); added.put(subj, ocSet); } } } else if (oc instanceof SetSymmetric) { SetSymmetric change = (SetSymmetric) oc; if (code.equals("ATTRIB")) { if (change.isSymmetric() && change.getProperty().equals(subj)) { // only for property attributes, add a set of ontology changes as the value in the hashmap Set ocSet = new HashSet(); if (added.containsKey(subj)) ocSet = (HashSet) added.get(subj); ocSet.add(oc); added.put(subj, ocSet); } } } else if (oc instanceof AddSuperClass) { AddSuperClass change = (AddSuperClass) oc; if (code.equals("C-SUB") && change.getOWLClass().equals(subj)) added.put(change.getDescription(), oc); else if (code.equals("C-SUP") && change.getDescription().equals(subj)) added.put(change.getOWLClass(), oc); } else if (oc instanceof RemoveSuperClass) { RemoveSuperClass change = (RemoveSuperClass) oc; if (code.equals("C-SUB") && change.getOWLClass().equals(subj)) added.remove(change.getDescription()); else if (code.equals("C-SUP") && change.getDescription().equals(subj)) added.remove(change.getOWLClass()); } else if (oc instanceof AddEquivalentClass) { AddEquivalentClass change = (AddEquivalentClass) oc; if (code.equals("C-EQU") && change.getOWLClass().equals(subj)) added.put(change.getDescription(), oc); } else if (oc instanceof BooleanElementChange) { BooleanElementChange change = (BooleanElementChange) oc; if (code.equals("C-INT") && change.getChangeType().equals("Add") && change.getType().equals(OWLAnd.class) && change.getOWLClass().equals(subj)) { added.put(change.getOWLDescription(), oc); } else if (code.equals("C-UNI") && change.getChangeType().equals("Add") && change.getType().equals(OWLOr.class) && change.getOWLClass().equals(subj)) { added.put(change.getOWLDescription(), oc); } else if (code.equals("C-NOT") && change.getChangeType().equals("Add") && change.getType().equals(OWLNot.class) && change.getOWLClass().equals(subj)) { added.put(change.getOWLDescription(), oc); } } else if (oc instanceof RemoveEquivalentClass) { RemoveEquivalentClass change = (RemoveEquivalentClass) oc; if (code.equals("C-EQU") && change.getOWLClass().equals(subj) && !(change.getDescription() instanceof OWLAnd) && !(change.getDescription() instanceof OWLOr) && !(change.getDescription() instanceof OWLEnumeration)) added.remove(change.getDescription()); else if (code.equals("C-INT") && change.getOWLClass().equals(subj) && change.getDescription() instanceof OWLAnd) added.keySet().removeAll(((OWLAnd) change.getDescription()).getOperands()); else if (code.equals("C-UNI") && change.getOWLClass().equals(subj) && change.getDescription() instanceof OWLOr) added.keySet().removeAll(((OWLOr) change.getDescription()).getOperands()); } else if (oc instanceof AddClassAxiom) { if (code.equals("C-DIS")) { AddClassAxiom change = (AddClassAxiom) oc; if (change.getAxiom() instanceof OWLDisjointClassesAxiom) { OWLDisjointClassesAxiom disAxiom = (OWLDisjointClassesAxiom) change.getAxiom(); if (disAxiom.getDisjointClasses().contains(subj)) { Iterator j = disAxiom.getDisjointClasses().iterator(); while (j.hasNext()) added.put(j.next(), oc); added.remove(subj); } } } else if (code.equals("C-SUP")) { AddClassAxiom change = (AddClassAxiom) oc; if (change.getAxiom() instanceof OWLSubClassAxiom) { OWLSubClassAxiom subAxiom = (OWLSubClassAxiom) change.getAxiom(); if (subAxiom.getSuperClass().equals(subj)) { added.put(subAxiom.getSubClass(), oc); } } } } else if (oc instanceof AddDomain) { AddDomain change = (AddDomain) oc; if (code.equals("P-DOM") && change.getDomain().equals(subj)) { added.put(change.getProperty(), oc); } if (code.equals("C-HASDOM") && change.getProperty().equals(subj)) { added.put(change.getDomain(), oc); } } else if (oc instanceof AddObjectPropertyRange) { AddObjectPropertyRange change = (AddObjectPropertyRange) oc; if (code.equals("P-RAN") && change.getRange().equals(subj)) { added.put(change.getProperty(), oc); } if (code.equals("C-HASRAN") && change.getProperty().equals(subj)) { added.put(change.getRange(), oc); } } else if (oc instanceof AddInverse) { AddInverse change = (AddInverse) oc; if (code.equals("P-INV") && change.getProperty().equals(subj)) { added.put(change.getInverse(), oc); } // also inverse gets added if (code.equals("P-INV") && change.getInverse().equals(subj)) { added.put(change.getProperty(), oc); } } else if (oc instanceof AddDataPropertyRange) { AddDataPropertyRange change = (AddDataPropertyRange) oc; if (code.equals("P-RAN") && change.getRange().equals(subj)) { added.put(change.getProperty(), oc); } if (code.equals("C-HASRAN") && change.getProperty().equals(subj)) { added.put(change.getRange(), oc); } } else if (oc instanceof AddPropertyAxiom) { AddPropertyAxiom change = (AddPropertyAxiom) oc; if (change.getAxiom() instanceof OWLEquivalentPropertiesAxiom && code.equals("P-EQU")) { OWLEquivalentPropertiesAxiom propAxiom = (OWLEquivalentPropertiesAxiom) change.getAxiom(); if (code.equals("P-EQU") && propAxiom.getProperties().contains(subj)) { Set equSet = new HashSet(propAxiom.getProperties()); equSet.remove(subj); Iterator iter = equSet.iterator(); while (iter.hasNext()) { added.put(iter.next(), oc); } } } } if (oc instanceof AddSuperProperty) { AddSuperProperty change = (AddSuperProperty) oc; if ((code.equals("P-SUB")) && (change.getProperty().equals(subj))) { added.put(change.getSuperProperty(), oc); } if ((code.equals("P-SUP")) && (change.getSuperProperty().equals(subj))) { added.put(change.getProperty(), oc); } } else if (oc instanceof AddIndividualClass) { AddIndividualClass change = (AddIndividualClass) oc; OWLIndividual ind = change.getIndividual(); OWLDescription desc = change.getDescription(); if (code.equals("I-INS") && desc.equals(subj)) { added.put(change.getIndividual(), oc); } else if (code.equals("C-TYP") && ind.equals(subj)) { added.put(change.getDescription(), oc); } } else if (oc instanceof EnumElementChange) { EnumElementChange change = (EnumElementChange) oc; if ((code.equals("I-ONE")) && (change.getChangeType().equals("Add")) && (change.getOWLClass().equals(subj))) { added.put(change.getOWLIndividual(), oc); } } else if (oc instanceof RemoveEnumeration) { RemoveEnumeration change = (RemoveEnumeration) oc; if ((code.equals("I-ONE")) && (change.getOWLClass().equals(subj))) { OWLEnumeration enumElem = change.getEnumeration(); added.keySet().removeAll(enumElem.getIndividuals()); } } else if (oc instanceof AddIndividualAxiom) { AddIndividualAxiom change = (AddIndividualAxiom) oc; if (code.equals("I-SAM")) { if (change.getAxiom() instanceof OWLSameIndividualsAxiom) { OWLSameIndividualsAxiom sameAxiom = (OWLSameIndividualsAxiom) change.getAxiom(); if (sameAxiom.getIndividuals().contains(subj)) { Iterator j = sameAxiom.getIndividuals().iterator(); while (j.hasNext()) added.put(j.next(), oc); added.remove(subj); } } } if (code.equals("I-DIF")) { if (change.getAxiom() instanceof OWLDifferentIndividualsAxiom) { OWLDifferentIndividualsAxiom diffAxiom = (OWLDifferentIndividualsAxiom) change.getAxiom(); if (diffAxiom.getIndividuals().contains(subj)) { Iterator j = diffAxiom.getIndividuals().iterator(); while (j.hasNext()) added.put(j.next(), oc); added.remove(subj); } } } } } return added; } private void printConciseObject(OWLEntity obj) { try { if (obj == null) return; String objURI = obj.getURI().toString(); String objName = shortForm(obj.getURI()); // String imageURI = baseImageURI; // JAVA WEBSTART STUFF boolean showIcon = swoopModel.getShowIcons(); if (obj instanceof OWLClass && swoopModel.getEnableDebugging()) showIcon = true; if (showIcon || swoopModel.getEnableDebugging()) { String imageURI = "http://www.mindswap.org/2004/SWOOP/icons/"; // JAVA WEBSTART STUFF if (obj instanceof OWLClass) { boolean isConsistent = reasoner.isConsistent((OWLClass) obj); if (isConsistent) imageURI += "InconsistentClass.gif"; else imageURI += "Class.gif"; } //************************************************* //changed for Econns //************************************************* else if (obj instanceof OWLObjectProperty) { if (((OWLObjectProperty) obj).isLink()) { imageURI += "LinkProperty.GIF"; } else { imageURI += "Property.gif"; } } else if (obj instanceof OWLDataProperty) imageURI += "DataProperty.gif"; else if (obj instanceof OWLIndividual) imageURI += "Instance.gif"; if (imageURI.endsWith(".gif") || imageURI.endsWith(".GIF")) print("<img src=\"" + imageURI + "\">"); } print("<a href=\"" + StringEscapeUtils.escapeHtml(objURI) + "\">" + StringEscapeUtils.escapeHtml(objName) + "</a>"); } catch (Exception e) { e.printStackTrace(); } } private void printLine(OWLObject obj, String title) throws OWLException { String code = getCode(title); boolean explicit = isExplicit(displayedEntity, code, obj); OntologyChange oc = editorEnabled ? isDeleted(displayedEntity, code, obj) : null; boolean deleted = (oc != null); if (deleted) print("<font color=\"red\"><strike>"); else if (!explicit) print("<i>"); printObject(obj); if (editorEnabled && !deleted && explicit) { // add delete hyperlink in editable mode // store object hash addDelete(obj, title); } if (!explicit) { print("</i>"); if (reasoner.supportsExplanation()) addWhy(obj, title); } else if (deleted) { print("</strike></font>"); addUndo(oc, "Delete", title); } println(); } private void printCollection(Collection coll, String title) throws OWLException { if (coll.isEmpty()) return; if (title != null) { println(); println(title); } Iterator i = coll.iterator(); while (i.hasNext()) { Object obj = i.next(); // if there is more than one element for this line // we only print the first one. rest are either // equivalent classes (or properties) if (obj instanceof Collection) { if (((Collection) obj).size() > 0) obj = ((Collection) obj).iterator().next(); else return; // empty set } // if debugging is enabled, for each class description, check consistency if (swoopModel.getEnableDebugging() && obj instanceof OWLDescription && !(obj instanceof OWLClass)) { URL imageURI; // = baseImageURI; OWLDescription claExpr = (OWLDescription) obj; boolean isConsistent = reasoner.isConsistent(claExpr); if (!isConsistent) { imageURI = SwoopIcons.getImageURL("InconsistentClassExpression.gif"); } else { imageURI = SwoopIcons.getImageURL("ClassExpression.gif"); } String hashCode = String.valueOf(claExpr.hashCode()); OWLDescHash.put(hashCode, claExpr); print("<a href=\"<CE:" + hashCode + "\"><img src=\"" + imageURI + "\"></a>"); } printLine((OWLObject) obj, title); } insertAddedChanges(coll, displayedEntity, title, ""); } /** * Accepts a collection (coll) of objects already displayed, * gets all added objects on (displayedEntity), matching the (title)/code, * inserts added objects not present in collection * @param coll * @param displayedEntity * @param title * @param titleHead * @throws OWLException */ protected boolean insertAddedChanges(Collection coll, OWLEntity displayedEntity, String title, String titleHead) throws OWLException { boolean printed = false; String code = getCode(title); if (editorEnabled) { Map added = getAdded(displayedEntity, code); if (!added.isEmpty()) { printed = true; if (!titleHead.equals("")) { println(); println(titleHead + addTitle(code)); } Iterator j = added.entrySet().iterator(); while (j.hasNext()) { Map.Entry entry = (Map.Entry) j.next(); OWLObject obj = (OWLObject) entry.getKey(); if (coll.contains(obj)) continue; Object change = entry.getValue(); print("<font color=\"green\">"); printObject(obj); print("</font>"); addUndo(change, "Add", title); println(); } } } return printed; } protected void renderClass(OWLClass clazz) throws OWLException { // check if class being rendered is a class expression if (clazz.getURI().toString().indexOf("#ClassExpression") >= 0) { String uri = clazz.getURI().toString(); String hashCode = uri.substring(uri.indexOf("#ClassExpression") + 16, uri.length()); // obtain class expression from hash OWLDescription claExpr = swoopModel.getCEfromHash(hashCode); // turn editable off boolean saveEditable = this.editorEnabled; this.editorEnabled = false; // print class expression print("Class Expression: "); printLine((OWLObject) claExpr, ""); // print equivalent classes of CE String equTitle = "<b>Equivalent to:</b>"; Set eqs = reasoner.equivalentClassesOf(claExpr); printCollection(eqs, equTitle); // print subclasses of CE String subTitle = "<b>Sub-Class of:</b>"; Set sub = reasoner.superClassesOf(claExpr); printCollection(sub, subTitle); // print superclasses of CE String supTitle = "<b>Super-Class of:</b>"; Set sup = reasoner.subClassesOf(claExpr); printCollection(sup, supTitle); // restore editable setting this.editorEnabled = saveEditable; return; } // check if class is in current ontology or imported String importedLbl = ""; imported = false; if (!clazz.getOntologies().contains(swoopModel.getSelectedOntology())) { importedLbl = "Imported "; imported = true; } Iterator i = null; List notPrinted = new ArrayList(); OWLClass owlThing = reasoner.getOntology().getOWLDataFactory().getOWLThing(); OWLClass owlNothing = reasoner.getOntology().getOWLDataFactory().getOWLNothing(); //****** TESTING PURPOSES ONLY *************** // print("<a href=\"PELLET-SATURATION\">SATURATION TEST</a><br>"); // ******************************************* print("<b>" + importedLbl + "OWL-Class:</b> "); printObject(clazz); if (importedLbl.length() > 0) { println(); // print("<b>Imported from Ontology(s):</b> "); // also print where the class is imported from Iterator ontIter = clazz.getOntologies().iterator(); while (ontIter.hasNext()) { OWLOntology ont = (OWLOntology) ontIter.next(); String ontURI = ont.getURI().toString(); String ontName = ontURI.substring(ontURI.lastIndexOf("/") + 1, ontURI.length()); String classXPtrURI = clazz.getURI() + XPointers.asDefinedIn + "(" + ontURI + ")"; print("See its definition in Imported Ontology: <a href=\"" + escape(classXPtrURI) + "\">" + escape(ontName) + "</a>"); // print("<a href=\""+ontURI+"asDefinedIn("+ontURI+")\">"+className+"</a> "); println(); } println(); } println(); //*** explanations for inconsistent class if (!reasoner.isConsistent(clazz)) { println("<font color=\"red\"><b>Unsatisfiable concept</b></font>"); if (reasoner instanceof PelletReasoner && swoopModel.isDebugGlass()) { if (swoopModel.findAllMUPS) parseTime = 0; Timer mupsTimer = new Timer("MUPS Processing Time"); mupsTimer.start(); // create a set of sets for MUPS List MUPS = new ArrayList(); List explStr = new ArrayList(); // also get explanation strings if using tableau Set explanationSet = new HashSet(); if (swoopModel.isUseTableau()) { // call debugging version of Pellet instead List explSOS = this.getTableauSOS(swoopModel.getSelectedOntology(), clazz); // String explanation = explSOS.get(0).toString(); // get explanation set from pellet explanationSet = (HashSet) explSOS.get(1); explStr.add(explSOS.get(0).toString()); } else { // use black box method instead explanationSet = this.getBlackBoxSOS(swoopModel.getSelectedOntology(), clazz); } MUPS.add(explanationSet); // find all MUPS using Hitting Set Trees approach if (swoopModel.isFindAllMUPS()) HSTMUPS(explanationSet, swoopModel.getSelectedOntology(), MUPS, explStr, new HashSet(), new HashSet()); mupsTimer.stop(); System.out.println("------ MUPS PROCEDURE COMPLETE -------"); if (swoopModel.findAllMUPS) { System.out.println(mupsTimer); System.out.println("parse time: " + parseTime); System.out.println("net time: " + String.valueOf(mupsTimer.getTotal() - parseTime)); netTime = mupsTimer.getTotal() - parseTime; mupsCount = MUPS.size(); } Object[] explObj = explStr.toArray(); int o = 0; HashMap explMap = new HashMap(); Set mupsSet = new HashSet(); for (Iterator iter = MUPS.iterator(); iter.hasNext();) { Set explSet = (HashSet) iter.next(); mupsSet.add(explSet); if (o < explObj.length && explObj[o] != null) { String expl = explObj[o].toString(); explMap.put(explSet, expl); } o++; } for (Iterator iter = mupsSet.iterator(); iter.hasNext();) { Set m = (HashSet) iter.next(); print("<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); if (explMap.containsKey(m)) println(explMap.get(m).toString()); this.printExplanationSOS(m, clazz, false); } } } //*** // rules stuff if (swoopModel.getEnableRules()) { RulesExpressivity ruleExpr = swoopModel.getRuleExpr(); Set rules = ruleExpr.getRules(clazz); String ruleTitle = "<b>Rules:</b>"; if (editorEnabled) ruleTitle += addTitle("RULE"); pw.println("\n" + ruleTitle + " \n<br>"); for (Iterator iter = rules.iterator(); iter.hasNext();) { OWLRule rule = ((RuleValue) iter.next()).getRule(); String ruleDesc = rule.toString(); int ptr; ptr = ruleDesc.indexOf(">") + 1; String consequent = ruleDesc.substring(ptr, ruleDesc.indexOf(".")); String varConsequent = consequent.substring((consequent.indexOf("(") + 1), consequent.indexOf(")")); ruleDesc = ruleDesc.substring(0, ptr - 2) + "."; ruleDesc = consequent + " <b>:-</b> " + ruleDesc; ptr = 0; ruleDesc = " " + ruleDesc; String hyperRule = ruleDesc; while ((ptr = ruleDesc.indexOf("(", ptr)) >= 0) { String name = ruleDesc.substring(ruleDesc.lastIndexOf(" ", ptr), ptr); String uri = this.getURIForTerm(name.trim()); hyperRule = hyperRule.replaceAll(name, "<a href=\"" + uri + "\">" + name + "</a>"); ptr++; } if (editorEnabled) { pw.print(hyperRule); String hash = String.valueOf(rule.hashCode()); OWLDescHash.put(hash, rule); String titleCode = "RULE"; //getCode(title); pw.print(" (<font color=\"red\"><a href=\"<Delete:" + hash + ":" + titleCode + "\">Delete</a></font>) "); pw.print(" (<font color=\"red\"><a href=\"<Edit:" + hash + ":" + titleCode + "\">Edit</a></font>)"); pw.print(" (<font color=\"red\"><a href=\"<Publish:" + hash + ":" + titleCode + "\">Publish</a></font>)"); pw.println("<br>"); } else { pw.println(hyperRule + "<br>"); } } } if (showDivisions) { print("<table cellpadding=\"5\"><tr bgcolor=\"#FFF68F\"><FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); } boolean printedAnn = renderAnnotations(clazz); if (!printedAnn) notPrinted.add("A-ANN"); else if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); int notPrintedSize = notPrinted.size(); i = OWLDescriptionFinder.getIntersections(clazz, reasoner.getOntologies()).iterator(); if (!i.hasNext()) { // insert added elements boolean printed = insertAddedChanges(new HashSet(), clazz, "C-INT", "<b>Intersection of:</b>"); if (!printed) notPrinted.add("C-INT"); } while (i.hasNext()) { OWLAnd intersection = (OWLAnd) i.next(); String title = "<b>Intersection of:</b>"; if (editorEnabled) title += addTitle("C-INT"); // check for empty collection if (intersection.getOperands().size() == 0) { // copy from above boolean printed = insertAddedChanges(new HashSet(), clazz, "C-INT", "<b>Intersection of:</b>"); if (!printed) notPrinted.add("C-INT"); } else printCollection(intersection.getOperands(), title); } i = OWLDescriptionFinder.getUnions(clazz, reasoner.getOntologies()).iterator(); if (!i.hasNext()) { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-UNI", "<b>Union of:</b>"); if (!printed) notPrinted.add("C-UNI"); } while (i.hasNext()) { OWLOr union = (OWLOr) i.next(); String title = "<b>Union of:</b>"; if (editorEnabled) title += addTitle("C-UNI"); // check for empty collection if (union.getOperands().size() == 0) { //copy from above boolean printed = insertAddedChanges(new HashSet(), clazz, "C-UNI", "<b>Union of:</b>"); if (!printed) notPrinted.add("C-UNI"); } else printCollection(union.getOperands(), title); } i = OWLDescriptionFinder.getEnumerations(clazz, reasoner.getOntologies()).iterator(); if (!i.hasNext()) { boolean printed = insertAddedChanges(new HashSet(), clazz, "I-ONE", "<b>One of:</b>"); if (!printed) notPrinted.add("I-ONE"); } while (i.hasNext()) { OWLEnumeration oneOf = (OWLEnumeration) i.next(); String title = "<b>One of:</b>"; if (editorEnabled) title += addTitle("I-ONE"); // check for empty collection if (oneOf.getIndividuals().size() == 0) { //copy from above boolean printed = insertAddedChanges(new HashSet(), clazz, "I-ONE", "<b>One of:</b>"); if (!printed) notPrinted.add("I-ONE"); } else printCollection(oneOf.getIndividuals(), title); } if ((notPrinted.size() - notPrintedSize < 3) && (showDivisions)) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); // print equivalent classes String equTitle = "<b>Equivalent to:</b>"; if (editorEnabled) equTitle += addTitle("C-EQU"); // get defined equivalentclasses Set eqs = OWLDescriptionFinder.getEquivalentClasses(clazz, reasoner.getOntologies()); // remove all complements i = eqs.iterator(); while (i.hasNext()) { OWLDescription desc = (OWLDescription) i.next(); if (!(desc instanceof OWLClass || desc instanceof OWLRestriction)) i.remove(); } if (reasoner.isConsistent(clazz)) { // add all the named equivalent classes eqs.addAll(reasoner.equivalentClassesOf(clazz)); } else eqs.add(owlNothing); // title is not printed if there was no equivalent class if (!eqs.isEmpty()) { printCollection(eqs, equTitle); } else { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-EQU", "<b>Equivalent to:</b>"); if (!printed) notPrinted.add("C-EQU"); } // print complements String notTitle = "<b>Complement of:</b>"; if (editorEnabled) notTitle += addTitle("C-NOT"); // get complements Set nots = OWLDescriptionFinder.getComplements(clazz, reasoner.getOntologies()); if (nots.isEmpty()) { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-NOT", "<b>Complement of:</b>"); if (!printed) notPrinted.add("C-NOT"); } else { // if(reasoner.isConsistent(clazz)) { // // add all the named equivalent classes // nots.addAll(reasoner.equivalentClassesOf(clazz)); // } // else // nots.add(owlNothing); printCollection(nots, notTitle); } // print named disjoints String disTitle = "<b>Disjoint with:</b>"; Set disjoints = OWLDescriptionFinder.getDisjoints(clazz, reasoner.getOntologies()); if (disjoints.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-DIS", disTitle); if (!printed) notPrinted.add("C-DIS"); } else { if (editorEnabled) disTitle += addTitle("C-DIS"); printCollection(disjoints, disTitle); } // get defined superclasses Set supers = OWLDescriptionFinder.getSuperClasses(clazz, reasoner.getOntologies()); if (reasoner.isConsistent(clazz)) { // remove all the named classes because reasoner will eventually add them i = supers.iterator(); while (i.hasNext()) if (i.next() instanceof OWLClass) i.remove(); // add all the named superclasses supers.addAll(reasoner.superClassesOf(clazz)); // remove owl:Thing from the superclass set i = supers.iterator(); while (i.hasNext()) { Object o = i.next(); if (o instanceof Set && ((Set) o).contains(owlThing)) i.remove(); } } String subTitle = "<b>Subclass of:</b>"; if (supers.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-SUB", "<b>Subclass of:</b>"); if (!printed) notPrinted.add("C-SUB"); } else { if (editorEnabled) subTitle += addTitle("C-SUB"); printCollection(supers, subTitle); } // print named subclasses // and asserted complex subclasses String supTitle = "<b>Superclass of:</b>"; if (editorEnabled) supTitle += addTitle("C-SUP"); Set subs = reasoner.subClassesOf(clazz); subs = SetUtils.union(subs); subs.addAll(OWLDescriptionFinder.getSubClasses(clazz, reasoner.getOntologies())); subs.remove(owlNothing); subs.removeAll(reasoner.equivalentClassesOf(owlNothing)); if (subs.size() >= 1) printCollection(subs, supTitle); else { boolean printed = insertAddedChanges(new HashSet(), clazz, "C-SUP", "<b>Superclass of:</b>"); if (!printed) notPrinted.add("C-SUP"); } if ((notPrinted.size() - notPrintedSize < 5) && (showDivisions)) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); // start printing properties whose domain/range is this class String domTitle = "<b>Domain of:</b>"; if (editorEnabled) domTitle += addTitle("P-DOM"); if (getPropertiesWithDomain(clazz, showInherited).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), clazz, "P-DOM", "<b>Domain of:</b>"); if (!printed) notPrinted.add("P-DOM"); } else printCollection(getPropertiesWithDomain(clazz, showInherited), domTitle); String ranTitle = "<b>Range of:</b>"; if (editorEnabled) ranTitle += addTitle("P-RAN"); if (getPropertiesWithRange(clazz, showInherited).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), clazz, "P-RAN", "<b>Range of:</b>"); if (!printed) notPrinted.add("P-RAN"); } else printCollection(getPropertiesWithRange(clazz, showInherited), ranTitle); if ((notPrinted.size() - notPrintedSize < 2) && (showDivisions)) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); Set instances = new HashSet(); if (showInherited) instances = reasoner.allInstancesOf(clazz); else instances = reasoner.instancesOf(clazz); String insTitle = "<b>Instances:</b>"; if (editorEnabled) insTitle += addTitle("I-INS"); if (instances.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), clazz, "I-INS", "<b>Instances:</b>"); if (!printed) notPrinted.add("I-INS"); } else printCollection(instances, insTitle); if ((notPrinted.size() - notPrintedSize < 1) && (showDivisions)) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); if (showDivisions && !editorEnabled) { print("</tr>"); } // add unprinted titles at the bottom addUnprinted(notPrinted); } /** * Add all the unprinted parameters at the end of the CF pane if editor is enabled * @param notPrinted */ protected void addUnprinted(List notPrinted) { if (editorEnabled) { Iterator npIter = notPrinted.iterator(); boolean div1 = false, div2 = false, div3 = false, div4 = false, div5 = false, div6 = false, div7 = false; while (npIter.hasNext()) { String typeCode = npIter.next().toString(); if (typeCode.equals("A-ANN")) { println(); println(" <b>Annotations</b>:" + addTitle(typeCode)); if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); } if (typeCode.equals("C-INT")) { div1 = true; println(); println(" <b>Intersection of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-UNI")) { div1 = true; println(); println(" <b>Union of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("I-ONE")) { div1 = true; println(); println(" <b>One of:</b>" + addTitle(typeCode)); } else if (showDivisions && div1) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div1 = false; } if (typeCode.equals("C-EQU")) { div2 = true; println(); println(" <b>Equivalent to:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-NOT")) { div2 = true; println(); println(" <b>Complement of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-DIS")) { div2 = true; println(); println(" <b>Disjoint with:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-SUB")) { div2 = true; println(); println(" <b>Subclass of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-SUP")) { div2 = true; println(); println(" <b>Superclass of:</b>" + addTitle(typeCode)); } else if (showDivisions && div2) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div2 = false; } if (typeCode.equals("P-DOM")) { div3 = true; println(); println(" <b>Domain of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("P-RAN")) { div3 = true; println(); println(" <b>Range of:</b>" + addTitle(typeCode)); } else if (showDivisions && div3) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div3 = false; } if (typeCode.equals("I-INS")) { println(); println(" <b>Instances:</b>" + addTitle(typeCode)); } // render unassigned property axiom divisions if (typeCode.equals("P-EQU")) { div4 = true; println(); println(" <b>Equivalent to:</b>" + addTitle(typeCode)); } else if (typeCode.equals("P-INV")) { div4 = true; println(); println(" <b>Inverse of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("P-SUB")) { div4 = true; println(); println(" <b>Subproperty of:</b>" + addTitle(typeCode)); } else if (typeCode.equals("P-SUP")) { div4 = true; println(); println(" <b>Superproperty of:</b>" + addTitle(typeCode)); } else if (showDivisions && div4) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div4 = false; } if (typeCode.equals("C-HASDOM")) { div5 = true; println(); println(" <b>Has Domain:</b>" + addTitle(typeCode)); } else if (typeCode.equals("C-HASRAN")) { div5 = true; println(); println(" <b>Has Range:</b>" + addTitle(typeCode)); } else if (showDivisions && div5) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div5 = false; } if (typeCode.equals("ATTRIB")) { println(); println(" <b>Attributes:</b>" + addTitle(typeCode)); } // render individual related information if (typeCode.equals("C-TYP")) { println(); println("<b>Instance of:</b>" + addTitle(typeCode)); div6 = true; } else if (typeCode.equals("I-SAM")) { println(); println("<b>Same As:</b>" + addTitle(typeCode)); div6 = true; } else if (typeCode.equals("I-DIF")) { println(); println("<b>Different From:</b>" + addTitle(typeCode)); div6 = true; } else if (showDivisions && div6) { print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); div6 = false; } if (typeCode.equals("P-INSD")) { println(); println("<b>Datatype Assertions:</b>" + addTitle(typeCode)); div7 = true; } if (typeCode.equals("P-INSO")) { println(); println("<b>Object Assertions:</b>" + addTitle(typeCode)); div7 = true; } } } } protected String addTitle(String param) { String title = " (<font color=\"red\"><a href=\"<Add" + param + "\">Add</a></font>)"; return title; } protected String getCode(String title) { String titleCode = title; if (editorEnabled) { // remove hyperlink stuff and return code if (title.indexOf("red") >= 0) { int spos = title.indexOf("<a href=\"<") + 10; int epos = title.indexOf("\"", spos + 1); titleCode = title.substring(spos, epos); titleCode = titleCode.substring(3, titleCode.length()); // remove 'Add..' } } else { // return code directly if (title.equals("<b>Intersection of:</b>")) titleCode = "C-INT"; else if (title.equals("<b>Union of:</b>")) titleCode = "C-UNI"; else if (title.equals("<b>One of:</b>")) titleCode = "I-ONE"; else if (title.equals("<b>Equivalent to:</b>")) { if (displayedEntity instanceof OWLClass) titleCode = "C-EQU"; else titleCode = "P-EQU"; } else if (title.equals("<b>Disjoint with:</b>")) titleCode = "C-DIS"; else if (title.equals("<b>Complement of:</b>")) titleCode = "C-NOT"; else if (title.equals("<b>Subclass of:</b>")) titleCode = "C-SUB"; else if (title.equals("<b>Superclass of:</b>")) titleCode = "C-SUP"; else if (title.equals("<b>Domain of:</b>")) titleCode = "P-DOM"; else if (title.equals("<b>Range of:</b>")) titleCode = "P-RAN"; else if (title.equals("<b>Instances:</b>")) titleCode = "I-INS"; else if (title.equals("<b>Instance of:</b>")) titleCode = "C-TYP"; else if (title.equals("<b>Inverse of:</b>")) titleCode = "P-INV"; else if (title.equals("<b>Subproperty of:</b>")) titleCode = "P-SUB"; else if (title.equals("<b>Superproperty of:</b>")) titleCode = "P-SUP"; else if (title.equals("<b>Has domain:</b>")) titleCode = "C-HASDOM"; else if (title.equals("<b>Has range:</b>")) titleCode = "C-HASRAN"; } return titleCode; } protected void addWhy(Object obj, String title) { String hash = String.valueOf(obj.hashCode()); OWLDescHash.put(hash, obj); String titleCode = getCode(title); if (!imported) { print(" (<font color=\"red\"><a href=\"<Why:" + hash + ":" + titleCode + "\">Why?