litvinovg/vitro
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

improvements to blank node handling in bulk deletion

Browse source
This commit is contained in:
brianjlowe 2012-06-08 19:38:04 +00:00
parent cef7b583e2
commit b480cb2eea
78 changed files with 5882 additions and 605 deletions
Download patch file Download diff file Expand all files Collapse all files

76
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropEditController.java
View file

@ -1,44 +1,44 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.edit;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vedit.beans.EditProcessObject;
import edu.cornell.mannlib.vedit.beans.FormObject;
import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vedit.beans.EditProcessObject;
import edu.cornell.mannlib.vedit.beans.FormObject;
import edu.cornell.mannlib.vedit.controller.BaseEditController;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
public class DatapropEditController extends BaseEditController {
private static final Log log = LogFactory.getLog(DatapropEditController.class.getName());
public void doPost (HttpServletRequest request, HttpServletResponse response) {
if (!isAuthorizedToDisplayPage(request, response, SimplePermission.EDIT_ONTOLOGY.ACTIONS)) {
return;
}
VitroRequest vreq = new VitroRequest(request);
public void doPost (HttpServletRequest request, HttpServletResponse response) {
if (!isAuthorizedToDisplayPage(request, response, SimplePermission.EDIT_ONTOLOGY.ACTIONS)) {
return;
}
VitroRequest vreq = new VitroRequest(request);
final int NUM_COLS=15;
@ -56,7 +56,7 @@ public class DatapropEditController extends BaseEditController {
results.add("range datatype");
results.add("group");
results.add("display tier");
results.add("display limit");
results.add("data entry limit");
results.add("example");
results.add("description");
results.add("public description");
@ -169,8 +169,8 @@ public class DatapropEditController extends BaseEditController {
}
}
request.setAttribute("equivalentProperties", eqProperties);
ApplicationBean appBean = vreq.getAppBean();
ApplicationBean appBean = vreq.getAppBean();
request.setAttribute("epoKey",epo.getKey());
request.setAttribute("datatypeProperty", dp);

160
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListDatatypePropertiesController.java Normal file
View file

@ -0,0 +1,160 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
public class ListDatatypePropertiesController extends FreemarkerHttpServlet {
private static Log log = LogFactory.getLog( ListDatatypePropertiesController.class );
private static final String TEMPLATE_NAME = "siteAdmin-objectPropHierarchy.ftl";
@Override
protected Actions requiredActions(VitroRequest vreq) {
return SimplePermission.EDIT_ONTOLOGY.ACTIONS;
}
@Override
protected ResponseValues processRequest(VitroRequest vreq) {
Map<String, Object> body = new HashMap<String, Object>();
try {
body.put("displayOption", "all");
body.put("pageTitle", "All Data Properties");
body.put("propertyType", "data");
String noResultsMsgStr = "No data properties found";
String ontologyUri = vreq.getParameter("ontologyUri");
DataPropertyDao dao = vreq.getFullWebappDaoFactory().getDataPropertyDao();
VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
DatatypeDao dDao = vreq.getFullWebappDaoFactory().getDatatypeDao();
PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
List<DataProperty> props = new ArrayList<DataProperty>();
if (vreq.getParameter("propsForClass") != null) {
noResultsMsgStr = "There are no data properties that apply to this class.";
Collection <DataProperty> dataProps = dao.getDataPropertiesForVClass(vreq.getParameter("vclassUri"));
Iterator<DataProperty> dataPropIt = dataProps.iterator();
HashSet<String> propURIs = new HashSet<String>();
while (dataPropIt.hasNext()) {
DataProperty dp = dataPropIt.next();
if (!(propURIs.contains(dp.getURI()))) {
propURIs.add(dp.getURI());
DataProperty prop = dao.getDataPropertyByURI(dp.getURI());
if (prop != null) {
props.add(prop);
}
}
}
} else {
props = dao.getAllDataProperties();
}
if (ontologyUri != null) {
List<DataProperty> scratch = new ArrayList<DataProperty>();
for (DataProperty p: props) {
if (p.getNamespace().equals(ontologyUri)) {
scratch.add(p);
}
}
props = scratch;
}
if (props != null) {
Collections.sort(props);
}
String json = new String();
int counter = 0;
if (props != null) {
if (props.size()==0) {
json = "{ \"name\": \"" + noResultsMsgStr + "\" }";
} else {
for (DataProperty prop: props) {
if ( counter > 0 ) {
json += ", ";
}
String nameStr = prop.getPublicName()==null ? prop.getName()==null ? prop.getURI()==null ? "(no name)" : prop.getURI() : prop.getName() : prop.getPublicName();
try {
json += "{ \"name\": \"<a href='datapropEdit?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>" + nameStr + "</a>\", ";
} catch (Exception e) {
json += "{ \"name\": \"" + nameStr + "\", ";
}
json += "\"data\": { \"internalName\": \"" + prop.getLocalNameWithPrefix() + "\", ";
/* VClass vc = null;
String domainStr="";
if (prop.getDomainClassURI() != null) {
vc = vcDao.getVClassByURI(prop.getDomainClassURI());
if (vc != null) {
try {
domainStr="<a href=\"vclassEdit?uri="+URLEncoder.encode(prop.getDomainClassURI(),"UTF-8")+"\">"+vc.getName()+"</a>";
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
}
}
}
*/
VClass vc = (prop.getDomainClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainClassURI()) : null;
String domainStr = (vc != null) ? vc.getLocalNameWithPrefix() : "";
json += "\"domainVClass\": \"" + domainStr + "\", " ;
Datatype rangeDatatype = dDao.getDatatypeByURI(prop.getRangeDatatypeURI());
String rangeDatatypeStr = (rangeDatatype==null)?prop.getRangeDatatypeURI():rangeDatatype.getName();
json += "\"rangeVClass\": \"" + rangeDatatypeStr + "\", " ;
if (prop.getGroupURI() != null) {
PropertyGroup pGroup = pgDao.getGroupByURI(prop.getGroupURI());
json += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" } } " ;
} else {
json += "\"group\": \"unspecified\" } }" ;
}
counter += 1;
}
}
body.put("jsonTree",json);
}
} catch (Throwable t) {
t.printStackTrace();
}
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
}

190
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ListPropertyWebappsController.java Normal file
View file

