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Removing 1.4 (and before) specific migration logic (External Concepts, display model, recomputing mostSpecificType on startup)

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This commit is contained in:
stellamit 2012-02-27 18:38:33 +00:00
parent 24f5562626
commit fe044c759a
6 changed files with 4 additions and 345 deletions
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173
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -564,179 +564,6 @@ public class ABoxUpdater {
}
}
protected void migrateExternalConcepts() throws IOException {
Property hasResearchArea = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#hasResearchArea");
Property researchAreaOf = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#researchAreaOf");
Property hasSubjectArea = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#hasSubjectArea");
Property subjectAreaFor = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#subjectAreaFor");
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 linkAnchorText = ResourceFactory.createProperty("http://vivoweb.org/ontology/core#linkAnchorText");
HashSet<Resource> resourcesToDelete = new HashSet<Resource>();
HashSet<Resource> resourcesToDetype = new HashSet<Resource>();
Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
int subjectRefCount = 0;
int researchRefCount = 0;
int webpageCount = 0;
int typeCount = 0;
int count = 0;
aboxModel.enterCriticalSection(Lock.WRITE);
try {
StmtIterator iter = aboxModel.listStatements((Resource) null, sourceVocabularyReference, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
Resource subjectAreaResource = stmt.getSubject();
if (!stmt.getObject().isResource()) continue;
Resource vocabularySourceReferenceResource = stmt.getObject().asResource();
Resource externalConceptResource = null;
Resource webpageResource = null;
if (subjectAreaResource.hasProperty(webpage)) {
Statement webpageStmt = subjectAreaResource.getProperty(webpage);
RDFNode webpageObject = webpageStmt.getObject();
if (!webpageObject.isResource()) continue;
webpageResource = webpageObject.asResource();
if (!webpageResource.hasProperty(linkURI)) continue;
Statement linkURIStmt = webpageResource.asResource().getProperty(linkURI);
RDFNode linkURIObject = linkURIStmt.getObject();
if (!linkURIObject.isLiteral()) continue;
externalConceptResource = ResourceFactory.createResource(linkURIObject.asLiteral().getString());
if (externalConceptResource == null) continue;
resourcesToDelete.add(webpageResource.asResource());
resourcesToDetype.add(vocabularySourceReferenceResource);
additions.add(externalConceptResource,RDFS.isDefinedBy,vocabularySourceReferenceResource);
additions.add(externalConceptResource, RDF.type, OWL_THING);
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);
researchRefCount += migrateConceptReferences(externalConceptResource, subjectAreaResource, hasResearchArea, researchAreaOf, additions);
migrateRelatedConcepts(externalConceptResource, subjectAreaResource, additions);
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()) {
Statement typeStatement = typeiter.next();
if (!typeStatement.getObject().equals(OWL_THING)) {
retractions.add(typeStatement);
}
}
additions.add(resource, RDF.type, OWL_THING);
typeCount++;
}
aboxModel.add(additions);
aboxModel.remove(retractions);
} finally {
aboxModel.leaveCriticalSection();
}
record.recordAdditions(additions);
record.recordRetractions(retractions);
Iterator<Resource> iter = resourcesToDelete.iterator();
while (iter.hasNext()) {
Resource ind = iter.next();
deleteIndividual(ind);
}
if (count > 0) {
; 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) {
logger.log("migrated " + subjectRefCount + " " + hasSubjectArea.getLocalName() + " external concept reference" + ((subjectRefCount == 1) ? "" : "s"));
}
if (researchRefCount > 0) {
logger.log("migrated " + researchRefCount + " " + hasResearchArea.getLocalName() + " external concept reference" + ((researchRefCount == 1) ? "" : "s"));
}
return;
}
protected int migrateConceptReferences(Resource externalConceptResource, Resource subjectArea, Property hasConcept, Property conceptOf, Model additions) throws IOException {
int count = 0;
aboxModel.enterCriticalSection(Lock.WRITE);
try {
StmtIterator iter = aboxModel.listStatements((Resource) null, hasConcept, subjectArea);
while (iter.hasNext()) {
Statement stmt = iter.next();
Resource agent = stmt.getSubject();
if (!additions.contains(agent, hasConcept, externalConceptResource)) {
additions.add(agent, hasConcept, externalConceptResource);
count++;
}
if (!additions.contains(externalConceptResource, conceptOf, agent)) {
additions.add(externalConceptResource, conceptOf, agent);
}
}
} finally {
aboxModel.leaveCriticalSection();
}
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 {
logChange(oldStatement,false);
logChange(newStatement,true);