</a></font>)"); } } protected void addDelete(Object obj, String title) { String hash = String.valueOf(obj.hashCode()); OWLDescHash.put(hash, obj); String titleCode = getCode(title); if (!imported) { print(" (<font color=\"red\"><a href=\"<Delete:" + hash + ":" + titleCode + "\">Delete</a></font>)"); } } protected void addValueLink(OWLProperty prop) { String hash = String.valueOf(prop.hashCode()); OWLDescHash.put(hash, prop); print(" (<font color=\"red\"><a href=\"<AddV:" + hash + "\">Add Value</a></font>)"); } protected void deleteValueLink(OWLProperty prop, OWLDataValue dtv) { String hash1 = String.valueOf(prop.hashCode()); String hash2 = String.valueOf(dtv.hashCode()); OWLDescHash.put(hash1, prop); OWLDescHash.put(hash2, dtv); print(" (<font color=\"red\"><a href=\"<Delete:" + hash1 + ":P-VAL:" + hash2 + "\">Delete</a></font>)"); } protected void deleteValueLink(OWLProperty prop, OWLIndividual ind) { String hash1 = String.valueOf(prop.hashCode()); String hash2 = String.valueOf(ind.hashCode()); OWLDescHash.put(hash1, prop); OWLDescHash.put(hash2, ind); print(" (<font color=\"red\"><a href=\"<Delete:" + hash1 + ":P-VAL:" + hash2 + "\">Delete</a></font>)"); } protected void deleteTypeLink(OWLDescription cla) { String hash = String.valueOf(cla.hashCode()); OWLDescHash.put(hash, cla); print(" (<font color=\"red\"><a href=\"<Delete:" + hash + ":I-INS\">Delete</a></font>)"); } protected void addUndo(Object obj, String type, String title) { String hash = String.valueOf(obj.hashCode()); OWLDescHash.put(hash, obj); String titleCode = getCode(title); print(" (<font color=\"red\"><a href=\"<Undo:" + type + ":" + hash + ":" + titleCode + "\">Undo</a></font>)"); } protected String isImage(String url) { Set imageExtSet = new HashSet(); imageExtSet.add("jpg"); imageExtSet.add("gif"); if (url.indexOf("<a href=") >= 0) { int spos = url.indexOf("<a href=\"<") + 10; int epos = url.indexOf("\"", spos + 1); url = url.substring(spos, epos); String ext = url.substring(url.lastIndexOf(".") + 1, url.length()); if (imageExtSet.contains(ext)) { return url; } } return ""; } protected void renderIndividual(OWLIndividual ind) throws OWLException { // check if individual is in current ontology or imported String importedLbl = ""; imported = false; List unprinted = new ArrayList(); if (!ind.getOntologies().contains(swoopModel.getSelectedOntology())) { importedLbl = "Imported "; imported = true; } OWLClass owlThing = reasoner.getOntology().getOWLDataFactory().getOWLThing(); print("<b>" + importedLbl + "OWL-Individual:</b> "); if (ind.isAnonymous()) println("Anonymous "); else println(shortForm(ind.getURI()) + " "); if (importedLbl.length() > 0) { println(); // print("<b>Imported from Ontology(s):</b> "); // also print where the class is imported from Iterator ontIter = ind.getOntologies().iterator(); while (ontIter.hasNext()) { OWLOntology ont = (OWLOntology) ontIter.next(); String ontURI = ont.getURI().toString(); String ontName = ontURI.substring(ontURI.lastIndexOf("/") + 1, ontURI.length()); String indXPtrURI = ind.getURI() + XPointers.asDefinedIn + "(" + ontURI + ")"; print("See its definition in Imported Ontology: <a href=\"" + indXPtrURI + "\">" + ontName + "</a>"); // print("<a href=\""+ontURI+"asDefinedIn("+ontURI+")\">"+className+"</a> "); println(); } println(); } println(); if (showDivisions) { print("<table cellpadding=\"5\"><tr bgcolor=\"#FFF68F\"><FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); } boolean printedAnn = renderAnnotations(ind); if (!printedAnn) unprinted.add("A-ANN"); else // print the first division here (after annotations) if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); boolean div2 = false; // get defined types Set types = OWLDescriptionFinder.getTypes(ind, reasoner.getOntologies()); if (reasoner.isConsistent()) { // remove all the named classes because reasoner will eventually add them Iterator i = types.iterator(); while (i.hasNext()) if (i.next() instanceof OWLClass) i.remove(); // types.clear(); // *** turns out reasoner returns asserted types as well // add all the named superclasses types.addAll(reasoner.typesOf(ind)); } // remove owl:Thing from the superclass set Iterator i = types.iterator(); while (i.hasNext()) { Object o = i.next(); if (o instanceof Set && ((Set) o).contains(owlThing)) i.remove(); } boolean printedType = false; String title = "<b>Instance of:</b>"; if (types.size() == 0) { printedType = insertAddedChanges(new HashSet(), ind, "C-TYP", "<b>Instance of:</b>"); } else { if (editorEnabled) title += addTitle("C-TYP"); printCollection(types, title); printedType = true; } if (!printedType) unprinted.add("C-TYP"); else div2 = true; // print sameAs individuals title = "<b>Same As:</b>"; boolean printedSame = false; if (reasoner.isConsistent() && reasoner.getSameAsIndividuals(ind) != null && reasoner.getSameAsIndividuals(ind).size() > 0) { Set sameAs = reasoner.getSameAsIndividuals(ind); if (editorEnabled) title += addTitle("I-SAM"); printCollection(sameAs, title); printedSame = true; } else { printedSame = insertAddedChanges(new HashSet(), ind, "I-SAM", "<b>Same As:</b>"); } if (!printedSame) unprinted.add("I-SAM"); else div2 = true; // print diffFrom individuals boolean printedDiff = false; title = "<b>Different From:</b>"; if (reasoner.isConsistent() && reasoner.getDifferentFromIndividuals(ind) != null && reasoner.getDifferentFromIndividuals(ind).size() > 0) { Set diffFrom = reasoner.getDifferentFromIndividuals(ind); if (editorEnabled) title += addTitle("I-DIF"); printCollection(diffFrom, title); printedDiff = true; } else { printedDiff = insertAddedChanges(new HashSet(), ind, "I-DIF", "<b>Different From:</b>"); } if (!printedDiff) unprinted.add("I-DIF"); else div2 = true; // print second division here (after types, sameAs, diffFrom) if (div2) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); // get properties whose domain is the type of the individual HashMap propMap = new HashMap(); for (Iterator typeIter = types.iterator(); typeIter.hasNext();) { Object typ = typeIter.next(); if (typ instanceof Set) { Set equClas = (HashSet) typ; // set of equivalent class types for (Iterator ite = equClas.iterator(); ite.hasNext();) { OWLDescription type = (OWLDescription) ite.next(); if (!(type instanceof OWLClass)) continue; propMap.put(type, getPropertiesWithDomain((OWLClass) type, false)); if (showInherited) { Set ancSet = reasoner.ancestorClassesOf(type); for (Iterator supCIter = ancSet.iterator(); supCIter.hasNext();) { Set supCSet = (HashSet) supCIter.next(); OWLDescription supC = (OWLDescription) supCSet.iterator().next(); if (supC instanceof OWLClass) { propMap.put(supC, getPropertiesWithDomain((OWLClass) supC, false)); } } } } } } boolean div3 = false; // print all datatype properties and value pairs of instance Set instanceProps = new HashSet(); Map dataValues = new HashMap(); if (reasoner.isConsistent()) dataValues = reasoner.getDataPropertyValues(ind); boolean printedDataAssTitle = false; if (dataValues.size() > 0) { for (Iterator it = dataValues.keySet().iterator(); it.hasNext();) { OWLDataProperty prop = (OWLDataProperty) it.next(); boolean valLinkPrinted = false; Set vals = (Set) dataValues.get(prop); if (vals.size() > 0) { if (!printedDataAssTitle) { // just print title once println(); print("<b>Datatype Assertions:</b>"); if (editorEnabled) print(addTitle("P-INSD")); println(); printedDataAssTitle = true; } instanceProps.add(prop); } for (Iterator valIt = vals.iterator(); valIt.hasNext();) { OWLDataValue dtv = (OWLDataValue) valIt.next(); // check if DataPropertyInstance is deleted OntologyChange oc = editorEnabled ? isDeleted(prop, dtv) : null; boolean deleted = (oc != null); if (deleted) print("<font color=\"red\"><strike>"); visitor.reset(); dtv.accept(visitor); if (!isExplicit(ind, "P-INSD", prop, dtv)) print("<i>"); printConciseObject(prop); print(" : " + visitor.result()); if (!isExplicit(ind, "P-INSD", prop, dtv)) print("</i>"); if (deleted) { print("</strike></font>"); addUndo(oc, "Delete", "P-VAL"); } else if (editorEnabled && isExplicit(ind, "P-INSD", prop, dtv)) deleteValueLink(prop, dtv); if ((!valLinkPrinted) && (editorEnabled)) { addValueLink(prop); valLinkPrinted = true; // only display 'Add Value' link once for each property } if (valIt.hasNext()) { println(); } } if (printedDataAssTitle) println(); } } // print all AddDataPropertyInstance changes associated with this instance in green Iterator citer = changes.iterator(); while (citer.hasNext()) { OntologyChange oc = (OntologyChange) citer.next(); if (oc instanceof AddDataPropertyInstance) { AddDataPropertyInstance change = (AddDataPropertyInstance) oc; if (change.getSubject().equals(ind)) { if (!printedDataAssTitle) { println(); print("<b>Datatype Assertions:</b>"); if (editorEnabled) print(addTitle("P-INSD")); println(); printedDataAssTitle = true; } OWLDataProperty prop = change.getProperty(); instanceProps.add(prop); OWLDataValue dtv = change.getObject(); visitor.reset(); dtv.accept(visitor); print("<font color=\"green\">"); printConciseObject(prop); print(" : " + visitor.result()); addUndo(change, "Add", "V"); print("</font>"); println(); } } } if (!printedDataAssTitle) unprinted.add("P-INSD"); else div3 = true; // print all object properties and value pairs of instance Map propertyValues = new HashMap(); if (reasoner.isConsistent()) propertyValues = reasoner.getObjectPropertyValues(ind); boolean printedObjAssTitle = false; if (propertyValues.size() > 0) { for (Iterator it = propertyValues.keySet().iterator(); it.hasNext();) { OWLObjectProperty prop = (OWLObjectProperty) it.next(); boolean valLinkPrinted = false; Set vals = (Set) propertyValues.get(prop); if (vals.size() > 0) { if (!printedObjAssTitle) { // only print title once println(); print("<b>Object Assertions:</b>"); if (editorEnabled) print(addTitle("P-INSO")); println(); printedObjAssTitle = true; } instanceProps.add(prop); } for (Iterator valIt = vals.iterator(); valIt.hasNext();) { OWLIndividual oi = (OWLIndividual) valIt.next(); // check if ObjectPropertyInstance is deleted OntologyChange oc = editorEnabled ? isDeleted(prop, oi) : null; boolean deleted = (oc != null); if (deleted) print("<font color=\"red\"><strike>"); if (!isExplicit(ind, "P-INSO", prop, oi)) print("<i>"); printConciseObject(prop); visitor.reset(); boolean turnOnIcons = false; // turn off icons while rendering individuals // since we are rendering image values inline if (swoopModel.getShowIcons()) { turnOnIcons = true; swoopModel.setShowIcons(false, false); } oi.accept(visitor); String objValue = visitor.result(); if (isImage(objValue).equals("")) print(" : " + visitor.result()); else { // render image inline print(" : "); println("<P align=\"left\"><b><img border=\"3\" src=\"" + isImage(objValue) + "\" width=\"100\" height=\"100\"></b></P>"); } // check for turnOnIcons if (turnOnIcons) swoopModel.setShowIcons(true, false); if (!isExplicit(ind, "P-INSO", prop, oi)) { print("</i>"); if (reasoner.supportsExplanation()) { // add why link manually List propVal = new ArrayList(); propVal.add(prop); propVal.add(oi); String hash = String.valueOf(propVal.hashCode()); OWLDescHash.put(hash, propVal); if (!imported) { print(" (<font color=\"red\"><a href=\"<Why:" + hash + ":" + "P-INSO" + "\">Why?</a></font>)"); } } } if (deleted) { print("</strike></font>"); addUndo(oc, "Delete", "P-VAL"); } else if (editorEnabled && isExplicit(ind, "P-INSO", prop, oi)) deleteValueLink(prop, oi); if ((!valLinkPrinted) && (editorEnabled)) { addValueLink(prop); valLinkPrinted = true; // only display 'Add Value' link once for each property } if (valIt.hasNext()) { println(); } } if (printedObjAssTitle) println(); } } // print all AddObjectPropertyInstance changes associated with this instance in green citer = changes.iterator(); while (citer.hasNext()) { OntologyChange oc = (OntologyChange) citer.next(); if (oc instanceof AddObjectPropertyInstance) { AddObjectPropertyInstance change = (AddObjectPropertyInstance) oc; if (change.getSubject().equals(ind)) { if (!printedObjAssTitle) { println(); print("<b>Object Assertions:</b>"); if (editorEnabled) print(addTitle("P-INSO")); println(); printedObjAssTitle = true; } OWLObjectProperty prop = change.getProperty(); instanceProps.add(prop); OWLIndividual objInst = change.getObject(); print("<font color=\"green\">"); printConciseObject(prop); print(" : "); printConciseObject(objInst); addUndo(change, "Add", "V"); print("</font>"); println(); } } } if (!printedObjAssTitle) unprinted.add("P-INSO"); else div3 = true; if (div3) { if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + swoopModel.getFontSize() + ">"); } this.addUnprinted(unprinted); if (editorEnabled) { if (propMap.size() > 0) { if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); println(); println("<b>Likely Properties to Use:</b>"); for (Iterator iter = propMap.keySet().iterator(); iter.hasNext();) { OWLClass cla = (OWLClass) iter.next(); Set props = (HashSet) propMap.get(cla); for (Iterator pit = props.iterator(); pit.hasNext();) { OWLProperty prop = (OWLProperty) pit.next(); if (!instanceProps.contains(prop)) { print("(of "); printConciseObject(cla); print(") "); printConciseObject(prop); print(" : "); addValueLink(prop); println(); } } } } } } protected void renderAnnotationProperty(OWLAnnotationProperty prop) throws OWLException { println("<b>OWL-AnnotationProperty:</b> " + shortForm(prop.getURI()) + " "); } protected void renderObjectProperty(OWLObjectProperty prop) throws OWLException { // check if property is in current ontology or imported String importedLbl = ""; imported = false; if (!prop.getOntologies().contains(swoopModel.getSelectedOntology())) { importedLbl = "Imported "; imported = true; } List notPrinted = new ArrayList(); Iterator it = null; // print("<b>"+importedLbl+"OWL-ObjectProperty:</b> "); // printObject(prop); // // ********************************************* //Added for Econnections //********************************************** if (!prop.isLink()) { print("<b>" + importedLbl + "OWL-ObjectProperty:</b> "); printObject(prop); } else { print("<b>" + importedLbl + "OWL-LinkProperty:</b> "); printObject(prop); print("<br><b>" + "ForeignOntology:</b> "); URI linkURI = prop.getLinkTarget(); print("<a href=\"" + linkURI.toString() + "\">" + swoopModel.shortForm(linkURI) + "</a>"); } //*********************************************** if (importedLbl.length() > 0) { println(); // print("<b>Imported from Ontology(s):</b> "); // also print where the class is imported from Iterator ontIter = prop.getOntologies().iterator(); while (ontIter.hasNext()) { OWLOntology ont = (OWLOntology) ontIter.next(); String ontURI = ont.getURI().toString(); String ontName = ontURI.substring(ontURI.lastIndexOf("/") + 1, ontURI.length()); String propXPtrURI = prop.getURI() + XPointers.asDefinedIn + "(" + ontURI + ")"; print("See its definition in Imported Ontology: <a href=\"" + propXPtrURI + "\">" + ontName + "</a>"); // print("<a href=\""+ontURI+"asDefinedIn("+ontURI+")\">"+className+"</a> "); println(); } println(); } else if (editorEnabled) print(" <font color=\"red\">(<a href=\"<SwitchProp\">Switch</a>)</font>"); if (showDivisions) print("<table cellpadding=\"5\"><tr bgcolor=\"#FFF68F\"><FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); // **** rules stuff for object properties**** if (swoopModel.getEnableRules()) { RulesExpressivity ruleExpr = swoopModel.getRuleExpr(); System.out.println("number of rules:" + ruleExpr.getNumRules()); Set rules = ruleExpr.getRules(prop); //pw.println("<b> Rules: </b> <br>"); String ruleTitle = "<b> Rules: </b>"; if (editorEnabled) ruleTitle += addTitle("RULE"); pw.println(ruleTitle + " \n<br>"); for (Iterator iter = rules.iterator(); iter.hasNext();) { //OWLRule rule = (OWLRule) iter.next(); RuleValue rv = (RuleValue) iter.next(); OWLRule rule = rv.getRule(); String ruleDesc = rule.toString(); int ptr; ptr = ruleDesc.indexOf(">") + 1; String consequent = ruleDesc.substring(ptr, ruleDesc.indexOf(".")); String varConsequent = consequent.substring((consequent.indexOf("(") + 1), consequent.indexOf(")")); ruleDesc = ruleDesc.substring(0, ptr - 2) + "."; ruleDesc = consequent + " <b>:-</b> " + ruleDesc; ptr = 0; ruleDesc = " " + ruleDesc; String hyperRule = ruleDesc; while ((ptr = ruleDesc.indexOf("(", ptr)) >= 0) { String name = ruleDesc.substring(ruleDesc.lastIndexOf(" ", ptr), ptr); String uri = this.getURIForTerm(name.trim()); hyperRule = hyperRule.replaceAll(name, "<a href=\"" + uri + "\">" + name + "</a>"); ptr++; } if (editorEnabled) { pw.print(hyperRule); String hash = String.valueOf(rule.hashCode()); OWLDescHash.put(hash, rule); String titleCode = "RULE"; //getCode(title); pw.print(" (<font color=\"red\"><a href=\"<Delete:" + hash + ":" + titleCode + "\">Delete</a></font>) "); pw.print(" (<font color=\"red\"><a href=\"<Edit:" + hash + ":" + titleCode + "\">Edit</a></font>)"); pw.print(" (<font color=\"red\"><a href=\"<Publish:" + hash + ":" + titleCode + "\">Publish</a></font>)"); pw.println("<br>"); } else { pw.println(hyperRule + "<br>"); } } } boolean printedAnn = renderAnnotations(prop); if (!printedAnn) notPrinted.add("A-ANN"); else if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); int notPrintedSize = notPrinted.size(); String title = "<b>Equivalent to:</b>"; if (reasoner.equivalentPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-EQU", title); if (!printed) notPrinted.add("P-EQU"); } else { if (editorEnabled) title += addTitle("P-EQU"); printCollection(reasoner.equivalentPropertiesOf(prop), title); } title = "<b>Inverse of:</b>"; if (reasoner.inversePropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-INV", title); if (!printed) notPrinted.add("P-INV"); } else { if (editorEnabled) title += addTitle("P-INV"); printCollection(reasoner.inversePropertiesOf(prop), title); } title = "<b>Subproperty of:</b>"; if (reasoner.superPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-SUB", title); if (!printed) notPrinted.add("P-SUB"); } else { if (editorEnabled) title += addTitle("P-SUB"); printCollection(reasoner.superPropertiesOf(prop), title); } title = "<b>Superproperty of:</b>"; if (reasoner.subPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-SUP", title); if (!printed) notPrinted.add("P-SUP"); } else { if (editorEnabled) title += addTitle("P-SUP"); printCollection(reasoner.subPropertiesOf(prop), title); } if ((notPrinted.size() - notPrintedSize < 4) && showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); title = "<b>Has domain:</b>"; Set doms = reasoner.domainsOf(prop); doms.addAll(prop.getDomains(swoopModel.getSelectedOntology())); if (doms.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "C-HASDOM", title); if (!printed) notPrinted.add("C-HASDOM"); } else { if (editorEnabled) title += addTitle("C-HASDOM"); printCollection(doms, title); } title = "<b>Has range:</b>"; Set rans = reasoner.rangesOf(prop); rans.addAll(prop.getRanges(swoopModel.getSelectedOntology())); if (rans.