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miscellaneous small updates made while testing the 1.0 to 1.1 upgrade process.

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This commit is contained in:
sjm222 2010-07-12 01:41:44 +00:00
parent 4241506730
commit 42b0b79377
4 changed files with 95 additions and 96 deletions
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8
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
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@ -110,7 +110,7 @@ public class ABoxUpdater {
/** /**
* *
* Update a knowledge based on a class rename in the ontology. All references to the * Update the knowledge base for a class rename in the ontology. All references to the
* old class URI in either the subject or the object position of a statement are * old class URI in either the subject or the object position of a statement are
* changed to use the new class URI. * changed to use the new class URI.
* *
@ -212,7 +212,7 @@ public class ABoxUpdater {
/** /**
* *
* Examine a knowledge based on a class addition to the ontology and * Examine the knowledge base for a class addition to the ontology and
* add messages to the change log indicating where manual review is * add messages to the change log indicating where manual review is
* recommended. If the added class has a direct parent in the new ontology * recommended. If the added class has a direct parent in the new ontology
* that is not OWL.Thing, and if the knowledge base contains individuals * that is not OWL.Thing, and if the knowledge base contains individuals
@ -275,6 +275,7 @@ public class ABoxUpdater {
} }
} }
/** /**
* *
* Update a knowledge base to account for a class deletion in the ontology. * Update a knowledge base to account for a class deletion in the ontology.
@ -328,6 +329,7 @@ public class ABoxUpdater {
renameClass(chg); renameClass(chg);
} }
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();
while(propItr.hasNext()){ while(propItr.hasNext()){
@ -452,7 +454,7 @@ public class ABoxUpdater {
record.recordRetractions(renamePropRetractModel); record.recordRetractions(renamePropRetractModel);
if (renamePropRetractModel.size() > 0) { if (renamePropRetractModel.size() > 0) {
logger.log(renamePropRetractModel.size() + " statment" + logger.log(renamePropRetractModel.size() + " statement" +
((renamePropRetractModel.size() > 1) ? "s" : "") + ((renamePropRetractModel.size() > 1) ? "s" : "") +
" with predicate " + propObj.getSourceURI() + " " + " with predicate " + propObj.getSourceURI() + " " +
((renamePropRetractModel.size() > 1) ? "were" : "was") ((renamePropRetractModel.size() > 1) ? "were" : "was")

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

@ -2,7 +2,6 @@
package edu.cornell.mannlib.vitro.webapp.ontology.update; package edu.cornell.mannlib.vitro.webapp.ontology.update;
import com.hp.hpl.jena.ontology.OntModel;
/** /**
* *
* We need to document what is in source and destinationURI for each * We need to document what is in source and destinationURI for each

67
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -12,14 +12,8 @@ import java.io.InputStream;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.query.Query; import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution; import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
@ -27,9 +21,6 @@ import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.Syntax; import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
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.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
@ -45,9 +36,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
*/ */
public class OntologyUpdater { public class OntologyUpdater {
//private final Log log = LogFactory.getLog(OntologyUpdater.class);
private final Log log = LogFactory.getLog(OntologyUpdater.class);
private OntologyUpdateSettings settings; private OntologyUpdateSettings settings;
private OntologyChangeLogger logger; private OntologyChangeLogger logger;
@ -55,10 +44,8 @@ public class OntologyUpdater {
public OntologyUpdater(OntologyUpdateSettings settings) { public OntologyUpdater(OntologyUpdateSettings settings) {
this.settings = settings; this.settings = settings;
this.logger = new SimpleOntologyChangeLogger(settings.getLogFile(), this.logger = new SimpleOntologyChangeLogger(settings.getLogFile(), settings.getErrorLogFile());
settings.getErrorLogFile()); this.record = new SimpleOntologyChangeRecord(settings.getAddedDataFile(), settings.getRemovedDataFile());
this.record = new SimpleOntologyChangeRecord(
settings.getAddedDataFile(), settings.getRemovedDataFile());
} }
public boolean update() throws IOException { public boolean update() throws IOException {
