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VCard migration

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This commit is contained in:
brianjlowe 2013-09-06 16:40:17 -04:00
parent 57055a4efc
commit 91aedd5255
3 changed files with 133 additions and 121 deletions
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22
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java
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@ -616,22 +616,36 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
return classes; return classes;
} }
private static final int DEPTH_LIMIT = 20;
private List<Restriction> getRelatedRestrictions(OntClass ontClass) { private List<Restriction> getRelatedRestrictions(OntClass ontClass) {
List<Restriction> relatedRestrictions = new ArrayList<Restriction>(); return getRelatedRestrictions(ontClass, new ArrayList<Restriction>(), DEPTH_LIMIT);
}
private List<Restriction> getRelatedRestrictions(OntClass ontClass,
List<Restriction> relatedRestrictions, int limit) {
limit--;
if (ontClass.isRestriction()) { if (ontClass.isRestriction()) {
relatedRestrictions.add(ontClass.as(Restriction.class)); relatedRestrictions.add(ontClass.as(Restriction.class));
} else if (ontClass.isIntersectionClass()) { } else if (ontClass.isIntersectionClass()) {
IntersectionClass inter = ontClass.as(IntersectionClass.class); IntersectionClass inter = ontClass.as(IntersectionClass.class);
Iterator<? extends OntClass> operIt = inter.listOperands(); Iterator<? extends OntClass> operIt = inter.listOperands();
while (operIt.hasNext()) { while (operIt.hasNext()) {
relatedRestrictions.addAll(getRelatedRestrictions(operIt.next())); OntClass operand = operIt.next();
if (!relatedRestrictions.contains(operand) && limit > 0) {
relatedRestrictions.addAll(
getRelatedRestrictions(
operand, relatedRestrictions, limit));
}
} }
} else { } else {
List<OntClass> superClasses = listSuperClasses(ontClass); List<OntClass> superClasses = listSuperClasses(ontClass);
superClasses.addAll(listEquivalentClasses(ontClass)); superClasses.addAll(listEquivalentClasses(ontClass));
for (OntClass sup : superClasses) { for (OntClass sup : superClasses) {
if (!sup.equals(ontClass)) { if (sup.isAnon() && !sup.equals(ontClass)
relatedRestrictions.addAll(getRelatedRestrictions(sup)); && !relatedRestrictions.contains(ontClass) && limit > 0) {
relatedRestrictions.addAll(
getRelatedRestrictions(sup, relatedRestrictions, limit));
} }
} }
} }

221
webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/KnowledgeBaseUpdater.java
View file

