public MyOWLSubClassOfAxiom(OWLAxiom b, MyOWLOntology onto) throws Exception {
super(b, onto);
OWLClassExpression subA = ((OWLSubClassOfAxiom) b).getSubClass();
OWLClassExpression superA = ((OWLSubClassOfAxiom) b).getSuperClass();
subConcept = o.getOWLConcept(subA.asOWLClass().toStringID());
switch (superA.getClassExpressionType()) {
case OBJECT_SOME_VALUES_FROM:
{
OWLObjectProperty ra =
(OWLObjectProperty) ((OWLObjectSomeValuesFrom) superA).getProperty();
OWLClassExpression fa = ((OWLObjectSomeValuesFrom) superA).getFiller();
rel = o.getOWLRelation(ra.toStringID());
superConcept = o.getOWLConcept(fa.asOWLClass().toStringID());
break;
}
case OWL_CLASS:
{
superConcept = o.getOWLConcept(superA.asOWLClass().toStringID());
rel = null;
break;
}
default:
throw new Exception(
"We do not know how to deal with the OWLClassExpresions \n"
+ superA.getClassExpressionType());
}
}
public boolean isDomainOrRangeOfObjectProperty(OWLClass clase, OWLObjectProperty prop) {
for (OWLClass owlClass1 : _reasoner.getObjectPropertyDomains(prop, false).getFlattened()) {
if (owlClass1.getIRI().equals(clase.getIRI())) {
Log.d(
TAG,
"<isDomainOrRangeOfObjectProperty> "
+ clase.getIRI().getRemainder().get()
+ " dominio o rango de "
+ prop.getIRI().getRemainder().get()
+ "? SI!");
return true;
}
}
for (OWLClass owlClass1 : _reasoner.getObjectPropertyRanges(prop, false).getFlattened()) {
if (owlClass1.getIRI().equals(clase.getIRI())) {
Log.d(
TAG,
"<isDomainOrRangeOfObjectProperty> "
+ clase.getIRI().getRemainder().get()
+ " dominio o rango de "
+ prop.getIRI().getRemainder().get()
+ "? SI!");
return true;
}
}
Log.d(
TAG,
"<isDomainOrRangeOfObjectProperty> "
+ clase.getIRI().getRemainder().get()
+ " dominio o rango de "
+ prop.getIRI().getRemainder().get()
+ "? NO");
return false;
}
private void runWithSeparateFiles() {
if (owlFile == null) {
throw new NullPointerException("You have to specify an ontology file!");
}
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = null;
OBDADataFactory obdaDataFactory = OBDADataFactoryImpl.getInstance();
try {
ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile)));
if (disableReasoning) {
/*
* when reasoning is disabled, we extract only the declaration assertions for the vocabulary
*/
ontology = extractDeclarations(manager, ontology);
}
Collection<Predicate> predicates = new ArrayList<>();
for (OWLClass owlClass : ontology.getClassesInSignature()) {
Predicate predicate = obdaDataFactory.getClassPredicate(owlClass.getIRI().toString());
predicates.add(predicate);
}
for (OWLDataProperty owlDataProperty : ontology.getDataPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getDataPropertyPredicate(owlDataProperty.getIRI().toString());
predicates.add(predicate);
}
for (OWLObjectProperty owlObjectProperty : ontology.getObjectPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getObjectPropertyPredicate(owlObjectProperty.getIRI().toString());
predicates.add(predicate);
}
OBDAModel obdaModel = loadMappingFile(mappingFile);
Ontology inputOntology = OWLAPI3TranslatorUtility.translate(ontology);
obdaModel.declareAll(inputOntology.getVocabulary());
int numPredicates = predicates.size();
int i = 1;
for (Predicate predicate : predicates) {
System.err.println(String.format("Materializing %s (%d/%d)", predicate, i, numPredicates));
serializePredicate(ontology, inputOntology, obdaModel, predicate, outputFile, format);
i++;
}
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* This method makes sure is used to setup a new/fresh OBDA model. This is done by replacing the
* instance this.obdacontroller (the OBDA model) with a new object. On creation listeners for the
* datasources, mappings and queries are setup so that changes in these trigger and ontology
* change.
*
* <p>Additionally, this method configures all available OBDAOWLReasonerFacotry objects to have a
* reference to the newly created OBDA model and to the global preference object. This is
* necessary so that the factories are able to pass the OBDA model to the reasoner instances when
* they are created.