@ -67,7 +54,13 @@ public class OntologyUpdater {
boolean updateRequired = updateRequired(); boolean updateRequired = updateRequired();
if (updateRequired) { if (updateRequired) {
try {
performUpdate(); performUpdate();
} catch (Exception e) {
logger.logError(e.getMessage());
e.printStackTrace();
}
if (!logger.errorsWritten()) { if (!logger.errorsWritten()) {
// add assertions to the knowledge base showing that the // add assertions to the knowledge base showing that the
@ -78,6 +71,7 @@ public class OntologyUpdater {
record.writeChanges(); record.writeChanges();
logger.closeLogs(); logger.closeLogs();
} }
return updateRequired; return updateRequired;
@ -86,16 +80,13 @@ public class OntologyUpdater {
private void performUpdate() throws IOException { private void performUpdate() throws IOException {
performSparqlConstructs(settings.getSparqlConstructsDir(), performSparqlConstructs(settings.getSparqlConstructsDir(), settings.getOntModelSelector().getABoxModel());
settings.getOntModelSelector().getABoxModel());
List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges(); List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
AtomicOntologyChangeLists changes = AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,
new AtomicOntologyChangeLists(rawChanges,
settings.getNewTBoxModel(), settings.getNewTBoxModel(),
settings.getOldTBoxModel()); settings.getOldTBoxModel());
//process the TBox before the ABox //process the TBox before the ABox
updateTBoxAnnotations(); updateTBoxAnnotations();
@ -195,7 +186,8 @@ public class OntologyUpdater {
private void updateABox(AtomicOntologyChangeLists changes) private void updateABox(AtomicOntologyChangeLists changes)
throws IOException { throws IOException {
// TODO get models from somewhere
OntModel oldTBoxModel = settings.getOldTBoxModel(); OntModel oldTBoxModel = settings.getOldTBoxModel();
OntModel newTBoxModel = settings.getNewTBoxModel(); OntModel newTBoxModel = settings.getNewTBoxModel();
OntModel ABoxModel = settings.getOntModelSelector().getABoxModel(); OntModel ABoxModel = settings.getOntModelSelector().getABoxModel();
@ -204,7 +196,7 @@ public class OntologyUpdater {
settings.getNewTBoxAnnotationsModel(), logger, record); settings.getNewTBoxAnnotationsModel(), logger, record);
aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges()); aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
aboxUpdater.processClassChanges(changes.getAtomicClassChanges()); aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
// run additional SPARQL CONSTRUCTS
} }
private void updateTBoxAnnotations() throws IOException { private void updateTBoxAnnotations() throws IOException {
@ -255,6 +247,7 @@ public class OntologyUpdater {
private void assertSuccess() throws FileNotFoundException, IOException { private void assertSuccess() throws FileNotFoundException, IOException {
try { try {
Model m = settings.getOntModelSelector().getApplicationMetadataModel(); Model m = settings.getOntModelSelector().getApplicationMetadataModel();
File successAssertionsFile = File successAssertionsFile =
new File(settings.getSuccessAssertionsFile()); new File(settings.getSuccessAssertionsFile());
@ -292,35 +285,33 @@ public class OntologyUpdater {
OntModel oldTboxModel) throws IOException { OntModel oldTboxModel) throws IOException {
Iterator<AtomicOntologyChange> listItr = changeList.iterator(); Iterator<AtomicOntologyChange> listItr = changeList.iterator();
while(listItr.hasNext()){
while(listItr.hasNext()) {
AtomicOntologyChange changeObj = listItr.next(); AtomicOntologyChange changeObj = listItr.next();
if(changeObj.getSourceURI() != null){ if (changeObj.getSourceURI() != null){
if(oldTboxModel.getOntProperty(changeObj.
getSourceURI()) != null){ if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
atomicPropertyChanges.add(changeObj); atomicPropertyChanges.add(changeObj);
} }
else if(oldTboxModel.getOntClass(changeObj. else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
getSourceURI()) != null) {
atomicClassChanges.add(changeObj); atomicClassChanges.add(changeObj);
} }
else{ else{
logger.logError("Source URI is neither a Property" + logger.logError("Source URI is neither a Property" +
" nor a Class. " + "Change Object skipped"); " nor a Class. " + "Change Object skipped for sourceURI: " + changeObj.getSourceURI());
} }
} }
else if(changeObj.getDestinationURI() != null){ else if(changeObj.getDestinationURI() != null){
if(newTboxModel.getOntProperty(changeObj.
getDestinationURI()) != null){ if (newTboxModel.getOntProperty(changeObj.getDestinationURI()) != null) {
atomicPropertyChanges.add(changeObj); atomicPropertyChanges.add(changeObj);
} } else if(newTboxModel.getOntClass(changeObj.
