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Working on new navigation controllers and model. NIHVIVO-633

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bdc34 2010-06-22 21:34:13 +00:00
parent 1cdef7f6e4
commit 6c59f2185a
8 changed files with 332 additions and 6 deletions
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11
webapp/config/web.xml
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@ -99,7 +99,7 @@
</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. -->
<!-- Changing the class name sets the kinds of inferences that are materialized. -->
<!-- See documentation for details. -->
<!-- If used, must be run after JenaDataSourceSetup -->
@ -295,6 +295,15 @@
<url-pattern>/SearchIndex</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>NavigationController</servlet-name>
<servlet-class>edu.cornell.mannlib.vitro.webapp.controller.freemarker.NavigationController</servlet-class>
</servlet>
<servlet-mapping>
<servlet-name>NavigationController</servlet-name>
<url-pattern>/nav/*</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>TestController</servlet-name>
<servlet-class>edu.cornell.mannlib.vitro.webapp.controller.TestController</servlet-class>

215
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/NavigationController.java Normal file
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@ -0,0 +1,215 @@
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.NodeIterator;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.web.DisplayVocabulary;
public class NavigationController extends FreeMarkerHttpServlet {
private static final long serialVersionUID = 1L;
private static final Log log = LogFactory.getLog(NavigationController.class.getName());
//private Map<Pattern,String> urlPatternToURI;
private NavigationURLPatternListener urlPatterns;
@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
OntModel displayOntModel = (OntModel)config.getServletContext().getAttribute("displayOntModel");
this.urlPatterns = new NavigationURLPatternListener( );
displayOntModel.getBaseModel().register( urlPatterns );
}
@Override
protected String getBody() {
OntModel displayOntModel = (OntModel)getServletContext().getAttribute("displayOntModel");
OntModel jenaOntModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
//figure out what is being requested
Individual ind = urlPatterns.getDisplayIndividual(vreq.getPathInfo(),displayOntModel);
Map<String,Object> values = getValues(ind, displayOntModel,jenaOntModel, getValuesFromRequest(/*?*/) );
String template = getTemplate(ind, displayOntModel);
return mergeBodyToTemplate(template, values);
}
private Map<String,Object>getValuesFromRequest(){
// TODO: figure out how to get request for FreeMarkerHttpServlet.
return Collections.emptyMap();
}
private String getTemplate(Individual ind, OntModel displayOntModel) {
if( ind == null ) return "defaultBody";
// check vitroDisplay:requiresBodyTemplate
displayOntModel.enterCriticalSection(Model.READ);
StmtIterator it = displayOntModel.listStatements(ind, DisplayVocabulary.REQUIRES_BODY_TEMPLATE, (RDFNode) null);
//NodeIterator it = ind.listPropertyValues(DisplayVocabulary.REQUIRES_BODY_TEMPLATE);
try{
while(it.hasNext()){
Statement stmt = it.nextStatement();
if( stmt.getObject().isLiteral() ){
String template = ((Literal)stmt.getObject().as(Literal.class)).getLexicalForm();
if( template != null && template.length() > 0 ){
return template;
}
}
}
}finally{
it.close();
displayOntModel.leaveCriticalSection();
}
return "defaultBody";
}
Map<String,Object> getValues(Individual ind, OntModel displayOntModel, OntModel assertionModel, Map<String,Object> baseValues){
if( ind == null ) return Collections.emptyMap();
/* Figure out what ValueFactories are specified in the display ontology for this individual. */
Set<ValueFactory> valueFactories = new HashSet<ValueFactory>();
displayOntModel.enterCriticalSection(Model.READ);
StmtIterator stmts = ind.listProperties(DisplayVocabulary.REQUIRES_VALUES);
try{
while(stmts.hasNext()){
Statement stmt = stmts.nextStatement();
RDFNode obj = stmt.getObject();
valueFactories.addAll(getValueFactory(obj,displayOntModel));
}
}finally{
stmts.close();
displayOntModel.leaveCriticalSection();
}
/* Get values from the ValueFactories. */
HashMap<String,Object> values = new HashMap<String,Object>();
values.putAll(baseValues);
for(ValueFactory vf : valueFactories){
values.putAll( vf.getValues(assertionModel, values));
}
return values;
}
protected Set<ValueFactory> getValueFactory( RDFNode valueNode, OntModel displayOntModel) {
//maybe use jenabean or owl2java for this?
if( valueNode.isResource() ){
Resource res = (Resource)valueNode.as(Resource.class);
Statement stmt = res.getProperty(DisplayVocabulary.JAVA_CLASS_NAME);
if( stmt == null || !stmt.getObject().isLiteral() ){
log.debug("Cannot build value factory: java class was " + stmt.getObject());
return Collections.emptySet();
}
String javaClassName = ((Literal)stmt.getObject().as(Literal.class)).getLexicalForm();
if( javaClassName == null || javaClassName.length() == 0 ){
log.debug("Cannot build value factory: no java class was set.");
return Collections.emptySet();
}
Class<?> clazz;
Object newObj;
try {
clazz = Class.forName(javaClassName);
} catch (ClassNotFoundException e) {
log.debug("Cannot build value factory: no class found for " + javaClassName);
return Collections.emptySet();
}
try {
newObj = clazz.newInstance();
} catch (Exception e) {
log.debug("Cannot build value factory: exception while creating object of java class " + javaClassName + " " + e.getMessage());
return Collections.emptySet();
}
if( newObj instanceof ValueFactory){
ValueFactory valueFactory = (ValueFactory)newObj;
return Collections.singleton( valueFactory );
}else{
log.debug("Cannot build value factory: " + javaClassName + " does not implement " + ValueFactory.class.getName() );
return Collections.emptySet();
}
}else{
log.debug("Cannot build value factory for " + valueNode);
return Collections.emptySet();
}
}
interface ValueFactory {
void configure( Map<String,String> config);
Map<String,Object> getValues(OntModel model, Map<String,Object> values);
}
@Override
protected String getTitle() {
// TODO Auto-generated method stub
return super.getTitle();
}
private class NavigationURLPatternListener extends StatementListener {
private Map<Pattern,String> urlPatternToURI;
public synchronized Map<Pattern,String> getUrlPatternToURIMap(){
if( urlPatternToURI == null || urlPatternToURI.isEmpty() ){
this.urlPatternToURI = buildUrlPatternToURI();
}
return urlPatternToURI;
}
protected synchronized void invalidateURLPatternMap(){
this.urlPatternToURI = null;
}
public Individual getDisplayIndividual( String pathInfo , OntModel displayModel){
Map<Pattern,String> map = getUrlPatternToURIMap();
for( Pattern regex : map.keySet()){
Matcher m = regex.matcher(pathInfo);
if(m.matches() ){
return displayModel.getIndividual(map.get(regex));
}
}
return null;
}
protected synchronized Map<Pattern,String> buildUrlPatternToURI(){
OntModel displayModel = (OntModel)getServletContext().getAttribute("displayOntModel");
Map<Pattern,String> map = new HashMap<Pattern,String>();
StmtIterator stmts = displayModel.listStatements(null, DisplayVocabulary.URL_MAPPING,(Literal)null);
while(stmts.hasNext()){
Statement stmt = stmts.nextStatement();
if( stmt.getSubject().isURIResource() && stmt.getObject().isLiteral()){
Resource r = (Resource)stmt.getSubject().as( Resource.class);
Pattern regex = Pattern.compile(stmt.getLiteral().getLexicalForm());
map.put(regex,r.getURI());
}
}
return map;
}
@Override
public void addedStatement(Statement s) {
invalidateURLPatternMap();
}
@Override
public void removedStatement(Statement s) {
invalidateURLPatternMap();
}
}
}