*/
private void setupNewOBDAModel() {
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (activeOBDAModel != null) {
return;
}
activeOBDAModel = dfac.getOBDAModel();
activeOBDAModel.addSourcesListener(dlistener);
activeOBDAModel.addMappingsListener(mlistener);
queryController.addListener(qlistener);
OWLModelManager mmgr = owlEditorKit.getOWLWorkspace().getOWLModelManager();
Set<OWLOntology> ontologies = mmgr.getOntologies();
for (OWLOntology ontology : ontologies) {
// Setup the entity declarations
for (OWLClass c : ontology.getClassesInSignature()) {
OClass pred = ofac.createClass(c.getIRI().toString());
activeOBDAModel.declareClass(pred);
}
for (OWLObjectProperty r : ontology.getObjectPropertiesInSignature()) {
ObjectPropertyExpression pred = ofac.createObjectProperty(r.getIRI().toString());
activeOBDAModel.declareObjectProperty(pred);
}
for (OWLDataProperty p : ontology.getDataPropertiesInSignature()) {
DataPropertyExpression pred = ofac.createDataProperty(p.getIRI().toString());
activeOBDAModel.declareDataProperty(pred);
}
}
// Setup the prefixes
PrefixOWLOntologyFormat prefixManager =
PrefixUtilities.getPrefixOWLOntologyFormat(mmgr.getActiveOntology());
// addOBDACommonPrefixes(prefixManager);
PrefixManagerWrapper prefixwrapper = new PrefixManagerWrapper(prefixManager);
activeOBDAModel.setPrefixManager(prefixwrapper);
OWLOntology activeOntology = mmgr.getActiveOntology();
String defaultPrefix = prefixManager.getDefaultPrefix();
if (defaultPrefix == null) {
OWLOntologyID ontologyID = activeOntology.getOntologyID();
defaultPrefix = ontologyID.getOntologyIRI().toURI().toString();
}
activeOBDAModel.getPrefixManager().addPrefix(PrefixManager.DEFAULT_PREFIX, defaultPrefix);
// Add the model
URI modelUri = activeOntology.getOntologyID().getOntologyIRI().toURI();
obdamodels.put(modelUri, activeOBDAModel);
}
private Iterable<Concept> getDomainsConcepts(OWLOntology o, OWLObjectProperty objectProperty) {
String uri = objectProperty.getIRI().toString();
if (objectProperty.getDomains(o).size() == 0) {
throw new LumifyException("Invalid number of domain properties on " + uri);
}
List<Concept> domains = new ArrayList<Concept>();
for (OWLClassExpression rangeClassExpr : objectProperty.getDomains(o)) {
OWLClass rangeClass = rangeClassExpr.asOWLClass();
String rangeClassUri = rangeClass.getIRI().toString();
Concept ontologyClass = getConceptByIRI(rangeClassUri);
checkNotNull(ontologyClass, "Could not find class with uri: " + rangeClassUri);
domains.add(ontologyClass);
}
return domains;
}
protected void importInverseOf(OWLOntology o, OWLObjectProperty objectProperty) {
String iri = objectProperty.getIRI().toString();
Relationship fromRelationship = null;
for (OWLObjectPropertyExpression inverseOf : objectProperty.getInverses(o)) {
if (inverseOf instanceof OWLObjectProperty) {
if (fromRelationship == null) {
fromRelationship = getRelationshipByIRI(iri);
}
OWLObjectProperty inverseOfOWLObjectProperty = (OWLObjectProperty) inverseOf;
String inverseOfIri = inverseOfOWLObjectProperty.getIRI().toString();
Relationship inverseOfRelationship = getRelationshipByIRI(inverseOfIri);
getOrCreateInverseOfRelationship(fromRelationship, inverseOfRelationship);
}
}
}
// TODO optimize translatin: (e) can be discarded for roles for which there
// aren't assertions
private Set<Rule> translation(QLAxiomsTranslator axiomsTranslator) {
final Set<Rule> result = new HashSet<Rule>();
for (final OWLClassAssertionAxiom assertion : ontologyNormalization.conceptAssertions())
result.addAll(axiomsTranslator.assertionTranslation(assertion));
for (final OWLObjectPropertyAssertionAxiom assertion : ontologyNormalization.roleAssertions())
result.addAll(axiomsTranslator.assertionTranslation(assertion));
for (final OWLDataPropertyAssertionAxiom assertion : ontologyNormalization.dataAssertions())
result.addAll(axiomsTranslator.assertionTranslation(assertion));
for (final OWLSubClassOfAxiom subsumption : ontologyNormalization.conceptSubsumptions())
result.addAll(
axiomsTranslator.subsumptionTranslation(
subsumption.getSubClass(), subsumption.getSuperClass()));
for (final OWLSubPropertyAxiom<?> subsumption : ontologyNormalization.roleSubsumptions())
if (subsumption instanceof OWLSubObjectPropertyOfAxiom) {
result.addAll(
axiomsTranslator.subsumptionTranslation(
subsumption.getSubProperty(), subsumption.getSuperProperty()));
final OWLSubObjectPropertyOfAxiom axiom = (OWLSubObjectPropertyOfAxiom) subsumption;
final OWLObjectPropertyExpression ope1 = axiom.getSubProperty();
final OWLObjectPropertyExpression ope2 = axiom.getSuperProperty();
final OWLObjectPropertyExpression invOpe1 = ope1.getInverseProperty().getSimplified();
final OWLObjectPropertyExpression invOpe2 = ope2.getInverseProperty().getSimplified();
if ((ontologyNormalization.isSuper(some(ope1)) || ontologyNormalization.isSuper(ope1))
&& (ontologyNormalization.isSub(some(ope2)) || ontologyNormalization.isSub(ope2)))
result.add(
axiomsTranslator.domainSubsumptionTranslation(
axiom.getSubProperty(), axiom.getSuperProperty()));
if ((ontologyNormalization.isSuper(some(invOpe1)) || ontologyNormalization.isSuper(invOpe1))
&& (ontologyNormalization.isSub(some(invOpe2)) || ontologyNormalization.isSub(invOpe2)))
result.add(axiomsTranslator.rangeSubsumptionTranslation(invOpe1, invOpe2));
} else if (subsumption instanceof OWLSubDataPropertyOfAxiom)
result.addAll(
axiomsTranslator.subsumptionTranslation(
subsumption.getSubProperty(), subsumption.getSuperProperty()));
for (final OWLPropertyExpression ope : ontologyNormalization.getRoles())
if (ope instanceof OWLObjectPropertyExpression) {
final OWLObjectProperty p = ((OWLObjectPropertyExpression) ope).getNamedProperty();
final OWLObjectPropertyExpression invP = p.getInverseProperty();
if (ontologyNormalization.isSub(some(p)) || ontologyNormalization.isSub(p))
result.add(axiomsTranslator.domainTranslation(p));
if (ontologyNormalization.isSub(some(invP)) || ontologyNormalization.isSub(invP))
result.add(axiomsTranslator.rangeTranslation(p));
