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NIHVIVO-2753 improved getUpdatedSinceIterator() and NIHVIVO-2448 visibility of workflows in arbitrary SDB graphs

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This commit is contained in:
brianjlowe 2011-06-22 21:10:48 +00:00
parent 4e9fa02a3f
commit 9b3a97c736
2 changed files with 72 additions and 70 deletions
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110
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java
View file

@ -66,14 +66,18 @@ public class IndividualDaoSDB extends IndividualDaoJena {
protected Individual makeIndividual(String individualURI) { protected Individual makeIndividual(String individualURI) {
try { try {
return new IndividualSDB(individualURI, this.dwf, datasetMode, getWebappDaoFactory()); return new IndividualSDB(individualURI,
this.dwf,
datasetMode,
getWebappDaoFactory());
} catch (IndividualNotFoundException e) { } catch (IndividualNotFoundException e) {
// If the individual does not exist, return null. // If the individual does not exist, return null.
return null; return null;
} }
} }
private static final Log log = LogFactory.getLog(IndividualDaoSDB.class.getName()); private static final Log log = LogFactory.getLog(
IndividualDaoSDB.class.getName());
@Override @Override
protected OntModel getOntModel() { protected OntModel getOntModel() {
@ -83,7 +87,9 @@ public class IndividualDaoSDB extends IndividualDaoJena {
private static final boolean SKIP_INITIALIZATION = true; private static final boolean SKIP_INITIALIZATION = true;
@Override @Override
public List getIndividualsByVClassURI(String vclassURI, int offset, int quantity ) { public List getIndividualsByVClassURI(String vclassURI,
int offset,
int quantity ) {
if (vclassURI==null) { if (vclassURI==null) {
return null; return null;
@ -253,7 +259,9 @@ public class IndividualDaoSDB extends IndividualDaoJena {
return filteredIndividualList; return filteredIndividualList;
} }
private Individual makeIndividual(String uri, String label, String moniker) { private Individual makeIndividual(String uri,
String label,
String moniker) {
Individual ent = new IndividualSDB(uri, Individual ent = new IndividualSDB(uri,
this.dwf, datasetMode, getWebappDaoFactory(), this.dwf, datasetMode, getWebappDaoFactory(),
SKIP_INITIALIZATION); SKIP_INITIALIZATION);
@ -272,7 +280,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
} }
/** /**
* fills in the Individual objects needed for any ObjectPropertyStatements attached to the specified individual. * fills in the Individual objects needed for any ObjectPropertyStatements
* attached to the specified individual.
* @param entity * @param entity
*/ */
private void fillIndividualsForObjectPropertyStatements(Individual entity){ private void fillIndividualsForObjectPropertyStatements(Individual entity){
@ -280,7 +289,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
try { try {
Iterator e2eIt = entity.getObjectPropertyStatements().iterator(); Iterator e2eIt = entity.getObjectPropertyStatements().iterator();
while (e2eIt.hasNext()) { while (e2eIt.hasNext()) {
ObjectPropertyStatement e2e = (ObjectPropertyStatement) e2eIt.next(); ObjectPropertyStatement e2e =
(ObjectPropertyStatement) e2eIt.next();
e2e.setSubject(makeIndividual(e2e.getSubjectURI())); e2e.setSubject(makeIndividual(e2e.getSubjectURI()));
e2e.setObject(makeIndividual(e2e.getObjectURI())); e2e.setObject(makeIndividual(e2e.getObjectURI()));
} }
@ -298,7 +308,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
* ontology as a data property -- only that it behaves as one. * ontology as a data property -- only that it behaves as one.