else if(newTboxModel.getOntClass(changeObj. getDestinationURI()) != null) {
getDestinationURI()) != null){
atomicClassChanges.add(changeObj); atomicClassChanges.add(changeObj);
} } else{
else{
logger.logError("Destination URI is neither a Property" + logger.logError("Destination URI is neither a Property" +
" nor a Class. " + "Change Object skipped"); " nor a Class. " + "Change Object skipped for destinationURI: " + changeObj.getDestinationURI());
} }
} }
else{ else{

87
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -22,8 +22,8 @@ import com.hp.hpl.jena.shared.Lock;
*/ */
public class TBoxUpdater { public class TBoxUpdater {
private OntModel oldTboxModel; private OntModel oldTboxAnnotationsModel;
private OntModel newTboxModel; private OntModel newTboxAnnotationsModel;
private OntModel siteModel; private OntModel siteModel;
private OntologyChangeLogger logger; private OntologyChangeLogger logger;
private OntologyChangeRecord record; private OntologyChangeRecord record;
@ -32,8 +32,8 @@ public class TBoxUpdater {
* *
* Constructor * Constructor
* *
* @param oldTboxModel - previous version of the ontology * @param oldTboxAnnotationsModel - previous version of the annotations in the ontology
* @param newTboxModel - new version of the ontology * @param newTboxAnnotationsModel - new version of the annotations in the ontology
* @param siteModel - the knowledge base to be updated * @param siteModel - the knowledge base to be updated
* @param logger - for writing to the change log * @param logger - for writing to the change log
* and the error log. * and the error log.
@ -41,14 +41,14 @@ public class TBoxUpdater {
* and the retractions model. * and the retractions model.
* *
*/ */
public TBoxUpdater(OntModel oldTboxModel, public TBoxUpdater(OntModel oldTboxAnnotationsModel,
OntModel newTboxModel, OntModel newTboxAnnotationsModel,
OntModel siteModel, OntModel siteModel,
OntologyChangeLogger logger, OntologyChangeLogger logger,
OntologyChangeRecord record) { OntologyChangeRecord record) {
this.oldTboxModel = oldTboxModel; this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
this.newTboxModel = newTboxModel; this.newTboxAnnotationsModel = newTboxAnnotationsModel;
this.siteModel = siteModel; this.siteModel = siteModel;
this.logger = logger; this.logger = logger;
this.record = record; this.record = record;
@ -56,12 +56,12 @@ public class TBoxUpdater {
/** /**
* *
* Update a knowledge base to align with changes vitro annotation property default * 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 * 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 * knowledge base to be updated are provided in the class constructor and are
* referenced via class level variables. * referenced via class level variables.
* *
* If the default value (i.e. the value that is provided in the vivo-core- * 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 * 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 * 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. * base, then update the value in the site knowledge base to be the new default.
@ -76,7 +76,7 @@ public class TBoxUpdater {
* Writes to the change log file, the error log file, and the incremental change * Writes to the change log file, the error log file, and the incremental change
* knowledge base. * knowledge base.
* *
* Note: as specified, this method for now assume that no new vitro annotation * Note: as specified, this method for now assumes that no new vitro annotation
* properties have been introduced. This should be updated for future versions. * properties have been introduced. This should be updated for future versions.
*/ */
public void updateVitroPropertyDefaultValues() throws IOException { public void updateVitroPropertyDefaultValues() throws IOException {
@ -92,7 +92,7 @@ public class TBoxUpdater {
// if the default has changed in the new version of the ontology AND if // 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. // the site hasn't overidden the previous default in their knowledge base.