}
return result;
}
protected void importObjectProperty(OWLOntology o, OWLObjectProperty objectProperty) {
String iri = objectProperty.getIRI().toString();
String label = getLabel(o, objectProperty);
checkNotNull(label, "label cannot be null or empty for " + iri);
LOGGER.info("Importing ontology object property " + iri + " (label: " + label + ")");
for (Concept domain : getDomainsConcepts(o, objectProperty)) {
for (Concept range : getRangesConcepts(o, objectProperty)) {
getOrCreateRelationshipType(domain, range, iri, label);
}
}
}
public LintReport<OWLObjectProperty> detected(Collection<? extends OWLOntology> targets)
throws LintException {
SimpleMatchBasedLintReport<OWLObjectProperty> report =
new SimpleMatchBasedLintReport<OWLObjectProperty>(this);
for (OWLOntology ontology : targets) {
for (OWLObjectProperty objectProperty : ontology.getObjectPropertiesInSignature()) {
if (objectProperty.isTransitive(ontology)) {
Set<OWLObjectPropertyExpression> superProperties =
objectProperty.getSuperProperties(ontology);
for (OWLObjectPropertyExpression objectPropertyExpression : superProperties) {
if (objectPropertyExpression.isTransitive(ontology)) {
report.add(
objectProperty,
ontology,
"The property "
+ objectProperty.toString()
+ " is transitive and has a transitive super property");
}
}
}
}
}
return report;
}
@Override
public void visit(OWLObjectProperty property) {
handleObject(property);
property.getIRI().accept(this);
}
@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> changes) throws OWLException {
Map<OWLEntity, OWLEntity> renamings = new HashMap<OWLEntity, OWLEntity>();
Set<OWLEntity> removals = new HashSet<OWLEntity>();
for (int idx = 0; idx < changes.size(); idx++) {
OWLOntologyChange change = changes.get(idx);
if (change instanceof SetOntologyID) {
IRI newiri = ((SetOntologyID) change).getNewOntologyID().getOntologyIRI();
if (newiri == null) continue;
IRI oldiri = ((SetOntologyID) change).getOriginalOntologyID().getOntologyIRI();
log.debug("Ontology ID changed");
log.debug("Old ID: {}", oldiri);
log.debug("New ID: {}", newiri);
OBDAModel model = obdamodels.get(oldiri.toURI());
if (model == null) {
setupNewOBDAModel();
model = getActiveOBDAModel();
}
PrefixManager prefixManager = model.getPrefixManager();
prefixManager.addPrefix(PrefixManager.DEFAULT_PREFIX, newiri.toURI().toString());
obdamodels.remove(oldiri.toURI());
obdamodels.put(newiri.toURI(), model);
continue;
} else if (change instanceof AddAxiom) {
OWLAxiom axiom = change.getAxiom();
if (axiom instanceof OWLDeclarationAxiom) {
OWLEntity entity = ((OWLDeclarationAxiom) axiom).getEntity();
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (entity instanceof OWLClass) {
OWLClass oc = (OWLClass) entity;
OClass c = ofac.createClass(oc.getIRI().toString());
activeOBDAModel.declareClass(c);
} else if (entity instanceof OWLObjectProperty) {
OWLObjectProperty or = (OWLObjectProperty) entity;
ObjectPropertyExpression r = ofac.createObjectProperty(or.getIRI().toString());
activeOBDAModel.declareObjectProperty(r);
} else if (entity instanceof OWLDataProperty) {
OWLDataProperty op = (OWLDataProperty) entity;
DataPropertyExpression p = ofac.createDataProperty(op.getIRI().toString());
activeOBDAModel.declareDataProperty(p);
}
}
} else if (change instanceof RemoveAxiom) {
OWLAxiom axiom = change.getAxiom();
if (axiom instanceof OWLDeclarationAxiom) {
OWLEntity entity = ((OWLDeclarationAxiom) axiom).getEntity();
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (entity instanceof OWLClass) {
OWLClass oc = (OWLClass) entity;
OClass c = ofac.createClass(oc.getIRI().toString());
activeOBDAModel.unDeclareClass(c);
} else if (entity instanceof OWLObjectProperty) {
OWLObjectProperty or = (OWLObjectProperty) entity;
ObjectPropertyExpression r = ofac.createObjectProperty(or.getIRI().toString());
activeOBDAModel.unDeclareObjectProperty(r);
} else if (entity instanceof OWLDataProperty) {
OWLDataProperty op = (OWLDataProperty) entity;
DataPropertyExpression p = ofac.createDataProperty(op.getIRI().toString());
activeOBDAModel.unDeclareDataProperty(p);
}
}
}
if (idx + 1 >= changes.size()) {
continue;
}
if (change instanceof RemoveAxiom && changes.get(idx + 1) instanceof AddAxiom) {
// Found the pattern of a renaming refactoring
RemoveAxiom remove = (RemoveAxiom) change;
AddAxiom add = (AddAxiom) changes.get(idx + 1);
if (!(remove.getAxiom() instanceof OWLDeclarationAxiom
&& add.getAxiom() instanceof OWLDeclarationAxiom)) {
continue;
}
// Found the patter we are looking for, a remove and add of
// declaration axioms
OWLEntity olde = ((OWLDeclarationAxiom) remove.getAxiom()).getEntity();
OWLEntity newe = ((OWLDeclarationAxiom) add.getAxiom()).getEntity();
renamings.put(olde, newe);
} else if (change instanceof RemoveAxiom
&& ((RemoveAxiom) change).getAxiom() instanceof OWLDeclarationAxiom) {
// Found the pattern of a deletion
OWLDeclarationAxiom declaration = (OWLDeclarationAxiom) ((RemoveAxiom) change).getAxiom();
OWLEntity removedEntity = declaration.getEntity();
removals.add(removedEntity);
}
}
// Applying the renaming to the OBDA model
OBDAModel obdamodel = getActiveOBDAModel();
for (OWLEntity olde : renamings.keySet()) {
OWLEntity removedEntity = olde;
OWLEntity newEntity = renamings.get(removedEntity);
// This set of changes appears to be a "renaming" operation,
// hence we will modify the OBDA model accordingly
Predicate removedPredicate = getPredicate(removedEntity);
Predicate newPredicate = getPredicate(newEntity);
obdamodel.renamePredicate(removedPredicate, newPredicate);
}
// Applying the deletions to the obda model
for (OWLEntity removede : removals) {
Predicate removedPredicate = getPredicate(removede);
obdamodel.deletePredicate(removedPredicate);
}
}
public ArrowElementVis(OWLObjectProperty property) {
this.property = property;
this.labelElement = property.getIRI().getFragment();
this.backgroudColor = Color.LIGHT_GRAY;
}
/*
* (non-Javadoc)
*
* @seeorg.semanticweb.owlapi.model.OWLPropertyExpressionVisitor#visit(org.
