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incremental development for NIHVIVO-1286

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This commit is contained in:
sjm222 2011-01-12 00:55:49 +00:00
parent b52832208d
commit 98d569d3fa
4 changed files with 96 additions and 23 deletions
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13
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
View file

@ -634,17 +634,14 @@ public class ABoxUpdater {
}
public void logChange(Statement statement, boolean add) throws IOException {
logger.log( (add ? "Added " : "Removed") + "Statement: subject = " + statement.getSubject().getURI() +
" property = " + statement.getPredicate().getURI() +
" object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm()
: ((Resource)statement.getObject()).getURI()));
logger.log( (add ? "Added" : "Removed") + stmtString(statement));
}
public static String stmtString(Statement statement) {
return " subject = " + statement.getSubject().getURI() +
" property = " + statement.getPredicate().getURI() +
" object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
: ((Resource)statement.getObject()).getURI() + " (Resource)");
return " [subject = " + statement.getSubject().getURI() +
"] [property = " + statement.getPredicate().getURI() +
"] [object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
: ((Resource)statement.getObject()).getURI() + " (Resource)") + "]";
}
}

17
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/DateTimeMigration.java
View file

@ -175,7 +175,7 @@ public class DateTimeMigration {
newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
} catch (ParseException pe) {
logger.log("Parse Exception for year literal: " + stmt.getObject().asLiteral().getLexicalForm() +
". The following statement has been removed from the knowledge base " + stmtString(stmt));
". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
}
} else if (ymPrecisionURI.equals(precision)) {
try {
@ -183,7 +183,7 @@ public class DateTimeMigration {
newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
} catch (ParseException pe) {
logger.log("Parse Exception for yearMonth literal: " + stmt.getObject().asLiteral().getLexicalForm() +
". The following statement has been removed from the knowledge base " + stmtString(stmt));
". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
}
} else if (ymdPrecisionURI.equals(precision)) {
try {
@ -191,14 +191,14 @@ public class DateTimeMigration {
newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
} catch (ParseException pe) {
logger.log("Parse Exception for yearMonthDay literal: " + stmt.getObject().asLiteral().getLexicalForm() +
". The following statement has been removed from the knowledge base " + stmtString(stmt));
". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
}
} else if (ymdtPrecisionURI.equals(precision)) {
logger.log("WARNING: unhandled precision found for individual " + stmt.getSubject().getURI() + ": " + precision +
". The following statement has been removed from the knowledge base " + stmtString(stmt));
". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
} else {
logger.log("WARNING: unrecognized precision found for individual " + stmt.getSubject().getURI() + ": " + precision +
". The following statement has been removed from the knowledge base " + stmtString(stmt));
". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
}
retractions.add(stmt);
@ -256,11 +256,4 @@ public class DateTimeMigration {
String dateString = dt.toString().substring(0, dt.toString().length()-1);
return ResourceFactory.createTypedLiteral(dateString, XSDDatatype.XSDdateTime);
}
public static String stmtString(Statement statement) {
return " subject = " + statement.getSubject().getURI() +
" property = " + statement.getPredicate().getURI() +
" object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
: ((Resource)statement.getObject()).getURI() + " (Resource)");
}
}

10
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -243,9 +243,13 @@ public class OntologyUpdater {
}
private void updateTBoxAnnotations() throws IOException {
(new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
settings.getNewTBoxAnnotationsModel(),
settings.getOntModelSelector().getABoxModel(), logger, record)).updateVitroPropertyDefaultValues();
TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
settings.getNewTBoxAnnotationsModel(),
settings.getOntModelSelector().getABoxModel(), logger, record);
tboxUpdater.updateVitroPropertyDefaultValues();
tboxUpdater.updateVitroAnnotationsModel();
}
/**

79
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -5,7 +5,9 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
import java.io.IOException;
import java.util.List;
import com.hp.hpl.jena.ontology.DatatypeProperty;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
@ -16,6 +18,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
@ -32,6 +35,11 @@ public class TBoxUpdater {
private OntologyChangeLogger logger;
private OntologyChangeRecord 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);
/**
*
@ -297,4 +305,75 @@ public class TBoxUpdater {
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 updateVitroAnnotationsModel() 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.
// TODO: the site will have classes asserted to be in it if we have switched
// the default assignment in the new version but haven't migration yet. How
// to handle this?
siteModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
int count = 0;
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
count++;
retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
}
}
if (retractions.size() > 0) {
siteModel.remove(retractions);
record.recordRetractions(retractions);
// log summary of changes
if (retractions.size() > 0) {
logger.log("Removed " + count + " Class Group" + (count > 1 ? "s" : "") + " from the annotations model.");
}
}
} finally {
siteModel.leaveCriticalSection();
}
// 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.
}
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();
}
}
}