@ -0,0 +1,190 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
public class ListPropertyWebappsController extends FreemarkerHttpServlet {
private static Log log = LogFactory.getLog( ListPropertyWebappsController.class );
private static final String TEMPLATE_NAME = "siteAdmin-objectPropHierarchy.ftl";
@Override
protected Actions requiredActions(VitroRequest vreq) {
return SimplePermission.EDIT_ONTOLOGY.ACTIONS;
}
@Override
protected ResponseValues processRequest(VitroRequest vreq) {
Map<String, Object> body = new HashMap<String, Object>();
try {
body.put("displayOption", "all");
body.put("pageTitle", "All Object Properties");
body.put("propertyType", "object");
String noResultsMsgStr = "No object properties found";
String ontologyUri = vreq.getParameter("ontologyUri");
ObjectPropertyDao dao = vreq.getFullWebappDaoFactory().getObjectPropertyDao();
PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory().getPropertyInstanceDao();
VClassDao vcDao = vreq.getFullWebappDaoFactory().getVClassDao();
PropertyGroupDao pgDao = vreq.getFullWebappDaoFactory().getPropertyGroupDao();
String vclassURI = vreq.getParameter("vclassUri");
List props = new ArrayList();
if (vreq.getParameter("propsForClass") != null) {
noResultsMsgStr = "There are no object properties that apply to this class.";
// incomplete list of classes to check, but better than before
List<String> superclassURIs = vcDao.getAllSuperClassURIs(vclassURI);
superclassURIs.add(vclassURI);
superclassURIs.addAll(vcDao.getEquivalentClassURIs(vclassURI));
Map<String, PropertyInstance> propInstMap = new HashMap<String, PropertyInstance>();
for (String classURI : superclassURIs) {
Collection<PropertyInstance> propInsts = piDao.getAllPropInstByVClass(classURI);
for (PropertyInstance propInst : propInsts) {
propInstMap.put(propInst.getPropertyURI(), propInst);
}
}
List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
propInsts.addAll(propInstMap.values());
Collections.sort(propInsts);
Iterator propInstIt = propInsts.iterator();
HashSet propURIs = new HashSet();
while (propInstIt.hasNext()) {
PropertyInstance pi = (PropertyInstance) propInstIt.next();
if (!(propURIs.contains(pi.getPropertyURI()))) {
propURIs.add(pi.getPropertyURI());
ObjectProperty prop = (ObjectProperty) dao.getObjectPropertyByURI(pi.getPropertyURI());
if (prop != null) {
props.add(prop);
}
}
}
} else {
props = (vreq.getParameter("iffRoot")!=null)
? dao.getRootObjectProperties()
: dao.getAllObjectProperties();
}
OntologyDao oDao = vreq.getFullWebappDaoFactory().getOntologyDao();
HashMap<String,String> ontologyHash = new HashMap<String,String>();
Iterator propIt = props.iterator();
List<ObjectProperty> scratch = new ArrayList();
while (propIt.hasNext()) {
ObjectProperty p = (ObjectProperty) propIt.next();
if (p.getNamespace()!=null) {
if( !ontologyHash.containsKey( p.getNamespace() )){
Ontology o = (Ontology)oDao.getOntologyByURI(p.getNamespace());
if (o==null) {
if (!VitroVocabulary.vitroURI.equals(p.getNamespace())) {
log.debug("doGet(): no ontology object found for the namespace "+p.getNamespace());
}
} else {
ontologyHash.put(p.getNamespace(), o.getName() == null ? p.getNamespace() : o.getName());
}
}
if (ontologyUri != null && p.getNamespace().equals(ontologyUri)) {
scratch.add(p);
}
}
}
if (ontologyUri != null) {
props = scratch;
}
if (props != null) {
Collections.sort(props, new ShowObjectPropertyHierarchyController.ObjectPropertyAlphaComparator());
}
String json = new String();
int counter = 0;
if (props != null) {
if (props.size()==0) {
json = "{ \"name\": \"" + noResultsMsgStr + "\" }";
} else {
Iterator propsIt = props.iterator();
while (propsIt.hasNext()) {
if ( counter > 0 ) {
json += ", ";
}
ObjectProperty prop = (ObjectProperty) propsIt.next();
String propNameStr = ShowObjectPropertyHierarchyController.getDisplayLabel(prop);
try {
json += "{ \"name\": \"<a href='./propertyEdit?uri="+URLEncoder.encode(prop.getURI(),"UTF-8")+"'>"
+ propNameStr + "</a>\", ";
} catch (Exception e) {
json += "{ \"name\": \"" + propNameStr + "\", ";
}
json += "\"data\": { \"internalName\": \"" + prop.getLocalNameWithPrefix() + "\", ";
VClass vc = (prop.getDomainVClassURI() != null) ? vcDao.getVClassByURI(prop.getDomainVClassURI()) : null;
String domainStr = (vc != null) ? vc.getLocalNameWithPrefix() : "";
json += "\"domainVClass\": \"" + domainStr + "\", " ;
vc = (prop.getRangeVClassURI() != null) ? vcDao.getVClassByURI(prop.getRangeVClassURI()) : null;
String rangeStr = (vc != null) ? vc.getLocalNameWithPrefix() : "";
json += "\"rangeVClass\": \"" + rangeStr + "\", " ;
if (prop.getGroupURI() != null) {
PropertyGroup pGroup = pgDao.getGroupByURI(prop.getGroupURI());
json += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" } } " ;
} else {
json += "\"group\": \"unspecified\" } }" ;
}
counter += 1;
}
}
body.put("jsonTree",json);
}
} catch (Throwable t) {
t.printStackTrace();
}
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
}

13
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowClassHierarchyController.java
View file

@ -11,7 +11,6 @@ import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@ -30,7 +29,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.email.FreemarkerEmailFactory;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao;
@ -47,8 +45,6 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
private VClassDao vcDao = null;
private int previous_posn = 0;
private int childCount = 0;
private int uriCounter = 0;
@Override
protected Actions requiredActions(VitroRequest vreq) {
@ -116,7 +112,7 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
while (rootIt.hasNext()) {
VClass root = (VClass) rootIt.next();
if (root != null) {
json += addChildren(vreq.getFullWebappDaoFactory(), root, 0, ontologyUri,counter,"parent");
json += addChildren(vreq.getFullWebappDaoFactory(), root, 0, ontologyUri,counter);
counter += 1;
}
}
@ -134,7 +130,7 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
private String addChildren(WebappDaoFactory wadf, VClass parent, int position, String ontologyUri, int counter, String status) {
private String addChildren(WebappDaoFactory wadf, VClass parent, int position, String ontologyUri, int counter) {
String rowElts = addVClassDataToResultsList(wadf, parent, position, ontologyUri, counter);
int childShift = (rowElts.length() > 0) ? 1 : 0; // if addVClassDataToResultsList filtered out the result, don't shift the children over
int length = rowElts.length();
@ -157,7 +153,7 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
Iterator childClassIt = childClasses.iterator();
while (childClassIt.hasNext()) {
VClass child = (VClass) childClassIt.next();
leaves += addChildren(wadf, child, position + childShift, ontologyUri, counter, "child");
leaves += addChildren(wadf, child, position + childShift, ontologyUri, counter);
if (!childClassIt.hasNext()) {
if ( ontologyUri == null ) {
leaves += " }] ";
@ -166,15 +162,12 @@ public class ShowClassHierarchyController extends FreemarkerHttpServlet {
// need this for when we show the classes associated with an ontology
String ending = leaves.substring(leaves.length() - 2, leaves.length());
if ( ending.equals("] ") ) {
log.debug("[1] leaves += }]");
leaves += "}]";
}
else if ( ending.equals(" [") ){
log.debug("[2] leaves += ]");
leaves += "] ";
}
else {
log.debug("[3] leaves += }]");
leaves += "}]";
}
}

251
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowDataPropertyHierarchyController.java Normal file
View file

