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resolves NIHVIVO-263 'Write SPARQL CONSTRUCTS...'

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This commit is contained in:
bjl23 2010-04-02 00:18:18 +00:00
parent c28519a98e
commit 853df19c8b
3 changed files with 133 additions and 6 deletions
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44
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdateSettings.java
View file

@ -1,10 +1,13 @@
package edu.cornell.mannlib.vitro.webapp.ontology.update;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
public class OntologyUpdateSettings {
private String dataDir;
private String sparqlConstructsDir;
private String askQueryFile;
private String successAssertionsFile;
private String successRDFFormat = "N3";
@ -13,7 +16,12 @@ public class OntologyUpdateSettings {
private String errorLogFile;
private String addedDataFile;
private String removedDataFile;
private String defaultNamespace;
private OntModelSelector ontModelSelector;
private OntModel oldTBoxModel;
private OntModel newTBoxModel;
private OntModel oldTBoxAnnotationsModel;
private OntModel newTBoxAnnotationsModel;
public String getDataDir() {
return dataDir;
@ -21,6 +29,12 @@ public class OntologyUpdateSettings {
public void setDataDir(String dataDir) {
this.dataDir = dataDir;
}
public String getSparqlConstructsDir() {
return sparqlConstructsDir;
}
public void setSparqlConstructsDir(String sparqlConstructsDir) {
this.sparqlConstructsDir = sparqlConstructsDir;
}
public String getAskQueryFile() {
return askQueryFile;
}
@ -72,8 +86,38 @@ public class OntologyUpdateSettings {
public void setRemovedDataFile(String removedDataFile) {
this.removedDataFile = removedDataFile;
}
public String getDefaultNamespace() {
return defaultNamespace;
}
public void setDefaultNamespace(String defaultNamespace) {
this.defaultNamespace = defaultNamespace;
}
public void setOntModelSelector(OntModelSelector ontModelSelector) {
this.ontModelSelector = ontModelSelector;
}
public OntModel getOldTBoxModel() {
return oldTBoxModel;
}
public void setOldTBoxModel(OntModel oldTBoxModel) {
this.oldTBoxModel = oldTBoxModel;
}
public OntModel getNewTBoxModel() {
return newTBoxModel;
}
public void setNewTBoxModel(OntModel newTBoxModel) {
this.newTBoxModel = newTBoxModel;
}
public OntModel getOldTBoxAnnotationsModel() {
return oldTBoxAnnotationsModel;
}
public void setOldTBoxAnnotationsModel(OntModel oldTBoxAnnotationsModel) {
this.oldTBoxAnnotationsModel = oldTBoxAnnotationsModel;
}
public OntModel getNewTBoxAnnotationsModel() {
return newTBoxAnnotationsModel;
}
public void setNewTBoxAnnotationsModel(OntModel newTBoxAnnotationsModel) {
this.newTBoxAnnotationsModel = newTBoxAnnotationsModel;
}
}

