/**
* * Protege wont trigger a save action unless it detects that the OWLOntology currently opened
* has suffered a change. The OBDA plugin requires that protege triggers a save action also in the
* case when only the OBDA model has suffered chagnes. To acomplish this, this method will "fake"
* an ontology change by inserting and removing a class into the OWLModel.
*/
private void triggerOntologyChanged() {
if (loadingData) {
return;
}
OWLModelManager owlmm = owlEditorKit.getOWLModelManager();
OWLOntology ontology = owlmm.getActiveOntology();
if (ontology == null) {
return;
}
OWLClass newClass =
owlmm
.getOWLDataFactory()
.getOWLClass(IRI.create("http://www.unibz.it/krdb/obdaplugin#RandomClass6677841155"));
OWLAxiom axiom = owlmm.getOWLDataFactory().getOWLDeclarationAxiom(newClass);
try {
AddAxiom addChange = new AddAxiom(ontology, axiom);
owlmm.applyChange(addChange);
RemoveAxiom removeChange = new RemoveAxiom(ontology, axiom);
owlmm.applyChange(removeChange);
} catch (Exception e) {
log.warn(
"Exception forcing an ontology change. Your OWL model might contain a new class that you need to remove manually: {}",
newClass.getIRI());
log.warn(e.getMessage());
log.debug(e.getMessage(), e);
}
}
public void testIgnoreAnnotations() throws Exception {
OWLOntologyManager man = getManager(); // OWLManager.createOWLOntologyManager();
OWLOntology ont = man.createOntology();
OWLDataFactory df = man.getOWLDataFactory();
OWLClass clsA = df.getOWLClass(IRI.create("http://ont.com#A"));
OWLClass clsB = df.getOWLClass(IRI.create("http://ont.com#B"));
OWLSubClassOfAxiom sca = df.getOWLSubClassOfAxiom(clsA, clsB);
man.addAxiom(ont, sca);
OWLAnnotationProperty rdfsComment = df.getRDFSComment();
OWLLiteral lit = df.getOWLLiteral("Hello world");
OWLAnnotationAssertionAxiom annoAx1 =
df.getOWLAnnotationAssertionAxiom(rdfsComment, clsA.getIRI(), lit);
man.addAxiom(ont, annoAx1);
OWLAnnotationPropertyDomainAxiom annoAx2 =
df.getOWLAnnotationPropertyDomainAxiom(rdfsComment, clsA.getIRI());
man.addAxiom(ont, annoAx2);
OWLAnnotationPropertyRangeAxiom annoAx3 =
df.getOWLAnnotationPropertyRangeAxiom(rdfsComment, clsB.getIRI());
man.addAxiom(ont, annoAx3);
OWLAnnotationProperty myComment =
df.getOWLAnnotationProperty(IRI.create("http://ont.com#myComment"));
OWLSubAnnotationPropertyOfAxiom annoAx4 =
df.getOWLSubAnnotationPropertyOfAxiom(myComment, rdfsComment);
man.addAxiom(ont, annoAx4);
reload(ont, new RDFXMLOntologyFormat());
reload(ont, new OWLXMLOntologyFormat());
reload(ont, new TurtleOntologyFormat());
reload(ont, new OWLFunctionalSyntaxOntologyFormat());
}
protected Concept getParentConcept(
OWLOntology o, OWLClass ontologyClass, File inDir, Authorizations authorizations)
throws IOException {
Set<OWLClassExpression> superClasses = ontologyClass.getSuperClasses(o);
if (superClasses.size() == 0) {
return getEntityConcept();
} else if (superClasses.size() == 1) {
OWLClassExpression superClassExpr = superClasses.iterator().next();
OWLClass superClass = superClassExpr.asOWLClass();
String superClassUri = superClass.getIRI().toString();
Concept parent = getConceptByIRI(superClassUri);
if (parent != null) {
return parent;
}
parent = importOntologyClass(o, superClass, inDir, authorizations);
if (parent == null) {
throw new LumifyException("Could not find or create parent: " + superClass);
}
return parent;
} else {
throw new LumifyException(
"Unhandled multiple super classes. Found " + superClasses.size() + ", expected 0 or 1.");
}
}
protected void importDataProperty(OWLOntology o, OWLDataProperty dataTypeProperty) {
String propertyIRI = dataTypeProperty.getIRI().toString();
