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NIHVIVO-3860 update past and current migration metadata to not use blank nodes and to be stored in the application metadata graph

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This commit is contained in:
stellamit 2012-06-30 19:44:30 +00:00
parent c89953d73f
commit f43a268324
1 changed files with 52 additions and 12 deletions
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64
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
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@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.ontology.update; package edu.cornell.mannlib.vitro.webapp.ontology.update;
import java.io.BufferedReader; import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File; import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
@ -15,6 +16,8 @@ import java.util.List;
import javax.servlet.ServletContext; import javax.servlet.ServletContext;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
@ -67,7 +70,7 @@ public class KnowledgeBaseUpdater {
logger.log("Started knowledge base migration"); logger.log("Started knowledge base migration");
try { try {
performUpdate(); performUpdate(servletContext);
} catch (Exception e) { } catch (Exception e) {
logger.logError(e.getMessage()); logger.logError(e.getMessage());
e.printStackTrace(); e.printStackTrace();
@ -88,8 +91,7 @@ public class KnowledgeBaseUpdater {
return; return;
} }
private void performUpdate(ServletContext servletContext) throws Exception {
private void performUpdate() throws IOException {
List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges(); List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
@ -98,7 +100,14 @@ public class KnowledgeBaseUpdater {
//process the TBox before the ABox //process the TBox before the ABox
log.info("\tupdating tbox annotations"); log.info("\tupdating tbox annotations");
updateTBoxAnnotations(); updateTBoxAnnotations();
try {
migrateMigrationMetadata(servletContext);
logger.log("migrated migration metadata");
} catch (Exception e) {
logger.log("unable to migrate migration metadata " + e.getMessage());
}
log.info("\tupdating the abox"); log.info("\tupdating the abox");
updateABox(changes); updateABox(changes);
} }
@ -239,6 +248,39 @@ public class KnowledgeBaseUpdater {
aboxUpdater.processClassChanges(changes.getAtomicClassChanges()); aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
} }
// special for 1.5 - temporary code
// migrate past migration indicators to not use blank nodes and move them to app metadata model
// changing structure for pre 1.5 ones in the process
private void migrateMigrationMetadata(ServletContext servletContext) throws Exception {
String baseResourceURI = "http://vitro.mannlib.cornell.edu/ns/vitro/metadata/migration/";
String queryFile = "MigrationData.sparql";
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(servletContext).getRDFService();
String fmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructDeletionsDir() + "/" + queryFile));
Model toRemove = ModelFactory.createDefaultModel();
toRemove.read(rdfService.sparqlConstructQuery(fmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
String cmQuery = FileUtils.readFileToString(new File(settings.getSparqlConstructAdditionsDir() + "/" + queryFile));
Model toAdd = ModelFactory.createDefaultModel();
toAdd.read(rdfService.sparqlConstructQuery(cmQuery, RDFService.ModelSerializationFormat.RDFXML), null);
ByteArrayOutputStream outAdd = new ByteArrayOutputStream();
toAdd.write(outAdd);
InputStream inAdd = new ByteArrayInputStream(outAdd.toByteArray());
ChangeSet addChangeSet = rdfService.manufactureChangeSet();
addChangeSet.addAddition(inAdd, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
rdfService.changeSetUpdate(addChangeSet);
ByteArrayOutputStream outRemove = new ByteArrayOutputStream();
toRemove.write(outRemove);
InputStream inRemove = new ByteArrayInputStream(outRemove.toByteArray());
ChangeSet removeChangeSet = rdfService.manufactureChangeSet();
addChangeSet.addRemoval(inRemove, RDFService.ModelSerializationFormat.RDFXML, JenaDataSourceSetupBase.JENA_DB_MODEL);
rdfService.changeSetUpdate(removeChangeSet);
}
private void updateTBoxAnnotations() throws IOException { private void updateTBoxAnnotations() throws IOException {
TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(), TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
@ -254,7 +296,6 @@ public class KnowledgeBaseUpdater {
* needs to be updated to conform to a new ontology version * needs to be updated to conform to a new ontology version
*/ */
public boolean updateRequired(ServletContext servletContext) throws IOException { public boolean updateRequired(ServletContext servletContext) throws IOException {
boolean required = false; boolean required = false;
String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile()); String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile());
@ -287,7 +328,7 @@ public class KnowledgeBaseUpdater {
return required; return required;
} }
/** /**
* loads a SPARQL ASK query from a text file * loads a SPARQL ASK query from a text file
* @param filePath * @param filePath
@ -311,19 +352,18 @@ public class KnowledgeBaseUpdater {
private void assertSuccess(ServletContext servletContext) throws FileNotFoundException, IOException { private void assertSuccess(ServletContext servletContext) throws FileNotFoundException, IOException {
try { try {
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(servletContext).getRDFService(); RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(servletContext).getRDFService();
ChangeSet changeSet = rdfService.manufactureChangeSet();
ChangeSet changeSet = rdfService.manufactureChangeSet();
File successAssertionsFile = new File(settings.getSuccessAssertionsFile()); File successAssertionsFile = new File(settings.getSuccessAssertionsFile());
InputStream inStream = new FileInputStream(successAssertionsFile); InputStream inStream = new FileInputStream(successAssertionsFile);
changeSet.addAddition(inStream, RDFService.ModelSerializationFormat.N3, JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL);
changeSet.addAddition(inStream, RDFService.ModelSerializationFormat.N3, JenaDataSourceSetupBase.JENA_DB_MODEL);
rdfService.changeSetUpdate(changeSet); rdfService.changeSetUpdate(changeSet);
} catch (Exception e) { } catch (Exception e) {
log.error("unable to make RDF assertions about successful " + log.error("unable to make RDF assertions about successful " +
" update to new ontology version: ", e); " update to new ontology version: ", e);
} }
} }
/** /**
* A class that allows to access two different ontology change lists, * A class that allows to access two different ontology change lists,
* one for class changes and the other for property changes. The * one for class changes and the other for property changes. The