private Model createModelFromDatabase() throws DataBaseNotAccessibleException {
HashMap<String, Vector<String>> res = this.getMetaInfoFromDataBase();
OntModel m = ModelFactory.createOntologyModel();
String ns = "http://www.lirmm.fr/metaInfo#";
m.setNsPrefix("metaInfos", ns);
OntClass maDataBase = m.createClass(ns + "DATABASE");
OntClass nameDataBase = m.createClass(ns + database.getDatabaseName());
nameDataBase.addSuperClass(maDataBase);
OntClass maSuperClasse = m.createClass(ns + "TABLE");
for (String cle : res.keySet()) {
OntClass c = m.createClass(ns + cle);
c.addSuperClass(maSuperClasse);
for (int i = 0; i < res.get(cle).size(); i++) {
OntClass c2 = m.createClass(ns + res.get(cle).get(i));
OntProperty prop =
m.createOntProperty(ns + "COLONNE_" + c.getLocalName() + "_" + c2.getLocalName());
prop.setRange(c2);
prop.setDomain(c);
c2.addSuperClass(maSuperClasse);
}
}
return m;
}
/** Prints out the inferred classes of the aligned ontology */
public void printInfClasses(Model model) {
ExtendedIterator<OntClass> classes = ((OntModel) model).listClasses();
while (classes.hasNext()) {
OntClass thisClass = (OntClass) classes.next();
if (thisClass.getLocalName() != null) {
System.out.println("Found class: " + thisClass.getLocalName());
ExtendedIterator inst = thisClass.listInstances();
while (inst.hasNext()) {
Individual thisInstance = (Individual) inst.next();
System.out.println("\tFound instance: " + thisInstance.getLocalName());
}
}
}
} // printInfClasses
private void addSubtypes(Frame frame) {
Iterator<OntClass> sequence = frame.asOntClass().listSubClasses(true);
while (sequence.hasNext()) {
OntClass type = sequence.next();
String subURI = type.getURI();
if (subURI == null) continue;
Frame subFrame = manager.getFrameByUri(subURI);
if (subFrame == null) {
subFrame = manager.getListTypeByListUri(subURI);
}
if (subFrame != null) {
frame.getSubtypeList().add(subFrame);
} else {
Datatype datatype = manager.getDatatypeByUri(subURI);
if (datatype != null) {
frame.addSubdatatype(datatype);
continue;
}
if (isStandard(subURI)) continue;
logger.warn(
"Ignoring supertype of " + type.getLocalName() + " because frame not found: " + subURI);
}
}
}
/**
* Initialises the anchor, finding the node's compulsory and optional properties and their NL
* representations and ordering it all in lists and maps, using the submenus.
*
* @param c OntClass corresponding to this anchor
* @param query true if this is an anchor for a node in the QueryGraph
* @throws BadAnchorException if the given SGNode does not need an anchor
*/
public void init(OntClass c, boolean query) throws BadAnchorException {
Map<String, Integer[]> map = reader.getCardinalities(c.getLocalName());
List<OntProperty> list = reader.getDomainProperties(c.getLocalName());
for (int i = 0; i < list.size(); i++) {
OntProperty p = list.get(i);
String name = p.getLocalName();
int nr =
node.getOutgoingEdges(name).size(); // number of times the node already has this property
String inverse = reader.getInverse(name); // , n.getLabel(), null);
if (inverse != null)
nr +=
node.getIncomingEdges(inverse)
.size(); // plus the number of times the inverse has this node as range
if (map.containsKey(name)) {
int min =
map.get(name)[0]; // if the minimum cardinality is not satisfied, add to 'compulsory'
int max = map.get(name)[1];
if (query) optional.add(p); // for the query, cardinality constraints do not matter
else if ((min != 0)
&& (min > nr)) // if the minimum cardinality > 0, add the property to compulsory
compulsory.add(p);
else if ((max == 0)
|| (max > nr)) // if the maximum cardinality will not be violated, add to optional
optional.add(p);
} else optional.add(p); // no cardinality constraints, so add to optional
}
if (!compulsory.isEmpty()) // if there are compulsory properties, this is a red anchor
redAnchor = true;
else if (optional.isEmpty()) // compulsory and optional both empty - means this is not an anchor
