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various migration issues and VIVO-265 blank node deletion optimization

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This commit is contained in:
brianjlowe 2013-09-19 13:05:00 -04:00
parent 618b90e5d7
commit eb1c2d4890
6 changed files with 139 additions and 31 deletions
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10
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
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@ -420,7 +420,7 @@ public class ABoxUpdater {
Iterator<AtomicOntologyChange> propItr = changes.iterator();
while(propItr.hasNext()){
AtomicOntologyChange propChangeObj = propItr.next();
log.info("processing " + propChangeObj);
log.debug("processing " + propChangeObj);
try {
if (propChangeObj.getAtomicChangeType() == null) {
log.error("Missing change type; skipping " + propChangeObj);
@ -428,19 +428,19 @@ public class ABoxUpdater {
}
switch (propChangeObj.getAtomicChangeType()){
case ADD:
log.info("add");
log.debug("add");
addProperty(propChangeObj);
break;
case DELETE:
log.info("delete");
log.debug("delete");
deleteProperty(propChangeObj);
break;
case RENAME:
log.info("rename");
log.debug("rename");
renameProperty(propChangeObj);
break;
default:
log.info("unknown");
log.debug("unknown");
logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
break;
}

8
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -96,7 +96,7 @@ public class KnowledgeBaseUpdater {
//process the TBox before the ABox
try {
log.info("\tupdating tbox annotations");
log.debug("\tupdating tbox annotations");
updateTBoxAnnotations();
} catch (Exception e) {
log.error(e,e);
@ -396,13 +396,13 @@ public class KnowledgeBaseUpdater {
while(listItr.hasNext()) {
AtomicOntologyChange changeObj = listItr.next();
if (changeObj.getSourceURI() != null){
log.info("triaging " + changeObj);
log.debug("triaging " + changeObj);
if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
atomicPropertyChanges.add(changeObj);
log.info("added to property changes");
log.debug("added to property changes");
} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
atomicClassChanges.add(changeObj);
log.info("added to class changes");
log.debug("added to class changes");
} else if ("Prop".equals(changeObj.getNotes())) {
atomicPropertyChanges.add(changeObj);
} else if ("Class".equals(changeObj.getNotes())) {

15
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -454,20 +454,23 @@ public class TBoxUpdater {
}
public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
Dataset dataset = new RDFServiceDataset(settings.getRDFService());
Model userAnnotationsModel = dataset.getNamedModel(
JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
mergePropertyAnnotationsToPropertyConfig(changeObj);
mergePropertyAnnotationsToPropertyConfig(changeObj, userAnnotationsModel);
}
Resource renamedProperty = userAnnotationsModel.getResource(changeObj.getSourceURI());
userAnnotationsModel.removeAll(renamedProperty, null, (RDFNode) null);
userAnnotationsModel.removeAll(null, null, renamedProperty);
}
private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj) throws IOException {
private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj,
Model userAnnotationsModel) 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" +

75
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java
View file

@ -6,13 +6,16 @@ import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.ConcurrentLinkedQueue;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.DataSource;
import com.hp.hpl.jena.query.Dataset;
@ -21,11 +24,9 @@ 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.query.QueryParseException;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
@ -129,7 +130,7 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
Resource s2 = (Resource) n;
// now run yet another describe query
String smallerTree = makeDescribe(s2);
log.info(smallerTree);
log.debug(smallerTree);
Query smallerTreeQuery = QueryFactory.create(smallerTree);
QueryExecution qe3 = QueryExecutionFactory.create(
smallerTreeQuery, tree);
@ -173,19 +174,23 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
StringBuffer queryBuff = new StringBuffer();
queryBuff.append("CONSTRUCT { \n");
addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
List<Statement> stmts = stmtIt.toList();
stmts = sort(stmts);
addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
queryBuff.append("} WHERE { \n");
if (graphURI != null) {
queryBuff.append(" GRAPH <" + graphURI + "> { \n");
}
stmtIt = model.listStatements();
addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
stmts = stmtIt.toList();
stmts = sort(stmts);
addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
if (graphURI != null) {
queryBuff.append(" } \n");
}
queryBuff.append("} \n");
log.info(queryBuff.toString());
log.debug(queryBuff.toString());
Query construct = QueryFactory.create(queryBuff.toString());
// make a plain dataset to force the query to be run in a way that
@ -209,11 +214,61 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
}
}
private List<Statement> sort(List<Statement> stmts) {
List<Statement> output = new ArrayList<Statement>();
int originalSize = stmts.size();
List <Statement> remaining = stmts;
ConcurrentLinkedQueue<Resource> subjQueue = new ConcurrentLinkedQueue<Resource>();
for(Statement stmt : remaining) {
if(stmt.getSubject().isURIResource()) {
subjQueue.add(stmt.getSubject());
break;
}
}
if (subjQueue.isEmpty()) {
throw new RuntimeException("No named subject in statement patterns");
}
while(remaining.size() > 0) {
if(subjQueue.isEmpty()) {
subjQueue.add(remaining.get(0).getSubject());
}
while(!subjQueue.isEmpty()) {
Resource subj = subjQueue.poll();
List<Statement> temp = new ArrayList<Statement>();
for (Statement stmt : remaining) {
if(stmt.getSubject().equals(subj)) {
output.add(stmt);
if (stmt.getObject().isResource()) {
subjQueue.add((Resource) stmt.getObject());
}
} else {
temp.add(stmt);
}
}
remaining = temp;
}
}
if(output.size() != originalSize) {
throw new RuntimeException("original list size was " + originalSize +
" but sorted size is " + output.size());
}
return output;
}
private String getHexString(Node node) {
String label = node.getBlankNodeLabel().replaceAll("\\W", "").toUpperCase();
if (label.length() > 7) {
return label.substring(label.length() - 7);
} else {
return label;
}
}
private static final boolean WHERE_CLAUSE = true;
private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
while(stmtIt.hasNext()) {
Triple t = stmtIt.next().asTriple();
private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
for(Statement stmt : stmts) {
Triple t = stmt.asTriple();
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
patternBuff.append(" ");
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