* semanticweb.owlapi.model.OWLObjectProperty)
*/
@Override
public void visit(OWLObjectProperty axiom) {
sb.append(print(axiom.toString()));
}
@Override
public String getAsText() {
/** Get the text value of this object - for displaying in GUIS, etc */
return value.toStringID();
}
@Override
protected void writeObjectPropertyComment(OWLObjectProperty prop) {
writeComment(prop.getIRI().toString());
}
// Main wrapping for adding non-ontology documents to GOlr.
// Also see OntologySolrLoader.
private void add(Bioentity e) {
String eid = e.getId();
String esym = e.getSymbol();
String edb = e.getDb();
String etype = e.getTypeCls();
String ename = e.getFullName();
String edbid = e.getDBID();
// LOG.info("Adding: " + eid + " " + esym);
SolrInputDocument bioentity_doc = new SolrInputDocument();
// Bioentity document base.
bioentity_doc.addField("document_category", "bioentity");
bioentity_doc.addField("id", eid);
bioentity_doc.addField("bioentity", eid);
bioentity_doc.addField("bioentity_internal_id", edbid);
bioentity_doc.addField("bioentity_label", esym);
bioentity_doc.addField("bioentity_name", ename);
bioentity_doc.addField("source", edb);
bioentity_doc.addField("type", etype);
// A little more work for the synonyms.
List<String> esynonyms = e.getSynonyms();
if (!esynonyms.isEmpty()) {
bioentity_doc.addField("synonym", esynonyms);
}
// Various taxon and taxon closure calculations, including map.
String etaxid = e.getNcbiTaxonId();
TaxonDetails taxonDetails = null;
if (etaxid != null) {
taxonDetails = createTaxonDetails(etaxid);
taxonDetails.addToSolrDocument(bioentity_doc);
}
// Optionally, pull information from the PANTHER file set.
List<String> pantherFamilyIDs = new ArrayList<String>();
List<String> pantherFamilyLabels = new ArrayList<String>();
List<String> pantherTreeGraphs = new ArrayList<String>();
// List<String> pantherTreeAnnAncestors = new ArrayList<String>();
// List<String> pantherTreeAnnDescendants = new ArrayList<String>();
if (pset != null && pset.getNumberOfFilesInSet() > 0) {
Set<PANTHERTree> pTrees = pset.getAssociatedTrees(eid);
if (pTrees != null) {
Iterator<PANTHERTree> piter = pTrees.iterator();
int pcnt = 0; // DEBUG
while (piter.hasNext()) {
pcnt++; // DEBUG
PANTHERTree ptree = piter.next();
pantherFamilyIDs.add(ptree.getPANTHERID());
pantherFamilyLabels.add(StringUtils.lowerCase(ptree.getTreeLabel()));
pantherTreeGraphs.add(ptree.getOWLShuntGraph().toJSON());
// pantherTreeAnnAncestors = new ArrayList<String>(ptree.getAncestorAnnotations(eid));
// pantherTreeAnnDescendants = new ArrayList<String>(ptree.getDescendantAnnotations(eid));
if (pcnt > 1) { // DEBUG
LOG.info(
"Belongs to multiple families ("
+ eid
+ "): "
+ StringUtils.join(pantherFamilyIDs, ", "));
}
// Store that we saw this for later use in the tree.
ptree.addAssociatedGeneProduct(eid, esym);
}
}
}
// Optionally, actually /add/ the PANTHER family data to the document.
if (!pantherFamilyIDs.isEmpty()) {
// BUG/TODO (but probably not ours): We only store the one tree for now as we're assuming that
// there is just one family.
// Unfortunately, PANTHER still produces data that sez sometimes something belongs to more
// than one
// family (eg something with fly in PTHR10919 PTHR10032), so we block it and just choose the
// first.
bioentity_doc.addField("panther_family", pantherFamilyIDs.get(0));
bioentity_doc.addField("panther_family_label", pantherFamilyLabels.get(0));
bioentity_doc.addField("phylo_graph_json", pantherTreeGraphs.get(0));
// if( ! pantherTreeAnnAncestors.isEmpty() ){
// bioentity_doc.addField("phylo_ancestor_closure", pantherTreeAnnAncestors);
// }
// if( ! pantherTreeAnnDescendants.isEmpty() ){
// bioentity_doc.addField("phylo_descendant_closure", pantherTreeAnnDescendants);
// }
}
// We're also going to want to make note of the direct annotations to this bioentity.
// This will mean getting ready and then storing all of c5 when we pass through through
// the annotation loop. We'll add to the document on the other side.
// Collect information: ids and labels.
Map<String, String> direct_list_map = new HashMap<String, String>();
// Something that we'll need for the annotation evidence aggregate later.
Map<String, SolrInputDocument> evAggDocMap = new HashMap<String, SolrInputDocument>();
// Annotation doc.
// We'll also need to be collecting some aggregate information, like for the GP term closures,
// which will be
// added at the end of this section.
Map<String, String> isap_map = new HashMap<String, String>();
Map<String, String> reg_map = new HashMap<String, String>();
for (GeneAnnotation a : gafDocument.getGeneAnnotations(e.getId())) {
SolrInputDocument annotation_doc = new SolrInputDocument();
String clsId = a.getCls();
// Annotation document base from static and previous bioentity.
annotation_doc.addField("document_category", "annotation"); // n/a
annotation_doc.addField("source", edb); // Col. 1 (from bioentity above)
annotation_doc.addField("bioentity", eid); // n/a, should be c1+c2.
annotation_doc.addField("bioentity_internal_id", edbid); // Col. 2 (from bioentity above)
annotation_doc.addField("bioentity_label", esym); // Col. 3 (from bioentity above)
// NOTE: Col. 4 generation is below...
annotation_doc.addField("annotation_class", clsId); // Col. 5
addLabelField(annotation_doc, "annotation_class_label", clsId); // n/a
// NOTE: Col. 6 generation is below...