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "C-HASRAN", title); if (!printed) notPrinted.add("C-HASRAN"); } else { if (editorEnabled) title += addTitle("C-HASRAN"); //printCollection(reasoner.rangesOf(prop), title); printCollection(rans, title); } if ((notPrinted.size() - notPrintedSize < 2) && showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); String OWL = OWLVocabularyAdapter.OWL; title = "<b>Attributes:</b>"; boolean printedAttribs = false; if (prop.isTransitive(reasoner.getOntologies()) || prop.isFunctional(reasoner.getOntologies()) || prop.isInverseFunctional(reasoner.getOntologies()) || prop.isSymmetric(reasoner.getOntologies())) { printedAttribs = true; println(); if (editorEnabled) title += addTitle("ATTRIB"); println(title); if (prop.isFunctional(reasoner.getOntologies())) { OntologyChange isDeleted = isDeleted(prop, "P-FUN"); if (editorEnabled) { if (isDeleted != null) { print("<font color=\"red\"><strike><a href=\"" + OWL + "FunctionalProperty\">Functional</a></strike></font>"); addUndo(isDeleted, "Delete", title); } else { print("<a href=\"" + OWL + "FunctionalProperty\">Functional</a>"); addDelete(prop, "P-FUN"); } } else print("<a href=\"" + OWL + "FunctionalProperty\">Functional</a>"); println(); } if (prop.isInverseFunctional(reasoner.getOntologies())) { OntologyChange isDeleted = isDeleted(prop, "P-IFUN"); if (editorEnabled) { if (isDeleted != null) { print("<font color=\"red\"><strike><a href=\"" + OWL + "InverseFunctionalProperty\">Inverse Functional</a></strike></font>"); addUndo(isDeleted, "Delete", title); } else { print("<a href=\"" + OWL + "InverseFunctionalProperty\">Inverse Functional</a>"); addDelete(prop, "P-IFUN"); } } else print("<a href=\"" + OWL + "InverseFunctionalProperty\">Inverse Functional</a>"); println(); } if (prop.isTransitive(reasoner.getOntologies())) { OntologyChange isDeleted = isDeleted(prop, "P-TRA"); if (editorEnabled) { if (isDeleted != null) { print("<font color=\"red\"><strike><a href=\"" + OWL + "TransitiveProperty\">Transitive</a></strike></font>"); addUndo(isDeleted, "Delete", title); } else { print("<a href=\"" + OWL + "TransitiveProperty\">Transitive</a>"); addDelete(prop, "P-TRA"); } } else print("<a href=\"" + OWL + "TransitiveProperty\">Transitive</a>"); println(); } if (prop.isSymmetric(reasoner.getOntologies())) { OntologyChange isDeleted = isDeleted(prop, "P-SYM"); if (editorEnabled) { if (isDeleted != null) { print("<font color=\"red\"><strike><a href=\"" + OWL + "SymmetricProperty\">Symmetric</a></strike></font>"); addUndo(isDeleted, "Delete", title); } else { print("<a href=\"" + OWL + "SymmetricProperty\">Symmetric</a>"); addDelete(prop, "P-SYM"); } } else print("<a href=\"" + OWL + "SymmetricProperty\">Symmetric</a>"); println(); } } // print temporarily added attribute changes Map added = this.getAdded(prop, "ATTRIB"); if (!added.isEmpty()) { if (!printedAttribs) { printedAttribs = true; if (editorEnabled) title += addTitle("ATTRIB"); println(title); } Iterator j = added.entrySet().iterator(); while (j.hasNext()) { Map.Entry entry = (Map.Entry) j.next(); OWLObject obj = (OWLObject) entry.getKey(); Set changes = (HashSet) entry.getValue(); for (Iterator changeIter = changes.iterator(); changeIter.hasNext();) { OntologyChange change = (OntologyChange) changeIter.next(); print("<font color=\"green\">"); if (change instanceof SetFunctional) { print("Functional"); } else if (change instanceof SetInverseFunctional) { print("Inverse Functional"); } else if (change instanceof SetTransitive) { print("Transitive"); } else if (change instanceof SetSymmetric) print("Symmetric"); print("</font>"); addUndo(change, "Add", title); println(); } } } if (swoopModel.getEditorEnabled() && !printedAttribs) notPrinted.add("ATTRIB"); if (showDivisions && printedAttribs) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); // add unprinted titles at the bottom addUnprinted(notPrinted); } // recursively find all MUPS using HST principle public void HSTMUPS(Set mups, OWLOntology onto, List MUPS, List explStr, Set satPaths, Set currPath) { // key step - make a backup of onto OWLOntology backup = swoopModel.cloneOntology(onto); try { for (Iterator iter = mups.iterator(); iter.hasNext();) { // reset ontology OWLOntology copyOnt = swoopModel.cloneOntology(backup); OWLObject axiom = (OWLObject) iter.next(); currPath.add(axiom); // System.out.println(axiom); // **** remove axiom from copyOnt ***** if (axiom instanceof OWLDisjointClassesAxiom) { OWLDisjointClassesAxiom dis = (OWLDisjointClassesAxiom) axiom; Set disSet = dis.getDisjointClasses(); Set newDisSet = new HashSet(); for (Iterator iter2 = disSet.iterator(); iter2.hasNext();) { OWLDescription desc = (OWLDescription) iter2.next(); if (desc instanceof OWLClass) newDisSet.add(copyOnt.getClass(((OWLClass) desc).getURI())); else newDisSet.add(desc); } OWLDisjointClassesAxiom newDis = copyOnt.getOWLDataFactory() .getOWLDisjointClassesAxiom(newDisSet); RemoveClassAxiom r = new RemoveClassAxiom(copyOnt, (OWLClassAxiom) newDis, null); r.accept((ChangeVisitor) copyOnt); } else if (axiom instanceof OWLEquivalentClassesAxiom) { OWLEquivalentClassesAxiom equ = (OWLEquivalentClassesAxiom) axiom; Set equSet = equ.getEquivalentClasses(); Set newEquSet = new HashSet(); List equList = new ArrayList(); for (Iterator iter2 = equSet.iterator(); iter2.hasNext();) { OWLDescription desc = (OWLDescription) iter2.next(); if (desc instanceof OWLClass) { newEquSet.add(copyOnt.getClass(((OWLClass) desc).getURI())); equList.add(copyOnt.getClass(((OWLClass) desc).getURI())); } else { newEquSet.add(desc); equList.add(desc); } } OWLEquivalentClassesAxiom newEqu = copyOnt.getOWLDataFactory() .getOWLEquivalentClassesAxiom(newEquSet); RemoveClassAxiom r = new RemoveClassAxiom(copyOnt, (OWLClassAxiom) newEqu, null); r.accept((ChangeVisitor) copyOnt); if (equList.size() == 2) { OWLDescription desc1 = (OWLDescription) equList.get(0); OWLDescription desc2 = (OWLDescription) equList.get(0); if (desc1 instanceof OWLClass) { RemoveEquivalentClass re = new RemoveEquivalentClass(copyOnt, (OWLClass) desc1, desc2, null); re.accept((ChangeVisitor) copyOnt); } if (desc2 instanceof OWLClass) { RemoveEquivalentClass re = new RemoveEquivalentClass(copyOnt, (OWLClass) desc2, desc1, null); re.accept((ChangeVisitor) copyOnt); } } } else if (axiom instanceof OWLSubClassAxiom) { OWLSubClassAxiom subA = (OWLSubClassAxiom) axiom; OWLDescription sub = subA.getSubClass(); OWLDescription sup = subA.getSuperClass(); OWLDescription newSub = sub; if (sub instanceof OWLClass) newSub = copyOnt.getClass(((OWLClass) sub).getURI()); OWLDescription newSup = sup; if (sup instanceof OWLClass) newSup = copyOnt.getClass(((OWLClass) sup).getURI()); OWLSubClassAxiom newSubA = copyOnt.getOWLDataFactory().getOWLSubClassAxiom(newSub, newSup); OntologyChange r = new RemoveClassAxiom(copyOnt, (OWLClassAxiom) newSubA, null); r.accept((ChangeVisitor) copyOnt); if (newSub instanceof OWLClass) { r = new RemoveSuperClass(copyOnt, (OWLClass) newSub, newSup, null); r.accept((ChangeVisitor) copyOnt); } } else if (axiom instanceof OWLPropertyDomainAxiom) { OWLPropertyDomainAxiom opd = (OWLPropertyDomainAxiom) axiom; OWLProperty prop = opd.getProperty(); OWLProperty newProp = null; if (prop instanceof OWLDataProperty) newProp = copyOnt.getDataProperty(prop.getURI()); else newProp = copyOnt.getObjectProperty(prop.getURI()); OWLDescription desc = opd.getDomain(); OWLDescription newDesc = desc; if (desc instanceof OWLClass) newDesc = copyOnt.getClass(((OWLClass) desc).getURI()); RemoveDomain rd = new RemoveDomain(copyOnt, newProp, newDesc, null); rd.accept((ChangeVisitor) copyOnt); } else if (axiom instanceof OWLObjectPropertyRangeAxiom) { OWLObjectPropertyRangeAxiom opd = (OWLObjectPropertyRangeAxiom) axiom; OWLObjectProperty prop = opd.getProperty(); OWLObjectProperty newProp = copyOnt.getObjectProperty(prop.getURI()); OWLDescription desc = opd.getRange(); OWLDescription newDesc = desc; if (desc instanceof OWLClass) newDesc = copyOnt.getClass(((OWLClass) desc).getURI()); RemoveObjectPropertyRange ropr = new RemoveObjectPropertyRange(copyOnt, newProp, newDesc, null); ropr.accept((ChangeVisitor) copyOnt); } else if (axiom instanceof OWLObjectPropertyInstance) { OWLObjectPropertyInstance oop = (OWLObjectPropertyInstance) axiom; OWLIndividual sub = copyOnt.getIndividual(oop.getSubject().getURI()); OWLObjectProperty prop = copyOnt.getObjectProperty(oop.getProperty().getURI()); OWLIndividual obj = copyOnt.getIndividual(oop.getObject().getURI()); RemoveObjectPropertyInstance ropi = new RemoveObjectPropertyInstance(copyOnt, sub, prop, obj, null); ropi.accept((ChangeVisitor) copyOnt); } else if (axiom instanceof OWLSameIndividualsAxiom) { OWLSameIndividualsAxiom osi = (OWLSameIndividualsAxiom) axiom; Set newInd = new HashSet(); for (Iterator it = osi.getIndividuals().iterator(); it.hasNext();) { newInd.add(copyOnt.getIndividual(((OWLIndividual) it.next()).getURI())); } OWLSameIndividualsAxiom copyInd = copyOnt.getOWLDataFactory() .getOWLSameIndividualsAxiom(newInd); RemoveIndividualAxiom ria = new RemoveIndividualAxiom(copyOnt, copyInd, null); ria.accept((ChangeVisitor) copyOnt); } else if (axiom instanceof OWLDifferentIndividualsAxiom) { OWLDifferentIndividualsAxiom osi = (OWLDifferentIndividualsAxiom) axiom; Set newInd = new HashSet(); for (Iterator it = osi.getIndividuals().iterator(); it.hasNext();) { newInd.add(copyOnt.getIndividual(((OWLIndividual) it.next()).getURI())); } OWLDifferentIndividualsAxiom copyInd = copyOnt.getOWLDataFactory() .getOWLDifferentIndividualsAxiom(newInd); RemoveIndividualAxiom ria = new RemoveIndividualAxiom(copyOnt, copyInd, null); ria.accept((ChangeVisitor) copyOnt); } //TODO: more removal! // test if copyOnt has changed //FIXME: not working when individual obj prop assertions are actually removed // if (copyOnt.equals(onto)) { // System.out.println("Ontology hasn't changed after removing axiom "+axiom); // continue; // } // get class in copyOnt OWLClass cla = null; if (swoopModel.getSelectedEntity() != null) cla = copyOnt.getClass(swoopModel.getSelectedEntity().getURI()); // early path termination boolean earlyTermination = false; for (Iterator i = satPaths.iterator(); i.hasNext();) { Set satPath = (HashSet) i.next(); if (satPath.containsAll(currPath)) { System.out.println("EARLY PATH TERMINATION!"); earlyTermination = true; break; } } if (!earlyTermination) { // check if there is a new mups of class Set newMUPS = new HashSet(); String expl = ""; if (swoopModel.isUseTableau()) { // use tableau tracing List explList = this.getTableauSOS(copyOnt, cla); expl = explList.get(0).toString(); newMUPS = (HashSet) explList.get(1); } else { // use black box newMUPS = this.getBlackBoxSOS(copyOnt, cla); } if (!newMUPS.isEmpty()) { if (!MUPS.contains(newMUPS)) { // print explanation for new MUPS MUPS.add(newMUPS); explStr.add(expl); System.out.println("FOUND NEW MUPS - MUPS COUNT: " + MUPS.size()); // recurse! HSTMUPS(newMUPS, copyOnt, MUPS, explStr, satPaths, currPath); } } else { satPaths.add(new HashSet(currPath)); } } currPath.remove(axiom); } } catch (Exception ex) { ex.printStackTrace(); } } //************************************************************ //Added for Econnections //************************************************************ protected void renderForeignEntity(OWLEntity e) throws OWLException { if (e instanceof OWLClass) { print("<b> OWL-ForeignClass:</b> "); printObject(e); print("<br><b> ForeignOntology </b> "); print("<a href=\"" + swoopModel.getSelectedOntology().getForeignEntities().get(e).toString() + "\">" + swoopModel.shortForm(((URI) swoopModel.getSelectedOntology().getForeignEntities().get(e))) + "</a>"); } if (e instanceof OWLObjectProperty) { if (!((OWLObjectProperty) e).isLink()) { print("<b> OWL-ForeignObjectProperty:</b> "); printObject(e); } else { print("<b> OWL-ForeignLinkProperty:</b> "); printObject(e); } print("<br><b> ForeignOntology </b> "); print("<a href=\"" + swoopModel.getSelectedOntology().getForeignEntities().get(e).toString() + "\">" + swoopModel.shortForm(((URI) swoopModel.getSelectedOntology().getForeignEntities().get(e))) + "</a>"); } if (e instanceof OWLDataProperty) { print("<b> OWL-ForeignDatatypeProperty:</b> "); printObject(e); print("<br><b> ForeignOntology </b> "); print("<a href=\"" + swoopModel.getSelectedOntology().getForeignEntities().get(e).toString() + "\">" + swoopModel.shortForm(((URI) swoopModel.getSelectedOntology().getForeignEntities().get(e))) + "</a>"); } if (e instanceof OWLIndividual) { print("<b> OWL-ForeignIndividual:</b> "); printObject(e); print("<br><b> ForeignOntology </b> "); print("<a href=\"" + swoopModel.getSelectedOntology().getForeignEntities().get(e).toString() + "\">" + swoopModel.shortForm(((URI) swoopModel.getSelectedOntology().getForeignEntities().get(e))) + "</a>"); } } //*********************************************************** protected void renderDataProperty(OWLDataProperty prop) throws OWLException { // check if property is in current ontology or imported String importedLbl = ""; imported = false; if (!prop.getOntologies().contains(swoopModel.getSelectedOntology())) { importedLbl = "Imported "; imported = true; } Iterator it = null; List notPrinted = new ArrayList(); print("<b>" + importedLbl + "OWL-DatatypeProperty:</b> "); printObject(prop); if (importedLbl.length() > 0) { println(); // print("<b>Imported from Ontology(s):</b> "); // also print where the class is imported from Iterator ontIter = prop.getOntologies().iterator(); while (ontIter.hasNext()) { OWLOntology ont = (OWLOntology) ontIter.next(); String ontURI = ont.getURI().toString(); String ontName = ontURI.substring(ontURI.lastIndexOf("/") + 1, ontURI.length()); String propXPtrURI = prop.getURI() + XPointers.asDefinedIn + "(" + ontURI + ")"; print("See its definition in Imported Ontology: <a href=\"" + escape(propXPtrURI) + "\">" + escape(ontName) + "</a>"); // print("<a href=\""+ontURI+"asDefinedIn("+ontURI+")\">"+className+"</a> "); println(); } println(); } else if (editorEnabled) print(" <font color=\"red\">(<a href=\"<SwitchProp\">Switch</a>)</font>"); if (showDivisions) { print("<table cellpadding=\"5\"><tr bgcolor=\"#FFF68F\"><FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); } boolean printedAnn = renderAnnotations(prop); if (!printedAnn) notPrinted.add("A-ANN"); else if (showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); int notPrintedSize = notPrinted.size(); String title = "<b>Equivalent to:</b>"; if (reasoner.equivalentPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-EQU", title); if (!printed) notPrinted.add("P-EQU"); } else { if (editorEnabled) title += addTitle("P-EQU"); printCollection(reasoner.equivalentPropertiesOf(prop), title); } title = "<b>Subproperty of:</b>"; if (reasoner.superPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-SUB", title); if (!printed) notPrinted.add("P-SUB"); } else { if (editorEnabled) title += addTitle("P-SUB"); printCollection(reasoner.superPropertiesOf(prop), title); } title = "<b>Superproperty of:</b>"; if (reasoner.subPropertiesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "P-SUP", title); if (!printed) notPrinted.add("P-SUP"); } else { if (editorEnabled) title += addTitle("P-SUP"); printCollection(reasoner.subPropertiesOf(prop), title); } if ((notPrinted.size() - notPrintedSize < 3) && showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); title = "<b>Has domain:</b>"; Set doms = reasoner.domainsOf(prop); doms.addAll(prop.getDomains(swoopModel.getSelectedOntology())); if (doms.size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "C-HASDOM", title); if (!printed) notPrinted.add("C-HASDOM"); } else { if (editorEnabled) title += addTitle("C-HASDOM"); printCollection(doms, title); } title = "<b>Has range:</b>"; if (reasoner.rangesOf(prop).size() == 0) { boolean printed = insertAddedChanges(new HashSet(), prop, "C-HASRAN", title); if (!printed) notPrinted.add("C-HASRAN"); } else { if (editorEnabled) title += addTitle("C-HASRAN"); printCollection(reasoner.rangesOf(prop), title); } if ((notPrinted.size() - notPrintedSize < 2) && showDivisions) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); notPrintedSize = notPrinted.size(); title = "<b>Attributes</b>:"; String OWL = OWLVocabularyAdapter.OWL; boolean printedAttribs = false; if (prop.isFunctional(reasoner.getOntologies())) { printedAttribs = true; if (editorEnabled) title += addTitle("ATTRIB"); println(title); OntologyChange isDeleted = isDeleted(prop, "P-FUN"); if (editorEnabled) { if (isDeleted != null) { print("<font color=\"red\"><strike><a href=\"" + OWL + "FunctionalProperty\">Functional</a></strike></font>"); addUndo(isDeleted, "Delete", title); } else { print("<a href=\"" + OWL + "FunctionalProperty\">Functional</a>"); addDelete(prop, "P-FUN"); } } else print("<a href=\"" + OWL + "FunctionalProperty\">Functional</a>"); println(); } // print temporarily added attribute changes Map added = this.getAdded(prop, "ATTRIB"); if (!added.isEmpty()) { if (!printedAttribs) { printedAttribs = true; if (editorEnabled) title += addTitle("ATTRIB"); println(title); } Iterator j = added.entrySet().iterator(); while (j.hasNext()) { Map.Entry entry = (Map.Entry) j.next(); OWLObject obj = (OWLObject) entry.getKey(); Set changes = (HashSet) entry.getValue(); for (Iterator changeIter = changes.iterator(); changeIter.hasNext();) { OntologyChange change = (OntologyChange) changeIter.next(); print("<font color=\"green\">"); if (change instanceof SetFunctional) print("Functional"); print("</font>"); addUndo(change, "Add", title); println(); } } } if (swoopModel.getEditorEnabled() && !printedAttribs) notPrinted.add("ATTRIB"); if (showDivisions && printedAttribs) print(HR + "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=" + fontSize + ">"); // rules stuff if (swoopModel.getEnableRules()) { RulesExpressivity ruleExpr = swoopModel.getRuleExpr(); Set rules = ruleExpr.getRules(prop); pw.println("<b> Rules: </b> <br>"); for (Iterator iter = rules.iterator(); iter.hasNext();) { String ruleDesc = ((RuleValue) iter.next()).getRule().toString(); int ptr; ptr = ruleDesc.indexOf(">") + 1; String consequent = ruleDesc.substring(ptr, ruleDesc.indexOf(".")); ruleDesc = ruleDesc.substring(0, ptr - 2) + "."; ruleDesc = consequent + " <b>:- </b> " + ruleDesc; ptr = 0; ruleDesc = " " + ruleDesc; String hyperRule = ruleDesc; while ((ptr = ruleDesc.indexOf("(", ptr)) >= 0) { String name = ruleDesc.substring(ruleDesc.lastIndexOf(" ", ptr), ptr); String uri = this.getURIForTerm(name.trim()); hyperRule = hyperRule.replaceAll(name, "<a href=\"" + uri + "\">" + name + "</a>"); ptr++; } pw.println(hyperRule + "<br>"); } } // add unprinted titles at the bottom addUnprinted(notPrinted); } protected void renderDataType(OWLDataType datatype) throws OWLException { println("<b>OWL-Datatype:</b> " + shortForm(datatype.getURI()) + " "); } protected void println() { pw.println("<br>"); } public void setEditorEnabled(boolean mode) { this.editorEnabled = mode; //if(mode) changes = new ArrayList(); } private void reset() { OWLDescHash.clear(); } public void render(OWLEntity entity, SwoopModel swoopModel, Writer writer) throws RendererException { changes = swoopModel.getUncommittedChanges(); reset(); displayedEntity = entity; StringWriter sw = new StringWriter(); PrintWriter buffer = new PrintWriter(sw); super.render(entity, swoopModel, buffer); String output = postProcess(sw.getBuffer().toString()); try { writer.write(output); } catch (IOException e) { e.printStackTrace(); } } /** * Method that handles the Add* operation when the user clicks on the * corresponding hyperlink in the Concise Format Pane (eg. Add SuperClass) * It calls the appropriate PopupAdd* Java Class depending on the type of add operation * @param hLink - code representing type of Add operation * @return * @throws OWLException */ public List handleAddLink(String hLink) throws OWLException { OWLOntology ontology = reasoner.getOntology(); // remove the prefixed "<" if (hLink.startsWith("<")) hLink = hLink.substring(1, hLink.length()); else System.out.println("hyperlink error: " + hLink); // new rules addition if (hLink.equals("AddRULE")) { PopupAddRule test = new PopupAddRule(swoopModel, displayedEntity); test.show(); } if (hLink.equals("AddA-ANN")) { // add annotation PopupAddAnnotation popup = new PopupAddAnnotation(swoopModel, false); popup.setLocation(200, 200); popup.show(); return new ArrayList(); } if (hLink.equals("AddATTRIB")) { // add property attribute - Functional etc JList attribList = new JList(); //attribList.setFont(new Font("Tahoma", Font.PLAIN, 10)); List attribs = new ArrayList(); OWLProperty prop = (OWLProperty) swoopModel.getSelectedEntity(); if (!prop.isFunctional(reasoner.getOntologies())) attribs.add("Functional"); if (prop instanceof OWLObjectProperty) { if (!((OWLObjectProperty) prop).isInverseFunctional(reasoner.getOntologies())) attribs.add("Inverse Functional"); if (!((OWLObjectProperty) prop).isTransitive(reasoner.getOntologies())) attribs.add("Transitive"); if (!((OWLObjectProperty) prop).isSymmetric(reasoner.getOntologies())) attribs.add("Symmetric"); } if (attribs.size() == 0) { JOptionPane.showMessageDialog(null, "Property already has all possible attributes", "Unable to Add", JOptionPane.INFORMATION_MESSAGE); return new ArrayList(); } attribList.setListData(attribs.toArray()); int attr = JOptionPane.showConfirmDialog(null, new JScrollPane(attribList), "Specify Property Attribute:", JOptionPane.YES_NO_OPTION); if (attr == 0) { OntologyChange change = null; String sel = attribList.getSelectedValue().toString(); if (sel.equals("Functional")) change = new SetFunctional(ontology, prop, true, null); else if (sel.equals("Inverse Functional")) change = new SetInverseFunctional(ontology, (OWLObjectProperty) prop, true, null); else if (sel.equals("Transitive")) change = new SetTransitive(ontology, (OWLObjectProperty) prop, true, null); else if (sel.equals("Symmetric")) change = new SetSymmetric(ontology, (OWLObjectProperty) prop, true, null); swoopModel.addUncommittedChange(change); } return new ArrayList(); } if (hLink.startsWith("AddC")) { // popup Add Class Frame String type = hLink.substring(hLink.indexOf("-") + 1, hLink.length()); PopupAddClass popup = new PopupAddClass(reasoner, type, swoopModel); popup.setLocation(200, 200); popup.show(); return popup.changes; } if (hLink.startsWith("AddP")) { // popup Add Property Frame boolean DP = true, OP = true; if (hLink.startsWith("AddP-INSO")) DP = false; if (hLink.startsWith("AddP-INSD")) OP = false; String type = hLink.substring(hLink.indexOf("-") + 1, hLink.length()); PopupAddProperty popup = new PopupAddProperty(reasoner, type, swoopModel, DP, OP); popup.setLocation(200, 200); popup.show(); return popup.changes; } if (hLink.startsWith("AddI-SAM") || hLink.startsWith("AddI-DIF") || hLink.startsWith("AddI-ONE") || hLink.startsWith("AddI-INS")) { // popup Add Individual Frame String type = hLink.substring(hLink.indexOf("-") + 1, hLink.length()); PopupAddIndividual popup = new PopupAddIndividual(reasoner, type, swoopModel); popup.setLocation(200, 200); popup.show(); return popup.changes; } if (hLink.startsWith("AddV")) { // add value for property String hash = hLink.substring(hLink.indexOf(":") + 1, hLink.length()); OWLProperty prop = (OWLProperty) OWLDescHash.get(hash); //*********************************************************** //changed for Econnections //*********************************************************** OWLEntity entit = swoopModel.getSelectedEntity(); if (prop instanceof OWLObjectProperty) { if (((OWLObjectProperty) prop).isLink()) { URI u = ((OWLObjectProperty) prop).getLinkTarget(); OWLOntology foreignOnto = swoopModel.getOntology(u); reasoner.setOntology(foreignOnto); swoopModel.setSelectedOntology(foreignOnto); } } PopupAddValue popup = new PopupAddValue(reasoner, swoopModel, prop); popup.setLocation(200, 200); popup.show(); if (prop instanceof OWLObjectProperty) { if (((OWLObjectProperty) prop).isLink()) { reasoner.setOntology(ontology); swoopModel.setSelectedOntology(ontology); swoopModel.setSelectedEntity(entit); } } return popup.changes; } return null; } public List handlePublishLink(String hLink) throws OWLException { OWLOntology ontology = reasoner.getOntology(); // parse DELETE hyper-link int pos1 = hLink.indexOf(":"); int pos2 = hLink.indexOf(":", pos1 + 1); String hashCode = hLink.substring(pos1 + 1, pos2); String titleCode = hLink.substring(pos2 + 1, hLink.length()); Object obj = OWLDescHash.get(hashCode); OWLRule rule = (OWLRule) obj; if (titleCode.startsWith("RULE")) { //System.out.println( "Deleting Rule" ); //String n3 = swoopModel.getRuleExpr().toN3(); ExternalRuleSubmitter submitter = new ExternalRuleSubmitter(swoopModel, rule); } //no changes to return return null; } /** * * Returns a list of changes that are required to fufill the requirements of clicking a * delete link. A delete operation may involve various steps of changes and may also * cause some other changes to happen. The list will contain all the atomic changes * required for this operation * * @param hLink the link clicked on the editor pane * @return A list of OntologyChange objects * @throws OWLException */ public List handleDeleteLink(String hLink) throws OWLException { List changes = new ArrayList(); OWLOntology ontology = reasoner.getOntology(); // parse DELETE hyper-link int pos1 = hLink.indexOf(":"); int pos2 = hLink.indexOf(":", pos1 + 1); String hashCode = hLink.substring(pos1 + 1, pos2); String titleCode = hLink.substring(pos2 + 1, hLink.length()); Object obj = OWLDescHash.get(hashCode); if (titleCode.equals("P-FUN")) { // Remove Functional Attribute // *** Note: Change is effective immediately for property attribute SetFunctional change = new SetFunctional(ontology, (OWLProperty) obj, false, null); swoopModel.addUncommittedChange(change); return new ArrayList(); } if (titleCode.equals("P-IFUN")) { // Remove InverseFunctional Attribute // *** Note: Change is effective immediately for property attribute SetInverseFunctional change = new SetInverseFunctional(ontology, (OWLObjectProperty) obj, false, null); swoopModel.addUncommittedChange(change); return new ArrayList(); } if (titleCode.equals("P-TRA")) { // Remove Transitive Attribute // *** Note: Change is effective immediately for property attribute SetTransitive change = new SetTransitive(ontology, (OWLObjectProperty) obj, false, null); swoopModel.addUncommittedChange(change); return new ArrayList(); } if (titleCode.equals("P-SYM")) { // Remove Symmetric Attribute // *** Note: Change is effective immediately for property attribute SetSymmetric change = new SetSymmetric(ontology, (OWLObjectProperty) obj, false, null); swoopModel.addUncommittedChange(change); return new ArrayList(); } if (titleCode.equals("A-ANN")) { // Remove Annotation Instance OWLEntity currEntity = swoopModel.getSelectedEntity(); if (obj instanceof OWLAnnotationInstance) { OWLAnnotationInstance oai = (OWLAnnotationInstance) obj; RemoveAnnotationInstance change = new RemoveAnnotationInstance(ontology, currEntity, oai.getProperty(), oai.getContent(), null); swoopModel.addUncommittedChange(change); } return new ArrayList(); } if (titleCode.equals("I-SAM") || titleCode.equals("I-DIF")) { // delete sameAs axiom Set indSet = new HashSet(); indSet.add((OWLIndividual) displayedEntity); indSet.add((OWLIndividual) obj); OWLIndividualAxiom indAxiom = null; if (titleCode.equals("I-SAM")) indAxiom = ontology.getOWLDataFactory().getOWLSameIndividualsAxiom(indSet); else indAxiom = ontology.getOWLDataFactory().getOWLDifferentIndividualsAxiom(indSet); RemoveIndividualAxiom change = new RemoveIndividualAxiom(ontology, indAxiom, null); changes.add(change); } if (titleCode.equals("C-EQU")) { // delete equivalent class OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; RemoveEquivalentClass change = new RemoveEquivalentClass(ontology, displayedClass, desc, null); changes.add(change); } else { Iterator descIter = ((Collection) obj).iterator(); while (descIter.hasNext()) { OWLDescription desc = (OWLDescription) descIter.next(); RemoveEquivalentClass change = new RemoveEquivalentClass(ontology, displayedClass, desc, null); changes.add(change); } } } else if (titleCode.equals("C-DIS")) { // delete disjoint class OWLClass displayedClass = (OWLClass) displayedEntity; Set disSet = new HashSet(); if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; disSet.add(desc); disSet.add(displayedClass); } else { disSet.add(displayedClass); disSet.addAll((Collection) obj); } OWLDisjointClassesAxiom disAxiom = ontology.getOWLDataFactory().getOWLDisjointClassesAxiom(disSet); RemoveClassAxiom change = new RemoveClassAxiom(ontology, disAxiom, null); changes.add(change); } else if (titleCode.equals("C-SUB")) { // delete super-class OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; if (displayedClass.getSuperClasses(ontology).contains(obj)) { // add RemoveSuperClass change in this case RemoveSuperClass change = new RemoveSuperClass(ontology, displayedClass, desc, null); changes.add(change); } else { // remove specific axiom in the other case OWLSubClassAxiom axiom = ontology.getOWLDataFactory().getOWLSubClassAxiom(displayedClass, desc); RemoveClassAxiom change2 = new RemoveClassAxiom(ontology, axiom, null); changes.add(change2); } } else { Iterator descIter = ((Collection) obj).iterator(); while (descIter.hasNext()) { OWLDescription desc = (OWLDescription) descIter.next(); if (displayedClass.getSuperClasses(ontology).contains(obj)) { RemoveSuperClass change = new RemoveSuperClass(ontology, displayedClass, desc, null); changes.add(change); } else { // remove specific axiom if present OWLSubClassAxiom axiom = ontology.getOWLDataFactory().getOWLSubClassAxiom(displayedClass, desc); RemoveClassAxiom change2 = new RemoveClassAxiom(ontology, axiom, null); changes.add(change2); } } } } else if (titleCode.equals("C-SUP")) { // delete super-class OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLClass) { // super classes can be defined in two ways // check to see what kind of change needs to be put OWLClass desc = (OWLClass) obj; if (desc.getSuperClasses(ontology).contains(displayedClass)) { RemoveSuperClass change = new RemoveSuperClass(ontology, desc, displayedClass, null); changes.add(change); } else { // remove specific axiom if present OWLSubClassAxiom axiom = ontology.getOWLDataFactory().getOWLSubClassAxiom(desc, displayedClass); RemoveClassAxiom change2 = new RemoveClassAxiom(ontology, axiom, null); changes.add(change2); } } else { OWLDescription desc = (OWLDescription) obj; // remove specific axiom if present OWLSubClassAxiom axiom = ontology.getOWLDataFactory().getOWLSubClassAxiom(desc, displayedClass); RemoveClassAxiom change2 = new RemoveClassAxiom(ontology, axiom, null); changes.add(change2); } } else if (titleCode.equals("C-INT")) { // delete intersection element // remove whole intersection and add remaining elements OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; deleteFromBooleanDesc(ontology, displayedClass, desc, OWLAnd.class, changes); } else { Iterator descIter = ((Collection) obj).iterator(); while (descIter.hasNext()) { OWLClass desc = (OWLClass) descIter.next(); deleteFromBooleanDesc(ontology, displayedClass, desc, OWLAnd.class, changes); } } } else if (titleCode.equals("C-UNI")) { // delete union element // remove whole union and add remaining elements OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; deleteFromBooleanDesc(ontology, displayedClass, desc, OWLOr.class, changes); } else { Iterator descIter = ((Collection) obj).iterator(); while (descIter.hasNext()) { OWLClass desc = (OWLClass) descIter.next(); deleteFromBooleanDesc(ontology, displayedClass, desc, OWLOr.class, changes); } } } else if (titleCode.equals("C-NOT")) { // delete complement element OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLDescription) { BooleanElementChange change = new BooleanElementChange(OWLNot.class, "Remove", ontology, displayedClass, (OWLDescription) obj, null); changes.add(change); } } else if (titleCode.equals("I-ONE")) { // delete one-of element OWLClass displayedClass = (OWLClass) displayedEntity; if (obj instanceof OWLIndividual) { OWLIndividual desc = (OWLIndividual) obj; updateEnumerations(ontology, displayedClass, desc, changes); } } else if (titleCode.equals("I-INS")) { // delete instance RemoveIndividualClass change = new RemoveIndividualClass(ontology, (OWLIndividual) obj, (OWLDescription) displayedEntity, null); changes.add(change); } else if (titleCode.equals("C-TYP")) { // delete type RemoveIndividualClass change = new RemoveIndividualClass(ontology, (OWLIndividual) displayedEntity, (OWLDescription) obj, null); changes.add(change); } else if (titleCode.equals("C-HASDOM")) { // delete property domain OWLProperty prop = (OWLProperty) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; RemoveDomain change = new RemoveDomain(ontology, prop, desc, null); changes.add(change); } } else