57
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java
View file

@ -9,6 +9,7 @@ import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.ConcurrentLinkedQueue;
import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
@ -715,7 +716,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
if (graphURI != null) {
queryBuff.append(" GRAPH <" + graphURI + "> { \n");
}
addStatementPatterns(stmtIt, queryBuff, !WHERE_CLAUSE);
List<Statement> stmts = stmtIt.toList();
sort(stmts);
addStatementPatterns(stmts, queryBuff, !WHERE_CLAUSE);
if (graphURI != null) {
queryBuff.append(" } \n");
}
@ -724,7 +727,9 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
queryBuff.append(" GRAPH <" + graphURI + "> { \n");
}
stmtIt = model.listStatements();
addStatementPatterns(stmtIt, queryBuff, WHERE_CLAUSE);
stmts = stmtIt.toList();
sort(stmts);
addStatementPatterns(stmts, queryBuff, WHERE_CLAUSE);
if (graphURI != null) {
queryBuff.append(" } \n");
}
@ -736,11 +741,53 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
executeUpdate(queryBuff.toString());
}
private List<Statement> sort(List<Statement> stmts) {
List<Statement> output = new ArrayList<Statement>();
int originalSize = stmts.size();
List <Statement> remaining = stmts;
ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource> subjQueue =
new ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource>();
for(Statement stmt : remaining) {
if(stmt.getSubject().isURIResource()) {
subjQueue.add(stmt.getSubject());
break;
}
}
if (subjQueue.isEmpty()) {
throw new RuntimeException("No named subject in statement patterns");
}
while(remaining.size() > 0) {
if(subjQueue.isEmpty()) {
subjQueue.add(remaining.get(0).getSubject());
}
while(!subjQueue.isEmpty()) {
com.hp.hpl.jena.rdf.model.Resource subj = subjQueue.poll();
List<Statement> temp = new ArrayList<Statement>();
for (Statement stmt : remaining) {
if(stmt.getSubject().equals(subj)) {
output.add(stmt);
if (stmt.getObject().isResource()) {
subjQueue.add((com.hp.hpl.jena.rdf.model.Resource) stmt.getObject());
}
} else {
temp.add(stmt);
}
}
remaining = temp;
}
}
if(output.size() != originalSize) {
throw new RuntimeException("original list size was " + originalSize +
" but sorted size is " + output.size());
}
return output;
}
private static final boolean WHERE_CLAUSE = true;
private void addStatementPatterns(StmtIterator stmtIt, StringBuffer patternBuff, boolean whereClause) {
while(stmtIt.hasNext()) {
Triple t = stmtIt.next().asTriple();
private void addStatementPatterns(List<Statement> stmts, StringBuffer patternBuff, boolean whereClause) {
for(Statement stmt : stmts) {
Triple t = stmt.asTriple();
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getSubject(), null));
patternBuff.append(" ");
patternBuff.append(SparqlGraph.sparqlNodeDelete(t.getPredicate(), null));

5
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -122,7 +122,10 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
} catch (Exception e) {
} catch (ModelFileNotFoundException e) {
// expected if no display migration was intended
tryMigrateDisplay = false;
} catch (Exception e) {
log.info("Unable to read display model migration files. ", e);
tryMigrateDisplay = false;
}