String propertyDisplayName = getLabel(o, dataTypeProperty);
PropertyType propertyType = getPropertyType(o, dataTypeProperty);
boolean userVisible = getUserVisible(o, dataTypeProperty);
boolean searchable = getSearchable(o, dataTypeProperty);
Boolean displayTime = getDisplayTime(o, dataTypeProperty);
Double boost = getBoost(o, dataTypeProperty);
if (propertyType == null) {
throw new LumifyException("Could not get property type on data property " + propertyIRI);
}
for (OWLClassExpression domainClassExpr : dataTypeProperty.getDomains(o)) {
OWLClass domainClass = domainClassExpr.asOWLClass();
String domainClassUri = domainClass.getIRI().toString();
Concept domainConcept = getConceptByIRI(domainClassUri);
checkNotNull(domainConcept, "Could not find class with uri: " + domainClassUri);
LOGGER.info("Adding data property " + propertyIRI + " to class " + domainConcept.getTitle());
ArrayList<PossibleValueType> possibleValues = getPossibleValues(o, dataTypeProperty);
Collection<TextIndexHint> textIndexHints = getTextIndexHints(o, dataTypeProperty);
addPropertyTo(
domainConcept,
propertyIRI,
propertyDisplayName,
propertyType,
possibleValues,
textIndexHints,
userVisible,
searchable,
displayTime,
boost);
}
}
public void addAncestor(OWLClass s, OWLClass t) {
if (!ancestors.containsKey(s.getIRI())) {
ancestors.put(s.getIRI(), t.getIRI());
} else {
throw new IllegalStateException("Child with more than 1 parent ! " + s + " " + t);
}
}
/**
* Создаем фрагмент запроса из списка именованных классов аксиомы и переданной sparql переменной,
* привоенной субаксиоме.
*/
public String getSparqlQueryPart(ArrayList<OWLClass> clsList, String SxAxVar) {
LOGGER.info(" ===getSparqlQueryPart==");
String fragmentOfQuery = "";
for (OWLClass cls : clsList) {
// Находи концепт в ОПП
IRI conceptIRI =
UPOont.getUPOont()
.getConceptByIRIinAnnotationValue(
IRI.create(ConstantsOntConverter.SKOS_HIDDEN_LABEL), cls.getIRI());
// Берем его переменную - нет переменная должна быть равна
// переменной субаксиомы
// String var = ontUPO.getAnnotationValue(conceptIRI,
// IRI.create(UPO_SPARQL_VARIABLE_LABEL) );
// Добавляем строку в запрос
fragmentOfQuery =
fragmentOfQuery
+ (SxAxVar
+ " "
+ ConstantsOntConverter.IRI_RDF_TYPE_SHORT
+ " <"
+ conceptIRI
+ ">"
+ ".\n");
LOGGER.info(" ConceptIRI:" + conceptIRI);
LOGGER.info(" Var of subAx:" + SxAxVar);
LOGGER.info(" Fragment:" + fragmentOfQuery);
}
LOGGER.info(" ===END-getSparqlQueryPart==");
return fragmentOfQuery;
}
private Set<OWLClassExpression> getInferredParents(
OWLOntology sourceOntology, OWLClass child, Set<OWLClass> viewed) {
Set<OWLClassExpression> result = new TreeSet<OWLClassExpression>();
if (!viewed.contains(child)) {
viewed.add(child);
Set<OWLClassExpression> parents = new TreeSet<OWLClassExpression>();
parents.addAll(child.getSuperClasses(sourceOntology));
parents.addAll(child.getEquivalentClasses(sourceOntology));
for (OWLClassExpression parent : parents) {
if (parent instanceof OWLClass) {
result.add(parent);
result.addAll(getInferredParents(sourceOntology, (OWLClass) parent, viewed));
} else if (parent instanceof OWLObjectIntersectionOf) {
Set<OWLClassExpression> inferredParents =
((OWLObjectIntersectionOf) parent).getOperands();
result.addAll(inferredParents);
for (OWLClassExpression inferredParent : inferredParents) {
if (inferredParent instanceof OWLClass) {
result.addAll(getInferredParents(sourceOntology, (OWLClass) inferredParent, viewed));
}
}
} else {
result.add(parent);
}
}
}
return result;
}
@Test
public void testNegAllValuesFrom() {
OWLObjectProperty property = ObjectProperty(getIRI("p"));
OWLClass filler = Class(getIRI("A"));
