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annotation data migration

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This commit is contained in:
brianjlowe 2013-09-18 16:21:36 -04:00
parent e739a94222
commit c062201a9a
7 changed files with 569 additions and 402 deletions
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2
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java
View file

@ -12,6 +12,8 @@ public class VitroVocabulary {
public static final String VITRO_AUTH = "http://vitro.mannlib.cornell.edu/ns/vitro/authorization#";
public static final String VITRO_PUBLIC = "http://vitro.mannlib.cornell.edu/ns/vitro/public#";
public static final String VITRO_PUBLIC_ONTOLOGY = "http://vitro.mannlib.cornell.edu/ns/vitro/public";
// TODO change the following before 1.6 release
public static final String PROPERTY_CONFIG_DATA = "http://example.org/appConfig/";
/** BJL23 2008-02-25:

1
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
View file

@ -949,7 +949,6 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
" { ?property display:listViewConfigFile ?filename \n" +
" } UNION { \n" +
" ?configuration config:listViewConfigFile ?filename . \n " +
// " ?configuration config:hasListView ?lv . " +
" ?context config:hasConfiguration ?configuration . \n" +
" ?context config:configContextFor ?property . \n" +
" ?context config:qualifiedBy ?range . \n" +

16
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -44,6 +44,7 @@ public class ABoxUpdater {
private Dataset dataset;
private RDFService rdfService;
private OntModel newTBoxAnnotationsModel;
private TBoxUpdater tboxUpdater;
private ChangeLogger logger;
private ChangeRecord record;
private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
@ -61,20 +62,19 @@ public class ABoxUpdater {
* and the retractions model.
*
*/
public ABoxUpdater(OntModel oldTboxModel,
OntModel newTboxModel,
RDFService rdfService,
OntModel newAnnotationsModel,
public ABoxUpdater(UpdateSettings settings,
ChangeLogger logger,
ChangeRecord record) {
this.oldTboxModel = oldTboxModel;
this.newTboxModel = newTboxModel;
this.oldTboxModel = settings.getOldTBoxModel();
this.newTboxModel = settings.getNewTBoxModel();
RDFService rdfService = settings.getRDFService();
this.dataset = new RDFServiceDataset(rdfService);
this.rdfService = rdfService;
this.newTBoxAnnotationsModel = newAnnotationsModel;
this.newTBoxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
this.logger = logger;
this.record = record;
this.tboxUpdater = new TBoxUpdater(settings, logger, record);
}
/**
@ -632,6 +632,8 @@ public class ABoxUpdater {
propObj.getDestinationURI() + " instead");
}
}
tboxUpdater.renameProperty(propObj);
}
public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {

41
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -64,7 +64,6 @@ public class KnowledgeBaseUpdater {
}
long startTime = System.currentTimeMillis();
System.out.println("Migrating the knowledge base");
log.info("Migrating the knowledge base");
logger.log("Started knowledge base migration");
@ -84,7 +83,6 @@ public class KnowledgeBaseUpdater {
logger.closeLogs();
long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;
System.out.println("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
return;
@ -110,20 +108,15 @@ public class KnowledgeBaseUpdater {
} catch (Exception e) {
log.error("unable to migrate migration metadata " + e.getMessage());
}
log.warn("KnowledgeBaseUpdater needs to be modified to work on all graphs!");
OntModel readModel = settings.getUnionOntModelSelector().getABoxModel();
OntModel writeModel = settings.getAssertionOntModelSelector().getABoxModel();
// TODO make sure the ABox update applies to all graphs
log.info("\tupdating the abox");
updateABox(changes);
log.info("performing SPARQL CONSTRUCT additions");
performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
log.info("performing SPARQL CONSTRUCT retractions");
performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
log.info("\tupdating the abox");
updateABox(changes);
}
@ -249,10 +242,8 @@ public class KnowledgeBaseUpdater {
private void updateABox(AtomicOntologyChangeLists changes)
throws IOException {
OntModel oldTBoxModel = settings.getOldTBoxModel();
OntModel newTBoxModel = settings.getNewTBoxModel();
RDFService rdfService = settings.getRDFService();
ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, rdfService, settings.getNewTBoxAnnotationsModel(), logger, record);
ABoxUpdater aboxUpdater = new ABoxUpdater(settings, logger, record);
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
}
@ -290,14 +281,18 @@ public class KnowledgeBaseUpdater {
rdfService.changeSetUpdate(removeChangeSet);
}
private void updateTBoxAnnotations() throws IOException {
TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
settings.getNewTBoxAnnotationsModel(),
settings.getAssertionOntModelSelector().getTBoxModel(), logger, record);
tboxUpdater.updateDefaultAnnotationValues();
//tboxUpdater.updateAnnotationModel();
private void updateTBoxAnnotations() {
TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);
try {
tboxUpdater.modifyPropertyQualifications();
} catch (Exception e) {
log.error("Unable to modify qualified property config file ", e);
}
try {
tboxUpdater.updateDefaultAnnotationValues();
} catch (Exception e) {
log.error("Unable to update default annotation values ", e);
}
}
/**

886
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -2,11 +2,22 @@
package edu.cornell.mannlib.vitro.webapp.ontology.update;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.List;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
@ -14,6 +25,7 @@ import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock;
@ -21,403 +33,539 @@ import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
/**
* Performs knowledge base updates to the tbox to align with a new ontology version
*
*/
* Performs knowledge base updates to the tbox to align with a new ontology version
*
*/
public class TBoxUpdater {
private OntModel oldTboxAnnotationsModel;
private OntModel newTboxAnnotationsModel;
private OntModel siteModel;
private ChangeLogger logger;
private ChangeRecord record;
private boolean detailLogs = false;
private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
private Resource classGroupClass = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource(classGroupURI);
private static final String inClassGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inClassGroup";
private Property inClassGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty(inClassGroupURI);
private static final Log log = LogFactory.getLog(TBoxUpdater.class);
/**
*
* Constructor
*
* @param oldTboxAnnotationsModel - previous version of the annotations in the ontology
* @param newTboxAnnotationsModel - new version of the annotations in the ontology
* @param siteModel - the knowledge base to be updated
* @param logger - for writing to the change log
* and the error log.
* @param record - for writing to the additions model
* and the retractions model.
*
*/
public TBoxUpdater(OntModel oldTboxAnnotationsModel,
OntModel newTboxAnnotationsModel,
OntModel siteModel,
ChangeLogger logger,
ChangeRecord record) {
this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
this.newTboxAnnotationsModel = newTboxAnnotationsModel;
this.siteModel = siteModel;
this.logger = logger;
this.record = record;
}
/**
*
* Update a knowledge base to align with changes to vitro annotation property default
* values in a new version of the ontology. The two versions of the ontology and the
* knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables.
*
* If the default value (i.e. the value that is provided in the vivo-core
* annotations files) of a vitro annotation property has been changed for a vivo
* core class, and that default value has not been changed in the site knowledge
* base, then update the value in the site knowledge base to be the new default.
* Also, if a new vitro annotation property setting (i.e. either an existing
* setting applied to an existing class where it wasn't applied before, or
* an existing setting applied to a new class) has been applied to a vivo
* core class then copy that new property statement into the site model.
* If a property setting for a class exists in the old ontology but
* not in the new one, then that statement will be removed from the
* site knowledge base.
*
* Writes to the change log file, the error log file, and the incremental change
* knowledge base.
*
* Note: as specified, this method for now assumes that no new vitro annotation
* properties have been introduced. This should be updated for future versions.
