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NIHVIVO-3206 data migration of external concepts

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stellamit 2011-11-10 16:49:55 +00:00
parent 3b4f8e11ca
commit c7d357f89f
1 changed files with 89 additions and 29 deletions
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106
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
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@ -382,6 +382,7 @@ public class ABoxUpdater {
return refCount; return refCount;
} }
public void processPropertyChanges(List<AtomicOntologyChange> changes) throws IOException { public void processPropertyChanges(List<AtomicOntologyChange> changes) throws IOException {
Iterator<AtomicOntologyChange> propItr = changes.iterator(); Iterator<AtomicOntologyChange> propItr = changes.iterator();
@ -571,15 +572,21 @@ public class ABoxUpdater {
Property subjectAreaFor = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#subjectAreaFor"); Property subjectAreaFor = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#subjectAreaFor");
Property sourceVocabularyReference = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#sourceVocabularyReference"); Property sourceVocabularyReference = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#sourceVocabularyReference");
Property webpage = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#webpage");
Property linkURI = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkURI"); Property linkURI = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkURI");
Property linkAnchorText = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkAnchorText"); Property linkAnchorText = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkAnchorText");
HashSet<Resource> resourcesToDelete = new HashSet<Resource>(); HashSet<Resource> resourcesToDelete = new HashSet<Resource>();
HashSet<Resource> resourcesToDetype = new HashSet<Resource>();
Model additions = ModelFactory.createDefaultModel(); Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
int subjectRefCount = 0; int subjectRefCount = 0;
int researchRefCount = 0; int researchRefCount = 0;
int webpageCount = 0;
int typeCount = 0;
int count = 0;
aboxModel.enterCriticalSection(Lock.WRITE); aboxModel.enterCriticalSection(Lock.WRITE);
try { try {
@ -591,57 +598,87 @@ public class ABoxUpdater {
if (!stmt.getObject().isResource()) continue; if (!stmt.getObject().isResource()) continue;
Resource vocabularySourceReference = stmt.getObject().asResource(); Resource vocabularySourceReferenceResource = stmt.getObject().asResource();
Resource externalConceptResource = null;
Resource webpageResource = null;
Statement linkURIStmt = aboxModel.getProperty(vocabularySourceReference, linkURI); if (subjectAreaResource.hasProperty(webpage)) {
Statement webpageStmt = subjectAreaResource.getProperty(webpage);
if (linkURIStmt == null || !linkURIStmt.getObject().isLiteral()) continue; RDFNode webpageObject = webpageStmt.getObject();
if (!webpageObject.isResource()) continue;
Resource externalConceptResource = ResourceFactory.createResource(linkURIStmt.getObject().asLiteral().getString()); webpageResource = webpageObject.asResource();
if (!webpageResource.hasProperty(linkURI)) continue;
if (externalConceptResource == null) continue; Statement linkURIStmt = webpageResource.asResource().getProperty(linkURI);
RDFNode linkURIObject = linkURIStmt.getObject();
Statement conceptLabelStmt = aboxModel.getProperty(vocabularySourceReference, linkAnchorText); if (!linkURIObject.isLiteral()) continue;
externalConceptResource = ResourceFactory.createResource(linkURIObject.asLiteral().getString());
if (conceptLabelStmt == null) { if (externalConceptResource == null) continue;
conceptLabelStmt = aboxModel.getProperty(subjectAreaResource, RDFS.label); resourcesToDelete.add(webpageResource.asResource());
} resourcesToDetype.add(vocabularySourceReferenceResource);
additions.add(externalConceptResource,RDFS.isDefinedBy,vocabularySourceReferenceResource);
if (conceptLabelStmt != null) { additions.add(externalConceptResource, RDF.type, OWL_THING);
additions.add(externalConceptResource, RDFS.label, conceptLabelStmt.getObject().asLiteral()); Statement conceptLabelStmt = subjectAreaResource.getProperty(RDFS.label);