@ -0,0 +1,251 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.net.URLEncoder;
import java.text.Collator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Datatype;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
public class ShowDataPropertyHierarchyController extends FreemarkerHttpServlet {
private static final Log log = LogFactory.getLog(ShowDataPropertyHierarchyController.class.getName());
private static final String TEMPLATE_NAME = "siteAdmin-objectPropHierarchy.ftl";
private int MAXDEPTH = 5;
private DataPropertyDao dpDao = null;
private VClassDao vcDao = null;
private PropertyGroupDao pgDao = null;
private DatatypeDao dDao = null;
private int previous_posn = 0;
@Override
protected Actions requiredActions(VitroRequest vreq) {
return SimplePermission.EDIT_ONTOLOGY.ACTIONS;
}
@Override
protected ResponseValues processRequest(VitroRequest vreq) {
Map<String, Object> body = new HashMap<String, Object>();
try {
String displayOption = "";
if ( vreq.getParameter("displayOption") != null ) {
displayOption = vreq.getParameter("displayOption");
}
else {
displayOption = "hierarchy";
}
body.put("displayOption", displayOption);
if ( displayOption.equals("all") ) {
body.put("pageTitle", "All Data Properties");
}
else {
body.put("pageTitle", "Data Property Hierarchy");
}
body.put("propertyType", "data");
dpDao = vreq.getAssertionsWebappDaoFactory().getDataPropertyDao();
vcDao = vreq.getAssertionsWebappDaoFactory().getVClassDao();
pgDao = vreq.getAssertionsWebappDaoFactory().getPropertyGroupDao();
dDao = vreq.getAssertionsWebappDaoFactory().getDatatypeDao();
String json = new String();
String ontologyUri = vreq.getParameter("ontologyUri");
String startPropertyUri = vreq.getParameter("propertyUri");
List<DataProperty> roots = null;
if (startPropertyUri != null) {
roots = new LinkedList<DataProperty>();
roots.add(dpDao.getDataPropertyByURI(startPropertyUri));
} else {
roots = dpDao.getRootDataProperties();
if (roots!=null){
Collections.sort(roots);
}
}
int counter = 0;
if (roots!=null) {
Iterator<DataProperty> rootIt = roots.iterator();
if (!rootIt.hasNext()) {
DataProperty dp = new DataProperty();
dp.setURI(ontologyUri+"fake");
String notFoundMessage = "<strong>No data properties found.</strong>";
dp.setName(notFoundMessage);
dp.setName(notFoundMessage);
json += addDataPropertyDataToResultsList(dp, 0, ontologyUri, counter);
} else {
while (rootIt.hasNext()) {
DataProperty root = rootIt.next();
if ( (ontologyUri==null) || ( (ontologyUri!=null) && (root.getNamespace()!=null) && (ontologyUri.equals(root.getNamespace())) ) ) {
json += addChildren(root, 0, ontologyUri, counter);
counter += 1;
}
}
int length = json.length();
if ( length > 0 ) {
json += " }";
}
}
}
body.put("jsonTree",json);
} catch (Throwable t) {
t.printStackTrace();
}
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
private String addChildren(DataProperty parent, int position, String ontologyUri, int counter) {
if (parent == null) {
return "";
}
String details = addDataPropertyDataToResultsList(parent, position, ontologyUri, counter);
int length = details.length();
String leaves = "";
leaves += details;
List childURIstrs = dpDao.getSubPropertyURIs(parent.getURI());
if ((childURIstrs.size()>0) && position<MAXDEPTH) {
List childProps = new ArrayList();
Iterator childURIstrIt = childURIstrs.iterator();
while (childURIstrIt.hasNext()) {
String URIstr = (String) childURIstrIt.next();
DataProperty child = (DataProperty) dpDao.getDataPropertyByURI(URIstr);
childProps.add(child);
}
Collections.sort(childProps);
Iterator childPropIt = childProps.iterator();
while (childPropIt.hasNext()) {
DataProperty child = (DataProperty) childPropIt.next();
leaves += addChildren(child, position+1, ontologyUri, counter);
if (!childPropIt.hasNext()) {
if ( ontologyUri == null ) {
leaves += " }] ";
}
else if ( ontologyUri != null && length > 0 ) {
// need this for when we show the classes associated with an ontology
String ending = leaves.substring(leaves.length() - 2, leaves.length());
if ( ending.equals("] ") ) {
leaves += "}]";
}
else if ( ending.equals(" [") ){
leaves += "] ";
}
else {
leaves += "}]";
}
}
}
}
}
else {
if ( ontologyUri == null ) {
leaves += "] ";
}
else if ( ontologyUri != null && length > 0 ) {
leaves += "] ";
}
}
return leaves;
}
private String addDataPropertyDataToResultsList(DataProperty dp, int position, String ontologyUri, int counter) {
String tempString = "";
if (dp == null) {
return tempString;
}
if (ontologyUri == null || ( (dp.getNamespace()!=null) && (dp.getNamespace().equals(ontologyUri)) ) ) {
if ( counter < 1 && position < 1 ) {
tempString += "{ \"name\": ";
}
else if ( position == previous_posn ) {
tempString += "}, { \"name\": ";
}
else if ( position > previous_posn ) {
tempString += " { \"name\": ";
}
else if ( position < previous_posn ) {
tempString += "}, { \"name\": ";
}
String nameStr = dp.getPublicName()==null ? dp.getName()==null ? dp.getURI()==null ? "(no name)" : dp.getURI() : dp.getName() : dp.getPublicName();
try {
tempString += "\"<a href='datapropEdit?uri="+URLEncoder.encode(dp.getURI(),"UTF-8")+"'>" + nameStr + "</a>\", ";
} catch (Exception e) {
tempString += "\"" + nameStr + "\", ";
log.error("Unsupported: URLEncoder.encode() with UTF-8");
}
tempString += "\"data\": { \"internalName\": \"" + dp.getLocalNameWithPrefix() + "\", ";
VClass tmp = null;
try {
tempString += "\"domainVClass\": \"" + (((tmp = vcDao.getVClassByURI(dp.getDomainClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(dp.getDomainClassURI()).getLocalNameWithPrefix()) + "\", " ;
} catch (NullPointerException e) {
tempString += "\"domainVClass\": \"\",";
}
try {
Datatype rangeDatatype = dDao.getDatatypeByURI(dp.getRangeDatatypeURI());
String rangeDatatypeStr = (rangeDatatype==null)?dp.getRangeDatatypeURI():rangeDatatype.getName();
tempString += "\"rangeVClass\": \"" + ((rangeDatatypeStr != null) ? rangeDatatypeStr : "") + "\", " ;
} catch (NullPointerException e) {
tempString += "\"rangeVClass\": \"\",";
}
if (dp.getGroupURI() != null) {
PropertyGroup pGroup = pgDao.getGroupByURI(dp.getGroupURI());
tempString += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" " ;
} else {
tempString += "\"group\": \"unspecified\"";
}
tempString += "}, \"children\": [";
previous_posn = position;
}
return tempString;
}
private class DataPropertyAlphaComparator implements Comparator {
public int compare(Object o1, Object o2) {
return Collator.getInstance().compare( ((DataProperty)o1).getName(), ((DataProperty)o2).getName());
}
}
}

275
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ShowObjectPropertyHierarchyController.java Normal file
View file