String a_ev_type = a.getShortEvidence();
annotation_doc.addField("evidence_type", a_ev_type); // Col. 7
// NOTE: Col. 8 generation is below...
String a_aspect = a.getAspect();
annotation_doc.addField("aspect", a_aspect); // Col. 9
annotation_doc.addField("bioentity_name", ename); // Col. 10 (from bioentity above)
annotation_doc.addField("synonym", esynonyms); // Col. 11 (from bioentity above)
annotation_doc.addField("type", etype); // Col. 12 (from bioentity above)
String adate = a.getLastUpdateDate();
annotation_doc.addField("date", adate); // Col. 14
String assgnb = a.getAssignedBy();
annotation_doc.addField("assigned_by", assgnb); // Col. 15
// NOTE: Col. generation is 16 below...
annotation_doc.addField("bioentity_isoform", a.getGeneProductForm()); // Col. 17
// Optionally, if there is enough taxon for a map, add the collections to the document.
if (taxonDetails != null) {
taxonDetails.addToSolrDocument(annotation_doc);
}
// Optionally, actually /add/ the PANTHER family data to the document.
if (!pantherFamilyIDs.isEmpty()) {
annotation_doc.addField("panther_family", pantherFamilyIDs.get(0));
annotation_doc.addField("panther_family_label", pantherFamilyLabels.get(0));
}
// Evidence type closure.
Set<OWLClass> ecoClasses = eco.getClassesForGoCode(a_ev_type);
Set<OWLClass> ecoSuper = eco.getAncestors(ecoClasses, true);
List<String> ecoIDClosure = new ArrayList<String>();
for (OWLClass es : ecoSuper) {
String itemID = es.toStringID();
ecoIDClosure.add(itemID);
}
addLabelFields(annotation_doc, "evidence_type_closure", ecoIDClosure);
// Col 4: qualifier generation.
String comb_aqual = "";
if (a.hasQualifiers()) {
if (a.isNegated()) {
comb_aqual = comb_aqual + "not";
annotation_doc.addField("qualifier", "not");
}
if (a.isContributesTo()) {
comb_aqual = comb_aqual + "contributes_to";
annotation_doc.addField("qualifier", "contributes_to");
}
if (a.isIntegralTo()) {
comb_aqual = comb_aqual + "integral_to";
annotation_doc.addField("qualifier", "integral_to");
}
if (a.isColocatesWith()) {
comb_aqual = comb_aqual + "colocalizes_with";
annotation_doc.addField("qualifier", "colocalizes_with");
}
if (a.isCut()) {
comb_aqual = comb_aqual + "cut";
annotation_doc.addField("qualifier", "cut");
}
}
// Drag in the reference (col 6)
List<String> refIds = a.getReferenceIds();
String refIdList = ""; // used to help make unique ID.
for (String refId : refIds) {
annotation_doc.addField("reference", refId);
refIdList = refIdList + "_" + refId;
}
// Drag in "with" (col 8).
// annotation_doc.addField("evidence_with", a.getWithExpression());
String withList = ""; // used to help make unique ID.
for (String wi : a.getWithInfos()) {
annotation_doc.addField("evidence_with", wi);
withList = withList + "_" + wi;
}
///
/// isa_partof_closure
///
OWLObject cls = graph.getOWLObjectByIdentifier(clsId);
// TODO: This may be a bug workaround, or it may be the way things are.
// getOWLObjectByIdentifier returns null on alt_ids, so skip them for now.
if (cls != null) {
// System.err.println(clsId);
// Is-a part-of closures.
ArrayList<String> isap = new ArrayList<String>();
isap.add("BFO:0000050");
Map<String, String> curr_isap_map =
addClosureToAnnAndBio(
isap,
"isa_partof_closure",
"isa_partof_closure_label",
"isa_partof_closure_map",
cls,
graph,
annotation_doc,
bioentity_doc,
a.isNegated());
isap_map.putAll(curr_isap_map); // add to aggregate map
// // Add to annotation and bioentity isa_partof closures; label and id.
// List<String> idClosure = graph.getRelationIDClosure(cls, isap);
// List<String> labelClosure = graph.getRelationLabelClosure(cls, isap);
// annotation_doc.addField("isa_partof_closure", idClosure);
// annotation_doc.addField("isa_partof_closure_label", labelClosure);
// for( String tlabel : labelClosure){
// addFieldUnique(bioentity_doc, "isa_partof_closure_label", tlabel);
// }
// for( String tid : idClosure){
// addFieldUnique(bioentity_doc, "isa_partof_closure", tid);
// }
//
// // Compile closure maps to JSON.
// Map<String, String> isa_partof_map = graph.getRelationClosureMap(cls, isap);
// if( ! isa_partof_map.isEmpty() ){
// String jsonized_isa_partof_map = gson.toJson(isa_partof_map);
// annotation_doc.addField("isa_partof_closure_map", jsonized_isa_partof_map);
// }
// Regulates closures.
List<String> reg = RelationSets.getRelationSet(RelationSets.COMMON);
Map<String, String> curr_reg_map =
addClosureToAnnAndBio(
reg,
"regulates_closure",
"regulates_closure_label",
"regulates_closure_map",
cls,
graph,
annotation_doc,
bioentity_doc,
a.isNegated());
reg_map.putAll(curr_reg_map); // add to aggregate map
// ///
// /// Next, work on the evidence aggregate...
// ///
//
// // Bug/TODO: This is a bit os a slowdown since we're not reusing our work from above
// here anymore.
// List<String> idIsapClosure = graph.getRelationIDClosure(cls, isap);
// Map<String, String> isaPartofMap = graph.getRelationClosureMap(cls, isap);
//
// // When we cycle, we'll also want to do some stuff to track all of the evidence codes
// we see.
// List<String> aggEvIDClosure = new ArrayList<String>();
// List<String> aggEvWiths = new ArrayList<String>();
//
// // Cycle through and pick up all the associated bits for the terms in the closure.
// SolrInputDocument ev_agg_doc = null;
// for( String tid : idIsapClosure ){
//
// String tlabel = isaPartofMap.get(tid);
// //OWLObject c = graph.getOWLObjectByIdentifier(tid);
//
// // Only have to do the annotation evidence aggregate base once.