} if (conceptLabelStmt == null) {
conceptLabelStmt = webpageResource.asResource().getProperty(RDFS.label);
}
if (conceptLabelStmt != null) {
additions.add(externalConceptResource, RDFS.label, conceptLabelStmt.getObject().asLiteral());
}
} else {
continue;
}
subjectRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasSubjectArea, subjectAreaFor, additions); subjectRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasSubjectArea, subjectAreaFor, additions);
researchRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasResearchArea, researchAreaOf, additions); researchRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasResearchArea, researchAreaOf, additions);
migrateRelatedConcepts(externalConceptResource, subjectAreaResource, additions);
resourcesToDelete.add(subjectAreaResource); resourcesToDelete.add(subjectAreaResource);
if (webpageResource != null) {
resourcesToDelete.add(webpageResource);
webpageCount++;
}
count++;
} }
Iterator<Resource> vsrIter = resourcesToDetype.iterator();
while (vsrIter.hasNext()) {
Resource resource = vsrIter.next();
StmtIterator typeiter = resource.listProperties(RDF.type);
while (typeiter.hasNext()) {
retractions.add(typeiter.next());
}
additions.add(resource,RDF.type, OWL_THING);
typeCount++;
}
aboxModel.add(additions); aboxModel.add(additions);
aboxModel.remove(retractions);
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
record.recordAdditions(additions); record.recordAdditions(additions);
record.recordRetractions(retractions);
int count = 0;
Iterator<Resource> iter = resourcesToDelete.iterator(); Iterator<Resource> iter = resourcesToDelete.iterator();
while (iter.hasNext()) { while (iter.hasNext()) {
Resource ind = iter.next(); Resource ind = iter.next();
deleteIndividual(ind); deleteIndividual(ind);
count++;
} }
if (count > 0) { if (count > 0) {
logger.log("migrated " + count + " external concept" + ((count == 1) ? "" : "s")); ; logger.log("migrated " + count + " external concept" + ((count == 1) ? "" : "s") + ", which involved deleting " +
count + " vivo:SubjectArea individual" + ((count == 1) ? "" : "s") + " and " +
webpageCount + " vivo:URLLink individual" + ((webpageCount == 1) ? "" : "s") +
", and changing the type for " + typeCount + " vivo:VocabularySourceReference individual" + ((typeCount == 1) ? "" : "s") + " to owl:Thing");
} }
if (subjectRefCount > 0) { if (subjectRefCount > 0) {
logger.log("migrated " + subjectRefCount + " external " + hasSubjectArea.getLocalName() + " reference" + ((subjectRefCount == 1) ? "" : "s")); logger.log("migrated " + subjectRefCount + " " + hasSubjectArea.getLocalName() + " external concept reference" + ((subjectRefCount == 1) ? "" : "s"));
} }
if (researchRefCount > 0) { if (researchRefCount > 0) {
logger.log("migrated " + researchRefCount + " external " + hasResearchArea.getLocalName() + " reference" + ((researchRefCount == 1) ? "" : "s")); logger.log("migrated " + researchRefCount + " " + hasResearchArea.getLocalName() + " external concept reference" + ((researchRefCount == 1) ? "" : "s"));
} }
return; return;
@ -674,6 +711,29 @@ public class ABoxUpdater {
return count; return count;
} }
protected void migrateRelatedConcepts(Resource externalConceptResource, Resource subjectAreaResource, Model additions) throws IOException {
Property related = ResourceFactory.createProperty("http://www.w3.org/2004/02/skos/core#related");
aboxModel.enterCriticalSection(Lock.WRITE);
try {
StmtIterator iter = subjectAreaResource.listProperties(related);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!stmt.getObject().isResource()) continue;
Resource relatedConcept = stmt.getObject().asResource();
if (!additions.contains(externalConceptResource, related, relatedConcept)) {
additions.add(externalConceptResource, related, relatedConcept);
}
if (!additions.contains(relatedConcept, related, externalConceptResource)) {
additions.add(relatedConcept, related, externalConceptResource);
}
}
} finally {
aboxModel.leaveCriticalSection();
}
}
public void logChanges(Statement oldStatement, Statement newStatement) throws IOException { public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {
logChange(oldStatement,false); logChange(oldStatement,false);
logChange(newStatement,true); logChange(newStatement,true);