1
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -236,7 +236,6 @@ public class KnowledgeBaseUpdater {
OntModel newTBoxModel = settings.getNewTBoxModel();
OntModel ABoxModel = settings.getAssertionOntModelSelector().getABoxModel();
ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, ABoxModel,settings.getNewTBoxAnnotationsModel(), logger, record);
aboxUpdater.migrateExternalConcepts();
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
}

60
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -912,66 +912,6 @@ public class SimpleReasoner extends StatementListener {
log.info("ABox inference model updated");
}
public synchronized void computeMostSpecificType() {
recomputing = true;
try {
doComputeMostSpecificType();
} finally {
recomputing = false;
}
}
/*
* Special for version 1.4
*/
public synchronized void doComputeMostSpecificType() {
log.info("Computing mostSpecificType annotations.");
HashSet<String> unknownTypes = new HashSet<String>();
try {
String queryString = "select distinct ?subject where {?subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2004/02/skos/core#Concept>}";
ArrayList<String> individuals = this.getIndividualURIs(queryString);
int numStmts = 0;
for (String individualURI : individuals ) {
Resource individual = ResourceFactory.createResource(individualURI);
try {
setMostSpecificTypes(individual, inferenceModel, unknownTypes);
} catch (NullPointerException npe) {
log.error("a NullPointerException was received while computing mostSpecificType annotations. Halting inference computation.");
return;
} catch (JenaException je) {
if (je.getMessage().equals("Statement models must no be null")) {
log.error("Exception while computing mostSpecificType annotations.: " + je.getMessage() + ". Halting inference computation.");
return;
}
log.error("Exception while computing mostSpecificType annotations.: " + je.getMessage());
} catch (Exception e) {
log.error("Exception while computing mostSpecificType annotations", e);
}
numStmts++;
if ((numStmts % 10000) == 0) {
log.info("Still computing mostSpecificType annotations...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during computeMostSpecificType. Halting Processing.");
return;
}
}
} catch (Exception e) {
log.error("Exception while computing mostSpecificType annotations", e);
return;
}
log.info("Finished computing mostSpecificType annotations");
}
public synchronized boolean isABoxReasoningAsynchronous() {
if (batchMode1 || batchMode2) {
return true;

17
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java
View file

@ -129,10 +129,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
new Thread(new ABoxRecomputer(simpleReasoner),"ABoxRecomputer").start();
}
} else if ( isMSTComputeRequired(sce.getServletContext()) ) {
log.info("mostSpecificType computation required. It will be done in a separate thread.");
waitForTBoxReasoning(pelletListener);
new Thread(new MostSpecificTypeRecomputer(simpleReasoner),"MostSpecificTypeComputer").start();
}
SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
@ -232,19 +228,6 @@ public class SimpleReasonerSetup implements ServletContextListener {
}
}
private class MostSpecificTypeRecomputer implements Runnable {
private SimpleReasoner simpleReasoner;
public MostSpecificTypeRecomputer(SimpleReasoner simpleReasoner) {
this.simpleReasoner = simpleReasoner;
}
public void run() {
simpleReasoner.computeMostSpecificType();
}
}
/**
* Read the names of the plugin classes classes.
*