throw new BadAnchorException(
"Node " + node.getLabel() + " is not an anchor anymore; all its relations are specified");
sort(query);
}
/** Initialise the page with proper layout and all. */
public void init() {
content.removeAll();
GridBagConstraints constraint = new GridBagConstraints();
JTextArea area =
new JTextArea(
"Editing the Label of the class '"
+ ontClass.getLocalName()
+ "'. You need to define which property will be used to identify a particular instance of this class. "
+ "For example, to identify a paper you can use the title of that paper. "
+ "You can either directly use one of the property of this class or specify the property of a related class "
+ "(e.g. for an ourSpaces account, you might want to use the name of the Person that holds that account)");
area.setEditable(false);
area.setLineWrap(true);
area.setWrapStyleWord(true);
constraint.insets = new Insets(10, 10, 10, 10);
constraint.fill = GridBagConstraints.HORIZONTAL;
constraint.anchor = GridBagConstraints.CENTER;
constraint.weightx = 1.0;
constraint.gridx = 0;
constraint.gridy = 0;
constraint.gridwidth = 2;
content.add(area, constraint);
directPropertyTypeButton = new JRadioButton("Direct");
directPropertyTypeButton.setActionCommand("direct");
directPropertyTypeButton.setSelected(true);
indirectPropertyTypeButton = new JRadioButton("Indirect");
indirectPropertyTypeButton.setActionCommand("indirect");
// Group the radio buttons.
ButtonGroup group = new ButtonGroup();
group.add(directPropertyTypeButton);
group.add(indirectPropertyTypeButton);
// Register a listener for the radio buttons.
directPropertyTypeButton.addActionListener(this);
indirectPropertyTypeButton.addActionListener(this);
// Put the radio buttons in a column in a panel.
JPanel radioPanel = new JPanel(new GridLayout(1, 0));
JLabel propTypeLabel = new JLabel("Property Type: ");
radioPanel.add(propTypeLabel);
radioPanel.add(directPropertyTypeButton);
radioPanel.add(indirectPropertyTypeButton);
constraint.gridy = 1;
content.add(radioPanel, constraint);
// Initialise list of direct properties
initDirectPropertyList();
// Create Panel for direct properties
constraint.weightx = 1;
constraint.weighty = 0.7; // add extra space to the tree widget, so it can expand
constraint.anchor = GridBagConstraints.FIRST_LINE_START;
constraint.gridx = 1;
constraint.gridy = 2;
constraint.fill = GridBagConstraints.BOTH;
constraint.gridwidth = 1;
propertyList.setSelectionMode(DefaultListSelectionModel.SINGLE_SELECTION);
directPropertyPane = new JScrollPane(propertyList);
Border blackBorder = BorderFactory.createLineBorder(Color.black);
directPropertyPane.setBorder(blackBorder);
content.add(directPropertyPane, constraint);
// Create Panel for indirect properties at the same place as the direct prop panel, so that only
// one is displayed at a time
indirectPropertyPanel = new JPanel(new GridLayout(0, 2));
indirectPropertyPanel.setBorder(blackBorder);
JLabel linkingPropLabel = new JLabel(" Property linking to another class: ");
linkingPropField = new JTextField(20);
classSubjectPropCheckBox = new JCheckBox("This class is the subject of the above property");
JLabel relatedClassPropLabel =
new JLabel(" Property of the related class that identify the original class: ");
relatedClassPropField = new JTextField(20);
indirectPropertyPanel.add(linkingPropLabel);
indirectPropertyPanel.add(linkingPropField);
indirectPropertyPanel.add(classSubjectPropCheckBox);
indirectPropertyPanel.add(new JLabel());
indirectPropertyPanel.add(relatedClassPropLabel);
indirectPropertyPanel.add(relatedClassPropField);
content.add(indirectPropertyPanel, constraint);
/** TODO: Add a list to allow user to add more than one property used as label */
// List of properties used as label
// constraint.gridy = 3;
// constraint.weighty = 0.3;
// String[] testList = {"test", "poi", "sdfs"};