*/
public void updateDefaultAnnotationValues() throws IOException {
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
// Update defaults values for vitro annotation properties in the site model
// if the default has changed in the new version of the ontology AND if
// the site hasn't overidden the previous default in their knowledge base.
if(oldTboxAnnotationsModel == null) {
logger.log("oldTboxAnnotationModel is null; aborting update of annotation values");
return;
}
StmtIterator iter = oldTboxAnnotationsModel.listStatements();
while (iter.hasNext()) {
Statement stmt = iter.next();
Resource subject = stmt.getSubject();
Property predicate = stmt.getPredicate();
RDFNode oldObject = stmt.getObject();
if (! ( (RDFS.getURI().equals(predicate.getNameSpace())) ||
(VitroVocabulary.vitroURI.equals(predicate.getNameSpace()))
) ) {
// this annotation updater is only concerned with properties
// such as rdfs:comment and properties in the vitro application
// namespace
continue;
}
NodeIterator newObjects = newTboxAnnotationsModel.listObjectsOfProperty(subject, predicate);
if ((newObjects == null) || (!newObjects.hasNext()) ) {
// first check to see if the site has a local value change
// that should override the deletion
List<RDFNode> siteObjects = siteModel.listObjectsOfProperty(subject, predicate).toList();
if (siteObjects.size() > 1) {
/*
private UpdateSettings settings;
private OntModel oldTboxAnnotationsModel;
private OntModel newTboxAnnotationsModel;
private OntModel siteModel;
private ChangeLogger logger;
private ChangeRecord record;
private boolean detailLogs = false;
private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
private Resource classGroupClass = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource(classGroupURI);
private static final String inClassGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inClassGroup";
private Property inClassGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty(inClassGroupURI);
/**
*
* Constructor
*
* @param oldTboxAnnotationsModel - previous version of the annotations in the ontology
* @param newTboxAnnotationsModel - new version of the annotations in the ontology
* @param siteModel - the knowledge base to be updated
* @param logger - for writing to the change log
* and the error log.
* @param record - for writing to the additions model
* and the retractions model.
*
*/
public TBoxUpdater(UpdateSettings settings,
ChangeLogger logger,
ChangeRecord record) {
this.settings = settings;
this.oldTboxAnnotationsModel = settings.getOldTBoxAnnotationsModel();
this.newTboxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
this.siteModel = settings.getAssertionOntModelSelector().getTBoxModel();
this.logger = logger;
this.record = record;
}
/**
* Update application ontology data for domain and range-qualified properties
* to use any applicable settings from obsolete subproperties
*/
public void modifyPropertyQualifications() throws IOException {
}
private Model mergeConfigurations(Model oldConfig, Model newConfig) {
return null;
}
public void updateDefaultAnnotationValues() throws IOException {
updateDefaultAnnotationValues(null);
}
/**
*
* Update a knowledge base to align with changes to vitro annotation property default
* values in a new version of the ontology. The two versions of the ontology and the
* knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables.
*
* If the default value (i.e. the value that is provided in the vivo-core
* annotations files) of a vitro annotation property has been changed for a vivo
* core class, and that default value has not been changed in the site knowledge
* base, then update the value in the site knowledge base to be the new default.
* Also, if a new vitro annotation property setting (i.e. either an existing
* setting applied to an existing class where it wasn't applied before, or
* an existing setting applied to a new class) has been applied to a vivo
* core class then copy that new property statement into the site model.
* If a property setting for a class exists in the old ontology but
* not in the new one, then that statement will be removed from the
* site knowledge base.
*
* Writes to the change log file, the error log file, and the incremental change
* knowledge base.
*
* Note: as specified, this method for now assumes that no new vitro annotation
* properties have been introduced. This should be updated for future versions.
*/
public void updateDefaultAnnotationValues(String subjectURI) throws IOException {
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model additions = ModelFactory.createDefaultModel();
Model retractions = ModelFactory.createDefaultModel();
// Update defaults values for vitro annotation properties in the site model
// if the default has changed in the new version of the ontology AND if
// the site hasn't overidden the previous default in their knowledge base.
