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continued work on ISF conversion and data migration

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This commit is contained in:
brianjlowe 2013-08-09 16:23:01 -04:00
parent cbdbe629d1
commit dffc40dd3b
7 changed files with 42 additions and 105 deletions
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4
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java
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@ -955,7 +955,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
} }
} else { } else {
String filename = soln.getLiteral("filename").getLexicalForm(); String filename = soln.getLiteral("filename").getLexicalForm();
log.info("putting " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map"); log.debug("putting " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map");
customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename); customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename);
} }
} }
@ -964,7 +964,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI())); String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI()));
if (customListViewConfigFileName == null) { if (customListViewConfigFileName == null) {
log.info("no list view found for " + op.getURI() + " qualified by " + op.getRangeVClassURI()); log.debug("no list view found for " + op.getURI() + " qualified by " + op.getRangeVClassURI());
customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI())); customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI()));
} }

8
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyDaoJena.java
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@ -721,7 +721,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties)); propInsts.add(getPropInstForPropertyAndRange(op, rangeRes, applicableProperties));
List<String> additionalFauxSubpropertyRangeURIs = getAdditionalFauxSubpropertyRangeURIsForPropertyURI(propertyURI); List<String> additionalFauxSubpropertyRangeURIs = getAdditionalFauxSubpropertyRangeURIsForPropertyURI(propertyURI);
for (String rangeURI : additionalFauxSubpropertyRangeURIs) { for (String rangeURI : additionalFauxSubpropertyRangeURIs) {
if (getWebappDaoFactory().getVClassDao().isSubClassOf(rangeURI, rangeRes.getURI())) { if (rangeRes == null || getWebappDaoFactory().getVClassDao().isSubClassOf(rangeURI, rangeRes.getURI())) {
propInsts.add(getPropInstForPropertyAndRange( propInsts.add(getPropInstForPropertyAndRange(
op, ResourceFactory.createResource(rangeURI), applicableProperties)); op, ResourceFactory.createResource(rangeURI), applicableProperties));
} }
@ -740,7 +740,9 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
Map<String, Resource[]> applicableProperties) { Map<String, Resource[]> applicableProperties) {
PropertyInstance pi = new PropertyInstance(); PropertyInstance pi = new PropertyInstance();
String domainURIStr = getURIStr(op.getDomain()); String domainURIStr = getURIStr(op.getDomain());
if (rangeRes != null) { if (rangeRes == null) {
pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
} else {
String rangeClassURI; String rangeClassURI;
if (rangeRes.isAnon()) { if (rangeRes.isAnon()) {
rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId() rangeClassURI = PSEUDO_BNODE_NS + rangeRes.getId()
@ -757,8 +759,6 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
range.setName(range.getLocalName()); range.setName(range.getLocalName());
} }
pi.setRangeClassName(range.getName()); pi.setRangeClassName(range.getName());
} else {
pi.setRangeClassURI(OWL.Thing.getURI()); // TODO see above
} }
pi.setDomainClassURI(domainURIStr); pi.setDomainClassURI(domainURIStr);
VClass domain = getWebappDaoFactory().getVClassDao() VClass domain = getWebappDaoFactory().getVClassDao()

8
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoJena.java
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@ -462,9 +462,11 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
while (classIt.hasNext()) { while (classIt.hasNext()) {
try { try {
Individual classInd = classIt.next(); Individual classInd = classIt.next();
OntClass cls = classInd.as(OntClass.class); if(classInd.canAs(OntClass.class)) {
if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) { OntClass cls = classInd.as(OntClass.class);
classes.add(new VClassJena(cls,getWebappDaoFactory())); if (!cls.isAnon() && !(NONUSER_NAMESPACES.contains(cls.getNameSpace()))) {
classes.add(new VClassJena(cls,getWebappDaoFactory()));
}
} }
} catch (ClassCastException cce) { } catch (ClassCastException cce) {
log.error(cce, cce); log.error(cce, cce);