// content.add(new JScrollPane(new JList(testList)), constraint);
// content.repaint();
constraint.fill = GridBagConstraints.NONE;
constraint.anchor = GridBagConstraints.PAGE_START;
constraint.weighty = 0;
constraint.weightx = 0;
constraint.gridx = 0;
constraint.gridy = 4;
constraint.gridwidth = 2;
backBtn.addActionListener(this);
saveBtn.addActionListener(this);
// exampleBtn.addActionListener(this);
Container cont = new Container();
cont.add(backBtn);
cont.add(saveBtn);
// cont.add(exampleBtn);
cont.setLayout(new FlowLayout(FlowLayout.CENTER, 20, 20));
content.add(cont, constraint);
content.validate();
}
private void ImportRelationsInheritanceOrEquivalence(int typeRelation) throws Exception {
List<OntClass> classes = this.jena.listClasses().toList();
for (OntClass jenaClass : classes) {
Class mobiClass = new Class(jenaClass.getLocalName());
// this.mobi.getClass(jenaClass.getLocalName());
if (mobiClass != null) {
List<OntClass> subClasses = null;
if (typeRelation == Relation.INHERITANCE)
subClasses = this.OntClassInheritanceChain(jenaClass.listSubClasses().toList());
else if (typeRelation == Relation.EQUIVALENCE)
subClasses = jenaClass.listEquivalentClasses().toList();
for (OntClass jenaSubClass : subClasses) {
if (jenaSubClass != null
&& !jenaSubClass.getLocalName().equals(mobiClass.getUri())
&& jenaSubClass.listInstances().hasNext()) {
// this.mobi.addConcept(mobiClass);
Class mobiSubClass = new Class(jenaSubClass.getLocalName());
Relation relation = null;
if (typeRelation == Relation.INHERITANCE)
relation = this.mobi.createInheritanceRelation("isSuper");
else if (typeRelation == Relation.EQUIVALENCE)
relation = this.mobi.createEquivalenceRelation("equals");
relation.setClassA(mobiClass);
relation.setClassB(mobiSubClass);
List<? extends OntResource> individualsClassA = jenaClass.listInstances().toList();
List<? extends OntResource> individualsClassB = jenaSubClass.listInstances().toList();
for (OntResource resourceA : individualsClassA) {
Individual individualA = resourceA.asIndividual();
Instance instanceA = new Instance(individualA.getLocalName());
// this.mobi.getInstance(individualA.getLocalName());
for (OntResource resourceB : individualsClassB) {
Individual individualB = resourceB.asIndividual();
Instance instanceB = new Instance(individualB.getLocalName());
// this.mobi.getInstance(individualB.getLocalName());
if (instanceB != null && instanceA.getUri().equals(instanceB.getUri())) {
this.mobi.addConcept(mobiClass);
this.mobi.addConcept(mobiSubClass);
this.mobi.addConcept(instanceA);
this.mobi.addConcept(instanceB);
try {
this.mobi.isOneOf(instanceA, mobiClass);
this.mobi.isOneOf(instanceB, mobiSubClass);
} catch (ExceptionURI e) {
}
this.mobi.addConcept(instanceB);
relation.addInstanceRelation(instanceA, instanceB);
}
}
}
relation.processCardinality();
if (relation.getInstanceRelationMapA().size() > 0) this.mobi.addConcept(relation);
}
}
}
}
}
private void ImportRelationsComposition() throws Exception {
List<ObjectProperty> properties = this.jena.listObjectProperties().toList();
for (ObjectProperty property : properties) {
OntClass domain = property.listDomain().next().asClass();
if (domain.isUnionClass()) domain = domain.asUnionClass().listOperands().toList().get(0);
OntClass range = property.listRange().next().asClass();
if (range.isUnionClass()) range = range.asUnionClass().listOperands().toList().get(0);
Relation r = null;
if (property.isSymmetricProperty())
r =
this.mobi.createSymmetricRelation(
this.getNameObjectProperty(
property.getLocalName(),
domain.getLocalName().length(),
range.getLocalName().length()));
else if (property.getInverse() == null)
r =
this.mobi.createUnidirecionalCompositionRelationship(
this.getNameObjectProperty(
property.getLocalName(),
domain.getLocalName().length(),
range.getLocalName().length()));
else if (property.getInverse() != null)