*/ */
@Override @Override
public List<Individual> getIndividualsByDataProperty(String dataPropertyUri, String value){ public List<Individual> getIndividualsByDataProperty(String dataPropertyUri,
String value){
Property prop = null; Property prop = null;
if( RDFS.label.getURI().equals( dataPropertyUri )){ if( RDFS.label.getURI().equals( dataPropertyUri )){
prop = RDFS.label; prop = RDFS.label;
@ -324,7 +335,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
//warning: this assumes that any language tags will be EN //warning: this assumes that any language tags will be EN
Literal litv3 = getOntModel().createLiteral(value,"EN"); Literal litv3 = getOntModel().createLiteral(value,"EN");
HashMap<String,Individual> individualsMap = new HashMap<String, Individual>(); HashMap<String,Individual> individualsMap =
new HashMap<String, Individual>();
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
int count = 0; int count = 0;
@ -411,14 +423,16 @@ public class IndividualDaoSDB extends IndividualDaoJena {
} }
@Override @Override
public Iterator getAllOfThisTypeIterator() { public Iterator<Individual> getAllOfThisTypeIterator() {
final List<String> list = final List<String> list =
new LinkedList<String>(); new LinkedList<String>();
// get all labeled resources from any non-tbox and non-metadata graphs. // get all labeled resources from any non-tbox and non-metadata graphs.
String query = "SELECT DISTINCT ?ind WHERE { \n" + String query = "SELECT DISTINCT ?ind WHERE { \n" +
" GRAPH ?g { ?ind <" + RDFS.label.getURI() + "> ?label } \n" + " GRAPH ?g { ?ind <" + RDFS.label.getURI() +
" FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + "> " + "> ?label } \n" +
" FILTER (?g != <" + JenaDataSourceSetupBase
.JENA_APPLICATION_METADATA_MODEL + "> " +
" && !regex(str(?g),\"tbox\")) \n " + " && !regex(str(?g),\"tbox\")) \n " +
"}"; "}";
@ -441,14 +455,21 @@ public class IndividualDaoSDB extends IndividualDaoJena {
w.close(); w.close();
} }
if (list.size() >0){ return getIndividualIterator(list);
log.info("Number of individuals from source: " + list.size());
return new Iterator(){ }
Iterator<String> innerIt = list.iterator();
private Iterator<Individual> getIndividualIterator(
final List<String> individualURIs) {
if (individualURIs.size() >0){
log.info("Number of individuals from source: "
+ individualURIs.size());
return new Iterator<Individual>(){
Iterator<String> innerIt = individualURIs.iterator();
public boolean hasNext() { public boolean hasNext() {
return innerIt.hasNext(); return innerIt.hasNext();
} }
public Object next() { public Individual next() {
String indURI = innerIt.next(); String indURI = innerIt.next();
Individual ind = makeIndividual(indURI); Individual ind = makeIndividual(indURI);
if (ind != null) { if (ind != null) {
@ -467,78 +488,59 @@ public class IndividualDaoSDB extends IndividualDaoJena {
} }
@Override @Override
public Iterator getAllOfThisVClassIterator(String vClassURI) { public Iterator<Individual> getAllOfThisVClassIterator(String vClassURI) {
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
try { try {
List ents = new LinkedList(); List<String> individualURIs = new ArrayList<String>();
OntClass cls = getOntModel().getOntClass(vClassURI); OntClass cls = getOntModel().getOntClass(vClassURI);
Iterator indIt = cls.listInstances(); Iterator indIt = cls.listInstances();
while (indIt.hasNext()) { while (indIt.hasNext()) {
com.hp.hpl.jena.ontology.Individual ind = (com.hp.hpl.jena.ontology.Individual) indIt.next(); com.hp.hpl.jena.ontology.Individual ind =
Individual ent = makeIndividual(ind.getURI()); (com.hp.hpl.jena.ontology.Individual) indIt.next();
if (ent != null) { if (ind.getURI() != null) {
ents.add(ent); individualURIs.add(ind.getURI());
} }
} }
return ents.iterator(); return getIndividualIterator(individualURIs);
} finally { } finally {
getOntModel().leaveCriticalSection(); getOntModel().leaveCriticalSection();
} }
} }
@Override @Override
public Iterator getUpdatedSinceIterator(long updatedSince){ public Iterator<Individual> getUpdatedSinceIterator(long updatedSince){
List ents = new ArrayList(); List<String> individualURIs = new ArrayList<String>();
Date since = new DateTime(updatedSince).toDate(); Date since = new DateTime(updatedSince).toDate();
String sinceStr = xsdDateTimeFormat.format(since); String sinceStr = xsdDateTimeFormat.format(since);
getOntModel().enterCriticalSection(Lock.READ); getOntModel().enterCriticalSection(Lock.READ);
try { try {
Property modTimeProp = MODTIME;
if (modTimeProp == null)
modTimeProp = getOntModel().getProperty(VitroVocabulary.MODTIME);
if (modTimeProp == null)
return null; // throw an exception?