7
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SimpleOntModelSelector.java
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@ -21,6 +21,7 @@ public class SimpleOntModelSelector implements OntModelSelector {
private OntModel userAccountsModel;
private OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
private OntModel displayModel;
/**
* Construct an OntModelSelector with a bunch of empty models
@ -116,4 +117,10 @@ public class SimpleOntModelSelector implements OntModelSelector {
this.userAccountsModel = userAccountsModel;
}
public void setDisplayModel(OntModel displayModel) {
this.displayModel = displayModel;
}
public OntModel getDisplayModel(){
return this.displayModel;
}
}

9
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetup.java
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@ -8,7 +8,6 @@ import javax.servlet.ServletContextEvent;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
@ -17,7 +16,6 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ClosableIterator;
import com.hp.hpl.jena.vocabulary.OWL;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
@ -61,6 +59,13 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
inferenceOms.setUserAccountsModel(userAccountsModel);
unionOms.setUserAccountsModel(userAccountsModel);
OntModel displayModel = ontModelFromContextAttribute(sce.getServletContext(),"displayOntModel");
OntModel displayUnionModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(displayModel, unionModel));
sce.getServletContext().setAttribute("displayOntModel", displayUnionModel);
baseOms.setDisplayModel(displayModel);
inferenceOms.setDisplayModel(displayModel);
unionOms.setDisplayModel(displayModel);
sce.getServletContext().setAttribute("baseOntModel", memModel);
WebappDaoFactory baseWadf = new WebappDaoFactoryJena(baseOms, defaultNamespace, null, null);
sce.getServletContext().setAttribute("assertionsWebappDaoFactory",baseWadf);