@ -0,0 +1,275 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.text.Collator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
public class ShowObjectPropertyHierarchyController extends FreemarkerHttpServlet {
private static final Log log = LogFactory.getLog(ShowObjectPropertyHierarchyController.class.getName());
private static final String TEMPLATE_NAME = "siteAdmin-objectPropHierarchy.ftl";
private int MAXDEPTH = 5;
private ObjectPropertyDao opDao = null;
private VClassDao vcDao = null;
private PropertyGroupDao pgDao = null;
private int previous_posn = 0;
@Override
protected Actions requiredActions(VitroRequest vreq) {
return SimplePermission.EDIT_ONTOLOGY.ACTIONS;
}
@Override
protected ResponseValues processRequest(VitroRequest vreq) {
Map<String, Object> body = new HashMap<String, Object>();
try {
String displayOption = "";
if ( vreq.getParameter("displayOption") != null ) {
displayOption = vreq.getParameter("displayOption");
}
else {
displayOption = "hierarchy";
}
body.put("displayOption", displayOption);
if ( displayOption.equals("all") ) {
body.put("pageTitle", "All Object Properties");
}
else {
body.put("pageTitle", "Object Property Hierarchy");
}
body.put("propertyType", "object");
opDao = vreq.getAssertionsWebappDaoFactory().getObjectPropertyDao();
vcDao = vreq.getAssertionsWebappDaoFactory().getVClassDao();
pgDao = vreq.getAssertionsWebappDaoFactory().getPropertyGroupDao();
String json = new String();
String ontologyUri = vreq.getParameter("ontologyUri");
String startPropertyUri = vreq.getParameter("propertyUri");
List<ObjectProperty> roots = null;
if (startPropertyUri != null) {
roots = new LinkedList<ObjectProperty>();
ObjectProperty op = opDao.getObjectPropertyByURI(startPropertyUri);
if (op == null) {
op = new ObjectProperty();
op.setURI(startPropertyUri);
}
roots.add(op);
} else {
roots = opDao.getRootObjectProperties();
if (roots!=null){
Collections.sort(roots, new ObjectPropertyAlphaComparator()); // sorts by domain public
}
}
int counter = 0;
if (roots != null) {
Iterator<ObjectProperty> rootIt = roots.iterator();
if (!rootIt.hasNext()) {
ObjectProperty op = new ObjectProperty();
op.setURI(ontologyUri+"fake");
String notFoundMessage = "<strong>No object properties found.</strong>";
op.setDomainPublic(notFoundMessage);
json += addObjectPropertyDataToResultsList(op, 0, ontologyUri, counter);
} else {
while (rootIt.hasNext()) {
ObjectProperty root = rootIt.next();
if ( (ontologyUri==null) ||
( (ontologyUri != null)
&& (root.getNamespace() != null)
&& (ontologyUri.equals(root.getNamespace())) ) ) {
json += addChildren(root, 0, ontologyUri, counter);
counter += 1;
}
}
int length = json.length();
if ( length > 0 ) {
json += " }";
}
}
}
body.put("jsonTree",json);
} catch (Throwable t) {
t.printStackTrace();
}
return new TemplateResponseValues(TEMPLATE_NAME, body);
}
private String addChildren(ObjectProperty parent, int position, String ontologyUri, int counter) {
String details = addObjectPropertyDataToResultsList(parent, position, ontologyUri, counter);
int length = details.length();
String leaves = "";
leaves += details;
List childURIstrs = opDao.getSubPropertyURIs(parent.getURI());
if ((childURIstrs.size()>0) && position<MAXDEPTH) {
List childProps = new ArrayList();
Iterator childURIstrIt = childURIstrs.iterator();
while (childURIstrIt.hasNext()) {
String URIstr = (String) childURIstrIt.next();
ObjectProperty child = (ObjectProperty) opDao.getObjectPropertyByURI(URIstr);
childProps.add(child);
}
Collections.sort(childProps);
Iterator childPropIt = childProps.iterator();
while (childPropIt.hasNext()) {
ObjectProperty child = (ObjectProperty) childPropIt.next();
leaves += addChildren(child, position+1, ontologyUri, counter);
if (!childPropIt.hasNext()) {
if ( ontologyUri == null ) {
leaves += " }] ";
}
else if ( ontologyUri != null && length > 0 ) {
// need this for when we show the classes associated with an ontology
String ending = leaves.substring(leaves.length() - 2, leaves.length());
if ( ending.equals("] ") ) {
leaves += "}]";
}
else if ( ending.equals(" [") ){
leaves += "] ";
}
else {
leaves += "}]";
}
}
}
}
}
else {
if ( ontologyUri == null ) {
leaves += "] ";
}
else if ( ontologyUri != null && length > 0 ) {
leaves += "] ";
}
}
return leaves;
}
private String addObjectPropertyDataToResultsList(ObjectProperty op, int position, String ontologyUri, int counter) {
String tempString = "";
if (ontologyUri == null || ( (op.getNamespace()!=null) && (op.getNamespace().equals(ontologyUri)) ) ) {
// first if statement ensures that the first class begins with correct format
if ( counter < 1 && position < 1 ) {
tempString += "{ \"name\": ";
}
else if ( position == previous_posn ) {
tempString += "}, { \"name\": ";
}
else if ( position > previous_posn ) {
tempString += " { \"name\": ";
}
else if ( position < previous_posn ) {
tempString += "}, { \"name\": ";
}
try {
tempString += "\"<a href='propertyEdit?uri="+URLEncoder.encode(op.getURI(),"UTF-8") + "'>" + getDisplayLabel(op)+"</a>\", ";
} catch (UnsupportedEncodingException uee) {
tempString += "\"" + getDisplayLabel(op) + "\"";
log.error("Unsupported: URLEncoder.encode() with UTF-8");
}
tempString += "\"data\": { \"internalName\": \"" + op.getLocalNameWithPrefix() + "\", ";
VClass tmp = null;
try {
tempString += "\"domainVClass\": \"" + (((tmp = vcDao.getVClassByURI(op.getDomainVClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(op.getDomainVClassURI()).getLocalNameWithPrefix()) + "\", " ;
} catch (NullPointerException e) {
tempString += "\"domainVClass\": \"\",";
}
try {
tempString += "\"rangeVClass\": \"" + (((tmp = vcDao.getVClassByURI(op.getRangeVClassURI())) != null && (tmp.getLocalNameWithPrefix() == null)) ? "" : vcDao.getVClassByURI(op.getRangeVClassURI()).getLocalNameWithPrefix()) + "\", " ;
} catch (NullPointerException e) {
tempString += "\"rangeVClass\": \"\",";
}
if (op.getGroupURI() != null) {
PropertyGroup pGroup = pgDao.getGroupByURI(op.getGroupURI());
tempString += "\"group\": \"" + ((pGroup == null) ? "unknown group" : pGroup.getName()) + "\" " ;
} else {
tempString += "\"group\": \"unspecified\"";
}
tempString += "}, \"children\": [";
previous_posn = position;
}
return tempString;
}
public static class ObjectPropertyAlphaComparator implements Comparator<ObjectProperty> {
public int compare(ObjectProperty op1, ObjectProperty op2) {
if (op1 == null) {
return 1;
} else if (op2 == null) {
return -1;
}
String propLabel1 = getDisplayLabel(op1);
String propLabel2 = getDisplayLabel(op2);
if (propLabel1 == null) {
return 1;
} else if (propLabel2 == null) {
return -1;
} else {
return Collator.getInstance().compare( propLabel1, propLabel2 );
}
}
}
/*
* should never be null
*/
public static String getDisplayLabel(ObjectProperty op) {
String domainPublic = op.getDomainPublic();
String displayLabel = (domainPublic != null && domainPublic.length() > 0)
? domainPublic
: op.getLocalName();
return (displayLabel != null) ? displayLabel : "[object property]" ;
}
}

28
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualResponseBuilder.java
View file

@ -2,9 +2,15 @@
package edu.cornell.mannlib.vitro.webapp.controller.individual;
import java.io.IOException;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
@ -22,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.web.beanswrappers.ReadOnlyBeansWrapper;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividual;
import edu.ucsf.vitro.opensocial.OpenSocialManager;
import freemarker.ext.beans.BeansWrapper;
import freemarker.template.TemplateModel;
import freemarker.template.TemplateModelException;
@ -33,6 +40,9 @@ import freemarker.template.TemplateModelException;
* TODO clean this up.
*/
class IndividualResponseBuilder {
private static final Log log = LogFactory
.getLog(IndividualResponseBuilder.class);
private static final Map<String, String> namespaces = new HashMap<String, String>() {{
put("display", VitroVocabulary.DISPLAY);
put("vitro", VitroVocabulary.vitroURI);
@ -78,6 +88,24 @@ class IndividualResponseBuilder {
//If special values required for individuals like menu, include values in template values
body.putAll(getSpecialEditingValues());
// VIVO OpenSocial Extension by UCSF
try {
OpenSocialManager openSocialManager = new OpenSocialManager(vreq,
itm.isEditable() ? "individual-EDIT-MODE" : "individual", itm.isEditable());
openSocialManager.setPubsubData(OpenSocialManager.JSON_PERSONID_CHANNEL,
OpenSocialManager.buildJSONPersonIds(individual, "1 person found"));
body.put(OpenSocialManager.TAG_NAME, openSocialManager);
if (openSocialManager.isVisible()) {
body.put("bodyOnload", "my.init();");
}
} catch (JSONException e) {
log.error("JSONException in doTemplate()", e);
} catch (IOException e) {
log.error("IOException in doTemplate()", e);
} catch (SQLException e) {
log.error("SQLException in doTemplate()", e);
}
String template = new IndividualTemplateLocator(vreq, individual).findTemplate();
return new TemplateResponseValues(template, body);