// // Otherwise, just skip over and add the multi fields separately.
// String evAggId = eid + "_:ev:_" + clsId;
// if (evAggDocMap.containsKey(evAggId)) {
// ev_agg_doc = evAggDocMap.get(evAggId);
// } else {
// ev_agg_doc = new SolrInputDocument();
// evAggDocMap.put(evAggId, ev_agg_doc);
// ev_agg_doc.addField("id", evAggId);
// ev_agg_doc.addField("document_category", "annotation_evidence_aggregate");
// ev_agg_doc.addField("bioentity", eid);
// ev_agg_doc.addField("bioentity_label", esym);
// ev_agg_doc.addField("annotation_class", tid);
// ev_agg_doc.addField("annotation_class_label", tlabel);
// ev_agg_doc.addField("taxon", etaxid);
// addLabelField(ev_agg_doc, "taxon_label", etaxid);
//
// // Optionally, if there is enough taxon for a map, add the collections to the
// document.
// if( jsonized_taxon_map != null ){
// ev_agg_doc.addField("taxon_closure", taxIDClosure);
// ev_agg_doc.addField("taxon_closure_label", taxLabelClosure);
// ev_agg_doc.addField("taxon_closure_map", jsonized_taxon_map);
// }
//
// // Optionally, actually /add/ the PANTHER family data to the document.
// if( ! pantherFamilyIDs.isEmpty() ){
// ev_agg_doc.addField("panther_family", pantherFamilyIDs.get(0));
// ev_agg_doc.addField("panther_family_label", pantherFamilyLabels.get(0));
// }
// }
//
// // Drag in "with" (col 8), this time for ev_agg.
// for (String wi : a.getWithInfos()) {
// aggEvWiths.add(wi);
// }
//
// // Make note for the evidence type closure.
// aggEvIDClosure.add(a.getShortEvidence());
// }
//
// // If there was actually a doc created/there, add the cumulative fields to it.
// if( ev_agg_doc != null ){
// addLabelFields(ev_agg_doc, "evidence_type_closure", aggEvIDClosure);
// addLabelFields(ev_agg_doc, "evidence_with", aggEvWiths);
// }
}
// Let's piggyback on a little of the work above and cache the extra stuff that we'll be
// adding to the bioenity at the end
// for the direct annotations. c5 and ???.
if (a.isNegated() == false) {
String dlbl = graph.getLabel(cls);
direct_list_map.put(clsId, dlbl);
}
// Map<String,String> isa_partof_map = new HashMap<String,String>(); // capture labels/ids
// OWLObject c = graph.getOWLObjectByIdentifier(clsId);
// Set<OWLPropertyExpression> ps =
// Collections.singleton((OWLPropertyExpression)getPartOfProperty());
// Set<OWLObject> ancs = graph.getAncestors(c, ps);
// for (OWLObject t : ancs) {
// if (! (t instanceof OWLClass))
// continue;
// String tid = graph.getIdentifier(t);
// //System.out.println(edge+" TGT:"+tid);
// String tlabel = null;
// if (t != null)
// tlabel = graph.getLabel(t);
// annotation_doc.addField("isa_partof_closure", tid);
// addFieldUnique(bioentity_doc, "isa_partof_closure", tid);
// if (tlabel != null) {
// annotation_doc.addField("isa_partof_closure_label", tlabel);
// addFieldUnique(bioentity_doc, "isa_partof_closure_label", tlabel);
// // Map both ways.
// // TODO: collisions shouldn't be an issue here?
// isa_partof_map.put(tid, tlabel);
// isa_partof_map.put(tlabel, tid);
// }else{
// // For the time being at least, I want to ensure that the id and label closures
// // mirror eachother as much as possible (for facets and mapping, etc.). Without
// // this, in some cases there is simply nothing returned to drill on.
// annotation_doc.addField("isa_partof_closure_label", tid);
// addFieldUnique(bioentity_doc, "isa_partof_closure_label", tid);
// // Map just the one way I guess--see above.
// isa_partof_map.put(tid, tid);
// }
//
// // Annotation evidence aggregate base.
// String evAggId = eid + "_:ev:_" + clsId;
// SolrInputDocument ev_agg_doc;
// if (evAggDocMap.containsKey(evAggId)) {
// ev_agg_doc = evAggDocMap.get(evAggId);
// }
// else {
// ev_agg_doc = new SolrInputDocument();
// evAggDocMap.put(evAggId, ev_agg_doc);
// ev_agg_doc.addField("id", evAggId);
// ev_agg_doc.addField("document_category", "annotation_evidence_aggregate");
// ev_agg_doc.addField("bioentity", eid);
// ev_agg_doc.addField("bioentity_label", esym);
// ev_agg_doc.addField("annotation_class", tid);
// ev_agg_doc.addField("annotation_class_label", tlabel);
// ev_agg_doc.addField("taxon", taxId);
// addLabelField(ev_agg_doc, "taxon_label", taxId);
// }
//
// //evidence_type is single valued
// //aggDoc.addField("evidence_type", a.getEvidenceCls());
//
// // Drag in "with" (col 8), this time for ev_agg.
// for (WithInfo wi : a.getWithInfos()) {
// ev_agg_doc.addField("evidence_with", wi.getWithXref());
// }
//
// //aggDoc.getFieldValues(name)
// // TODO:
// ev_agg_doc.addField("evidence_type_closure", a.getEvidenceCls());
// }
// Column 16.
// We only want to climb the is_a/part_of parts here.
ArrayList<String> aecc_rels = new ArrayList<String>();
aecc_rels.add("BFO:0000050");
// And capture the label and ID mappings for when we're done the loop.