@ -11,6 +11,8 @@ import java.io.FileReader;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
@ -112,126 +114,123 @@ public class KnowledgeBaseUpdater {
log.error("unable to migrate migration metadata " + e.getMessage()); log.error("unable to migrate migration metadata " + e.getMessage());
} }
log.warn("KnowledgeBaseUpdater needs to be modified to work on all graphs!");
OntModel readModel = settings.getUnionOntModelSelector().getABoxModel();
OntModel writeModel = settings.getAssertionOntModelSelector().getABoxModel();
// TODO make sure the ABox update applies to all graphs
log.info("\tupdating the abox"); log.info("\tupdating the abox");
updateABox(changes); updateABox(changes);
}
private void performSparqlConstructAdditions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException { log.info("performing SPARQL CONSTRUCT additions");
performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), readModel, writeModel, ADD);
Model anonModel = performSparqlConstructs(sparqlConstructDir, readModel, true); log.info("performing SPARQL CONSTRUCT retractions");
performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), readModel, writeModel, RETRACT);
if (anonModel == null) {
return;
}
writeModel.enterCriticalSection(Lock.WRITE);
try {
JenaIngestUtils jiu = new JenaIngestUtils();
Model additions = jiu.renameBNodes(anonModel, settings.getDefaultNamespace() + "n", writeModel);
Model actualAdditions = ModelFactory.createDefaultModel();
StmtIterator stmtIt = additions.listStatements();
while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement();
if (!writeModel.contains(stmt)) {
actualAdditions.add(stmt);
}
}
writeModel.add(actualAdditions);
record.recordAdditions(actualAdditions);
} finally {
writeModel.leaveCriticalSection();
}
}
private void performSparqlConstructRetractions(String sparqlConstructDir, OntModel readModel, OntModel writeModel) throws IOException {
Model retractions = performSparqlConstructs(sparqlConstructDir, readModel, false);
if (retractions == null) {
return;
}
writeModel.enterCriticalSection(Lock.WRITE);
try {
writeModel.remove(retractions);
record.recordRetractions(retractions);
} finally {
writeModel.leaveCriticalSection();
}
} }
/** private static final boolean ADD = true;
* Performs a set of arbitrary SPARQL CONSTRUCT queries on the private static final boolean RETRACT = !ADD;
* 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 Model performSparqlConstructs(String sparqlConstructDir,
OntModel readModel,
boolean add) throws IOException {
Model anonModel = ModelFactory.createDefaultModel(); /**
File sparqlConstructDirectory = new File(sparqlConstructDir); * Performs a set of arbitrary SPARQL CONSTRUCT queries on the
* data, for changes that cannot be expressed as simple property
if (!sparqlConstructDirectory.isDirectory()) { * or class additions, deletions, or renamings.
logger.logError(this.getClass().getName() + * Blank nodes created by the queries are given random URIs.
"performSparqlConstructs() expected to find a directory " + * @param sparqlConstructDir
" at " + sparqlConstructDir + ". Unable to execute " + * @param readModel
" SPARQL CONSTRUCTS."); * @param writeModel
return null; * @param add (add = true; retract = false)
} */
private void performSparqlConstructs(String sparqlConstructDir,
File[] sparqlFiles = sparqlConstructDirectory.listFiles(); OntModel readModel, OntModel writeModel,
for (int i = 0; i < sparqlFiles.length; i ++) { boolean add) throws IOException {
File sparqlFile = sparqlFiles[i]; File sparqlConstructDirectory = new File(sparqlConstructDir);
try { log.info("Using SPARQL CONSTRUCT director " + sparqlConstructDirectory);
BufferedReader reader = new BufferedReader(new FileReader(sparqlFile)); if (!sparqlConstructDirectory.isDirectory()) {
StringBuffer fileContents = new StringBuffer(); String logMsg = this.getClass().getName() +
String ln; "performSparqlConstructs() expected to find a directory " +
" at " + sparqlConstructDir + ". Unable to execute " +
while ( (ln = reader.readLine()) != null) { " SPARQL CONSTRUCTS.";
fileContents.append(ln).append('\n'); logger.logError(logMsg);
} log.error(logMsg);
return;
try { }
log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFiles[i].getName()); List<File> sparqlFiles = Arrays.asList(sparqlConstructDirectory.listFiles());
Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ); Collections.sort(sparqlFiles); // queries may depend on being run in a certain order
readModel.enterCriticalSection(Lock.READ); JenaIngestUtils jiu = new JenaIngestUtils();
try { for (File sparqlFile : sparqlFiles) {
QueryExecution qe = QueryExecutionFactory.create(q, readModel); Model anonModel = ModelFactory.createDefaultModel();
long numBefore = anonModel.size(); StringBuffer fileContents = new StringBuffer();
qe.execConstruct(anonModel); try {
long numAfter = anonModel.size(); BufferedReader reader = new BufferedReader(new FileReader(sparqlFile));
long num = numAfter - numBefore; String ln;
while ( (ln = reader.readLine()) != null) {
if (num > 0) { fileContents.append(ln).append('\n');
logger.log((add ? "Added " : "Removed ") + num + }
" statement" + ((num > 1) ? "s" : "") + } catch (FileNotFoundException fnfe) {
" using the SPARQL construct query from file " + sparqlFiles[i].getParentFile().getName() + "/" + sparqlFiles[i].getName()); String logMsg = "WARNING: performSparqlConstructs() could not find " +
" SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.";
logger.log(logMsg);
log.info(logMsg);
continue;
}
try {
log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
Query q = QueryFactory.create(fileContents.toString(), Syntax.syntaxARQ);
readModel.enterCriticalSection(Lock.READ);
try {
QueryExecution qe = QueryExecutionFactory.create(q, readModel);
long numBefore = anonModel.size();
qe.execConstruct(anonModel);
long numAfter = anonModel.size();
long num = numAfter - numBefore;
if (num > 0) {
String logMsg = (add ? "Added " : "Removed ") + num +
" statement" + ((num > 1) ? "s" : "") +
" using the SPARQL construct query from file " +
sparqlFile.getParentFile().getName() +
"/" + sparqlFile.getName();
logger.log(logMsg);
log.info(logMsg);
}
qe.close();
} finally {
readModel.leaveCriticalSection();
}
} catch (Exception e) {
logger.logError(this.getClass().getName() +
".performSparqlConstructs() unable to execute " +
"query at " + sparqlFile + ". Error message is: " + e.getMessage());
log.error(e,e);
}
writeModel.enterCriticalSection(Lock.WRITE);
try {
if(!add) {
writeModel.remove(anonModel);
record.recordRetractions(anonModel);
//log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
} else {
Model additions = jiu.renameBNodes(
anonModel, settings.getDefaultNamespace() + "n", writeModel);
Model actualAdditions = ModelFactory.createDefaultModel();
StmtIterator stmtIt = additions.listStatements();
while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement();
if (!writeModel.contains(stmt)) {
actualAdditions.add(stmt);
} }
qe.close(); }
} finally { writeModel.add(actualAdditions);
readModel.leaveCriticalSection(); //log.info("added " + actualAdditions.size() + " statements from SPARQL CONSTRUCTs");
} record.recordAdditions(actualAdditions);
} catch (Exception e) { }
logger.logError(this.getClass().getName() + } finally {
".performSparqlConstructs() unable to execute " + writeModel.leaveCriticalSection();
"query at " + sparqlFile + ". Error message is: " + e.getMessage()); }
} }
} catch (FileNotFoundException fnfe) { }
logger.log("WARNING: performSparqlConstructs() could not find " +
" SPARQL CONSTRUCT file " + sparqlFile + ". Skipping.");
}
}
return anonModel;
}
private List<AtomicOntologyChange> getAtomicOntologyChanges() private List<AtomicOntologyChange> getAtomicOntologyChanges()