if (titleCode.equals("P-DOM")) { // delete property domain OWLClass cla = (OWLClass) displayedEntity; if (obj instanceof OWLProperty) { RemoveDomain change = new RemoveDomain(ontology, (OWLProperty) obj, cla, null); changes.add(change); } } else if (titleCode.equals("C-HASRAN")) { // delete property range // check if datatype or object property if (displayedEntity instanceof OWLObjectProperty) { OWLObjectProperty prop = (OWLObjectProperty) displayedEntity; if (obj instanceof OWLDescription) { OWLDescription desc = (OWLDescription) obj; RemoveObjectPropertyRange change = new RemoveObjectPropertyRange(ontology, prop, desc, null); changes.add(change); } } else { OWLDataProperty prop = (OWLDataProperty) displayedEntity; if (obj instanceof OWLDataRange) { OWLDataRange dran = (OWLDataRange) obj; RemoveDataPropertyRange change = new RemoveDataPropertyRange(ontology, prop, dran, null); changes.add(change); } } } else if (titleCode.equals("P-RAN")) { // delete property range OWLClass cla = (OWLClass) displayedEntity; if (obj instanceof OWLObjectProperty) { RemoveObjectPropertyRange change = new RemoveObjectPropertyRange(ontology, (OWLObjectProperty) obj, cla, null); changes.add(change); } } else if (titleCode.equals("P-SUB")) { // remove super property if (obj instanceof OWLProperty) { if (((OWLProperty) displayedEntity).getSuperProperties(ontology).contains(obj)) { RemoveSuperProperty change = new RemoveSuperProperty(ontology, (OWLProperty) displayedEntity, (OWLProperty) obj, null); changes.add(change); } else { // remove specific axiom if present OWLSubPropertyAxiom axiom = ontology.getOWLDataFactory() .getOWLSubPropertyAxiom((OWLProperty) displayedEntity, (OWLProperty) obj); RemovePropertyAxiom change2 = new RemovePropertyAxiom(ontology, axiom, null); changes.add(change2); } } } else if (titleCode.equals("P-SUP")) { // remove sub property if (obj instanceof OWLProperty) { if (((OWLProperty) obj).getSuperProperties(ontology).contains(displayedEntity)) { RemoveSuperProperty change = new RemoveSuperProperty(ontology, (OWLProperty) obj, (OWLProperty) displayedEntity, null); changes.add(change); } else { // remove specific axiom if present OWLSubPropertyAxiom axiom = ontology.getOWLDataFactory() .getOWLSubPropertyAxiom((OWLProperty) obj, (OWLProperty) displayedEntity); RemovePropertyAxiom change2 = new RemovePropertyAxiom(ontology, axiom, null); changes.add(change2); } } } else if (titleCode.equals("P-EQU")) { // remove equivalent property if (obj instanceof OWLProperty) { Set propSet = new HashSet(); propSet.add((OWLProperty) obj); propSet.add((OWLProperty) displayedEntity); OWLEquivalentPropertiesAxiom axiom = ontology.getOWLDataFactory() .getOWLEquivalentPropertiesAxiom(propSet); RemovePropertyAxiom change = new RemovePropertyAxiom(ontology, axiom, null); changes.add(change); } } else if (titleCode.equals("P-INV")) { // remove inverse property if (obj instanceof OWLObjectProperty) { OWLObjectProperty prop = (OWLObjectProperty) displayedEntity; OWLObjectProperty inverse = (OWLObjectProperty) obj; RemoveInverse change = new RemoveInverse(ontology, prop, inverse, null); changes.add(change); } } else if (titleCode.startsWith(("P-VAL"))) { // remove property value pair // also obtain value from hash table String valueHashKey = titleCode.substring(titleCode.lastIndexOf(":") + 1, titleCode.length()); Object value = OWLDescHash.get(valueHashKey); if (obj instanceof OWLObjectProperty) { RemoveObjectPropertyInstance change = new RemoveObjectPropertyInstance(ontology, (OWLIndividual) displayedEntity, (OWLObjectProperty) obj, (OWLIndividual) value, null); changes.add(change); } else if (obj instanceof OWLDataProperty) { RemoveDataPropertyInstance change = new RemoveDataPropertyInstance(ontology, (OWLIndividual) displayedEntity, (OWLDataProperty) obj, (OWLDataValue) value, null); changes.add(change); } } else if (titleCode.startsWith("RULE")) { System.out.println("Deleting Rule"); //String n3 = swoopModel.getRuleExpr().publishRulesToPychinko(); // obj is OWLRule // go through the rulemap and remove this rule OWLRule rule = (OWLRule) obj; //get the rule and its friggin expressivity (exactly why are they bundled together?) OWLRuleAtom consAtom = (OWLRuleAtom) rule.getConsequents().iterator().next(); OWLObject key = null; if (consAtom instanceof OWLRuleClassAtom) { key = ((OWLRuleClassAtom) consAtom).getDescription(); } else { if (consAtom instanceof OWLRuleDataPropertyAtom) { key = ((OWLRuleDataPropertyAtom) consAtom).getProperty(); } else { if (consAtom instanceof OWLRuleObjectPropertyAtom) { key = ((OWLRuleObjectPropertyAtom) consAtom).getProperty(); } } } HashSet rulesSet = (HashSet) swoopModel.getRuleExpr().getRuleMap().get(key); //find the rule we want to delete RuleValue rvDelete = null; Iterator it = rulesSet.iterator(); while (it.hasNext()) { RuleValue rv = (RuleValue) it.next(); if (rv.getRule().equals(obj)) { rvDelete = rv; } } rulesSet.remove(rvDelete); swoopModel.getRuleExpr().getRuleMap().put(key, rulesSet); } return changes; } /** * Handle what happens when the reasoner supports explanation, a "Why?" link is displayed * next to an inference and the user clicks on the link. * In this case, we call reasoner's explanation tool to display reason */ public List handleWhyLink(String hLink) throws Exception { OWLOntology ontology = reasoner.getOntology(); OWLDataFactory ontDF = ontology.getOWLDataFactory(); // parse WHY hyper-link int pos1 = hLink.indexOf(":"); int pos2 = hLink.indexOf(":", pos1 + 1); String hashCode = hLink.substring(pos1 + 1, pos2); String titleCode = hLink.substring(pos2 + 1, hLink.length()); Object obj = OWLDescHash.get(hashCode); OWLEntity entity = swoopModel.getSelectedEntity(); // create description of inference String infSubj = "", infObj = "", infRel = ""; if (entity instanceof OWLNamedObject) { infSubj = swoopModel.shortForm(((OWLNamedObject) entity).getURI()); // add entity URI to highlightSet in ConciseFormatVisitor ((ConciseFormatVisitor) visitor).highlightMap.put(((OWLNamedObject) entity).getURI(), "<font color=\"green\">"); } if (obj instanceof OWLNamedObject) { infObj = swoopModel.shortForm(((OWLNamedObject) obj).getURI()); // add obj URI to highlightSet in ConciseFormatVisitor ((ConciseFormatVisitor) visitor).highlightMap.put(((OWLNamedObject) obj).getURI(), "<font color=\"green\">"); } OWLDescription satClazz = null; List restoreChanges = new ArrayList(); Set sos = new HashSet(); if (titleCode.equals("C-SUB")) { // explanation for why entity subClassOf obj // check sat. of C ^ ~D infRel = infSubj + " " + ConciseFormat.SUBSET + " " + infObj; Set and = new HashSet(); and.add(entity); and.add(ontDF.getOWLNot((OWLDescription) obj)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("C-SUP")) { // check sat. of D ^ ~C infRel = infObj + " " + ConciseFormat.SUBSET + " " + infSubj; Set and = new HashSet(); and.add(obj); and.add(ontDF.getOWLNot((OWLDescription) entity)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("C-EQU")) { // check sat. of (C ^ ~D) v (~C ^ D) infRel = infSubj + " " + ConciseFormat.EQUIVALENT + " " + infObj; Set and1 = new HashSet(); and1.add(entity); and1.add(ontDF.getOWLNot((OWLDescription) obj)); Set and2 = new HashSet(); and2.add(obj); and2.add(ontDF.getOWLNot((OWLDescription) entity)); Set or = new HashSet(); or.add(ontDF.getOWLAnd(and1)); or.add(ontDF.getOWLAnd(and2)); satClazz = ontDF.getOWLOr(or); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("C-DIS")) { // check sat. of C ^ D infRel = infSubj + " " + ConciseFormat.SUBSET + ConciseFormat.COMPLEMENT + " " + infObj; Set and = new HashSet(); and.add(obj); and.add(entity); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("C-HASDOM")) { // check sat. of (\exists P. Top ^ ~C) infRel = infSubj + " rdfs:domain " + infObj; OWLProperty prop = (OWLProperty) entity; OWLDescription dom = (OWLDescription) obj; OWLDescription existsPT = null; OWLClass thing = ontDF.getOWLThing(); if (prop instanceof OWLDataProperty) existsPT = ontDF.getOWLDataCardinalityAtLeastRestriction((OWLDataProperty) prop, 1); else existsPT = ontDF.getOWLObjectSomeRestriction((OWLObjectProperty) prop, thing); Set and = new HashSet(); and.add(existsPT); and.add(ontDF.getOWLNot(dom)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("P-DOM")) { // check sat. of (\exists P. Top ^ ~C) infRel = infObj + " rdfs:domain " + infSubj; OWLProperty prop = (OWLProperty) obj; OWLClass dom = (OWLClass) entity; OWLDescription existsPT = null; OWLClass thing = ontDF.getOWLThing(); if (prop instanceof OWLDataProperty) existsPT = ontDF.getOWLDataCardinalityAtLeastRestriction((OWLDataProperty) prop, 1); else existsPT = ontDF.getOWLObjectSomeRestriction((OWLObjectProperty) prop, thing); Set and = new HashSet(); and.add(existsPT); and.add(ontDF.getOWLNot(dom)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("C-HASRAN") && entity instanceof OWLObjectProperty) { // check sat. of (Thing ^ ~(\forall P.C)) infRel = infSubj + " rdfs:range " + infObj; OWLObjectProperty prop = (OWLObjectProperty) entity; OWLDescription ran = (OWLDescription) obj; OWLDescription forallPR = null; OWLClass thing = ontDF.getOWLThing(); forallPR = ontDF.getOWLObjectAllRestriction(prop, ran); Set and = new HashSet(); and.add(thing); and.add(ontDF.getOWLNot(forallPR)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("P-RAN") && obj instanceof OWLObjectProperty) { // check sat. of (Thing ^ ~(\forall P.C)) infRel = infObj + " rdfs:range " + infSubj; OWLObjectProperty prop = (OWLObjectProperty) obj; OWLClass ran = (OWLClass) entity; OWLDescription forallPR = null; OWLClass thing = ontDF.getOWLThing(); forallPR = ontDF.getOWLObjectAllRestriction(prop, ran); Set and = new HashSet(); and.add(thing); and.add(ontDF.getOWLNot(forallPR)); satClazz = ontDF.getOWLAnd(and); sos = this.getSOS(ontology, satClazz); } else if (titleCode.equals("I-INS")) { infRel = infObj + " rdf:type " + infSubj; OWLClass cla = (OWLClass) entity; OWLIndividual ind = (OWLIndividual) obj; OWLDescription notC = ontDF.getOWLNot(cla); // temporarily add assertion to ontology for getting explanation AddIndividualClass ai = new AddIndividualClass(ontology, ind, notC, null); ai.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveIndividualClass(ontology, ind, notC, null)); satClazz = notC; sos = this.getSOS(ontology, satClazz); // remove type assertion from sos for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { Object axiom = iter.next(); if (axiom instanceof OWLIndividualTypeAssertion) { OWLIndividualTypeAssertion oit = (OWLIndividualTypeAssertion) axiom; if (oit.getIndividual().equals(ind) && oit.getType().equals(notC)) { sos.remove(axiom); break; } } } } else if (titleCode.equals("C-TYP")) { infRel = infSubj + " rdf:type " + infObj; OWLDescription cla = (OWLDescription) obj; OWLIndividual ind = (OWLIndividual) entity; OWLDescription notC = ontDF.getOWLNot(cla); // temporarily add assertion to ontology for getting explanation AddIndividualClass ai = new AddIndividualClass(ontology, ind, notC, null); ai.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveIndividualClass(ontology, ind, notC, null)); satClazz = notC; sos = this.getSOS(ontology, satClazz); // remove type assertion from sos for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { Object axiom = iter.next(); if (axiom instanceof OWLIndividualTypeAssertion) { OWLIndividualTypeAssertion oit = (OWLIndividualTypeAssertion) axiom; if (oit.getIndividual().equals(ind) && oit.getType().equals(notC)) { sos.remove(axiom); break; } } } } else if (titleCode.startsWith(("P-INSO")) && obj instanceof List) { // also obtain value from hash table List pvTuple = (List) obj; OWLIndividual value = (OWLIndividual) pvTuple.get(1); OWLIndividual ind = (OWLIndividual) entity; OWLObjectProperty prop = (OWLObjectProperty) pvTuple.get(0); // \exists R \neg {o} //TODO: infRel = infSubj + " subClassOf " + infObj; Set one = new HashSet(); one.add(value); OWLEnumeration oneOf = ontDF.getOWLEnumeration(one); OWLDescription negOne = ontDF.getOWLNot(oneOf); OWLDescription existsNeg = ontDF.getOWLObjectAllRestriction(prop, negOne); AddIndividualClass ai = new AddIndividualClass(ontology, ind, existsNeg, null); restoreChanges.add(new RemoveIndividualClass(ontology, ind, existsNeg, null)); ai.accept((ChangeVisitor) ontology); satClazz = existsNeg; sos = this.getSOS(ontology, satClazz); // remove type assertion from sos for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { Object axiom = iter.next(); if (axiom instanceof OWLIndividualTypeAssertion) { OWLIndividualTypeAssertion oit = (OWLIndividualTypeAssertion) axiom; if (oit.getIndividual().equals(ind) && oit.getType().equals(existsNeg)) { sos.remove(axiom); break; } } } } else if (titleCode.startsWith(("I-SAM"))) { // add different from assertion infRel = infSubj + " " + ConciseFormat.EQU + " " + infObj; OWLClass temp1 = ontDF.getOWLClass(new URI("temp1")); AddEntity ae = new AddEntity(ontology, temp1, null); ae.accept((ChangeVisitor) ontology); OWLClass temp2 = ontDF.getOWLClass(new URI("temp2")); AddEntity ae2 = new AddEntity(ontology, temp2, null); ae2.accept((ChangeVisitor) ontology); Set enum1 = new HashSet(); enum1.add((OWLIndividual) displayedEntity); OWLEnumeration en1 = ontDF.getOWLEnumeration(enum1); AddEquivalentClass aec = new AddEquivalentClass(ontology, temp1, en1, null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp1, en1, null)); Set enum2 = new HashSet(); enum2.add((OWLIndividual) obj); OWLEnumeration en2 = ontDF.getOWLEnumeration(enum2); aec = new AddEquivalentClass(ontology, temp2, en2, null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp2, en2, null)); aec = new AddEquivalentClass(ontology, temp1, ontDF.getOWLNot(temp2), null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp1, ontDF.getOWLNot(temp2), null)); restoreChanges.add(new RemoveEntity(ontology, temp1, null)); restoreChanges.add(new RemoveEntity(ontology, temp2, null)); satClazz = temp1; sos = this.getSOS(ontology, satClazz); // remove axioms contains temp1 or temp2 for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); if (axiom instanceof OWLEquivalentClassesAxiom) { OWLEquivalentClassesAxiom equ = (OWLEquivalentClassesAxiom) axiom; boolean remove = false; for (Iterator iter2 = equ.getEquivalentClasses().iterator(); iter2.hasNext();) { OWLDescription desc = (OWLDescription) iter2.next(); if (desc instanceof OWLClass && (((OWLClass) desc).getURI().equals(new URI("temp1")) || ((OWLClass) desc).getURI().equals(new URI("temp2")))) { remove = true; break; } } if (remove) sos.remove(axiom); } } } else if (titleCode.startsWith(("I-DIF"))) { // add sameAs assertion infRel = infSubj + " " + ConciseFormat.DISJOINT + " " + infObj; OWLClass temp1 = ontDF.getOWLClass(new URI("temp1")); AddEntity ae = new AddEntity(ontology, temp1, null); ae.accept((ChangeVisitor) ontology); OWLClass temp2 = ontDF.getOWLClass(new URI("temp2")); AddEntity ae2 = new AddEntity(ontology, temp2, null); ae2.accept((ChangeVisitor) ontology); Set enum1 = new HashSet(); enum1.add((OWLIndividual) displayedEntity); OWLEnumeration en1 = ontDF.getOWLEnumeration(enum1); AddEquivalentClass aec = new AddEquivalentClass(ontology, temp1, en1, null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp1, en1, null)); Set enum2 = new HashSet(); enum2.add((OWLIndividual) obj); OWLEnumeration en2 = ontDF.getOWLEnumeration(enum2); aec = new AddEquivalentClass(ontology, temp2, en2, null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp2, en2, null)); aec = new AddEquivalentClass(ontology, temp1, temp2, null); aec.accept((ChangeVisitor) ontology); restoreChanges.add(new RemoveEquivalentClass(ontology, temp1, temp2, null)); restoreChanges.add(new RemoveEntity(ontology, temp1, null)); restoreChanges.add(new RemoveEntity(ontology, temp2, null)); satClazz = temp1; sos = this.getSOS(ontology, satClazz); // remove axioms containing temp1 or temp2 for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { Object axiom = iter.next(); if (axiom instanceof OWLEquivalentClassesAxiom) { OWLEquivalentClassesAxiom equ = (OWLEquivalentClassesAxiom) axiom; boolean remove = false; for (Iterator iter2 = equ.getEquivalentClasses().iterator(); iter2.hasNext();) { OWLDescription desc = (OWLDescription) iter2.next(); if (desc instanceof OWLClass && (((OWLClass) desc).getURI().equals(new URI("temp1")) || ((OWLClass) desc).getURI().equals(new URI("temp2")))) { remove = true; break; } } if (remove) sos.remove(axiom); } } } else { List sosStr = new ArrayList(); sosStr.add("No explanation support yet for this