StmtIterator iter = oldTboxModel.listStatements(); StmtIterator iter = oldTboxAnnotationsModel.listStatements();
int stmtCount = 0; int stmtCount = 0;
@ -104,39 +104,49 @@ public class TBoxUpdater {
Property predicate = stmt.getPredicate(); Property predicate = stmt.getPredicate();
RDFNode oldObject = stmt.getObject(); RDFNode oldObject = stmt.getObject();
NodeIterator objects = newTboxModel.listObjectsOfProperty(subject, predicate); NodeIterator newObjects = newTboxAnnotationsModel.listObjectsOfProperty(subject, predicate);
if ((objects == null) || (!objects.hasNext()) ) { if ((newObjects == null) || (!newObjects.hasNext()) ) {
retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null)); retractions.add(siteModel.listStatements(subject, predicate, (RDFNode) null));
//logger.log("Error: found a statement for subject = " + subject.getURI() +
// " and property = " + predicate.getURI() +
// " in the old version but not the new version of the ontology.");
continue; continue;
} }
RDFNode newObject = objects.next(); RDFNode newObject = newObjects.next();
if (objects.hasNext()) {
logger.logError("Error: found " + objects.toList().size() + int i = 1;
while (newObjects.hasNext()) {
i++;
newObjects.next();
}
if (i > 1) {
logger.log("WARNING: found " + i +
" statements with subject = " + subject.getURI() + " statements with subject = " + subject.getURI() +
" and property = " + predicate.getURI() + " and property = " + predicate.getURI() +
" in the new version of the ontology. (maximum of one is expected)"); " in the new version of the annotations ontology. (maximum of one is expected)");
continue; continue;
} }
if (!newObject.equals(oldObject)) { if (!newObject.equals(oldObject)) {
objects = siteModel.listObjectsOfProperty(subject,predicate); NodeIterator siteObjects = siteModel.listObjectsOfProperty(subject,predicate);
if (!objects.hasNext()) { if (siteObjects == null || !siteObjects.hasNext()) {
continue; continue;
} }
RDFNode siteObject = objects.next(); RDFNode siteObject = siteObjects.next();
if (objects.hasNext()) {
logger.logError("Warning: found " + objects.toList().size() + i = 1;
while (siteObjects.hasNext()) {
i++;
siteObjects.next();
}
if (i > 1) {
logger.log("WARNING: found " + i +
" statements with subject = " + subject.getURI() + " statements with subject = " + subject.getURI() +
" and property = " + predicate.getURI() + " and property = " + predicate.getURI() +
" in the site model (maximum of one is expected). +" + " in the site annotations model. (maximum of one is expected). ");
" did not perform any update on this property");
continue; continue;
} }
@ -180,7 +190,7 @@ public class TBoxUpdater {
// log summary of changes // log summary of changes
if (actualAdditions.size() > 0) { if (actualAdditions.size() > 0) {
logger.log("Updated the default vitro annotation value for " + logger.log("Updated the default vitro annotation value for " +
actualAdditions.size() + " statments in the knowledge base."); actualAdditions.size() + " statements in the knowledge base.");
} }
long numRemoved = actualRetractions.size() - actualAdditions.size(); long numRemoved = actualRetractions.size() - actualAdditions.size();
@ -193,15 +203,22 @@ public class TBoxUpdater {
// into the site model. // into the site model.
// //
Model newAnnotationSettings = newTboxModel.difference(oldTboxModel); Model newAnnotationSettings = newTboxAnnotationsModel.difference(oldTboxAnnotationsModel);
Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel(); Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
StmtIterator newStmtIt = newAnnotationSettings.listStatements(); StmtIterator newStmtIt = newAnnotationSettings.listStatements();
while (newStmtIt.hasNext()) { while (newStmtIt.hasNext()) {
Statement stmt = newStmtIt.next(); Statement stmt = newStmtIt.next();
if (!siteModel.contains(stmt)) { if (!siteModel.contains(stmt)) {
newAnnotationSettingsToAdd.add(stmt); newAnnotationSettingsToAdd.add(stmt);
// TODO remove this for production
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); siteModel.add(newAnnotationSettingsToAdd);
record.recordAdditions(newAnnotationSettingsToAdd); record.recordAdditions(newAnnotationSettingsToAdd);
@ -213,16 +230,6 @@ public class TBoxUpdater {
"existing annotation properties applied to existing classes where they weren't applied before, or existing " + "existing annotation properties applied to existing classes where they weren't applied before, or existing " +
"properties applied to new classes. No new annotation properties have been introduced."); "properties applied to new classes. No new annotation properties have been introduced.");
} }
//details
while (iter.hasNext()) {
Statement statement = iter.next();
logger.log( "added Statement: subject = " + statement.getSubject().getURI() +
" property = " + statement.getPredicate().getURI() +
" object = " + (statement.getObject().isLiteral() ? ((Resource)statement.getObject()).getURI()
: ((Literal)statement.getObject()).getLexicalForm()));
}
} finally { } finally {
siteModel.leaveCriticalSection(); siteModel.leaveCriticalSection();