Map<String, String> ann_ext_map = new HashMap<String, String>(); // capture labels/ids
for (List<ExtensionExpression> groups : a.getExtensionExpressions()) {
// TODO handle extension expression groups
for (ExtensionExpression ee : groups) {
String eeid = ee.getCls();
OWLObject eObj = graph.getOWLObjectByIdentifier(eeid);
annotation_doc.addField("annotation_extension_class", eeid);
String eLabel = addLabelField(annotation_doc, "annotation_extension_class_label", eeid);
if (eLabel == null) eLabel = eeid; // ensure the label
///////////////
// New
///////////////
// Get the closure maps.
if (eObj != null) {
Map<String, String> aecc_cmap = graph.getRelationClosureMap(eObj, aecc_rels);
if (!aecc_cmap.isEmpty()) {
for (String aecc_id : aecc_cmap.keySet()) {
String aecc_lbl = aecc_cmap.get(aecc_id);
// Add all items to the document.
annotation_doc.addField("annotation_extension_class_closure", aecc_id);
annotation_doc.addField("annotation_extension_class_closure_label", aecc_lbl);
// And make sure that both id and label are in the per-term map.
ann_ext_map.put(aecc_lbl, aecc_id);
ann_ext_map.put(aecc_id, aecc_lbl);
}
}
}
// ///////////////
// // Old
// ///////////////
//
// if (eObj != null) {
// for (OWLGraphEdge edge : graph.getOutgoingEdgesClosureReflexive(eObj)) {
// OWLObject t = edge.getTarget();
// if (!(t instanceof OWLClass))
// continue;
// String annExtID = graph.getIdentifier(t);
// String annExtLabel = graph.getLabel(edge.getTarget());
// annotation_doc.addField("annotation_extension_class_closure", annExtID);
// annotation_doc.addField("annotation_extension_class_closure_label", annExtLabel);
// ann_ext_map.put(annExtID, annExtLabel);
// ann_ext_map.put(annExtLabel, annExtID);
// }
// }
// Ugly. Hand roll out the data for the c16 special handler. Have mercy on me--I'm going
// to just do this by hand since it's a limited case and I don't want to mess with Gson
// right now.
String complicated_c16r = ee.getRelation();
if (complicated_c16r != null) {
List<OWLObjectProperty> relations = graph.getRelationOrChain(complicated_c16r);
if (relations != null) {
ArrayList<String> relChunk = new ArrayList<String>();
for (OWLObjectProperty rel : relations) {
// Use the IRI to get the BFO:0000050 as ID for the part_of OWLObjectProperty
String rID = graph.getIdentifier(rel.getIRI());
String rLabel = graph.getLabel(rel);
if (rLabel == null) rLabel = rID; // ensure the label
relChunk.add("{\"id\": \"" + rID + "\", \"label\": \"" + rLabel + "\"}");
}
String finalSpan = StringUtils.join(relChunk, ", ");
// Assemble final JSON blob.
String aeJSON =
"{\"relationship\": {\"relation\": ["
+ finalSpan
+ "], \"id\": \""
+ eeid
+ "\", \"label\": \""
+ eLabel
+ "\"}}";
annotation_doc.addField("annotation_extension_json", aeJSON);
// LOG.info("added complicated c16: (" + eeid + ", " + eLabel + ") " + aeJSON);
} else {
// The c16r is unknown to the ontology--render it as just a normal label, without the
// link.
annotation_doc.addField("annotation_extension_json", complicated_c16r);
LOG.info("added unknown c16: " + complicated_c16r);
}
}
}
}
// Add annotation ext closure map to annotation doc (needs to be outside loop since there are
// multiple extensions).
if (!ann_ext_map.isEmpty()) {
String jsonized_ann_ext_map = gson.toJson(ann_ext_map);
annotation_doc.addField("annotation_extension_class_closure_map", jsonized_ann_ext_map);
}
// Final doc assembly; make the ID /really/ unique.
// WARNING: We're relying on the current truth that the toString() method returns a nice
// concatenated version
// of the GAF line, which is fundamentally unique (or should be). If this changes, revert to
// what we were
// doing here pre-20150930, which was assembling out own unique line manually.
annotation_doc.addField("id", a.toString());
// Finally add doc.
add(annotation_doc);
}
// Add the necessary aggregates to the bio doc. These cannot be done incrementally like the
// multi-valued closures
// sonce there can only be a single map.
if (!isap_map.isEmpty()) {
String jsonized_cmap = gson.toJson(isap_map);
bioentity_doc.addField("isa_partof_closure_map", jsonized_cmap);
}
if (!reg_map.isEmpty()) {
String jsonized_cmap = gson.toJson(reg_map);
bioentity_doc.addField("regulates_closure_map", jsonized_cmap);
}
// Add c5 to bioentity.
// Compile closure map to JSON and add to the document.
String jsonized_direct_map = null;
if (!direct_list_map.isEmpty()) {
jsonized_direct_map = gson.toJson(direct_list_map);
}
// Optionally, if there is enough direct annotations for a map, add the collections to the
// document.
if (jsonized_direct_map != null) {
List<String> directIDList = new ArrayList<String>(direct_list_map.keySet());
List<String> directLabelList = new ArrayList<String>(direct_list_map.values());
bioentity_doc.addField("annotation_class_list", directIDList);
bioentity_doc.addField("annotation_class_list_label", directLabelList);
bioentity_doc.addField("annotation_class_list_map", jsonized_direct_map);
}
add(bioentity_doc);
for (SolrInputDocument ev_agg_doc : evAggDocMap.values()) {
add(ev_agg_doc);
}
// Now repeat some of the same to help populate the "general" index for bioentities.