String queryStr = "PREFIX vitro: <"+ VitroVocabulary.vitroURI+"> " + String queryStr = "PREFIX vitro: <"+ VitroVocabulary.vitroURI+"> " +
"PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>" + "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>"+
"SELECT ?ent " + "SELECT ?ent " +
"WHERE { " + "WHERE { " +
" ?ent vitro:modTime ?modTime ." + " ?ent vitro:modTime ?modTime ." +
" FILTER (xsd:dateTime(?modTime) >= \""+sinceStr+"\"^^xsd:dateTime) " + " FILTER (xsd:dateTime(?modTime) >= \""
+ sinceStr + "\"^^xsd:dateTime) " +
"}"; "}";
Query query = QueryFactory.create(queryStr); Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.create(query,getOntModel()); QueryExecution qe = QueryExecutionFactory.create(
query,getOntModel());
try {
ResultSet results = qe.execSelect(); ResultSet results = qe.execSelect();
while (results.hasNext()) { while (results.hasNext()) {
QuerySolution qs = (QuerySolution) results.next(); QuerySolution qs = (QuerySolution) results.next();
Resource res = (Resource) qs.get("?ent"); Resource res = (Resource) qs.get("?ent");
com.hp.hpl.jena.ontology.Individual ent = getOntModel().getIndividual(res.getURI()); if (res.getURI() != null) {
if (ent != null) { individualURIs.add(res.getURI());
boolean userVisible = false;
ClosableIterator typeIt = ent.listRDFTypes(true);
try {
while (typeIt.hasNext()) {
Resource typeRes = (Resource) typeIt.next();
if (typeRes.getNameSpace() == null || (!NONUSER_NAMESPACES.contains(typeRes.getNameSpace()))) {
userVisible = true;
break;
} }
} }
} finally { } finally {
typeIt.close(); qe.close();
}
if (userVisible) {
Individual ind = makeIndividual(ent.getURI());
if (ind != null) {
ents.add(ind);
}
}
}
} }
} finally { } finally {
getOntModel().leaveCriticalSection(); getOntModel().leaveCriticalSection();
} }
return ents.iterator(); return getIndividualIterator(individualURIs);
} }
} }

12
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetup.java
View file

@ -23,7 +23,6 @@ import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory; import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.Syntax; import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -41,7 +40,6 @@ import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ClosableIterator; import com.hp.hpl.jena.util.iterator.ClosableIterator;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties; import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary; import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
@ -55,9 +53,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker; import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaSDBModelMaker;
import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB; import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactorySDB;
import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater; import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils; import edu.cornell.mannlib.vitro.webapp.utils.jena.InitialJenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.utils.jena.NamespaceMapperJena;
public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements javax.servlet.ServletContextListener { public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements javax.servlet.ServletContextListener {
@ -285,8 +281,12 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY); WebappDaoFactorySDB.SDBDatasetMode.INFERENCES_ONLY);
ctx.setAttribute("deductionsWebappDaoFactory", infWadf); ctx.setAttribute("deductionsWebappDaoFactory", infWadf);
OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, OntModel masterUnion = ModelFactory.createOntologyModel(
ModelFactory.createUnion(unionABoxModel, unionTBoxModel)); DB_ONT_MODEL_SPEC, makeDBModel(
bds, WebappDaoFactorySDB.UNION_GRAPH,
DB_ONT_MODEL_SPEC, TripleStoreType.SDB, ctx));
//OntModel masterUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
// ModelFactory.createUnion(unionABoxModel, unionTBoxModel));
unionOms.setFullModel(masterUnion); unionOms.setFullModel(masterUnion);
ctx.setAttribute("jenaOntModel", masterUnion); ctx.setAttribute("jenaOntModel", masterUnion);
WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, bds, storeDesc, defaultNamespace, null, null); WebappDaoFactory wadf = new WebappDaoFactorySDB(unionOms, bds, storeDesc, defaultNamespace, null, null);