14
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DataPropertyDao.java
View file

@ -1,5 +1,5 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.dao;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
@ -34,9 +34,11 @@ public interface DataPropertyDao extends PropertyDao {
List<DataProperty> getRootDataProperties();
boolean annotateDataPropertyAsExternalIdentifier(String dataPropertyURI);
public List<DataProperty> getDataPropertyList(Individual subject);
boolean annotateDataPropertyAsExternalIdentifier(String dataPropertyURI);
public List<DataProperty> getDataPropertyList(Individual subject);
public List<DataProperty> getDataPropertyList(String subjectUri);
public String getCustomListViewConfigFileName(DataProperty dataProperty);
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DataPropertyStatementDao.java
View file

@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.dao;
import java.util.Collection;
import java.util.List;
import java.util.Set;
import com.hp.hpl.jena.rdf.model.Literal;
@ -44,5 +45,9 @@ public interface DataPropertyStatementDao {
List<Literal> getDataPropertyValuesForIndividualByProperty(String subjectUri, String propertyUri);
List<Literal> getDataPropertyValuesForIndividualByProperty(Individual subject, DataProperty property, String queryString, Set<String> constructQueryStrings);
List<Literal> getDataPropertyValuesForIndividualByProperty(String subjectUri, String propertyUri, String queryString, Set<String> constructQueryStrings);
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/DisplayVocabulary.java
View file

@ -130,11 +130,14 @@ public class DisplayVocabulary {
public static final String HOME_MENU_ITEM = DISPLAY_NS + "HomeMenuItem";
/* some URIs of properties used with the SPARQL DataGetter */
/* some URIs of properties used with the SPARQL DataGetter, and save to var is saved for fixedHtml */
public static final String SAVE_TO_VAR = DISPLAY_NS + "saveToVar" ;
public static final String QUERY_MODEL = DISPLAY_NS + "queryModel";
public static final String QUERY = DISPLAY_NS + "query";
/* URI of property for Fixed HTML Generator */
public static final String FIXED_HTML_VALUE = DISPLAY_NS + "htmlValue";
//public static final Individual EVENTS = m_model.createIndividual( NS + "Events", PAGE );
//public static final Individual EVENTS_MENU_ITEM = m_model.createIndividual( NS + "EventsMenuItem", NAVIGATION_ELEMENT );

5
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/DataPropertyDaoFiltering.java
View file

@ -213,4 +213,9 @@ class DataPropertyDaoFiltering extends BaseFiltering implements DataPropertyDao{
return innerDataPropertyDao.getDataPropertyList(subjectUri);
}
@Override
public String getCustomListViewConfigFileName(DataProperty dataProperty) {
return innerDataPropertyDao.getCustomListViewConfigFileName(dataProperty);
}
}

46
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/DataPropertyStatementDaoFiltering.java
View file

@ -7,6 +7,7 @@ import java.util.Collection;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.hp.hpl.jena.rdf.model.Literal;
@ -18,6 +19,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
class DataPropertyStatementDaoFiltering extends BaseFiltering implements DataPropertyStatementDao{
final DataPropertyStatementDao innerDataPropertyStatementDao;
final VitroFilters filters;
@ -141,4 +143,48 @@ class DataPropertyStatementDaoFiltering extends BaseFiltering implements DataPro
}
@Override
public List<Literal> getDataPropertyValuesForIndividualByProperty(Individual subject, DataProperty property, String queryString, Set<String> constructQueryStrings) {
return getDataPropertyValuesForIndividualByProperty(subject.getURI(), property.getURI(), queryString, constructQueryStrings);
}
@Override
public List<Literal> getDataPropertyValuesForIndividualByProperty(String subjectUri, String propertyUri, String queryString, Set<String> constructQueryStrings) {
List<Literal> literals = innerDataPropertyStatementDao.getDataPropertyValuesForIndividualByProperty(subjectUri, propertyUri, queryString, constructQueryStrings);
/* Filter the data
*
* Filtering is applied to a list of DataPropertyStatement. Create these statements, mapped
* to the literal that they are built from, apply filtering to the statements, then get
* the associated literals out of the original list. Use a LinkedHashMap to preserve the ordering.
*/
Map<DataPropertyStatement, Literal> stmtsToLiterals =
new LinkedHashMap<DataPropertyStatement, Literal>(literals.size());
for (Literal literal : literals) {
String value = literal.getLexicalForm();
DataPropertyStatement statement = new DataPropertyStatementImpl(subjectUri, propertyUri, value);
statement.setDatatypeURI(literal.getDatatypeURI());
statement.setLanguage(literal.getLanguage());
stmtsToLiterals.put(statement, literal);
}
List<DataPropertyStatement> stmtList = new ArrayList<DataPropertyStatement>(stmtsToLiterals.keySet());
// Apply the filters to the list of statements
List<DataPropertyStatement> filteredStatements = filter(stmtList, filters.getDataPropertyStatementFilter());
// Get the literals associated with the filtered statements out of the original list
List<Literal> filteredLiterals = new ArrayList<Literal>(filteredStatements.size());
for (DataPropertyStatement dps : filteredStatements) {
if (dps instanceof DataPropertyStatementFiltering) {
dps = ((DataPropertyStatementFiltering)dps).innerStmt;
}
filteredLiterals.add(stmtsToLiterals.get(dps));
}
// Return the filtered list of literals
return filteredLiterals;
}
}

50
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
View file

@ -11,6 +11,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
@ -25,6 +26,8 @@ import com.hp.hpl.jena.ontology.ProfileException;
import com.hp.hpl.jena.ontology.Restriction;
import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
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.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
@ -729,5 +732,52 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
}
return properties;
}
protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
"PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#>" +
"SELECT ?property ?filename WHERE { \n" +
" ?property display:listViewConfigFile ?filename . \n" +
"}";
protected static Query listViewConfigFileQuery = null;
static {
try {
listViewConfigFileQuery = QueryFactory.create(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
} catch(Throwable th){
log.error("could not create SPARQL query for LIST_VIEW_CONFIG_FILE_QUERY_STRING " + th.getMessage());
log.error(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
}
}
Map<DataProperty, String> customListViewConfigFileMap = null;
@Override
public String getCustomListViewConfigFileName(DataProperty dp) {
if (customListViewConfigFileMap == null) {
customListViewConfigFileMap = new HashMap<DataProperty, String>();
OntModel displayModel = getOntModelSelector().getDisplayModel();
//Get all property to list view config file mappings in the system
QueryExecution qexec = QueryExecutionFactory.create(listViewConfigFileQuery, displayModel);
ResultSet results = qexec.execSelect();
//Iterate through mappings looking for the current property and setting up a hashmap for subsequent retrieval
while (results.hasNext()) {
QuerySolution soln = results.next();
String propertyUri = soln.getResource("property").getURI();
DataProperty prop = getDataPropertyByURI(propertyUri);
if (prop == null) {
//This is a warning only if this property is the one for which we're searching
if(dp.getURI().equals(propertyUri)){
log.warn("Can't find property for uri " + propertyUri);
} else {
log.debug("Can't find property for uri " + propertyUri);
}
} else {
String filename = soln.getLiteral("filename").getLexicalForm();
customListViewConfigFileMap.put(prop, filename);
}
}
qexec.close();
}
return customListViewConfigFileMap.get(dp);
}
}

