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work in progress on data migration and related changes to support ISF

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This commit is contained in:
brianjlowe 2013-08-05 16:48:23 -04:00
parent c00fefacfe
commit d8d704064e
8 changed files with 75 additions and 29 deletions
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15
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
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@ -77,11 +77,16 @@ public class RDFUploadController extends JenaIngestController {
VitroRequest request = new VitroRequest(req);
LoginStatusBean loginBean = LoginStatusBean.getBean(request);
String modelName = req.getParameter("modelName");
if(modelName!=null){
loadRDF(req,request,response);
return;
}
try {
String modelName = req.getParameter("modelName");
if(modelName!=null){
loadRDF(req,request,response);
return;
}
} catch (Exception e) {
log.error(e,e);
throw new RuntimeException(e);
}
boolean remove = "remove".equals(request.getParameter("mode"));
String verb = remove?"Removed":"Added";

6
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
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@ -905,8 +905,8 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
"SELECT ?property ?range ?filename WHERE { \n" +
" { ?property display:listViewConfigFile ?filename \n" +
" } UNION { \n" +
" ?lv config:listViewConfigFile ?filename . \n " +
" ?configuration config:hasListView ?lv . " +
" ?configuration config:listViewConfigFile ?filename . \n " +
// " ?configuration config:hasListView ?lv . " +
" ?context config:hasConfiguration ?configuration . \n" +
" ?context config:configContextFor ?property . \n" +
" ?context config:qualifiedBy ?range . \n" +
@ -955,6 +955,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
}
} else {
String filename = soln.getLiteral("filename").getLexicalForm();
log.info("putting " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map");
customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename);
}
}
@ -963,6 +964,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI()));
if (customListViewConfigFileName == null) {
log.info("no list view found for " + op.getURI() + " qualified by " + op.getRangeVClassURI());
customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI()));
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/uploadrequest/MultipartHttpServletRequest.java
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@ -57,6 +57,7 @@ public class MultipartHttpServletRequest extends FileUploadServletRequest {
throws IOException{
super(request);
storeFilesToTempDir = false;
setup(request);
}
@ -73,6 +74,7 @@ public class MultipartHttpServletRequest extends FileUploadServletRequest {
storeFilesToTempDir = true;
this.maxFileSize = maxFileSize;
this.tempDir = figureTemporaryDirectory(request);
setup(request);
}
private void setup(HttpServletRequest request){

49
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java
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@ -4,10 +4,12 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
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.OntModelSpec;
@ -24,7 +26,6 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
@ -34,6 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
*/
public class ABoxUpdater {
private final Log log = LogFactory.getLog(ABoxUpdater.class);
private OntModel oldTboxModel;
private OntModel newTboxModel;
private OntModel aboxModel;
@ -388,20 +390,33 @@ public class ABoxUpdater {
Iterator<AtomicOntologyChange> propItr = changes.iterator();
while(propItr.hasNext()){
AtomicOntologyChange propChangeObj = propItr.next();
switch (propChangeObj.getAtomicChangeType()){
case ADD:
addProperty(propChangeObj);
break;
case DELETE:
deleteProperty(propChangeObj);
break;
case RENAME:
renameProperty(propChangeObj);
break;
default:
logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
break;
}
log.info("processing " + propChangeObj);
try {
if (propChangeObj.getAtomicChangeType() == null) {
log.error("Missing change type; skipping " + propChangeObj);
continue;
}
switch (propChangeObj.getAtomicChangeType()){
case ADD:
log.info("add");
addProperty(propChangeObj);
break;
case DELETE:
log.info("delete");
deleteProperty(propChangeObj);
break;
case RENAME:
log.info("rename");
renameProperty(propChangeObj);
break;
default:
log.info("unknown");
logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
break;
}
} catch (Exception e) {
log.error(e,e);
}
}
}
@ -518,7 +533,7 @@ public class ABoxUpdater {
private void renameProperty(AtomicOntologyChange propObj) throws IOException {
//logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
OntProperty oldProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
OntProperty newProperty = newTboxModel.getOntProperty(propObj.getDestinationURI());

5
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/AtomicOntologyChange.java
View file

@ -30,6 +30,11 @@ public class AtomicOntologyChange {
this.notes = notes;
}
@Override
public String toString() {
return "Source: " + sourceURI + "; Destination: " + destinationURI +
"; Type: " + atomicChangeType + "; Notes:" + notes;
}
/**
* Contains the URI of a class or property in the previous version of

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

@ -98,14 +98,18 @@ public class KnowledgeBaseUpdater {
AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
//process the TBox before the ABox
log.info("\tupdating tbox annotations");
updateTBoxAnnotations();
try {
log.info("\tupdating tbox annotations");
updateTBoxAnnotations();
} catch (Exception e) {
log.error(e,e);
}
try {
migrateMigrationMetadata(servletContext);
logger.log("Migrated migration metadata");
} catch (Exception e) {
log.debug("unable to migrate migration metadata " + e.getMessage());
log.error("unable to migrate migration metadata " + e.getMessage());
}
log.info("\tupdating the abox");
@ -390,11 +394,13 @@ public class KnowledgeBaseUpdater {
while(listItr.hasNext()) {
AtomicOntologyChange changeObj = listItr.next();
if (changeObj.getSourceURI() != null){
log.info("triaging " + changeObj);
if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
atomicPropertyChanges.add(changeObj);
log.info("added to property changes");
} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
atomicClassChanges.add(changeObj);
log.info("added to class changes");
} else if ("Prop".equals(changeObj.getNotes())) {
atomicPropertyChanges.add(changeObj);
} else if ("Class".equals(changeObj.getNotes())) {

6
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java
View file

@ -9,6 +9,8 @@ import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.skife.csv.CSVReader;
import org.skife.csv.SimpleReader;
@ -23,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
public class OntologyChangeParser {
private final Log log = LogFactory.getLog(OntologyChangeParser.class);
private ChangeLogger logger;
public OntologyChangeParser(ChangeLogger logger) {
@ -85,6 +89,8 @@ public class OntologyChangeParser {
}
log.info(changeObj);
changeObjects.add(changeObj);
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -104,6 +104,11 @@ public class TBoxUpdater {
// 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()) {