51
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -109,10 +109,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
try {
if (ontologyUpdater.updateRequired()) {
ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
log.info("Migrating data model");
doMigrateDisplayModel(ctx);
log.info("Display model migrated");
ontologyUpdater.update();
}
} catch (IOException ioe) {
String errMsg = "IOException updating knowledge base " +
@ -137,53 +133,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
return;
}
OntModel displayModel = (OntModel) o;
migrateDisplayModel(displayModel);
}
public static void migrateDisplayModel(Model displayModel) {
Resource browseDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter");
Resource pageDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassGroupPageData");
Resource internalDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.InternalClassesDataGetter");
Resource individualsDataGetterClass = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.IndividualsForClassesDataGetter");
Resource homeDataGetter = ResourceFactory.createResource(DisplayVocabulary.DISPLAY_NS + "homeDataGetter");
Property dataGetterProperty = displayModel.getProperty(DisplayVocabulary.HAS_DATA_GETTER);
Resource homePage = displayModel.getResource(DisplayVocabulary.HOME_PAGE_URI);
Resource classGroupPage = displayModel.getResource(DisplayVocabulary.CLASSGROUP_PAGE_TYPE);
Resource internalClassesPage = displayModel.getResource(DisplayVocabulary.CLASSINDIVIDUALS_INTERNAL_TYPE);
Resource individualsPage = displayModel.getResource(DisplayVocabulary.CLASSINDIVIDUALS_PAGE_TYPE);
displayModel.add(homePage, dataGetterProperty, homeDataGetter);
displayModel.add(homeDataGetter, RDF.type, browseDataGetterClass);
Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
StmtIterator iter = displayModel.listStatements((Resource) null, RDF.type, internalClassesPage);
while (iter.hasNext()) {
Statement stmt = iter.next();
retractions.add(stmt);
additions.add(stmt.getSubject(), RDF.type, internalDataGetterClass);
}
iter = displayModel.listStatements((Resource) null, RDF.type, classGroupPage);
while (iter.hasNext()) {
Statement stmt = iter.next();
retractions.add(stmt);
additions.add(stmt.getSubject(), RDF.type, pageDataGetterClass);
}
iter = displayModel.listStatements((Resource) null, RDF.type, individualsPage);
while (iter.hasNext()) {
Statement stmt = iter.next();
retractions.add(stmt);
additions.add(stmt.getSubject(), RDF.type, individualsDataGetterClass);
}
displayModel.remove(retractions);
displayModel.add(additions);
}
private OntModel loadModelFromDirectory(String directoryPath) {

41
webapp/test/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBaseTest.java
View file

@ -13,47 +13,8 @@ import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
public class UpdateKnowledgeBaseTest extends AbstractTestClass {
//@org.junit.Test
public void testMigrateDisplayModel12() {
String version12DisplayModel = "\n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PrimaryLuceneIndex> " +
" a <http://www.w3.org/2002/07/owl#Thing> . \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations> \n" +
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#ClassGroupPage> , \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page> ; \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#forClassGroup> \n " +
" <http://vivoweb.org/ontology#vitroClassGrouporganizations> ; \n " +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#title> \n" +
" \"Organizations\" ; \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping> \n " +
" \"/organizations\" . ";
String version13DisplayModel = "\n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#SearchIndex> " +
" a <http://www.w3.org/2002/07/owl#Thing> . \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations> \n" +
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page> ; \n " +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#hasDataGetter> \n " +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsDataGetter1> ; " +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#title> \n " +
" \"Organizations\" ; \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping> \n" +
" \"/organizations\" . \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsDataGetter1> \n" +
" a <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#ClassGroupPage> ; \n" +
" <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#forClassGroup> \n" +
" <http://vivoweb.org/ontology#vitroClassGrouporganizations> .";
Model preMigrate = ModelFactory.createDefaultModel().read(new StringReader(version12DisplayModel), null, "N3");
Model postMigrate = ModelFactory.createDefaultModel().read(new StringReader(version13DisplayModel), null, "N3");
UpdateKnowledgeBase.migrateDisplayModel(preMigrate);
Assert.assertTrue(preMigrate.isIsomorphicWith(postMigrate));
}
@org.junit.Test
public void testMigrateDisplayModel13() {
public void testMigrateDisplayModel14() {
return;
}