130
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoJena.java
View file

@ -8,6 +8,7 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.hp.hpl.jena.datatypes.TypeMapper;
import com.hp.hpl.jena.ontology.OntModel;
@ -18,10 +19,15 @@ 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.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.AnonId;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
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.rdf.model.Statement;
@ -38,6 +44,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.edit.ReorderController;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualUpdateEvent;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ObjectPropertyStatementDaoJena;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -190,6 +197,7 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
Resource res = ResourceFactory.createResource(entity.getURI());
if (!VitroVocabulary.PSEUDO_BNODE_NS.equals(entity.getNamespace())) {
for (Literal lit : this.getDataPropertyValuesForIndividualByProperty(res.getURI(), datapropURI)) {
log.debug("Literal lit = " + lit);
DataPropertyStatement ed = new DataPropertyStatementImpl();
fillDataPropertyStatementWithJenaLiteral(ed, lit);
ed.setIndividualURI(entity.getURI());
@ -390,4 +398,126 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
}
}
@Override
public List<Literal> getDataPropertyValuesForIndividualByProperty(
Individual subject,
DataProperty property,
String queryString, Set<String> constructQueryStrings ) {
return getDataPropertyValuesForIndividualByProperty(subject.getURI(), property.getURI(), queryString, constructQueryStrings );
}
@Override
public List<Literal> getDataPropertyValuesForIndividualByProperty(
String subjectUri,
String propertyUri,
String queryString, Set<String> constructQueryStrings ) {
Model constructedModel = constructModelForSelectQueries(
subjectUri, propertyUri, constructQueryStrings);
log.debug("Query string for data property " + propertyUri + ": " + queryString);
Query query = null;
try {
query = QueryFactory.create(queryString, Syntax.syntaxARQ);
} catch(Throwable th){
log.error("Could not create SPARQL query for query string. " + th.getMessage());
log.error(queryString);
return Collections.emptyList();
}
QuerySolutionMap initialBindings = new QuerySolutionMap();
initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
initialBindings.add("property", ResourceFactory.createResource(propertyUri));
// Run the SPARQL query to get the properties
List<Literal> values = new ArrayList<Literal>();
DatasetWrapper w = dwf.getDatasetWrapper();
Dataset dataset = w.getDataset();
dataset.getLock().enterCriticalSection(Lock.READ);
QueryExecution qexec = null;
try {
qexec = (constructedModel == null)
? QueryExecutionFactory.create(
query, dataset, initialBindings)
: QueryExecutionFactory.create(
query, constructedModel, initialBindings);
ResultSet results = qexec.execSelect();
while (results.hasNext()) {
QuerySolution sol = results.next();
Literal value = sol.getLiteral("value");
values.add(value);
}
log.debug("values = " + values);
return values;
} catch (Exception e) {
log.error("Error getting data property values for subject " + subjectUri + " and property " + propertyUri);
return Collections.emptyList();
} finally {
dataset.getLock().leaveCriticalSection();
w.close();
if (qexec != null) {
qexec.close();
}
}
}
private Model constructModelForSelectQueries(String subjectUri,
String propertyUri,
Set<String> constructQueries) {
if (constructQueries == null) {
return null;
}
Model constructedModel = ModelFactory.createDefaultModel();
for (String queryString : constructQueries) {
log.debug("CONSTRUCT query string for object property " +
propertyUri + ": " + queryString);
Query query = null;
try {
query = QueryFactory.create(queryString, Syntax.syntaxARQ);
} catch(Throwable th){
log.error("Could not create CONSTRUCT SPARQL query for query " +
"string. " + th.getMessage());
log.error(queryString);
return constructedModel;
}
QuerySolutionMap initialBindings = new QuerySolutionMap();
initialBindings.add(
"subject", ResourceFactory.createResource(subjectUri));
initialBindings.add(
"property", ResourceFactory.createResource(propertyUri));
DatasetWrapper w = dwf.getDatasetWrapper();
Dataset dataset = w.getDataset();
dataset.getLock().enterCriticalSection(Lock.READ);
QueryExecution qe = null;
try {
qe = QueryExecutionFactory.create(
query, dataset, initialBindings);
qe.execConstruct(constructedModel);
} catch (Exception e) {
log.error("Error getting constructed model for subject " + subjectUri + " and property " + propertyUri);
} finally {
if (qe != null) {
qe.close();
}
dataset.getLock().leaveCriticalSection();
w.close();
}
}
return constructedModel;
}
}

39
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraph.java
View file

@ -1,6 +1,5 @@
package edu.cornell.mannlib.vitro.webapp.dao.jena;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
@ -49,8 +48,6 @@ public class RDFServiceGraph implements GraphWithPerform {
private PrefixMapping prefixMapping = new PrefixMappingImpl();
private GraphEventManager eventManager;
private Reifier reifier = new EmptyReifier(this);
private GraphStatisticsHandler graphStatisticsHandler;
private TransactionHandler transactionHandler;
private QueryHandler queryHandler;
/**
@ -83,26 +80,6 @@ public class RDFServiceGraph implements GraphWithPerform {
public void add(Triple arg0) throws AddDeniedException {
performAdd(arg0);
}
// public void executeUpdate(String updateString) {
// try {
// RepositoryConnection conn = getConnection();
// try {
// Update u = conn.prepareUpdate(QueryLanguage.SPARQL, updateString);
// u.execute();
// } catch (MalformedQueryException e) {
// throw new RuntimeException(e);
// } catch (UpdateExecutionException e) {
// log.error(e,e);
// log.error("Update command: \n" + updateString);
// throw new RuntimeException(e);
// } finally {
// conn.close();
// }
// } catch (RepositoryException re) {
// throw new RuntimeException(re);
// }
// }
private String serialize(Triple t) {
StringBuffer sb = new StringBuffer();
@ -130,8 +107,8 @@ public class RDFServiceGraph implements GraphWithPerform {
public void performDelete(Triple t) {
ChangeSet changeSet = rdfService.manufactureChangeSet();
try {
changeSet.addRemoval(new ByteArrayInputStream(
serialize(t).getBytes()), RDFService.ModelSerializationFormat.N3, graphURI);
changeSet.addRemoval(RDFServiceUtils.toInputStream(serialize(t)),
RDFService.ModelSerializationFormat.N3, graphURI);
rdfService.changeSetUpdate(changeSet);
} catch (RDFServiceException rdfse) {
throw new RuntimeException(rdfse);
@ -268,16 +245,8 @@ public class RDFServiceGraph implements GraphWithPerform {
findQuery.append("\n}");
String queryString = findQuery.toString();
//log.info(queryString);
// //TODO remove me
// if (queryString.contains("individual/AI") && queryString.contains("label")) {
// throw new RuntimeException("break!");
// }
ResultSet rs = execSelect(queryString);
//rs = execSelect(findQuery.toString());
//rs = execSelect(findQuery.toString());
List<Triple> triplist = new ArrayList<Triple>();
while (rs.hasNext()) {
@ -324,9 +293,6 @@ public class RDFServiceGraph implements GraphWithPerform {
@Override
public Reifier getReifier() {
//if (reifier == null) {
// reifier = new SimpleReifier(this, ReificationStyle.Standard);
//}
return reifier;
}
@ -354,7 +320,6 @@ public class RDFServiceGraph implements GraphWithPerform {
@Override
public boolean isIsomorphicWith(Graph arg0) {
log.info("Hey dummy!");
throw new UnsupportedOperationException("isIsomorphicWith() not supported " +
"by SPARQL graphs");
}

20
webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceGraphBulkUpdater.java
View file