if(oldTboxAnnotationsModel == null) {
logger.log("oldTboxAnnotationModel is null; aborting update of annotation values");
return;
}
Resource subj = (subjectURI == null) ? null : ResourceFactory.createResource(subjectURI);
StmtIterator iter = oldTboxAnnotationsModel.listStatements(subj, null, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
Resource subject = stmt.getSubject();
Property predicate = stmt.getPredicate();
RDFNode oldObject = stmt.getObject();
if (! ( (RDFS.getURI().equals(predicate.getNameSpace())) ||
(VitroVocabulary.vitroURI.equals(predicate.getNameSpace()))
) ) {
// this annotation updater is only concerned with properties
// such as rdfs:comment and properties in the vitro application
// namespace
continue;
}
NodeIterator newObjects = newTboxAnnotationsModel.listObjectsOfProperty(subject, predicate);
if ((newObjects == null) || (!newObjects.hasNext()) ) {
// first check to see if the site has a local value change
// that should override the deletion
List<RDFNode> siteObjects = siteModel.listObjectsOfProperty(subject, predicate).toList();
if (siteObjects.size() > 1) {
/*
logger.log("WARNING: found " + siteObjects.size() +
" statements with subject = " + subject.getURI() +
" and property = " + predicate.getURI() +
" in the site database (maximum of one is expected)");
*/
}
if (siteObjects.size() > 0) {
RDFNode siteNode = siteObjects.get(0);
if (siteNode.equals(oldObject)) {
retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null));
}
}
continue;
}
RDFNode newObject = newObjects.next();
int i = 1;
while (newObjects.hasNext()) {
i++;
newObjects.next();
}
if (i > 1) {
/*
*/
}
if (siteObjects.size() > 0) {
RDFNode siteNode = siteObjects.get(0);
if (siteNode.equals(oldObject)) {
retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null));
}
}
continue;
}
RDFNode newObject = newObjects.next();
int i = 1;
while (newObjects.hasNext()) {
i++;
newObjects.next();
}
if (i > 1) {
/*
logger.log("WARNING: found " + i +
" statements with subject = " + subject.getURI() +
" and property = " + predicate.getURI() +
" in the new version of the annotations ontology (maximum of one is expected)");
*/
continue;
}
// If a subject-property pair occurs in the old annotation TBox and the new annotations
// TBox, but not in the site model, then it is considered an erroneous deletion and
// the value from the new TBox is added into the site model.
// sjm: 7-16-2010. We want this here now to add back in annotations mistakenly dropped
// in the .9 to 1.0 migration, but I'm not sure we would want this here permanently.
// Shouldn't a site be allowed to delete annotations if they want to?
NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
if (siteObjects == null || !siteObjects.hasNext()) {
try {
additions.add(subject, predicate, newObject);
if (detailLogs) {
logger.log( "adding Statement: subject = " + subject.getURI() +
" property = " + predicate.getURI() +
" object = " + (newObject.isLiteral() ? ((Literal)newObject).getLexicalForm()
: ((Resource)newObject).getURI()));
}
} catch (Exception e) {
logger.logError("Error trying to add statement with property " + predicate.getURI() +
" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
}
continue;
}
if (!newObject.equals(oldObject)) {
*/
continue;
}
RDFNode siteObject = siteObjects.next();
// If a subject-property pair occurs in the old annotation TBox and the new annotations
// TBox, but not in the site model, then it is considered an erroneous deletion and
// the value from the new TBox is added into the site model.
// sjm: 7-16-2010. We want this here now to add back in annotations mistakenly dropped
// in the .9 to 1.0 migration, but I'm not sure we would want this here permanently.
// Shouldn't a site be allowed to delete annotations if they want to?