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

@ -73,7 +73,7 @@ public class KnowledgeBaseUpdater {
performUpdate(servletContext); performUpdate(servletContext);
} catch (Exception e) { } catch (Exception e) {
logger.logError(e.getMessage()); logger.logError(e.getMessage());
e.printStackTrace(); log.error(e,e);
} }
if (!logger.errorsWritten()) { if (!logger.errorsWritten()) {
@ -300,7 +300,7 @@ public class KnowledgeBaseUpdater {
* needs to be updated to conform to a new ontology version * needs to be updated to conform to a new ontology version
*/ */
public boolean updateRequired(ServletContext servletContext) throws IOException { public boolean updateRequired(ServletContext servletContext) throws IOException {
boolean required = false; boolean required = true;
String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile()); String sparqlQueryStr = loadSparqlQuery(settings.getAskUpdatedQueryFile());
if (sparqlQueryStr == null) { if (sparqlQueryStr == null) {
@ -342,7 +342,7 @@ public class KnowledgeBaseUpdater {
File file = new File(filePath); File file = new File(filePath);
if (!file.exists()) { if (!file.exists()) {
return null; throw new RuntimeException("SPARQL file not found at " + filePath);
} }
BufferedReader reader = new BufferedReader(new FileReader(file)); BufferedReader reader = new BufferedReader(new FileReader(file));
StringBuffer fileContents = new StringBuffer(); StringBuffer fileContents = new StringBuffer();

85
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/AssembleModelsSetup.java
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@ -1,85 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
import java.io.InputStream;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.assembler.Assembler;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelSynchronizer;
/**
* This is the beginning of a more sane and flexible model management system,
* especially necessary for DataStaR.
* Don't use it yet; it's going to change.
* (That part is still insane, I know.)
* @author bjl23
*/
public class AssembleModelsSetup implements ServletContextListener {
private static final Log log = LogFactory.getLog(AssembleModelsSetup.class);
private List<Model> assembledModels = new LinkedList<Model>();
private String ASSEMBLERS_DIR_PATH = "/WEB-INF/assemblers/";
private Resource ASSEMBLER_OBJECT = ResourceFactory.createProperty("http://jena.hpl.hp.com/2005/11/Assembler#Object");
private String SYNTAX = "N3";
public void contextInitialized(ServletContextEvent sce) {
OntModel jenaOntModel = ModelAccess.on(sce.getServletContext()).getBaseOntModel();
// read assemblers out of assemblers directory
Set pathSet = sce.getServletContext().getResourcePaths(ASSEMBLERS_DIR_PATH);
for (String path : (Set<String>)pathSet) {
InputStream assemblerInputStream = sce.getServletContext().getResourceAsStream(path);
Model assemblerModel = ModelFactory.createDefaultModel();
try {
assemblerModel.read(assemblerInputStream, null, SYNTAX);
ExtendedIterator assemblerIt = assemblerModel.listResourcesWithProperty(RDF.type,ASSEMBLER_OBJECT);
while (assemblerIt.hasNext()) {
Resource assemblerObj = (Resource) assemblerIt.next();
Model assembledModel = Assembler.general.openModel(assemblerObj);
/* special stuff here */
Model memModel = ModelFactory.createDefaultModel();
memModel.add(assembledModel);
memModel.register(new ModelSynchronizer(assembledModel));
/* end special stuff */
if (assembledModel != null) {
jenaOntModel.addSubModel(memModel);
}
}
if (assemblerIt != null) {
assemblerIt.close();
}
} catch (Exception e) {
log.error("Unable to use assembler at "+path);
}
}
System.out.println("ContextListener AssembleModelsSetup done");
}
public void contextDestroyed(ServletContextEvent sce) {
for (Model model : assembledModels) {
if (model != null) {
model.close();
}
}
}
}