2
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java
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@ -39,6 +39,7 @@ public class JenaDataSourceSetupBase {
protected static String USERPATH = BASE+"user/";
protected static String SYSTEMPATH = BASE+"system/";
protected static String AUTHPATH = BASE+"auth/";
protected static String APPPATH = BASE+"app/";
String DB_USER = "jenatest"; // database user id
String DB_PASSWD = "jenatest"; // database password
@ -49,6 +50,7 @@ public class JenaDataSourceSetupBase {
static final String JENA_INF_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-inf";
static final String JENA_USER_ACCOUNTS_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts";
static final String JENA_APPLICATION_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
static final String JENA_DISPLAY_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata";
static final String DEFAULT_DEFAULT_NAMESPACE = "http://vitro.mannlib.cornell.edu/ns/default#";

13
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaPersistentDataSourceSetup.java
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@ -104,6 +104,19 @@ public class JenaPersistentDataSourceSetup extends JenaDataSourceSetupBase imple
log.error("Unable to load user accounts model from DB", t);
}
// display, editing and navigation Model
try {
Model appDbModel = makeDBModelFromConfigurationProperties(JENA_DISPLAY_METADATA_MODEL, DB_ONT_MODEL_SPEC);
if (appDbModel.size() == 0)
readOntologyFilesInPathSet(APPPATH, sce.getServletContext(),appDbModel);
OntModel appModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
appModel.add(appDbModel);
appModel.getBaseModel().register(new ModelSynchronizer(appDbModel));
sce.getServletContext().setAttribute("displayOntModel", appModel);
} catch (Throwable t) {
log.error("Unable to load user application configuration model from DB", t);
}
sce.getServletContext().setAttribute("jenaOntModel", memModel);
}

74
webapp/src/edu/cornell/mannlib/vitro/webapp/web/DisplayVocabulary.java Normal file
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@ -0,0 +1,74 @@
package edu.cornell.mannlib.vitro.webapp.web;
import com.hp.hpl.jena.ontology.DatatypeProperty;
import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.ObjectProperty;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
/**
* Vocabulary definitions from /home/bdc34/swoop/display.rdf
* @author Auto-generated by schemagen on 18 Jun 2010 16:57
*/
public class DisplayVocabulary {
/** <p>The ontology model that holds the vocabulary terms</p> */
private static OntModel m_model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM, null );
/** <p>The namespace of the vocabulary as a string</p> */
public static final String NS = "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#";
/** <p>The namespace of the vocabulary as a string</p>
* @see #NS */
public static String getURI() {return NS;}
/** <p>The namespace of the vocabulary as a resource</p> */
public static final Resource NAMESPACE = m_model.createResource( NS );
public static final ObjectProperty REQUIRES_VALUES = m_model.createObjectProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#requiresValues" );
public static final ObjectProperty TO_PAGE = m_model.createObjectProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#toPage" );
/** <p>Java package and class name. ex edu.cornell.mannlib.vitro.webapps.functions.ExampleFunction</p> */
public static final DatatypeProperty JAVA_CLASS_NAME = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#javaClassName" );
public static final DatatypeProperty MENU_POSITION = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#menuPosition" );
public static final DatatypeProperty PARAMETER_NAME = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#parameterName" );
public static final DatatypeProperty PARAMETER_VALUE = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#parameterValue" );
public static final DatatypeProperty REQUIRES_BODY_TEMPLATE = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#requiresBodyTemplate" );
/** <p>Values from HttpRequest.getPathInfo() will be mapped to values from urlMapping.</p> */
public static final DatatypeProperty URL_MAPPING = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping" );
/** <p>This represents a menu item or other general navigation item.</p> */
public static final OntClass NAVIGATION_ELEMENT = m_model.createClass( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#NavigationElement" );
/** <p>Class of pages.</p> */
public static final OntClass PAGE = m_model.createClass( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page" );
//public static final Individual EVENTS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Events", PAGE );
//public static final Individual EVENTS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#EventsMenuItem", NAVIGATION_ELEMENT );
//public static final Individual HOME = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Home", PAGE );
//public static final Individual HOME_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#HomeMenuItem", NAVIGATION_ELEMENT );
//public static final Individual ORGANIZATIONS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations", PAGE );
//public static final Individual ORGANIZATIONS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsMenuItem", NAVIGATION_ELEMENT );
//public static final Individual PEOPLE = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#People", PAGE );
//public static final Individual PEOPLE_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PeopleMenuItem", NAVIGATION_ELEMENT );
//public static final Individual PUBLICATIONS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Publications", PAGE );
//public static final Individual PUBLICATIONS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PublicationsMenuItem", NAVIGATION_ELEMENT );
}

1
webapp/web/templates/freemarker/body/home.ftl Normal file
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@ -0,0 +1 @@
<h1>Welcome to VIVO</h1>