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improvements and bugfixes for NIHVIVO-205 ontology upgrade

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This commit is contained in:
bjl23 2010-04-02 18:16:22 +00:00
parent 03a2a13a37
commit 71a6fccd64
5 changed files with 43 additions and 26 deletions
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13
webapp/config/web.xml
View file

@ -72,18 +72,19 @@
<listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetup</listener-class>
</listener>
<!-- Invokes process to perform updates to align with ontology changes if needed -->
<!-- Needs to run before submodels are attached and Pellet is set up -->
<listener>
<listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase</listener-class>
</listener>
<!-- Attaching submodels permits extra RDF files to be made visible without storing the data in the DB. -->
<listener>
<listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.AttachSubmodels</listener-class>
</listener>
<!-- Invokes process to perform updates to align with ontology changes if needed -->
<listener>
<listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase</listener-class>
</listener>
<!-- Pellet setup enables reasoning. Inferences are cached in a separate DB graph. -->
<!-- Changing the class name sets the kindss of inferences that are materialized. -->
<!-- See documentation for details. -->

4
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -84,7 +84,7 @@ public class OntologyUpdater {
AtomicOntologyChangeLists changes =
new AtomicOntologyChangeLists(rawChanges,
settings.getOntModelSelector().getTBoxModel(),
settings.getNewTBoxModel(),
settings.getOldTBoxModel());
//updateTBox(changes);
@ -186,7 +186,7 @@ public class OntologyUpdater {
private void updateTBoxAnnotations() throws IOException {
(new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
settings.getNewTBoxAnnotationsModel(),
settings.getOntModelSelector().getTBoxModel(), logger, record))
settings.getOntModelSelector().getABoxModel(), logger, record))
.updateVitroPropertyDefaultValues();
}

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

@ -46,12 +46,16 @@ public class SimpleOntologyChangeRecord implements OntologyChangeRecord {
public void recordAdditions(Model incrementalAdditions) {
additionsModel.add(incrementalAdditions);
write(additionsModel, additionsFile);
if (additionsModel.size() > 0) {
write(additionsModel, additionsFile);
}
}
public void recordRetractions(Model incrementalRetractions) {
retractionsModel.add(incrementalRetractions);
write(retractionsModel, retractionsFile);
if (retractionsModel.size() > 0) {
write(retractionsModel, retractionsFile);
}
}
private void write(Model model, File file) {

40
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java
View file

@ -122,7 +122,11 @@ public class TBoxUpdater {
if (!newObject.equals(oldObject)) {
objects = siteModel.listObjectsOfProperty(subject,predicate);
if (!objects.hasNext()) {
continue;
}
RDFNode siteObject = objects.next();
if (objects.hasNext()) {
logger.logError("Warning: found " + objects.toList().size() +
@ -163,18 +167,18 @@ public class TBoxUpdater {
}
}
siteModel.add(additions);
record.recordAdditions(additions);
siteModel.remove(retractions);
record.recordRetractions(retractions);
Model actualAdditions = additions.difference(retractions);
siteModel.add(actualAdditions);
record.recordAdditions(actualAdditions);
Model actualRetractions = retractions.difference(additions);
siteModel.remove(actualRetractions);
record.recordRetractions(actualRetractions);
// log summary of changes
StmtIterator addedIter = additions.listStatements();
logger.log("Updated the default vitro annotation value for " +
addedIter.toList().size() + " statments in the knowledge base.");
actualAdditions.size() + " statments in the knowledge base.");
StmtIterator removedIter = retractions.listStatements();
int numRemoved = removedIter.toList().size() - addedIter.toList().size();
long numRemoved = actualRetractions.size() - actualAdditions.size();
logger.log("Removed " + numRemoved +
" superfluous vitro annotation property settings from the knowledge base.");
@ -183,15 +187,21 @@ public class TBoxUpdater {
//
Model newAnnotationSettings = newTboxModel.difference(oldTboxModel);
siteModel.add(newAnnotationSettings);
record.recordAdditions(newAnnotationSettings);
Model newAnnotationSettingsToAdd = ModelFactory.createDefaultModel();
StmtIterator newStmtIt = newAnnotationSettings.listStatements();
while (newStmtIt.hasNext()) {
Statement stmt = newStmtIt.next();
if (!siteModel.contains(stmt)) {
newAnnotationSettingsToAdd.add(stmt);
}
}
siteModel.add(newAnnotationSettingsToAdd);
record.recordAdditions(newAnnotationSettingsToAdd);
// log the additions
iter = newAnnotationSettings.listStatements();
//summary
logger.log("Added " + iter.toList().size() + " new annotation property settings to the knowledge base. This includes " +
"exsiting annotation properties applied to exsiting classes where they weren't applied before, or existing " +
logger.log("Added " + newAnnotationSettingsToAdd.size() + " new annotation property settings to the knowledge base. This includes " +
"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.");
//details

4
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -60,6 +60,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
private final String SPARQL_CONSTRUCTS_DIR = DATA_DIR + "sparqlConstructs/";
private final String MISC_REPLACEMENTS_FILE = DATA_DIR + "miscReplacements.rdf";
private final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";
private final String NEW_TBOX_MODEL_DIR = "/WEB-INF/submodels/";
private final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/";
private final String NEW_TBOX_ANNOTATIONS_DIR = "/WEB-INF/ontologies/user";
@ -91,7 +92,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setOntModelSelector(oms);
OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
settings.setOldTBoxModel(oldTBoxModel);
settings.setNewTBoxModel(oms.getTBoxModel());
OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
settings.setNewTBoxModel(newTBoxModel);
OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
OntModel newTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_ANNOTATIONS_DIR));