OWLObjectAllValuesFrom allValuesFrom = ObjectAllValuesFrom(property, filler);
OWLClassExpression cls = allValuesFrom.getObjectComplementOf();
OWLClassExpression nnf = ObjectSomeValuesFrom(property, filler.getObjectComplementOf());
assertEquals(cls.getNNF(), nnf);
}
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();
}
}
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;
}
public Set<OWLDataProperty> getDataPropertiesByDomain(OWLClass domain) {
Set<OWLDataProperty> propSet = new HashSet<OWLDataProperty>();
Set<OWLDataProperty> objProps = _ontology.getDataPropertiesInSignature();
for (OWLDataProperty prop : objProps) {
for (OWLClass owlClass : _reasoner.getDataPropertyDomains(prop, true).getFlattened()) {
if (owlClass.equals(domain)) {
propSet.add(prop);
}
}
}
return propSet;
}
/**
* 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 Set<String> getSuperClasses(OWLReasoner reasoner, OWLClass cl, OWLClass owlThing) {
Set<String> pset = new HashSet<String>();
Set<OWLClass> reasonerSuperClasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperClasses.add(cl);
reasonerSuperClasses.add(owlThing);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperClasses.add(iterator.next());
for (OWLClass scl : reasonerSuperClasses) pset.add(scl.toString());
return pset;
}
private void compareAndPrintEqualSizedClasses(
OWLClass cl, Set<OWLClass> reasonerSuperClasses, Set<String> superClasses, Jedis idReader)
throws Exception {
// compare each element of these 2 sets
boolean print = false;
for (OWLClass scl : reasonerSuperClasses) {
String sclID = conceptToID(scl.toString(), idReader);
if (!superClasses.contains(sclID)) {
print = true;
System.out.print(cl.toString() + " -e- " + scl.toString());
System.out.print(" , ");
}
}
if (print) System.out.println("\n");
}
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;
}
public Set<OWLObjectProperty> getObjectPropertiesByDomainAndRange(
OWLClass domain, OWLClass range) {
Set<OWLObjectProperty> propSet = new HashSet<OWLObjectProperty>();
for (OWLObjectProperty prop : _ontology.getObjectPropertiesInSignature()) {
for (OWLClass owlClass : _reasoner.getObjectPropertyDomains(prop, true).getFlattened()) {
if (owlClass.equals(domain)) {
for (OWLClass owlClass2 : _reasoner.getObjectPropertyRanges(prop, true).getFlattened()) {
if (owlClass2.equals(range)) {
propSet.add(prop);
}
}
}
}
}
return propSet;
}
private void recursiveAddTuple(
String termPath, OWLClass cls, OntologyLoader ontologyLoader, List<Tuple> tuples) {
String label = ontologyLoader.getLabel(cls).replaceAll("[^a-zA-Z0-9 ]", " ");
Set<String> synonyms = new HashSet<String>();
synonyms.add(label);
synonyms.addAll(ontologyLoader.getSynonyms(cls));
// listOfChildren.addAll(model.getAssociatedClasses(cls));
StringBuilder alternativeDefinitions = new StringBuilder();
for (Set<OWLClass> alternativeDefinition : ontologyLoader.getAssociatedClasses(cls)) {
StringBuilder newDefinition = new StringBuilder();
for (OWLClass associatedClass : alternativeDefinition) {
if (newDefinition.length() != 0) newDefinition.append(',');
newDefinition.append(associatedClass.getIRI().toString());
}
if (alternativeDefinitions.length() != 0 && newDefinition.length() != 0)
alternativeDefinitions.append("&&&");
alternativeDefinitions.append(newDefinition);
}
if (alternativeDefinitions.length() != 0) {
System.out.println(alternativeDefinitions.toString());
}
for (String synonym : synonyms) {
KeyValueTuple tuple = new KeyValueTuple();
tuple.set(NODE_PATH, termPath);
tuple.set(BOOST, false);
tuple.set(ONTOLOGY_IRI, ontologyIRI);
tuple.set(ONTOLOGY_NAME, ontologyName);
tuple.set(ONTOLOGY_TERM, label);