inference."); sosStr.add("No explanation support yet for this inference."); return sosStr; } // save current print writer PrintWriter copy = new PrintWriter(pw); // create new temp writer to render axioms StringWriter st = new StringWriter(); PrintWriter buffer = new PrintWriter(st); setWriter(buffer); // Note: choice of base below only effects ordering OWLNamedObject base = null; if (entity instanceof OWLNamedObject) base = (OWLNamedObject) entity; else if (obj instanceof OWLNamedObject) base = (OWLNamedObject) obj; else base = ontDF.getOWLThing(); printExplanationSOS(sos, base, false); String sosStr1 = st.toString(); sosStr1 = sosStr1.replaceAll("problem", "inference <br><font color=\"green\">" + infRel + "</font>"); // call printing again but turn highlighting on st = new StringWriter(); buffer = new PrintWriter(st); setWriter(buffer); printExplanationSOS(sos, base, true); String sosStr2 = st.toString(); sosStr2 = sosStr2.replaceAll("problem", "inference <br><font color=\"green\">" + infRel + "</font>"); // restore writer this.pw = copy; // restore highlightedSet in visitor to empty ((ConciseFormatVisitor) visitor).highlightMap.clear(); // also restore ontology to initial state if changed for (Iterator iter = restoreChanges.iterator(); iter.hasNext();) { OntologyChange res = (OntologyChange) iter.next(); res.accept((ChangeVisitor) ontology); } List sosStr = new ArrayList(); sosStr.add(sosStr1); sosStr.add(sosStr2); return sosStr; } public String getSudokuExplanation(OWLOntology gridOnt, OWLIndividual ind, OWLClass cla) { try { OWLOntology ontology = swoopModel.cloneOntology(gridOnt); ind = ontology.getIndividual(ind.getURI()); cla = ontology.getClass(cla.getURI()); OWLDescription notC = ontology.getOWLDataFactory().getOWLNot(cla); // temporarily add assertion to ontology for getting explanation AddIndividualClass ai = new AddIndividualClass(ontology, ind, notC, null); ai.accept((ChangeVisitor) ontology); OWLDescription satClazz = notC; Set sos = this.getSOS(ontology, satClazz); // remove type assertion from sos for (Iterator iter = new HashSet(sos).iterator(); iter.hasNext();) { Object axiom = iter.next(); if (axiom instanceof OWLIndividualTypeAssertion || axiom instanceof OWLSubClassAxiom) { sos.remove(axiom); } } // create new temp writer to render axioms StringWriter st = new StringWriter(); PrintWriter buffer = new PrintWriter(st); setWriter(buffer); // Note: choice of base below only effects ordering OWLNamedObject base = null; if (entity instanceof OWLNamedObject) base = (OWLNamedObject) entity; else if (cla instanceof OWLNamedObject) base = (OWLNamedObject) cla; else base = ontology.getOWLDataFactory().getOWLThing(); printExplanationSOS(sos, base, false); String sosStr = st.toString(); sosStr = sosStr.replaceAll("problem", "inference"); sosStr = "<html><font face=\"Verdana\" SIZE=2>" + sosStr + "</font></html>"; return sosStr; } catch (Exception ex) { ex.printStackTrace(); } return ""; } public List handleEditLink(String hLink) throws OWLException { List changes = new ArrayList(); OWLOntology ontology = reasoner.getOntology(); // parse EDIT hyper-link int pos1 = hLink.indexOf(":"); int pos2 = hLink.indexOf(":", pos1 + 1); String hashCode = hLink.substring(pos1 + 1, pos2); String titleCode = hLink.substring(pos2 + 1, hLink.length()); Object obj = OWLDescHash.get(hashCode); //System.out.println( "CODE: " + titleCode ); if (titleCode.startsWith("RULE")) { System.out.println("\nEDITING RULE\n"); OWLRule rule = (OWLRule) obj; PopupAddRule test = new PopupAddRule(swoopModel, rule); test.show(); } return changes; } /* * SwoopRenderer method * */ public Component getDisplayComponent(SwoopDisplayPanel panel) { if (!(panel instanceof TermsDisplay)) throw new IllegalArgumentException(); return getEditorPane(this.getContentType(), (TermsDisplay) panel); } private void deleteFromBooleanDesc(OWLOntology ontology, OWLClass displayedClass, OWLDescription desc, Class type, List changes) throws OWLException { BooleanElementChange change = new BooleanElementChange(type, "Remove", ontology, displayedClass, desc, null); changes.add(change); } /** Accepts an ontology, class, individual (changes) ; * Removes the enumeration on class that contains individual * Adds a new enumeration without the individual * Records changes */ private void updateEnumerations(OWLOntology ontology, OWLClass displayedClass, OWLIndividual desc, List changes) throws OWLException { EnumElementChange change = new EnumElementChange("Remove", ontology, displayedClass, desc, null); changes.add(change); } public boolean isEditableText() { return false; } /* * For debugging purposes: sort axioms in explanation set to explain trace better */ private List sortAxioms(URI baseURI, Map LHSmap, Map RHSmap, Set removed, int level) { List sort = new ArrayList(); try { for (Iterator iter = LHSmap.keySet().iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); List LHS = (List) LHSmap.get(axiom); for (Iterator iter2 = LHS.iterator(); iter2.hasNext();) { OWLNamedObject term = (OWLNamedObject) iter2.next(); if (baseURI == null || term.getURI().equals(baseURI)) { // match found, add axiom to source, tag removal if (!removed.contains(axiom)) { sort.add(axiom); sortLevelMap.put(axiom, String.valueOf(level)); } removed.add(axiom); // and remove from LHS/RHS maps Map newLHSmap = new HashMap(LHSmap); newLHSmap.remove(axiom); Map newRHSmap = new HashMap(RHSmap); newRHSmap.remove(axiom); // now check RHS and move baseURI here if possible List RHS = (List) RHSmap.get(axiom); URI newBaseURI = null; if (!RHS.isEmpty()) { for (int rctr = 0; rctr < RHS.size(); rctr++) { newBaseURI = ((OWLNamedObject) RHS.get(rctr)).getURI(); sort.addAll(sortAxioms(newBaseURI, newLHSmap, newRHSmap, removed, level + 1)); } } else { // else move to element in LHS List modLHS = new ArrayList(LHS); modLHS.remove(term); for (int lctr = 0; lctr < modLHS.size(); lctr++) { newBaseURI = ((OWLNamedObject) modLHS.get(lctr)).getURI(); sort.addAll(sortAxioms(newBaseURI, newLHSmap, newRHSmap, removed, level + 1)); } } } } } // // check for remaining axioms // for (Iterator iter = removed.iterator(); iter.hasNext();) { // OWLObject axiom = (OWLObject) iter.next(); // LHSmap.remove(axiom); // RHSmap.remove(axiom); // } // if (LHSmap.keySet().size()>0) { // sort.addAll(sortAxioms(null, LHSmap, RHSmap, new HashSet())); // } } catch (Exception ex) { ex.printStackTrace(); } return sort; } /* * Used to prune explanation set obtained from Pellet */ public boolean checkSatisfiability(Set axioms, OWLDescription clazz) { // create a new ontology with axioms // and check satisfiability of clazz boolean sat = false; try { OWLOntBuilder ontBuilder = new OWLOntBuilder(); // create new ontology using axioms // use OWLOntBuilder to build a new ontology given axioms for (Iterator iter = axioms.iterator(); iter.hasNext();) { OWLObject obj = (OWLObject) iter.next(); obj.accept(ontBuilder); } // if clazz is not in ontology, return true OWLOntology newOnt = ontBuilder.currentOnt; if (clazz != null && clazz instanceof OWLClass && newOnt.getClass(((OWLClass) clazz).getURI()) == null) return true; else if (clazz != null) { // get clazz in newOnt clazz = ontBuilder.visitDescription(clazz); } // create new instance of pellet and check sat. of clazz PelletReasoner newPellet = new PelletReasoner(); newPellet.setOntology(newOnt, false); if (clazz != null) sat = newPellet.isConsistent(clazz); else sat = newPellet.isConsistent(); // TESTING: // also add clazz to some ind type // try { // OWLIndividual dummy = newOnt.getOWLDataFactory().getOWLIndividual(new URI("dummy")); // AddEntity ae = new AddEntity(newOnt, dummy, null); // ae.accept((ChangeVisitor) newOnt); // AddIndividualClass aic = new AddIndividualClass(newOnt, dummy, clazz, null); // aic.accept((ChangeVisitor) newOnt); // } // catch (Exception ex) { // ex.printStackTrace(); // } // System.out.println(clazz + "satisfiability: " + sat); // CorrectedRDFRenderer rdf = new CorrectedRDFRenderer(); // StringWriter w = new StringWriter(); // rdf.renderOntology(newOnt, null, w); // System.out.println(w.toString()); } catch (Exception ex) { System.out.println(ex.getMessage()); // clazz (description) may not be in ontology! // ex.printStackTrace(); return true; } return sat; } private boolean checkSatisfiability(OWLOntBuilder ob, OWLDescription clazz) { // check satisfiability of clazz in ont in ob OWLOntology newOnt = ob.currentOnt; boolean sat = false; try { if (clazz != null && clazz instanceof OWLClass && newOnt.getClass(((OWLClass) clazz).getURI()) == null) return true; else if (clazz != null) { // get clazz in newOnt clazz = ob.visitDescription(clazz); } // create new instance of pellet and check sat. of clazz PelletReasoner newPellet = new PelletReasoner(); newPellet.setOntology(newOnt, false); Timer parseTimer = new Timer("parse time"); parseTimer.start(); if (clazz != null) sat = newPellet.isConsistent(clazz); else sat = newPellet.isConsistent(); parseTimer.stop(); parseTime += parseTimer.getTotal(); } catch (Throwable ex) { System.out.println(ex.getMessage()); // clazz (description) may not be in ontology! ex.printStackTrace(); return true; } return sat; } /* * check if entity is in ont, if not, create new entity and return it */ private OWLEntity checkEntity(OWLOntology ont, OWLEntity entity) { try { AddEntity ae = null; OWLDataFactory ontDF = ont.getOWLDataFactory(); if (entity instanceof OWLClass) { if (ont.getClass(entity.getURI()) == null) { entity = ontDF.getOWLClass(entity.getURI()); ae = new AddEntity(ont, entity, null); } else entity = ont.getClass(entity.getURI()); } else if (entity instanceof OWLDataProperty) { if (ont.getDataProperty(entity.getURI()) == null) { entity = ontDF.getOWLDataProperty(entity.getURI()); ae = new AddEntity(ont, entity, null); } else entity = ont.getDataProperty(entity.getURI()); } else if (entity instanceof OWLObjectProperty) { if (ont.getObjectProperty(entity.getURI()) == null) { entity = ontDF.getOWLObjectProperty(entity.getURI()); ae = new AddEntity(ont, entity, null); } else entity = ont.getObjectProperty(entity.getURI()); } else if (entity instanceof OWLIndividual) { if (ont.getIndividual(entity.getURI()) == null) { entity = ontDF.getOWLIndividual(entity.getURI()); ae = new AddEntity(ont, entity, null); } else entity = ont.getIndividual(entity.getURI()); } if (ae != null) ae.accept((ChangeVisitor) ont); } catch (Exception ex) { ex.printStackTrace(); } return entity; } /* * Prune the explanation set and print axioms */ public void printExplanationSOS(Set explanationSet, OWLNamedObject entity, boolean enableHighlights) { Set strikeSet = new HashSet(); try { if (explanationSet != null && !explanationSet.isEmpty()) { println("<b>Axioms causing the problem:</b>"); // need to sort axioms to explain trace better Iterator i = explanationSet.iterator(); // create instance of object container to check contents of axiom OWLObjectContainer owlCont = null; owlCont = new OWLObjectContainer(entity); Map LHSmap = new HashMap(); Map RHSmap = new HashMap(); Map objectCount = new HashMap(); while (i.hasNext()) { OWLObject axiom = (OWLObject) i.next(); owlCont.reset(); // visit axiom owlCont.visit(axiom); // get contained objects, LHS and RHS of axiom List objects = owlCont.getContainedObjects(); List LHS = owlCont.getLHS(); List RHS = owlCont.getRHS(); if (LHS.size() == 0 && RHS.size() == 0) LHS = objects; LHSmap.put(axiom, LHS); RHSmap.put(axiom, RHS); List total = new ArrayList(LHS); total.addAll(RHS); updateCount(objectCount, total); } // highlight based on entity count if (enableHighlights) { for (Iterator iter = objectCount.keySet().iterator(); iter.hasNext();) { URI objURI = (URI) iter.next(); String valStr = objectCount.get(objURI).toString(); int val = Integer.parseInt(valStr); // System.out.println(objURI + ":"+ val); if (val == 1 && !((ConciseFormatVisitor) visitor).highlightMap.containsKey(objURI)) { ((ConciseFormatVisitor) visitor).highlightMap.put(objURI, "<strike><font color=\"red\">"); strikeSet.add(objURI); } } } // now call sorting method after computing lhs/rhs of axioms URI baseURI = entity.getURI(); int count = 1; sortLevelMap = new HashMap(); // reset map which stores links between sorted axioms in their resp level (recursive depth) do { List axioms = sortAxioms(baseURI, LHSmap, RHSmap, new HashSet(), 0); // now print sorted axiom list for (Iterator iter = axioms.iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); int level = Integer.parseInt(sortLevelMap.get(axiom).toString()); print("<b>" + (count++) + ")</b> "); for (int ctr = 0; ctr < level * 2; ctr++) print(" "); if (level > 0) print("|_"); printObject(axiom); println(); LHSmap.remove(axiom); RHSmap.remove(axiom); } baseURI = null; } while ((count - 1) < explanationSet.size()); } print("<hr>"); } catch (Exception ex) { ex.printStackTrace(); } finally { // clear highlight map of all strikes ((ConciseFormatVisitor) visitor).highlightMap.keySet().removeAll(strikeSet); } } /* * Prune the explanation set and print axioms */ public void printRepairSOS(Set explanationSet, OWLNamedObject entity, boolean enableHighlights, RepairFrame repair) { Set strikeSet = new HashSet(); String insFont = "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=3>"; String tab = "_____"; // "; try { if (explanationSet != null && !explanationSet.isEmpty()) { println("<b>Axioms causing the problem:</b>"); // need to sort axioms to explain trace better Iterator i = explanationSet.iterator(); // create instance of object container to check contents of axiom OWLObjectContainer owlCont = null; owlCont = new OWLObjectContainer(entity); Map LHSmap = new HashMap(); Map RHSmap = new HashMap(); Map objectCount = new HashMap(); while (i.hasNext()) { OWLObject axiom = (OWLObject) i.next(); owlCont.reset(); // visit axiom owlCont.visit(axiom); // get contained objects, LHS and RHS of axiom List objects = owlCont.getContainedObjects(); List LHS = owlCont.getLHS(); List RHS = owlCont.getRHS(); if (LHS.size() == 0 && RHS.size() == 0) LHS = objects; LHSmap.put(axiom, LHS); RHSmap.put(axiom, RHS); List total = new ArrayList(LHS); total.addAll(RHS); updateCount(objectCount, total); } // highlight based on entity count if (enableHighlights) { for (Iterator iter = objectCount.keySet().iterator(); iter.hasNext();) { URI objURI = (URI) iter.next(); String valStr = objectCount.get(objURI).toString(); int val = Integer.parseInt(valStr); // System.out.println(objURI + ":"+ val); if (val == 1 && !