SolrInputDocument general_doc = new SolrInputDocument();
// Watch out for "id" collision!
general_doc.addField("id", "general_bioentity_" + eid);
general_doc.addField("entity", eid);
general_doc.addField("entity_label", esym);
general_doc.addField("document_category", "general");
general_doc.addField("category", "bioentity");
general_doc.addField(
"general_blob", ename + " " + edbid + " " + StringUtils.join(esynonyms, " "));
add(general_doc);
}
private OWLOntology parseWithReasoner(OWLOntologyManager manager, OWLOntology ontology) {
try {
PelletOptions.load(new URL("http://" + cssLocation + "pellet.properties"));
PelletReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(ontology);
reasoner.getKB().prepare();
List<InferredAxiomGenerator<? extends OWLAxiom>> generators =
new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
generators.add(new InferredSubClassAxiomGenerator());
generators.add(new InferredClassAssertionAxiomGenerator());
generators.add(new InferredDisjointClassesAxiomGenerator());
generators.add(new InferredEquivalentClassAxiomGenerator());
generators.add(new InferredEquivalentDataPropertiesAxiomGenerator());
generators.add(new InferredEquivalentObjectPropertyAxiomGenerator());
generators.add(new InferredInverseObjectPropertiesAxiomGenerator());
generators.add(new InferredPropertyAssertionGenerator());
generators.add(new InferredSubDataPropertyAxiomGenerator());
generators.add(new InferredSubObjectPropertyAxiomGenerator());
InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, generators);
OWLOntologyID id = ontology.getOntologyID();
Set<OWLImportsDeclaration> declarations = ontology.getImportsDeclarations();
Set<OWLAnnotation> annotations = ontology.getAnnotations();
Map<OWLEntity, Set<OWLAnnotationAssertionAxiom>> entityAnnotations =
new HashMap<OWLEntity, Set<OWLAnnotationAssertionAxiom>>();
for (OWLClass aEntity : ontology.getClassesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLObjectProperty aEntity : ontology.getObjectPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLDataProperty aEntity : ontology.getDataPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLNamedIndividual aEntity : ontology.getIndividualsInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLAnnotationProperty aEntity : ontology.getAnnotationPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLDatatype aEntity : ontology.getDatatypesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
manager.removeOntology(ontology);
OWLOntology inferred = manager.createOntology(id);
iog.fillOntology(manager, inferred);
for (OWLImportsDeclaration decl : declarations) {
manager.applyChange(new AddImport(inferred, decl));
}
for (OWLAnnotation ann : annotations) {
manager.applyChange(new AddOntologyAnnotation(inferred, ann));
}
for (OWLClass aEntity : inferred.getClassesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLObjectProperty aEntity : inferred.getObjectPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLDataProperty aEntity : inferred.getDataPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLNamedIndividual aEntity : inferred.getIndividualsInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLAnnotationProperty aEntity : inferred.getAnnotationPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLDatatype aEntity : inferred.getDatatypesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
return inferred;
} catch (FileNotFoundException e1) {
return ontology;
} catch (MalformedURLException e1) {
return ontology;
} catch (IOException e1) {
return ontology;
} catch (OWLOntologyCreationException e) {
return ontology;
}
}
public static void main(String[] args) throws Exception {
if (args.length == 0) {
// args = new String[] { "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl"};
args = new String[] {PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl"};
// args = new String[] { PagodaTester.onto_dir +
// "dbpedia/integratedOntology-all-in-one-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl" };
// args = new String[] { PagodaTester.onto_dir +
// "bio2rdf/reactome/biopax-level3-processed.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/uniprot/core-processed-noDis.owl"
// };
}
// OWLOntology ontology = OWLHelper.getMergedOntology(args[0], null);
// OWLHelper.correctDataTypeRangeAxioms(ontology);
OWLOntology ontology = OWLHelper.loadOntology(args[0]);
OWLOntologyManager manager = ontology.getOWLOntologyManager();
OWLDataFactory factory = manager.getOWLDataFactory();
// manager.saveOntology(ontology, new FileOutputStream(args[0].replace(".owl",
// "_owlapi.owl")));
if (outputFile != null) Utility.redirectCurrentOut(outputFile);
int queryID = 0;
for (OWLClass cls : ontology.getClassesInSignature(true)) {
if (cls.equals(factory.getOWLThing()) || cls.equals(factory.getOWLNothing())) continue;
if (!cls.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println(template.replace("@CLASS", cls.toStringID()));
System.out.println();
}
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT ?X ?Y");
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
String[] answerVars = new String[] {"?X", "?Y"};
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
for (int i = 0; i < answerVars.length; ++i) {
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT " + answerVars[i]);
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
}
if (outputFile != null) Utility.closeCurrentOut();
}
public void writeOntology() throws OWLRendererException {
if (ontologies.size() != 1) {
throw new OWLRuntimeException("Can only render one ontology");
}
OWLOntology ontology = getOntologies().iterator().next();
writePrefixMap();
writeNewLine();
writeOntologyHeader(ontology);
for (OWLAnnotationProperty prop : ontology.getAnnotationPropertiesInSignature()) {
write(prop);
}
for (OWLDatatype datatype : ontology.getDatatypesInSignature()) {
write(datatype);
}
for (OWLObjectProperty prop : ontology.getObjectPropertiesInSignature()) {
write(prop);
OWLObjectPropertyExpression invProp = prop.getInverseProperty();
if (!ontology.getAxioms(invProp).isEmpty()) {
write(invProp);
}
}
for (OWLDataProperty prop : ontology.getDataPropertiesInSignature()) {
write(prop);
}
for (OWLClass cls : ontology.getClassesInSignature()) {
write(cls);
}
for (OWLNamedIndividual ind : ontology.getIndividualsInSignature()) {
write(ind);
}
for (OWLAnonymousIndividual ind : ontology.getReferencedAnonymousIndividuals()) {
write(ind);
}
// Nary disjoint classes axioms
event = new RendererEvent(this, ontology);
for (OWLDisjointClassesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(DISJOINT_CLASSES, map, ",", false, ontology);
}
}
// Nary equivalent classes axioms
for (OWLEquivalentClassesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(EQUIVALENT_CLASSES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivlant properties
for (OWLEquivalentObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivalent properties
for (OWLEquivalentDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary different individuals
for (OWLDifferentIndividualsAxiom ax : ontology.getAxioms(AxiomType.DIFFERENT_INDIVIDUALS)) {
if (ax.getIndividuals().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getIndividuals(), ax);
writeSection(DIFFERENT_INDIVIDUALS, map, ",", false, ontology);
}
}
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
writeSection(RULE, Collections.singleton(rule), ", ", false);
}
flush();
}
@Override
public String getJavaInitializationString() {
/** This returns the value needed to reconstitute the object from a string */
return value.toStringID();
}