tuple.set(ONTOLOGY_TERM_IRI, cls.getIRI().toString());
tuple.set(ONTOLOGY_LABEL, ontologyLoader.getOntologyName());
tuple.set(ENTITY_TYPE, "ontologyTerm");
tuple.set(SYNONYMS, synonym.replaceAll("[^a-zA-Z0-9 ]", " "));
tuple.set(ALTERNATIVE_DEFINITION, alternativeDefinitions.toString());
tuples.add(tuple);
}
Set<OWLClass> listOfChildren = ontologyLoader.getChildClass(cls);
if (listOfChildren.size() > 0) {
int i = 0;
for (OWLClass childClass : listOfChildren) {
String childTermPath = termPath + "." + i;
recursiveAddTuple(childTermPath, childClass, ontologyLoader, tuples);
i++;
}
}
}
private void compareClassificationResults(
OWLOntology ontology, OWLReasoner reasoner, Jedis resultStore, Jedis idReader)
throws Exception {
Set<OWLClass> classes = ontology.getClassesInSignature();
Pipeline resultPipeline = resultStore.pipelined();
double classCount = 0;
int multiplier = 1;
double totalCount = 0;
for (OWLClass cl : classes) {
classCount++;
double classProgress = (classCount / classes.size()) * 100;
Set<OWLClass> reasonerSuperclasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperclasses.add(cl);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperclasses.add(iterator.next());
String classToCheckID = conceptToID(cl.toString(), idReader);
List<Response<Double>> responseList = new ArrayList<Response<Double>>();
for (OWLClass scl : reasonerSuperclasses) {
String key = conceptToID(scl.toString(), idReader);
responseList.add(resultPipeline.zscore(key, classToCheckID));
}
resultPipeline.sync();
double hitCount = 0;
for (Response<Double> response : responseList) {
if (response.get() != null) hitCount++;
}
totalCount += (hitCount / reasonerSuperclasses.size());
if (classProgress >= (5 * multiplier)) {
System.out.println(
"% of no. of classes looked at: "
+ classProgress
+ "\tProgress %: "
+ (totalCount / classCount) * 100);
multiplier++;
}
}
double progress = totalCount / classes.size();
System.out.println("\nProgress %: " + (progress * 100));
}
public String[] searchOntology(String term, String ontofilepath, String type) {
OWLAccessorImpl owlapi = new OWLAccessorImpl(new File(ontofilepath));
List<OWLClass> matches = owlapi.retrieveConcept(term);
Iterator<OWLClass> it = matches.iterator();
String[] result = null;
while (it.hasNext()) {
OWLClass c = it.next();
String label = owlapi.getLabel(c);
if (label.compareToIgnoreCase(term) == 0) {
result = new String[3];
result[0] = type;
result[1] =
c.toString()
.replaceFirst("http.*?(?=(PATO|TAO)_)", "")
.replaceFirst("_", ":")
.replaceFirst(">$", "");
result[2] = label;
return result;
}
}
it = matches.iterator();
result = new String[] {"", "", ""};
while (it.hasNext()) {
OWLClass c = it.next();
String label = owlapi.getLabel(c);
result[0] = type;
result[1] +=
c.toString()
.replaceFirst(".*http.*?(?=(PATO|TAO)_)", "")
.replaceFirst("_", ":")
.replaceFirst(">$", "")
+ ";";
result[2] += label + ";";
}
if (result != null) {
result[1] = result[1].replaceFirst(";$", "");
result[2] = result[2].replaceFirst(";$", "");
}
return result;
}
/*
* (non-Javadoc)
*
* @see ru.iimm.ontology.OWL2UPOConverter.SubAxiom#getNewTitle()
*/
@Override
protected String generateTitle() {
LOGGER.info("=== Generate title for SubAxiom:\n" + this.getSubAxOWL());
String namedTitle = "";
/* В название добавляем имена классов субавксиомы */
for (OWLClass cls : this.getClsList()) {
namedTitle += cls.getIRI().getFragment() + ConstantsOntConverter.UPO_TITLE_DELIMITER;
}
/* Формируем карту: свойство --- массив субаксиом [] */
HashMap<IRI, ArrayList<SubAxiom>> map = this.getPropSubaxMap(this.getPrpFromAxList());
/* Из карты формируем подзаголовки - для сложных субаксиом */