((ConciseFormatVisitor) visitor).highlightMap.containsKey(objURI)) { ((ConciseFormatVisitor) visitor).highlightMap.put(objURI, "<strike><font color=\"red\">"); strikeSet.add(objURI); } } } // now call sorting method after computing lhs/rhs of axioms URI baseURI = entity.getURI(); int count = 1; sortLevelMap = new HashMap(); // reset map which stores links between sorted axioms in their resp level (recursive depth) print("</b><hr><table border=\"1\">"); print("<tr><td>" + insFont + "<b>Erroneous Axioms</b></td><td>" + insFont + "<b><a href=\":ARITY\">Arity</a></b></td><td>" + insFont + "<b><a href=\":IMPACT\">Impact</a></b></td><td>" + insFont + "<b><a href=\":USAGE\">Usage</a></b></td><td>" + insFont + "<b><a href=\":RANK\">Rank</a></b></td>" + insFont + "<b>Status</b></td></tr>"); do { List axioms = sortAxioms(baseURI, LHSmap, RHSmap, new HashSet(), 0); // now print sorted axiom list for (Iterator iter = axioms.iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); if (repair.keptAxiomSet.contains(axiom)) print("<tr bgcolor=\"C3FDB8\"><td>"); else if (repair.removedAxiomSet.contains(axiom)) print("<tr bgcolor=\"FFDDDD\"><td>"); else print("<tr><td>"); print(insFont); int level = Integer.parseInt(sortLevelMap.get(axiom).toString()); print("<b>" + (count++) + ")</b> "); for (int ctr = 0; ctr < level * 2; ctr++) print(" "); if (level > 0) print("|_"); int arity = ((HashSet) repair.axiomUnsatClaMap.get(axiom)).size(); String color = "FFFFFF"; if (arity == 2) color = "FFFF88"; else if (arity == 3) color = "FFFF44"; else if (arity >= 4) color = "FFFF22"; print("<font size = 3 style=\"BACKGROUND-COLOR:" + color + "\">"); printObject(axiom); print("</td>"); // String hash = String.valueOf(repair.axiomUnsatClaMap.get(axiom).hashCode()); repair.objectMap.put(hash, repair.axiomUnsatClaMap.get(axiom)); print("<td>" + insFont + "<a href=\":HASH:Arity:" + hash + "\">" + String.valueOf(arity) + "</a></td>"); int impact = 0; Set impactSet = new HashSet(); if (repair.axiomSOSMap.containsKey(axiom)) impactSet = (HashSet) repair.axiomSOSMap.get(axiom); impact = impactSet.size(); hash = String.valueOf(impactSet.hashCode()); repair.objectMap.put(hash, impactSet); print("<td>" + insFont + "<a href=\":HASH:Impact:" + hash + "\">" + String.valueOf(impact) + "</a></td>"); int usage = ((HashSet) repair.axiomUsageMap.get(axiom)).size(); hash = String.valueOf(repair.axiomUsageMap.get(axiom).hashCode()); repair.objectMap.put(hash, repair.axiomUsageMap.get(axiom)); print("<td>" + insFont + "<a href=\":HASH:Usage:" + hash + "\">" + String.valueOf(usage) + "</a></td>"); String rank = "-"; if (repair.axiomRanksMap.containsKey(axiom)) rank = repair.axiomRanksMap.get(axiom).toString(); print("<td>" + insFont + rank + "</td>"); String rem = "R"; if (repair.removedAxiomSet.contains(axiom)) rem = "Undo"; print("<td>" + insFont + "<font color = \"red\">[<a href=\":FORCE:" + axiom.hashCode() + "\">" + rem + "</a>] </font>"); String keep = "K"; if (repair.keptAxiomSet.contains(axiom)) keep = "Undo"; print(insFont + "<font color = \"green\">[<a href =\":BLOCK:" + axiom.hashCode() + "\">" + keep + "</a>] </font></td>"); print("</tr>"); LHSmap.remove(axiom); RHSmap.remove(axiom); } baseURI = null; } while ((count - 1) < explanationSet.size()); print("</table>"); } print("<hr>"); } catch (Exception ex) { ex.printStackTrace(); } finally { // clear highlight map of all strikes ((ConciseFormatVisitor) visitor).highlightMap.keySet().removeAll(strikeSet); } } // also used in Why? explanation in Repair Frame :/ public void printRepairSOS(Set explanationSet, OWLNamedObject entity, RepairFrame repair) { Set strikeSet = new HashSet(); String insFont = "<FONT FACE=\"" + swoopModel.getFontFace() + "\" SIZE=3>"; try { if (explanationSet != null && !explanationSet.isEmpty()) { println("<b>Axioms causing the problem:</b>"); // need to sort axioms to explain trace better Iterator i = explanationSet.iterator(); // create instance of object container to check contents of axiom OWLObjectContainer owlCont = null; owlCont = new OWLObjectContainer(entity); Map LHSmap = new HashMap(); Map RHSmap = new HashMap(); Map objectCount = new HashMap(); while (i.hasNext()) { OWLObject axiom = (OWLObject) i.next(); owlCont.reset(); // visit axiom owlCont.visit(axiom); // get contained objects, LHS and RHS of axiom List objects = owlCont.getContainedObjects(); List LHS = owlCont.getLHS(); List RHS = owlCont.getRHS(); if (LHS.size() == 0 && RHS.size() == 0) LHS = objects; LHSmap.put(axiom, LHS); RHSmap.put(axiom, RHS); List total = new ArrayList(LHS); total.addAll(RHS); updateCount(objectCount, total); } // now call sorting method after computing lhs/rhs of axioms URI baseURI = entity.getURI(); int count = 1; sortLevelMap = new HashMap(); // reset map which stores links between sorted axioms in their resp level (recursive depth) do { List axioms = sortAxioms(baseURI, LHSmap, RHSmap, new HashSet(), 0); // now print sorted axiom list for (Iterator iter = axioms.iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); print(insFont); int level = Integer.parseInt(sortLevelMap.get(axiom).toString()); print("<b>" + (count++) + ")</b> "); for (int ctr = 0; ctr < level * 2; ctr++) print(" "); if (level > 0) print("|_"); if (repair.planSolnAxioms[0].contains(axiom)) print("<font color=\"red\"><b>[X]</b></font>"); printObject(axiom); print("<br>"); LHSmap.remove(axiom); RHSmap.remove(axiom); } baseURI = null; } while ((count - 1) < explanationSet.size()); } } catch (Exception ex) { ex.printStackTrace(); } } // expand axiom set iteratively public Set expandAxiomSet(Set axioms, OWLOntology ont, boolean expandMore) { try { Set newEntities = new HashSet(); for (Iterator iter = new HashSet(axioms).iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); if (signatureMap.containsKey(axiom)) { newEntities.addAll((HashSet) signatureMap.get(axiom)); } else { Set ents = swoopModel.getAxiomSignature(axiom, ont); signatureMap.put(axiom, ents); newEntities.addAll(ents); } if (expandMore) { // expand entity set to include usage entities for (Iterator iter2 = new HashSet(newEntities).iterator(); iter2.hasNext();) { Set usage = new HashSet(); OWLEntity ent = (OWLEntity) iter2.next(); // check in local cache first before using OntologyHelper if (usageMap.containsKey(ent.getURI())) { usage = (HashSet) usageMap.get(ent.getURI()); } else { usage = OntologyHelper.entityUsage(ont, ent); usageMap.put(ent.getURI(), usage); } // only add entities because axioms are returned for (Iterator it = usage.iterator(); it.hasNext();) { Object e = it.next(); if (e instanceof OWLEntity) newEntities.add(e); else if (e instanceof OWLObject) { if (signatureMap.containsKey(e)) { newEntities.addAll((HashSet) signatureMap.get(e)); } else { Set ents = swoopModel.getAxiomSignature((OWLObject) e, ont); signatureMap.put(e, ents); newEntities.addAll(ents); } } } } } } // get axioms for all newEntities either from local cache or from swoopModel Set newAxioms = new HashSet(); for (Iterator iter2 = newEntities.iterator(); iter2.hasNext();) { OWLEntity ent = (OWLEntity) iter2.next(); if (axiomMap.containsKey(ent.getURI())) { newAxioms.addAll((HashSet) axiomMap.get(ent.getURI())); } else { Set ax = swoopModel.getAxioms(ent, ont); axiomMap.put(ent.getURI(), ax); newAxioms.addAll(ax); } } if (axioms.containsAll(newAxioms)) { return new HashSet(); } else { // determine latest axioms Set before = new HashSet(axioms); Set latest = new HashSet(axioms); latest.addAll(newAxioms); latest.removeAll(before); // // set a limit on axioms to be added if (latest.size() > axiomLimit) { // only let limited entities remain in latest Set copyLatest = new HashSet(latest); latest.clear(); for (int ctr = 0; ctr < axiomLimit; ctr++) { Object ax = copyLatest.iterator().next(); latest.add(ax); copyLatest.remove(ax); } axiomLimit *= 1.25; // slowly increase axiom limit } newAxioms = latest; axioms.addAll(newAxioms); return newAxioms; } } catch (Exception ex) { ex.printStackTrace(); } return new HashSet(); } /* * find a single MUPS of an unsatisfiable class using the black box method */ public Set getBlackBoxSOS(OWLOntology ont, OWLClass cla) { // first check if cla is indeed unsatisfiable in ont try { PelletReasoner newPellet = new PelletReasoner(); newPellet.setOntology(ont, false); if (cla != null && newPellet.isConsistent(cla)) { System.out.println(swoopModel.shortForm(cla.getURI()) + " is satisfiable in " + swoopModel.shortForm(ont.getURI())); return new HashSet(); } // else if (cla==null && newPellet.isConsistent()) { // System.out.println(swoopModel.shortForm(ont.getURI())+" is consistent"); // return new HashSet(); // } } catch (Exception ex) { ex.printStackTrace(); } Set sos = new HashSet(); axiomLimit = 40; usageMap.clear(); axiomMap.clear(); signatureMap.clear(); Timer sosTimer = new Timer("find SOS black-box"); if (!swoopModel.findAllMUPS) parseTime = 0; sosTimer.start(); try { // add axioms related to class Set axioms = swoopModel.getAxioms(cla, ont); axiomMap.put(cla.getURI(), axioms); OWLOntBuilder ob = new OWLOntBuilder(); ob.addAxiom = true; // add axiom mode set to true // add all base axioms to testOnt via ob for (Iterator iter = axioms.iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); axiom.accept(ob); } // toggle a variable that considers entity usage while expanding axiom set boolean expandMore = false; // add linked references iteratively while (checkSatisfiability(ob, cla)) { Set newAxioms = this.expandAxiomSet(axioms, ont, expandMore); // System.out.println("Size of axioms: "+axioms.size()); // add axioms from latest to testOnt for (Iterator it = newAxioms.iterator(); it.hasNext();) { OWLObject axiom = (OWLObject) it.next(); axiom.accept(ob); } if (newAxioms.isEmpty() && expandMore) { System.out.println("ERROR: Could not find axioms responsible for error!"); CorrectedRDFRenderer rdfRend = new CorrectedRDFRenderer(); StringWriter st = new StringWriter(); rdfRend.renderOntology(ob.currentOnt, st); FileWriter fw = new FileWriter("testSOS.owl"); fw.write(st.toString()); fw.close(); System.out.println("Saved Test Ontology: testSOS.owl"); return sos; } else if (newAxioms.isEmpty()) { expandMore = true; } // System.out.println(axioms); } // now axioms contains cla unsatisfiable // remove one axiom at a time and if it turns satisfiable, add it to sos // System.out.println("Found concept unsatisfiable: #axioms = "+axioms.size()); // fast pruning List axiomList = new ArrayList(axioms); int pruneWindow = 10; if (axiomList.size() > pruneWindow) { axioms.clear(); int parts = axiomList.size() / pruneWindow; for (int part = 0; part < parts; part++) { for (int i = part * pruneWindow; i < part * pruneWindow + pruneWindow; i++) { ob.addAxiom = false; ((OWLObject) axiomList.get(i)).accept(ob); } if (checkSatisfiability(ob, cla)) { for (int i = part * pruneWindow; i < part * pruneWindow + pruneWindow; i++) { axioms.add(axiomList.get(i)); ob.addAxiom = true; ((OWLObject) axiomList.get(i)).accept(ob); } } } if (axiomList.size() > parts * pruneWindow) { // add remaining from list to axioms for (int i = parts * pruneWindow; i < axiomList.size(); i++) { axioms.add(axiomList.get(i)); } } } // System.out.println("After pruning axioms quickly: #axioms = "+axioms.size()); // slow pruning for (Iterator iter = new HashSet(axioms).iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); axioms.remove(axiom); ob.addAxiom = false; axiom.accept(ob); if (checkSatisfiability(ob, cla)) { sos.add(axiom); axioms.add(axiom); ob.addAxiom = true; axiom.accept(ob); } // System.out.println("Size of axioms: "+axioms.size()); } sosTimer.stop(); if (!swoopModel.findAllMUPS) { System.out.println(sosTimer); System.out.println("parse time: " + parseTime); System.out.println("net time: " + String.valueOf(sosTimer.getTotal() - parseTime)); netTime = sosTimer.getTotal() - parseTime; } } catch (Exception ex) { ex.printStackTrace(); } return sos; } /* * This method is mainly used by the explanations feature * to obtain the SOS for any OWLDescription */ public Set getSOS(OWLOntology ontology, OWLDescription satClazz) { Set sos = new HashSet(); if (!(satClazz instanceof OWLClass)) { try { // if its not an atomic class // create an atomic class and make it equivalent to the complex class OWLDataFactory ontDF = ontology.getOWLDataFactory(); OWLClass tempCla = ontDF.getOWLClass(new URI("tempClass")); AddEntity ae = new AddEntity(ontology, tempCla, null); ae.accept((ChangeVisitor) ontology); Set equs = new HashSet(); equs.add(tempCla); equs.add(satClazz); OWLEquivalentClassesAxiom equAxiom = ontDF.getOWLEquivalentClassesAxiom(equs); AddClassAxiom aca = new AddClassAxiom(ontology, equAxiom, null); aca.accept((ChangeVisitor) ontology); // get sos for new temp class if (swoopModel.isUseTableau()) { List sosExpl = getTableauSOS(ontology, tempCla); sos = (HashSet) sosExpl.get(1); } else { sos = getBlackBoxSOS(ontology, tempCla); } // remove equivalence axiom from sos sos.remove(equAxiom); // undo changes made to the ontology RemoveClassAxiom rec = new RemoveClassAxiom(ontology, equAxiom, null); rec.accept((ChangeVisitor) ontology); RemoveEntity re = new RemoveEntity(ontology, tempCla, null); re.accept((ChangeVisitor) ontology); } catch (Exception ex) { ex.printStackTrace(); } } else { // directly find sos of atomic class if (swoopModel.isUseTableau()) { List sosExpl = getTableauSOS(ontology, (OWLClass) satClazz); return (HashSet) sosExpl.get(1); } else return getBlackBoxSOS(ontology, (OWLClass) satClazz); } return sos; } /* * For a specific ontology and clazz, use debugging version of * Pellet to get string explanation and SOS */ public List getTableauSOS(OWLOntology ont, OWLDescription clazz) { List explSOS = new ArrayList(); try { Reasoner pelletDebug = new Reasoner(); pelletDebug.setOntology(ont); pelletDebug.getKB().setDoExplanation(true); pelletDebug.getKB().doDependencyTracking = true; boolean consistent = true; Timer timers = new Timer("Pellet Debugging Check"); timers.start(); if (clazz != null) consistent = pelletDebug.isConsistent(clazz); else consistent = pelletDebug.isConsistent(); timers.stop(); System.out.println(timers); if (consistent) { // no SOS cos ABox is consistent! System.out.println("No SOS since ABox is consistent"); explSOS.add("No Explanation"); explSOS.add(new HashSet()); // empty SOS return explSOS; } String explanation = ((PelletReasoner) reasoner).parseExplanation(this, pelletDebug.getKB().getExplanation()); Set explanationSet = pelletDebug.getKB().getExplanationSet(); // prune the axioms in case there are additional axioms Set prunedSet = new HashSet(explanationSet); for (Iterator iter = explanationSet.iterator(); iter.hasNext();) { OWLObject axiom = (OWLObject) iter.next(); prunedSet.remove(axiom); boolean sat = false; sat = this.checkSatisfiability(prunedSet, clazz); if (sat) prunedSet.add(axiom); } explanationSet = prunedSet; // end of pruning explSOS.add(explanation); explSOS.add(explanationSet); } catch (OWLException ex) { ex.printStackTrace(); } return explSOS; } public void setWriter(Writer w) { this.pw = (PrintWriter) w; } /* * update count for each entity appearing in an axiom */ private void updateCount(Map objectCount, List objects) { try { // Set once = new HashSet(); for (Iterator iter = objects.iterator(); iter.hasNext();) { OWLNamedObject obj = (OWLNamedObject) iter.next(); // if (once.contains(obj.getURI())) continue; ??? int val = 1; if (objectCount.containsKey(obj.getURI())) { String valStr = objectCount.get(obj.getURI()).toString(); val = Integer.parseInt(valStr) + 1; } // once.add(obj.getURI()); objectCount.put(obj.getURI(), String.valueOf(val)); } } catch (Exception ex) { ex.printStackTrace(); } } public void setReasoner(SwoopReasoner reas) { this.reasoner = reas; } /* * run all debugging tests w/ Pellet, RACER and KAON * IMPORTANT NOTE: TO MAKE THIS WORK CORRECTLY --- * Select "Debug->Use Black Box to compute MUPS" * Open required Test Ontology in Swoop * Select some class in ConciseFormat * Then click on "Advanced->Run Debug Tests" */ public void runDebugTests() throws Exception { // check anyway swoopModel.useTableau = false; swoopModel.setDebugGlass(true); // Single MUPS // w/ pellet String NEWLINE = System.getProperty("line.separator"); String log = ""; // read test cases OWLOntology ont = swoopModel.getSelectedOntology(); String fname = "testUniversity"; //// String fname = swoopModel.shortForm(ont.getURI()); List testCla = new ArrayList(); BufferedReader in = new BufferedReader(new FileReader(new File(fname + ".txt"))); String line = null; //not declared within while loop while ((line = in.readLine()) != null) { OWLClass cla = ont.getClass(new URI(line)); if (cla != null) testCla.add(cla); } // for (Iterator iter = swoopModel.getReasoner().equivalentClassesOf(swoopModel.getSelectedOntology().getOWLDataFactory().getOWLNothing()).iterator(); iter.hasNext();) { // testCla.add(iter.next()); // } // run tests // useRACER = false; // useKAON = false; // log += runReasonerTest(ont, testCla, "Pellet")+NEWLINE; // // useKAON = true; // log += runReasonerTest(ont, testCla, "KAON2")+NEWLINE; // useRACER = true; // useKAON = false; log += runReasonerTest(ont, testCla, "RACER") + NEWLINE; // System.out.println(log); FileWriter fw = new FileWriter(new File(fname + "DebugLog.txt")); fw.write(log); fw.close(); System.out.println("DONE: Log File written to " + fname + "DebugLog.txt"); } private String runReasonerTest(OWLOntology ont, List testCla, String reasStr) throws Exception { String NEWLINE = System.getProperty("line.separator"); String log = "Reasoner: " + reasStr + NEWLINE; log += "Single MUPS" + NEWLINE; swoopModel.findAllMUPS = false; for (Iterator iter = testCla.iterator(); iter.hasNext();) { OWLClass cla = (OWLClass) iter.next(); swoopModel.setSelectedEntity(cla); log += "| " + cla.getURI().toString() + " | " + netTime + " |" + NEWLINE; } log += "All MUPS" + NEWLINE; swoopModel.findAllMUPS = true; for (Iterator iter = testCla.iterator(); iter.hasNext();) { OWLClass cla = (OWLClass) iter.next(); swoopModel.setSelectedEntity(cla); log += "| " + cla.getURI().toString() + " (" + mupsCount + ") | " + netTime + " |" + NEWLINE; } System.out.println("--- Tests done for " + reasStr + "----"); return log; } public String getURIForTerm(String name) { try { for (Iterator iter = swoopModel.getOntologies().iterator(); iter.hasNext();) { OWLOntology ont = (OWLOntology) iter.next(); Set allURIs = OntologyHelper.allURIs(ont); for (Iterator iter2 = allURIs.iterator(); iter2.hasNext();) { String uri = iter2.next().toString(); if (uri.endsWith("#" + name) || uri.endsWith("/" + name)) { return uri; } } } } catch (OWLException ex) { ex.printStackTrace(); } return ""; } }