84
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java
View file

@ -11,6 +11,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -22,12 +23,16 @@ 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.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;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
/**
* Performs knowledge base updates if necessary to align with a
* new ontology version.
@ -47,6 +52,9 @@ public class OntologyUpdater {
private OntModel OLD_TBOX_MODEL = null; // TODO change this
private OntModel oldTBoxAnnotationsModel;
private OntModel newTBoxAnnotationsModel;
public OntologyUpdater(OntologyUpdateSettings settings) {
this.settings = settings;
this.logger = new SimpleOntologyChangeLogger(settings.getLogFile(),
@ -66,6 +74,10 @@ public class OntologyUpdater {
}
private void performUpdate() throws IOException {
performSparqlConstructs(settings.getSparqlConstructsDir(),
settings.getOntModelSelector().getABoxModel());
List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
AtomicOntologyChangeLists changes =
@ -83,6 +95,72 @@ public class OntologyUpdater {
// perform additional additions and retractions
}
/**
* Performs a set of arbitrary SPARQL CONSTRUCT queries on the
* data, for changes that cannot be expressed as simple property
* or class additions, deletions, or renamings.
* Blank nodes created by the queries are given random URIs.
* @param sparqlConstructDir
* @param aboxModel
*/
private void performSparqlConstructs(String sparqlConstructDir,
OntModel aboxModel) throws IOException {
Model anonModel = ModelFactory.createDefaultModel();
File sparqlConstructDirectory = new File(sparqlConstructDir);
if (!sparqlConstructDirectory.isDirectory()) {
logger.logError(this.getClass().getName() +
"performSparqlConstructs() expected to find a directory " +
" at " + sparqlConstructDir + ". Unable to execute " +
" SPARQL CONSTRUCTS.");
return;
}
File[] sparqlFiles = sparqlConstructDirectory.listFiles();
for (int i = 0; i < sparqlFiles.length; i ++) {
File sparqlFile = sparqlFiles[i];
try {
BufferedReader reader =
new BufferedReader(new FileReader(sparqlFile));
StringBuffer fileContents = new StringBuffer();
String ln;
while ( (ln = reader.readLine()) != null) {
fileContents.append(ln).append('\n');
}
try {
Query q = QueryFactory.create(fileContents.toString(),
Syntax.syntaxARQ);
aboxModel.enterCriticalSection(Lock.WRITE);
try {
QueryExecution qe = QueryExecutionFactory.create(q,
aboxModel);
qe.execConstruct(anonModel);
} finally {
aboxModel.leaveCriticalSection();
}
} catch (Exception e) {
logger.logError(this.getClass().getName() +
".performSparqlConstructs() unable to execute " +
"query at " + sparqlFile);
}
} catch (FileNotFoundException fnfe) {
logger.logError(this.getClass().getName() +
".performSparqlConstructs() could not find " +
" SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
}
}
aboxModel.enterCriticalSection(Lock.WRITE);
try {
JenaIngestUtils jiu = new JenaIngestUtils();
jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n",
aboxModel);
} finally {
aboxModel.leaveCriticalSection();
}
}
private List<AtomicOntologyChange> getAtomicOntologyChanges()
throws IOException {
return (new OntologyChangeParser()).parseFile(settings.getDiffFile());
@ -103,8 +181,10 @@ public class OntologyUpdater {
// run additional SPARQL CONSTRUCTS
}
private void updateTBoxAnnotations() {
// Stella's code is called here
private void updateTBoxAnnotations() throws IOException {
(new TBoxUpdater(oldTBoxAnnotationsModel, newTBoxAnnotationsModel,
settings.getOntModelSelector().getTBoxModel(), logger, record))
.updateVitroPropertyDefaultValues();
}
/**

9
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -10,6 +10,7 @@ import javax.servlet.ServletContextListener;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SimpleOntModelSelector;
@ -37,10 +38,11 @@ public class UpdateKnowledgeBase implements ServletContextListener {
"knowledgeBaseUpdate.error.log";
private final String REMOVED_DATA_FILE = DATA_DIR + REMOVED_DATA_DIR +
"removedData.rdf";
private final String SPARQL_CONSTRUCTS_DIR = DATA_DIR + "sparqlConstructs/";
public void contextInitialized(ServletContextEvent sce) {
/*
ServletContext ctx = sce.getServletContext();
@ -51,6 +53,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
OntologyUpdateSettings settings = new OntologyUpdateSettings();
settings.setAskQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
settings.setDataDir(ctx.getRealPath(DATA_DIR));
settings.setSparqlConstructsDir(ctx.getRealPath(SPARQL_CONSTRUCTS_DIR));
settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
settings.setSuccessAssertionsFile(
ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
@ -58,6 +61,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setLogFile(ctx.getRealPath(LOG_FILE));
settings.setErrorLogFile(ctx.getRealPath(ERROR_LOG_FILE));
settings.setRemovedDataFile(ctx.getRealPath(REMOVED_DATA_FILE));
WebappDaoFactory wadf = (WebappDaoFactory) ctx.getAttribute("webappDaoFactory");
settings.setDefaultNamespace(wadf.getDefaultNamespace());
try {
(new OntologyUpdater(settings)).update();
@ -71,8 +76,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
throw new RuntimeException(errMsg, ioe);
}
*/
}
public void contextDestroyed(ServletContextEvent arg0) {