@ -73,7 +73,6 @@ public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
@Override
public void add(Graph g, boolean arg1) {
log.info("bulk addGraph()");
Model[] model = separateStatementsWithBlankNodes(g);
addModel(model[1] /* nonBlankNodeModel */);
// replace following call with different method
@ -118,7 +117,6 @@ public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
}
public void addModel(Model model) {
log.info("bulk addModel()");
ChangeSet changeSet = graph.getRDFService().manufactureChangeSet();
ByteArrayOutputStream out = new ByteArrayOutputStream();
model.write(out, "N-TRIPLE");
@ -133,7 +131,6 @@ public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
}
public void deleteModel(Model model) {
log.info("bulk addModel()");
ChangeSet changeSet = graph.getRDFService().manufactureChangeSet();
ByteArrayOutputStream out = new ByteArrayOutputStream();
model.write(out, "N-TRIPLE");
@ -180,22 +177,7 @@ public class RDFServiceGraphBulkUpdater extends SimpleBulkUpdateHandler {
public static void removeAll( Graph g )
{
ExtendedIterator<Triple> it = GraphUtil.findAll(g);
try {
while (it.hasNext()) {
Triple t = it.next();
g.delete(t);
it.remove();
}
} finally {
it.close();
}
// get rid of remaining blank nodes using a SPARQL DELETE
if (g instanceof SparqlGraph) {
((SparqlGraph) g).removeAll();
}
g.getBulkUpdateHandler().delete(g);
}
}

9
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManagePageGenerator.java
View file

@ -13,6 +13,7 @@ import javax.servlet.http.HttpSession;
import com.hp.hpl.jena.ontology.OntModel;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -154,7 +155,7 @@ public class ManagePageGenerator extends BaseEditConfigurationGenerator implemen
//For the case of a new page
if(subjectUri == null) {
//Once added, return to pageList
editConfiguration.setUrlToReturnTo("/pageList");
editConfiguration.setUrlToReturnTo(UrlBuilder.getUrl("/pageList"));
editConfiguration.setEntityToReturnTo("?page");
editConfiguration.setPredicateUri(predicateUri);
@ -190,8 +191,10 @@ public class ManagePageGenerator extends BaseEditConfigurationGenerator implemen
//In the case where this is a new page, need to ensure page gets a new
private void setNewResources(EditConfigurationVTwo conf) {
//null makes default namespace be triggered
conf.addNewResource("page", defaultDisplayNs);
conf.addNewResource("menuItem", defaultDisplayNs);
//conf.addNewResource("page", defaultDisplayNs);
//conf.addNewResource("menuItem", defaultDisplayNs);
conf.addNewResource("page", null);
conf.addNewResource("menuItem", null);
}

64
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ManagePagePreprocessor.java
View file

@ -25,9 +25,11 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManagePageGenerator;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3Utils;
import net.sf.json.JSON;
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
import net.sf.json.util.JSONUtils;
public class ManagePagePreprocessor extends
BaseEditSubmissionPreprocessorVTwo {
@ -83,7 +85,7 @@ public class ManagePagePreprocessor extends
int counter = 0;
for(JSONObject jsonObject:pageContentUnitsJSON) {
String dataGetterClass = getDataGetterClass(jsonObject);
ProcessDataGetterN3 pn = ProcessDataGetterN3Utils.getDataGetterProcessorN3(dataGetterClass);
ProcessDataGetterN3 pn = ProcessDataGetterN3Utils.getDataGetterProcessorN3(dataGetterClass, jsonObject);
//Add n3 required
addN3Required(pn, counter);
//Add N3 Optional as well
@ -106,7 +108,13 @@ public class ManagePagePreprocessor extends
// TODO Auto-generated method stub
List<String> newResources = pn.getNewResources(counter);
for(String newResource:newResources) {
editConfiguration.addNewResource(newResource, ManagePageGenerator.defaultDisplayNs);
//Will null get us display vocabulary or something else?
editConfiguration.addNewResource(newResource, null);
//Weirdly enough, the defaultDisplayNS doesn't act as a namespace REALLY
//as it first gets assigned as the URI itself and this lead to an error
//instead of repetitively trying to get another URI
//editConfiguration.addNewResource(newResource, ManagePageGenerator.defaultDisplayNs );
}
}
@ -130,23 +138,51 @@ public class ManagePagePreprocessor extends
List<String> uriLabels = pn.getUriVarNamesBase();
for(String literalLabel:literalLabels) {
//TODO: Deal with multiple submission values
//This retrieves the value for this particular json object
String literalValue = jsonObject.getString(literalLabel);
//Var names will depend on which data getter object this is on the page, so depends on counter
List<String> literalValues = new ArrayList<String>();
Object jsonValue = jsonObject.get(literalLabel);
//Var names will depend on which data getter object this is on the page, so depends on counter
String submissionLiteralName = pn.getVarName(literalLabel, counter);
//Single value
if(jsonValue instanceof String) {
//TODO: Deal with multiple submission values
//This retrieves the value for this particular json object
literalValues.add(jsonObject.getString(literalLabel));
} else if(jsonValue instanceof JSONArray) {
JSONArray values = jsonObject.getJSONArray(literalLabel);
literalValues = (List<String>) JSONSerializer.toJava(values);
}
String[] literalValuesSubmission = new String[literalValues.size()];
literalValuesSubmission = literalValues.toArray(literalValuesSubmission);
//This adds literal, connecting the field with
submission.addLiteralToForm(editConfiguration, editConfiguration.getField(submissionLiteralName), submissionLiteralName, new String[]{literalValue});
submission.addLiteralToForm(editConfiguration,
editConfiguration.getField(submissionLiteralName),
submissionLiteralName,
literalValuesSubmission);
}
for(String uriLabel:uriLabels) {
//TODO: Deal with multiple submission values
//This retrieves the value for this particular json object
String uriValue = jsonObject.getString(uriLabel);
//Var names will depend on which data getter object this is on the page, so depends on counter
List<String> uriValues = new ArrayList<String>();
Object jsonValue = jsonObject.get(uriLabel);
//Var names will depend on which data getter object this is on the page, so depends on counter
String submissionUriName = pn.getVarName(uriLabel, counter);
//This adds literal, connecting the field with
submission.addLiteralToForm(editConfiguration, editConfiguration.getField(submissionUriName), submissionUriName, new String[]{uriValue});
//if single value, then, add to values
if(jsonValue instanceof String) {
//Var names will depend on which data getter object this is on the page, so depends on counter
//This retrieves the value for this particular json object and adds to list
uriValues.add(jsonObject.getString(uriLabel));
} else if(jsonValue instanceof JSONArray) {
//multiple values
JSONArray values = jsonObject.getJSONArray(uriLabel);
uriValues = (List<String>) JSONSerializer.toJava(values);
} else {
//This may include JSON Objects but no way to deal with these right now
}
String[] uriValuesSubmission = new String[uriValues.size()];
uriValuesSubmission = uriValues.toArray(uriValuesSubmission);
//This adds literal, connecting the field with the value
submission.addUriToForm(editConfiguration, submissionUriName, uriValuesSubmission);
}
//this needs to be different

95
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessClassGroupDataGetterN3.java Normal file
View file