i = 1;
while (siteObjects.hasNext()) {
i++;
siteObjects.next();
}
NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
if (i > 1) {
/*
if (siteObjects == null || !siteObjects.hasNext()) {
try {
additions.add(subject, predicate, newObject);
if (detailLogs) {
logger.log( "adding Statement: subject = " + subject.getURI() +
" property = " + predicate.getURI() +
" object = " + (newObject.isLiteral() ? ((Literal)newObject).getLexicalForm()
: ((Resource)newObject).getURI()));
}
} catch (Exception e) {
logger.logError("Error trying to add statement with property " + predicate.getURI() +
" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
}
continue;
}
if (!newObject.equals(oldObject)) {
RDFNode siteObject = siteObjects.next();
i = 1;
while (siteObjects.hasNext()) {
i++;
siteObjects.next();
}
if (i > 1) {
/*
logger.log("WARNING: found " + i +
" statements with subject = " + subject.getURI() +
" and property = " + predicate.getURI() +
" in the site annotations model (maximum of one is expected) ");
*/
continue;
}
if (siteObject.equals(oldObject)) {
try {
StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
while (it.hasNext()) {
retractions.add(it.next());
}
} catch (Exception e) {
logger.logError("Error removing statement for subject = " + subject.getURI() +
"and property = " + predicate.getURI() +
"from the knowledge base:\n" + e.getMessage());
}
*/
continue;
}
try {
additions.add(subject, predicate, newObject);
if (detailLogs) {
logger.log("Changed the value of property " + predicate.getURI() +
" of subject = " + subject.getURI() +
" from " +
(oldObject.isResource() ? ((Resource)oldObject).getURI() : ((Literal)oldObject).getLexicalForm()) +
" to " +
(newObject.isResource() ? ((Resource)newObject).getURI() : ((Literal)newObject).getLexicalForm()) +
" in the knowledge base:\n");
}
} catch (Exception e) {
logger.logError("Error trying to change the value of property " + predicate.getURI() +
" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
}
}
}
}
Model actualAdditions = additions.difference(retractions);
siteModel.add(actualAdditions);
record.recordAdditions(actualAdditions);
Model actualRetractions = retractions.difference(additions);
siteModel.remove(actualRetractions);
record.recordRetractions(actualRetractions);
long numAdded = actualAdditions.size();
long numRemoved = actualRetractions.size();
// log summary of changes
if (numAdded > 0) {
logger.log("Updated the default vitro annotation value for " +
numAdded + " statements in the knowledge base");
}
if (numRemoved > 0) {
logger.log("Removed " + numRemoved +
" outdated vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base");
}
// Copy annotation property settings that were introduced in the new ontology
// into the site model.
//
if (siteObject.equals(oldObject)) {
try {
StmtIterator it = siteModel.listStatements(subject, predicate, (RDFNode)null);
while (it.hasNext()) {
retractions.add(it.next());
}
} catch (Exception e) {
logger.logError("Error removing statement for subject = " + subject.getURI() +
"and property = " + predicate.getURI() +
"from the knowledge base:\n" + e.getMessage());
}
Model newAnnotationSettings = newTboxAnnotationsModel.difference(oldTboxAnnotationsModel);
Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
StmtIterator newStmtIt = newAnnotationSettings.listStatements();
while (newStmtIt.hasNext()) {
Statement stmt = newStmtIt.next();
if (!siteModel.contains(stmt)) {
newAnnotationSettingsToAdd.add(stmt);
if (detailLogs) {
logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
" property = " + stmt.getPredicate().getURI() +
" object = " + (stmt.getObject().isLiteral() ? ((Literal)stmt.getObject()).getLexicalForm()
: ((Resource)stmt.getObject()).getURI()));
}
}
}
siteModel.add(newAnnotationSettingsToAdd);
record.recordAdditions(newAnnotationSettingsToAdd);
// log the additions - summary
if (newAnnotationSettingsToAdd.size() > 0) {
boolean plural = (newAnnotationSettingsToAdd.size() > 1);
logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes only " +
"existing annotation properties applied to existing classes where they weren't applied before, or existing " +
"properties applied to new classes.");
}
} finally {
siteModel.leaveCriticalSection();
}
}
/**
*
* Update a knowledge base to align with changes to the vitro annotation model
* in a new version of the ontology. The two versions of the ontology and the
* knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables.
*
* Currently, this method only handles deletions of a ClassGroup
*
* Writes to the change log file, the error log file, and the incremental change
* knowledge base.