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

@ -158,6 +158,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
private void putNonReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) { private void putNonReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) {
settings.setAskUpdatedQueryFile(ctx.getRealPath(ASK_QUERY_FILE)); settings.setAskUpdatedQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
settings.setDiffFile(ctx.getRealPath(DIFF_FILE)); settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
settings.setSparqlConstructAdditionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/additions"));
settings.setSparqlConstructDeletionsDir(ctx.getRealPath(DATA_DIR + "sparqlConstructs/deletions"));
settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE)); settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
settings.setSuccessRDFFormat("N3"); settings.setSuccessRDFFormat("N3");
} }
@ -174,9 +176,6 @@ public class UpdateKnowledgeBase implements ServletContextListener {
settings.setDataDir(dataDir.toString()); settings.setDataDir(dataDir.toString());
StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'"); StartupStatus.getBean(ctx).info(this, "Updating knowledge base: reports are in '" + dataDir + "'");
settings.setSparqlConstructAdditionsDir(createDirectory(dataDir, "sparqlConstructs", "additions").toString());
settings.setSparqlConstructDeletionsDir(createDirectory(dataDir, "sparqlConstructs", "deletions").toString());
Path changedDir = createDirectory(dataDir, "changedData"); Path changedDir = createDirectory(dataDir, "changedData");
settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString()); settings.setAddedDataFile(changedDir.resolve("addedData.n3").toString());
settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString()); settings.setRemovedDataFile(changedDir.resolve("removedData.n3").toString());