for (IRI propIRI : map.keySet()) {
for (SubAxiom subax : map.get(propIRI))
// namedTitle += subax.getTitle()
namedTitle +=
propIRI.getFragment()
+ ConstantsOntConverter.UPO_PROP_VAL_DELIMITER
+ subax.getTitle()
+ ConstantsOntConverter.UPO_TITLE_DELIMITER;
}
/* Добавляем фрагмент имени от типизированных свойств */
namedTitle = namedTitle + this.getDatatypePropNameFragment(this.getDtpPrpList());
/* Отрезаем лишний делимитер (-) из конца аксиомы */
namedTitle =
namedTitle.length() > 0
? namedTitle.substring(
0, namedTitle.lastIndexOf(ConstantsOntConverter.UPO_TITLE_DELIMITER))
: namedTitle;
/* Обрамляем скобками субаксиому */
// namedTitle = namedTitle.length()>0 ? "[" + namedTitle + "]" : null;
namedTitle = namedTitle.length() > 0 ? UPOont.getSBrackedString(namedTitle) : null;
return namedTitle;
}
public Set<OWLDataProperty> getDataPropertiesByDomainExtended(OWLClass domain) {
Log.d(
TAG,
"<getDataPropertiesByDomainExtended> Buscando DataProperties con dominio "
+ domain.getIRI().toString());
Set<OWLDataProperty> propSet = new HashSet<OWLDataProperty>();
for (OWLDataProperty prop : _ontology.getDataPropertiesInSignature()) {
if (isDomainOfDataProperty(domain, prop)) {
propSet.add(prop);
}
}
return propSet;
}
private void compareAndPrintUnEqualSizedIndividuals(
OWLClass cl,
Set<OWLNamedIndividual> reasonerInstances,
Set<String> computedInstances,
Jedis idReader)
throws Exception {
// compare each element of these 2 sets
boolean print = false;
for (OWLNamedIndividual scl : reasonerInstances) {
String sclID = conceptToID(scl.toString(), idReader);
if (!computedInstances.contains(sclID)) {
print = true;
System.out.print(cl.toString() + " -ne- " + scl.toString());
System.out.print(" , ");
}
computedInstances.remove(sclID);
}
for (String s : computedInstances)
System.out.println("\t -- " + Util.idToConcept(s, idReader) + "(" + s + ")");
System.out.println();
}
@Override
public boolean compare(JSONObject jsonObject, OWLClass owlClass, OWLOntology owlOntology) {
Set<OWLClass> allClassesInAxiomsRelated = new HashSet<OWLClass>();
JSONArray jsonAnnotationsArray = (JSONArray) jsonObject.get("annotations");
Set<OWLAxiom> owlAxiomSet = owlClass.getReferencingAxioms(owlOntology);
Iterator<OWLAxiom> owlAxiomSetIterator = owlAxiomSet.iterator();
while (owlAxiomSetIterator.hasNext()) {
OWLAxiom owlAxiom = owlAxiomSetIterator.next();
Set<OWLClass> owlClassesInAxiom = owlAxiom.getClassesInSignature();
allClassesInAxiomsRelated.addAll(owlClassesInAxiom);
}
Set<String> owlClassesIds = new HashSet<String>();
Iterator<OWLClass> allClassesInAxiomsRelatedIterator = allClassesInAxiomsRelated.iterator();
while (allClassesInAxiomsRelatedIterator.hasNext()) {
OWLClass currentClass = allClassesInAxiomsRelatedIterator.next();
owlClassesIds.add(
OwlDataExtrators.getAttribute("id", currentClass, owlOntology).replace(":", "_"));
}
Set<String> jsonAnnotationsIdsSet = new HashSet<String>();
Iterator<JSONObject> jsonAnnotationsArrayIterator = jsonAnnotationsArray.iterator();
while (jsonAnnotationsArrayIterator.hasNext()) {
JSONObject jsonAnnottation = jsonAnnotationsArrayIterator.next();
String jsonAnnotationIdentifier = (String) jsonAnnottation.get("identifier");
jsonAnnotationsIdsSet.add(jsonAnnotationIdentifier);
}
Set<Set<String>> jsonAnnotationsIdPowerSet = SetsOperations.powerSet(jsonAnnotationsIdsSet);
Iterator<Set<String>> jsonAnnotationsIdPowerSetIterator = jsonAnnotationsIdPowerSet.iterator();
while (jsonAnnotationsIdPowerSetIterator.hasNext()) {
Set<String> idsSet = jsonAnnotationsIdPowerSetIterator.next();
if (idsSet.containsAll(owlClassesIds)) {
return true;
}
}