27
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
View file

@ -54,6 +54,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
private final static Log log = LogFactory.getLog(UpdateKnowledgeBase.class); private final static Log log = LogFactory.getLog(UpdateKnowledgeBase.class);
private static final String DATA_DIR = "/WEB-INF/ontologies/update/"; private static final String DATA_DIR = "/WEB-INF/ontologies/update/";
private static final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
private static final String ASK_QUERY_FILE = DATA_DIR + "askUpdated.sparql";
private static final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
private static final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/"; private static final String OLD_TBOX_MODEL_DIR = DATA_DIR + "oldVersion/";
private static final String NEW_TBOX_MODEL_DIR = "/WEB-INF/filegraph/tbox/"; private static final String NEW_TBOX_MODEL_DIR = "/WEB-INF/filegraph/tbox/";
private static final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/"; private static final String OLD_TBOX_ANNOTATIONS_DIR = DATA_DIR + "oldAnnotations/";
@ -75,6 +78,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
try { try {
UpdateSettings settings = new UpdateSettings(); UpdateSettings settings = new UpdateSettings();
putReportingPathsIntoSettings(ctx, settings); putReportingPathsIntoSettings(ctx, settings);
putNonReportingPathsIntoSettings(ctx, settings);
WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory(); WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
settings.setDefaultNamespace(wadf.getDefaultNamespace()); settings.setDefaultNamespace(wadf.getDefaultNamespace());
@ -113,7 +117,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH)); OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView); settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
} catch (Exception e) { } catch (Exception e) {
log.info("unable to read display model migration files, display model not migrated. " + e.getMessage()); log.info("Unable to read display model migration files. " + e.getMessage());
tryMigrateDisplay = false; tryMigrateDisplay = false;
} }
@ -121,8 +125,11 @@ public class UpdateKnowledgeBase implements ServletContextListener {
KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings); KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
try { try {
if (ontologyUpdater.updateRequired(ctx)) { if (!ontologyUpdater.updateRequired(ctx)) {
log.info("No data migration required.");
} else {
ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE); ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
log.info("Data migration required");
ontologyUpdater.update(ctx); ontologyUpdater.update(ctx);
if (tryMigrateDisplay) { if (tryMigrateDisplay) {
try { try {
@ -144,6 +151,17 @@ public class UpdateKnowledgeBase implements ServletContextListener {
} }
} }
/**
* Set the paths for the files that specify how to perform the update
*/
private void putNonReportingPathsIntoSettings(ServletContext ctx, UpdateSettings settings) {
settings.setAskUpdatedQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
settings.setSuccessRDFFormat("N3");
}
/** /**
* Create the directories where we will report on the update. * Create the directories where we will report on the update.
* Put the paths for the directories and files into the settings object. * Put the paths for the directories and files into the settings object.
@ -156,11 +174,6 @@ 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.setAskUpdatedQueryFile(dataDir.resolve("askUpdated.sparql").toString());
settings.setDiffFile(dataDir.resolve("diff.tab.txt").toString());
settings.setSuccessAssertionsFile(dataDir.resolve("success.n3").toString());
settings.setSuccessRDFFormat("N3");
settings.setSparqlConstructAdditionsDir(createDirectory(dataDir, "sparqlConstructs", "additions").toString()); settings.setSparqlConstructAdditionsDir(createDirectory(dataDir, "sparqlConstructs", "additions").toString());
settings.setSparqlConstructDeletionsDir(createDirectory(dataDir, "sparqlConstructs", "deletions").toString()); settings.setSparqlConstructDeletionsDir(createDirectory(dataDir, "sparqlConstructs", "deletions").toString());

9
webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/GroupedPropertyList.java
View file

@ -20,6 +20,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance; import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao; import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao; import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao; import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao; import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
@ -175,7 +176,13 @@ public class GroupedPropertyList extends BaseTemplateModel {
// There is no ObjectPropertyDao.getAllPossibleObjectPropertiesForIndividual() parallel to // There is no ObjectPropertyDao.getAllPossibleObjectPropertiesForIndividual() parallel to
// DataPropertyDao.getAllPossibleDatapropsForIndividual(). The comparable method for object properties // DataPropertyDao.getAllPossibleDatapropsForIndividual(). The comparable method for object properties
// is defined using PropertyInstance rather than ObjectProperty. // is defined using PropertyInstance rather than ObjectProperty.
PropertyInstanceDao piDao = wdf.getPropertyInstanceDao();
// Getting WebappDaoFactory from the session because we can't have the filtering
// that gets applied to the request. This breaks blank node structures in the
// restrictions that determine applicable properties.
WebappDaoFactory wadf = ModelAccess.on(vreq.getSession().getServletContext()).getWebappDaoFactory();
PropertyInstanceDao piDao = wadf.getPropertyInstanceDao();
Collection<PropertyInstance> allPropInstColl = piDao Collection<PropertyInstance> allPropInstColl = piDao
.getAllPossiblePropInstForIndividual(subject.getURI()); .getAllPossiblePropInstForIndividual(subject.getURI());
if (allPropInstColl != null) { if (allPropInstColl != null) {