r =
this.mobi.createBidirecionalCompositionRelationship(
this.getNameObjectProperty(
property.getLocalName(),
domain.getLocalName().length(),
range.getLocalName().length()),
this.getNameObjectProperty(
property.getInverse().getLocalName(),
range.getLocalName().length(),
domain.getLocalName().length()));
Class mobiDomain = new Class(domain.getLocalName());
// this.mobi.getClass(domain.getLocalName());
Class mobiRange = new Class(range.getLocalName());
// this.mobi.getClass(range.getLocalName());
if (mobiDomain != null && mobiRange != null) {
r.setClassA(mobiDomain);
r.setClassB(mobiRange);
List<? extends OntResource> individuals = domain.listInstances().toList();
for (OntResource resourceIndividual : individuals) {
Individual individualDomain = resourceIndividual.asIndividual();
NodeIterator propertyValues =
this.jena.getIndividual(individualDomain.getURI()).listPropertyValues(property);
while (propertyValues.hasNext()) {
RDFNode node = propertyValues.next();
Individual individualValue = node.as(Individual.class);
this.mobi.addConcept(mobiDomain);
this.mobi.addConcept(mobiRange);
Instance instanceDomain = new Instance(individualDomain.getLocalName());
Instance instanceRange = new Instance(individualValue.getLocalName());
try {
this.mobi.isOneOf(instanceDomain, mobiDomain);
this.mobi.isOneOf(instanceRange, mobiRange);
} catch (ExceptionURI e) {
}
r.addInstanceRelation(instanceDomain, instanceRange);
}
}
r.processCardinality();
if (r.getInstanceRelationMapA().size() > 0) this.mobi.addConcept(r);
}
}
}
@Override
public UpdateContainer doIt(VWorkspace vWorkspace) throws CommandException {
OntologyManager ontMgr = vWorkspace.getWorkspace().getOntologyManager();
JSONArray classesList = new JSONArray();
JSONArray classesMap = new JSONArray();
JSONArray propertiesList = new JSONArray();
JSONArray propertiesMap = new JSONArray();
Map<String, String> prefixMap = vWorkspace.getWorkspace().getOntologyManager().getPrefixMap();
ExtendedIterator<OntClass> iter = ontMgr.getOntModel().listNamedClasses();
// ExtendedIterator<DatatypeProperty> propsIter = ontMgr.getOntModel()
// .listDatatypeProperties();
ExtendedIterator<OntProperty> propsIter = ontMgr.getOntModel().listAllOntProperties();
final JSONObject outputObj = new JSONObject();
try {
while (iter.hasNext()) {
OntClass cls = iter.next();
String pr = prefixMap.get(cls.getNameSpace());
String classLabel = cls.getLocalName();
// if (cls.getLabel(null) != null && !cls.getLabel(null).equals(""))
// classLabel = cls.getLabel(null);
String clsStr = (pr != null && !pr.equals("")) ? pr + ":" + classLabel : classLabel;
classesList.put(clsStr);
JSONObject classKey = new JSONObject();
classKey.put(clsStr, cls.getURI());
classesMap.put(classKey);
}
while (propsIter.hasNext()) {
// DatatypeProperty prop = propsIter.next();
OntProperty prop = propsIter.next();
if (prop.isObjectProperty() && !prop.isDatatypeProperty()) continue;
String pr = prefixMap.get(prop.getNameSpace());
String propLabel = prop.getLocalName();
// if (prop.getLabel(null) != null && !prop.getLabel(null).equals(""))
// propLabel = prop.getLabel(null);
String propStr = (pr != null && !pr.equals("")) ? pr + ":" + propLabel : propLabel;
propertiesList.put(propStr);
JSONObject propKey = new JSONObject();
propKey.put(propStr, prop.getURI());
propertiesMap.put(propKey);
}
// Populate the JSON object that will hold everything in output
outputObj.put(JsonKeys.classList.name(), classesList);
outputObj.put(JsonKeys.classMap.name(), classesMap);
outputObj.put(JsonKeys.propertyList.name(), propertiesList);
outputObj.put(JsonKeys.propertyMap.name(), propertiesMap);
} catch (JSONException e) {
logger.error("Error populating JSON!");
}
UpdateContainer upd =
new UpdateContainer(
new AbstractUpdate() {
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
pw.print(outputObj.toString());
}
});
return upd;
}