return false;
}
private void handleNewSplitAxioms(
OWLClass newlyCreatedClass, OWLClass classThatWasSplit, EntityBasedDiff diff) {
OWLOntology sourceOntology = diffMap.getSourceOntology();
Map<OWLEntity, IRI> newTargetToSplitSource =
Collections.singletonMap((OWLEntity) newlyCreatedClass, classThatWasSplit.getIRI());
OWLObjectDuplicator duplicator =
new OWLObjectDuplicator(newTargetToSplitSource, diffMap.getOWLDataFactory());
Set<OWLClassExpression> inferredParents = getInferredParents(sourceOntology, classThatWasSplit);
for (MatchedAxiom match : new ArrayList<MatchedAxiom>(diff.getAxiomMatches())) {
if (match.getDescription().equals(MatchedAxiom.AXIOM_ADDED)
&& cameFromSourceOntology(
(OWLAxiom) duplicator.duplicateObject(match.getTargetAxiom()),
sourceOntology,
classThatWasSplit,
inferredParents)) {
MatchedAxiom modifiedBySplit =
new MatchedAxiom(null, match.getTargetAxiom(), COPIED_FROM_SPLIT);
changes.removeMatch(match);
changes.addMatch(modifiedBySplit);
}
}
}
public Set<OWLClass> getRootUnsatisfiableClasses() {
// StructureBasedRootClassFinder srd = new StructureBasedRootClassFinder(this.baseReasoner);
StructuralRootDerivedReasoner srd =
new StructuralRootDerivedReasoner(this.manager, this.baseReasoner, this.reasonerFactory);
Set<OWLClass> estimatedRoots = srd.getRootUnsatisfiableClasses();
this.cls2JustificationMap = new HashMap<OWLClass, Set<Explanation>>();
Set<OWLAxiom> allAxioms = new HashSet<OWLAxiom>();
for (OWLOntology ont : this.baseReasoner.getRootOntology().getImportsClosure()) {
allAxioms.addAll(ont.getLogicalAxioms());
}
for (OWLClass cls : estimatedRoots) {
this.cls2JustificationMap.put(cls, new HashSet<Explanation>());
System.out.println("POTENTIAL ROOT: " + cls);
}
System.out.println("Finding real roots from " + estimatedRoots.size() + " estimated roots");
int done = 0;
this.roots.addAll(estimatedRoots);
for (OWLClass estimatedRoot : estimatedRoots) {
try {
PelletExplanationGenerator gen =
new PelletExplanationGenerator(manager.createOntology(allAxioms));
OWLDataFactory df = this.manager.getOWLDataFactory();
Set<Explanation> expls =
gen.getExplanations(df.getOWLSubClassOfAxiom(estimatedRoot, df.getOWLNothing()));
cls2JustificationMap.get(estimatedRoot).addAll(expls);
++done;
System.out.println("Done " + done);
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
}
for (OWLClass clsA : estimatedRoots) {
for (OWLClass clsB : estimatedRoots)
if (!clsA.equals(clsB)) {
Set<Explanation> clsAExpls = cls2JustificationMap.get(clsA);
Set<Explanation> clsBExpls = cls2JustificationMap.get(clsB);
boolean clsARootForClsB = false;
boolean clsBRootForClsA = false;
for (Explanation clsAExpl : clsAExpls) {
for (Explanation clsBExpl : clsBExpls)
if (isRootFor(clsAExpl, clsBExpl)) {
clsARootForClsB = true;
} else if (isRootFor(clsBExpl, clsAExpl)) {
clsBRootForClsA = true;
}
}
Explanation clsAExpl;
if ((!clsARootForClsB) || (!clsBRootForClsA))
if (clsARootForClsB) {
this.roots.remove(clsB);
} else if (clsBRootForClsA) this.roots.remove(clsA);
}
}
OWLClass clsA;
return this.roots;
}
// 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);
}
@Override
public void visit(OWLClass cls) {
handleObject(cls);
cls.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);
}
}
/*
* (non-Javadoc)
*
* @see
* org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb
* .owlapi.model.OWLClass)
*/
@Override
public void visit(OWLClass axiom) {
sb.append(print(axiom.toString()));
}
public boolean isRestrictedInstantiator(OWLClass c) {
return c == null
|| c.isTopEntity()
|| m_ontologyOperator.getFlatteningTransformer().isIntermediary(c)
|| c.equals(m_referenceClass);
}