*
*/
public void updateAnnotationModel() throws IOException {
// for each ClassGroup in the old vitro annotations model: if it is not in
// the new vitro annotations model and the site has no classes asserted to
// be in that class group then delete it.
removeObsoleteAnnotations();
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
long pre = retractions.size();
retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
long post = retractions.size();
if ((post - pre) > 0) {
logger.log("Removed the " + stmt.getSubject().getURI() + " ClassGroup from the annotations model");
}
}
}
if (retractions.size() > 0) {
siteModel.remove(retractions);
record.recordRetractions(retractions);
}
} finally {
siteModel.leaveCriticalSection();
}
try {
additions.add(subject, predicate, newObject);
// If we were going to handle add, this is the logic:
// for each ClassGroup in new old vitro annotations model: if it is not in
// the old vitro annotations and it is not in the site model, then
// add it.
}
if (detailLogs) {
logger.log("Changed the value of property " + predicate.getURI() +
" of subject = " + subject.getURI() +
" from " +
(oldObject.isResource() ? ((Resource)oldObject).getURI() : ((Literal)oldObject).getLexicalForm()) +
" to " +
(newObject.isResource() ? ((Resource)newObject).getURI() : ((Literal)newObject).getLexicalForm()) +
" in the knowledge base:\n");
}
} catch (Exception e) {
logger.logError("Error trying to change the value of property " + predicate.getURI() +
" of class = " + subject.getURI() + " in the knowledge base:\n" + e.getMessage());
}
}
}
}
public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
model.enterCriticalSection(Lock.READ);
try {
return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
} finally {
model.leaveCriticalSection();
}
}
Model actualAdditions = additions.difference(retractions);
siteModel.add(actualAdditions);
record.recordAdditions(actualAdditions);
Model actualRetractions = retractions.difference(additions);
siteModel.remove(actualRetractions);
record.recordRetractions(actualRetractions);
public void removeObsoleteAnnotations() throws IOException {
Resource subj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology/florida#StatewideGoalAndFocusArea");
Resource obj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroClassGrouptopics");
Property subj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#divisionOfSponsoredResearchNumber");
Resource obj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupidentifiers");
Property subj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#statewideGoalAndFocusArea");
Resource obj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupoutreach");
Property inPropertyGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inPropertyGroup");
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
if (siteModel.contains(subj1, inClassGroupProp, obj1) ) {
retractions.add(subj1, inClassGroupProp, obj1);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj1, inClassGroupProp, obj1) + " from the knowledge base (assumed to be obsolete)");
long numAdded = actualAdditions.size();
long numRemoved = actualRetractions.size();
// log summary of changes
if (numAdded > 0) {
logger.log("Updated the default vitro annotation value for " +
numAdded + " statements in the knowledge base");
}
if (numRemoved > 0) {
logger.log("Removed " + numRemoved +
" outdated vitro annotation property setting" + ((numRemoved > 1) ? "s" : "") + " from the knowledge base");
}
// Copy annotation property settings that were introduced in the new ontology
// into the site model.
//
Model newAnnotationSettings = newTboxAnnotationsModel.difference(oldTboxAnnotationsModel);
Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
StmtIterator newStmtIt = newAnnotationSettings.listStatements();
while (newStmtIt.hasNext()) {
Statement stmt = newStmtIt.next();
if (!siteModel.contains(stmt)) {
newAnnotationSettingsToAdd.add(stmt);
if (detailLogs) {
logger.log( "adding Statement: subject = " + stmt.getSubject().getURI() +
" property = " + stmt.getPredicate().getURI() +
" object = " + (stmt.getObject().isLiteral() ? ((Literal)stmt.getObject()).getLexicalForm()
: ((Resource)stmt.getObject()).getURI()));
}
}
}
siteModel.add(newAnnotationSettingsToAdd);
record.recordAdditions(newAnnotationSettingsToAdd);
// log the additions - summary
if (newAnnotationSettingsToAdd.size() > 0) {
boolean plural = (newAnnotationSettingsToAdd.size() > 1);
logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property setting" + (plural ? "s" : "") + " to the knowledge base. This includes only " +
"existing annotation properties applied to existing classes where they weren't applied before, or existing " +
"properties applied to new classes.");
}
} finally {
siteModel.leaveCriticalSection();
}
}
/**
*
* Update a knowledge base to align with changes to the vitro annotation model
* in a new version of the ontology. The two versions of the ontology and the
* knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables.
*
* Currently, this method only handles deletions of a ClassGroup
*
* Writes to the change log file, the error log file, and the incremental change
* knowledge base.
*
*/
public void updateAnnotationModel() throws IOException {
// for each ClassGroup in the old vitro annotations model: if it is not in
// the new vitro annotations model and the site has no classes asserted to
// be in that class group then delete it.
removeObsoleteAnnotations();
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
long pre = retractions.size();
retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
long post = retractions.size();
if ((post - pre) > 0) {
logger.log("Removed the " + stmt.getSubject().getURI() + " ClassGroup from the annotations model");
}
}
}
if (retractions.size() > 0) {
siteModel.remove(retractions);
record.recordRetractions(retractions);
}
} finally {
siteModel.leaveCriticalSection();
}
if (siteModel.contains(subj2, inPropertyGroupProp, obj2) ) {
retractions.add(subj2, inPropertyGroupProp, obj2);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj2, inPropertyGroupProp, obj2) + " from the knowledge base (assumed to be obsolete)");
}
// If we were going to handle add, this is the logic:
// for each ClassGroup in new old vitro annotations model: if it is not in
// the old vitro annotations and it is not in the site model, then
// add it.
if (siteModel.contains(subj3, inPropertyGroupProp, obj3) ) {
retractions.add(subj3, inPropertyGroupProp, obj3);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj3, inPropertyGroupProp, obj3) + " from the knowledge base (assumed to be obsolete)");
}
public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
model.enterCriticalSection(Lock.READ);
try {
return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
} finally {
model.leaveCriticalSection();
}
if (retractions.size() > 0) {
siteModel.remove(retractions);
record.recordRetractions(retractions);
}
} finally {
siteModel.leaveCriticalSection();
}
}
}
public void removeObsoleteAnnotations() throws IOException {
Resource subj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology/florida#StatewideGoalAndFocusArea");
Resource obj1 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroClassGrouptopics");
Property subj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#divisionOfSponsoredResearchNumber");
Resource obj2 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupidentifiers");
Property subj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vivoweb.org/ontology/florida#statewideGoalAndFocusArea");
Resource obj3 = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource("http://vivoweb.org/ontology#vitroPropertyGroupoutreach");
Property inPropertyGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty("http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inPropertyGroup");
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
if (siteModel.contains(subj1, inClassGroupProp, obj1) ) {
retractions.add(subj1, inClassGroupProp, obj1);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj1, inClassGroupProp, obj1) + " from the knowledge base (assumed to be obsolete)");
}
if (siteModel.contains(subj2, inPropertyGroupProp, obj2) ) {
retractions.add(subj2, inPropertyGroupProp, obj2);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj2, inPropertyGroupProp, obj2) + " from the knowledge base (assumed to be obsolete)");
}
if (siteModel.contains(subj3, inPropertyGroupProp, obj3) ) {
retractions.add(subj3, inPropertyGroupProp, obj3);
logger.log("Removed statement " + ABoxUpdater.stmtString(subj3, inPropertyGroupProp, obj3) + " from the knowledge base (assumed to be obsolete)");
}
if (retractions.size() > 0) {
siteModel.remove(retractions);
record.recordRetractions(retractions);
}
} finally {
siteModel.leaveCriticalSection();
}
}
public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
mergePropertyAnnotationsToPropertyConfig(changeObj);
}
}
private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj) throws IOException {
String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
String oldPropertyURI = changeObj.getSourceURI();
Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
Dataset dataset = new RDFServiceDataset(settings.getRDFService());
Model userAnnotationsModel = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
String propertyAnnotationsQuery =
"PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
"CONSTRUCT { \n" +
" <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
" <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
" <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
" <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
" <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
" <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
"} WHERE { \n" +
" { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
" UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
" UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
" UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
" UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
" UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
"} \n" ;
Model userChangesModel = construct(
propertyAnnotationsQuery, userAnnotationsModel).difference(
construct(propertyAnnotationsQuery, oldAnnotationsModel));
String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
"CONSTRUCT { \n" +
" ?configuration config:propertyGroup ?group . \n" +
" ?configuration config:displayName ?label . \n" +
" ?configuration vitro:displayRankAnnot ?displayRank . \n" +
" ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
"} WHERE { \n" +
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
"} \n" ;
String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
"PREFIX vitro: <" + VitroVocabulary.vitroURI + "> \n" +
"CONSTRUCT { \n" +
" <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
" ?configuration config:displayName ?rlabel . \n" +
" ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
" ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +
"} WHERE { \n" +
" <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
" ?configuration config:propertyGroup ?rgroup } \n" +
" OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
" ?configuration config:displayName ?rlabel } \n " +
" OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
" ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
" OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
" ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
" ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
" OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
" ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
"} \n" ;
Model configModel = ModelFactory.createDefaultModel();
String configFileName = settings.getQualifiedPropertyConfigFile();
File file = new File(configFileName);
FileInputStream fis = new FileInputStream(file);
configModel.read(fis, null, "N3");
Model union = ModelFactory.createUnion(configModel,
userChangesModel);
Model additions = construct(addQuery, union);
Model retractions = construct(retractQuery, union);
if (additions.size() > 0 || retractions.size() > 0) {
configModel.remove(retractions);
log.info("Removing " + retractions.size() + " statements from " + contextURI);
configModel.add(additions);
log.info("Adding " + additions.size() + " statements from " + contextURI);
FileOutputStream fos = new FileOutputStream(file);
configModel.write(fos, "N3");
}
}
private Model construct(String queryStr, Model model) {
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.create(query, model);
try {
return qe.execConstruct();
} finally {
qe.close();
}
}
}

9
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java
View file

@ -21,6 +21,7 @@ public class UpdateSettings {
private String errorLogFile;
private String addedDataFile;
private String removedDataFile;
private String qualifiedPropertyConfigFile;
private String defaultNamespace;
private OntModelSelector assertionOntModelSelector;
private OntModelSelector inferenceOntModelSelector;
@ -121,7 +122,13 @@ public class UpdateSettings {
public void setRemovedDataFile(String removedDataFile) {
this.removedDataFile = removedDataFile;
}
public String getDefaultNamespace() {
public String getQualifiedPropertyConfigFile() {
return qualifiedPropertyConfigFile;
}
public void setQualifiedPropertyConfigFile(String qualifiedPropertyConfigFile) {
this.qualifiedPropertyConfigFile = qualifiedPropertyConfigFile;
}
public String getDefaultNamespace() {
return defaultNamespace;
}
public void setDefaultNamespace(String defaultNamespace) {

16
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -96,7 +96,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setNewTBoxModel(newTBoxModel);
OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString());
OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "firsttime").toString());
settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
@ -145,6 +145,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
log.warn("unable to successfully update display model: " + e.getMessage());
}
}
// reload the display model since the TBoxUpdater may have
// modified it
new ApplicationModelSetup().contextInitialized(sce);
}
} catch (Exception ioe) {
ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
@ -189,8 +192,19 @@ public class UpdateKnowledgeBase implements ServletContextListener {
Path logDir = createDirectory(dataDir, "logs");
settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());
settings.setErrorLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate.error", "log")).toString());
Path qualifiedPropertyConfigFile = getFilePath(homeDir, "rdf", "display", "everytime", "PropertyConfig.n3");
settings.setQualifiedPropertyConfigFile(qualifiedPropertyConfigFile.toString());
}
private Path getFilePath(Path parent, String... children) throws IOException {
Path path = parent;
for (String child : children) {
path = path.resolve(child);
}
return path;
}
private Path createDirectory(Path parent, String... children) throws IOException {
Path dir = parent;
for (String child : children) {