@ -0,0 +1,95 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.util.List;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
//Returns the appropriate n3 based on data getter
public class ProcessClassGroupDataGetterN3 extends ProcessDataGetterAbstract {
private static String classType = "java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData";
private static String classGroupVarBase = "classGroup";
public ProcessClassGroupDataGetterN3(){
}
//Pass in variable that represents the counter
//TODO: ensure correct model returned
//We shouldn't use the ACTUAL values here but generate the n3 required
public List<String> retrieveN3Required(int counter) {
return this.retrieveN3ForTypeAndClassGroup(counter);
}
public List<String> retrieveN3Optional(int counter) {
return null;
}
public List<String> retrieveN3ForTypeAndClassGroup(int counter) {
String n3ForType = this.getN3ForTypePartial(counter);
String n3 = n3ForType +"; \n" +
"<" + DisplayVocabulary.FOR_CLASSGROUP + "> " + getN3VarName(classGroupVarBase, counter) + " .";
List<String> n3List = new ArrayList<String>();
n3List.add(getPrefixes() + n3);
return n3List;
}
public String getN3ForTypePartial(int counter) {
String dataGetterVar = getDataGetterVar(counter);
String n3 = dataGetterVar + " a <" + getClassType() + ">";
return n3;
}
//These methods will return the literals and uris expected within the n3
//and the counter is used to ensure they are numbered correctly
public List<String> retrieveLiteralsOnForm(int counter) {
//no literals, just the class group URI
List<String> literalsOnForm = new ArrayList<String>();
return literalsOnForm;
}
public List<String> retrieveUrisOnForm(int counter) {
List<String> urisOnForm = new ArrayList<String>();
//Class group is a URI
urisOnForm.add(getVarName("classGroup", counter));
return urisOnForm;
}
public List<FieldVTwo> retrieveFields(int counter) {
List<FieldVTwo> fields = new ArrayList<FieldVTwo>();
fields.add(new FieldVTwo().setName(getVarName("classGroup", counter)));
return fields;
}
//These var names match the names of the elements within the json object returned with the info required for the data getter
public List<String> getLiteralVarNamesBase() {
return Arrays.asList();
}
//these are for the fields ON the form
public List<String> getUriVarNamesBase() {
return Arrays.asList("classGroup");
}
//This class can be extended so returning type here
public String getClassType() {
return classType;
}
}

53
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterAbstract.java Normal file
View file

@ -0,0 +1,53 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.util.List;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
//Returns the appropriate n3 based on data getter
public abstract class ProcessDataGetterAbstract implements ProcessDataGetterN3 {
public ProcessDataGetterAbstract(){
}
//placeholder so need "?" in front of the variable
public String getDataGetterVar(int counter) {
return "?dataGetter" + counter;
}
public String getPrefixes() {
return "@prefix display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> . \n" +
"@prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> . \n";
}
public String getVarName(String base, int counter) {
return base + counter;
}
//For use within n3 strings, need a "?"
public String getN3VarName(String base, int counter) {
return "?" + getVarName(base, counter);
}
//Return name of new resources
public List<String> getNewResources(int counter) {
//Each data getter requires a new resource
List<String> newResources = new ArrayList<String>();
newResources.add("dataGetter" + counter);
return newResources;
}
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3.java
View file

@ -10,7 +10,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
//Returns the appropriate n3 based on data getter
public interface ProcessDataGetterN3 {
public List<String> retrieveN3Required(int counter);
public List<String> retrieveN3Required(int counter);
public List<String> retrieveN3Optional(int counter);
public List<String >retrieveLiteralsOnForm(int counter);

33
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3Utils.java
View file

@ -2,6 +2,7 @@
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.lang.reflect.Constructor;
import java.util.HashMap;
import java.util.Map;
@ -20,6 +21,7 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
/*
* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
@ -29,18 +31,20 @@ public class ProcessDataGetterN3Utils {
public static HashMap<String, String> getDataGetterTypeToProcessorMap() {
HashMap<String, String> map = new HashMap<String, String>();
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSparqlDataGetterN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessClassGroupDataGetterN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessIndividualsForClassesDataGetterN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
return map;
}
public static ProcessDataGetterN3 getDataGetterProcessorN3(String dataGetterClass) {
public static ProcessDataGetterN3 getDataGetterProcessorN3(String dataGetterClass, JSONObject jsonObject) {
HashMap<String, String> map = getDataGetterTypeToProcessorMap();
//
if(map.containsKey(dataGetterClass)) {
String processorClass = map.get(dataGetterClass);
try {
Class<?> clz = Class.forName(processorClass);
//Don't actually need to pass in json object since that includes the actual submission values
ProcessDataGetterN3 pn = (ProcessDataGetterN3) clz.getConstructor().newInstance();
ProcessDataGetterN3 pn = instantiateClass(processorClass, jsonObject);
return pn;
} catch(Exception ex) {
log.error("Exception occurred in trying to get processor class for n3 for " + dataGetterClass, ex);
@ -50,4 +54,25 @@ public class ProcessDataGetterN3Utils {
return null;
}
private static ProcessDataGetterN3 instantiateClass(String processorClass, JSONObject jsonObject) {
ProcessDataGetterN3 pn = null;
try {
Class<?> clz = Class.forName(processorClass);
Constructor<?>[] ctList = clz.getConstructors();
for (Constructor<?> ct: ctList) {
Class<?>[] parameterTypes =ct.getParameterTypes();
if(parameterTypes.length > 0 && parameterTypes[0].isAssignableFrom(jsonObject.getClass())) {
pn = (ProcessDataGetterN3) ct.newInstance(jsonObject);
} else {
pn = (ProcessDataGetterN3) ct.newInstance();
}
}
} catch(Exception ex) {
log.error("Error occurred instantiating " + processorClass, ex);
}
return pn;
}
}

81
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessFixedHTMLN3.java Normal file
View file

@ -0,0 +1,81 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.util.List;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
//Returns the appropriate n3 based on data getter
public class ProcessFixedHTMLN3 extends ProcessDataGetterAbstract {
private static String classType = "java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter";
public ProcessFixedHTMLN3(){
}
//Pass in variable that represents the counter
//TODO: ensure correct model returned
//We shouldn't use the ACTUAL values here but generate the n3 required
public List<String> retrieveN3Required(int counter) {
String dataGetterVar = getDataGetterVar(counter);
String n3 = dataGetterVar + " a <" + classType + ">; \n" +
"display:saveToVar " + getN3VarName("saveToVar", counter) + "; \n" +
"display:htmlValue " + getN3VarName("htmlValue", counter) + " .";
List<String> requiredList = new ArrayList<String>();
requiredList.add(getPrefixes() + n3);
return requiredList;
}
public List<String> retrieveN3Optional(int counter) {
return null;
}
public List<String> retrieveLiteralsOnForm(int counter) {
List<String> literalsOnForm = new ArrayList<String>();
literalsOnForm.add(getVarName("saveToVar",counter));
literalsOnForm.add(getVarName("htmlValue", counter));
return literalsOnForm;
}
public List<String> retrieveUrisOnForm(int counter) {
List<String> urisOnForm = new ArrayList<String>();
return urisOnForm;
}
public List<FieldVTwo> retrieveFields(int counter) {
List<FieldVTwo> fields = new ArrayList<FieldVTwo>();
//fields.add(new FieldVTwo().setName(getVarName("dataGetter", counter)));
fields.add(new FieldVTwo().setName(getVarName("saveToVar", counter)));
fields.add(new FieldVTwo().setName(getVarName("htmlValue", counter)));
return fields;
}
public List<String> getLiteralVarNamesBase() {
return Arrays.asList("saveToVar", "htmlValue");
}
//these are for the fields ON the form
public List<String> getUriVarNamesBase() {
return Arrays.asList();
}
}

139
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessIndividualsForClassesDataGetterN3.java Normal file
View file

@ -0,0 +1,139 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.util.Collection;
import java.util.List;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import com.hp.hpl.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
//Returns the appropriate n3 for selection of classes from within class group
public class ProcessIndividualsForClassesDataGetterN3 extends ProcessClassGroupDataGetterN3 {
private static String classType = "java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter";
protected JSONObject values = null;
int classCount = 0;
protected static String individualClassVarNameBase = "classesSelectedInClassGroup";
public ProcessIndividualsForClassesDataGetterN3(JSONObject jsonObject){
this.values = jsonObject;
if(values != null && values.containsKey(individualClassVarNameBase)) {
//Check how many individual classes are in json object
JSONArray ja = values.getJSONArray(individualClassVarNameBase);
classCount = ja.size();
}
}
//Pass in variable that represents the counter
//TODO: ensure correct model returned
//We shouldn't use the ACTUAL values here but generate the n3 required
public List<String> retrieveN3Required(int counter) {
List<String> classGroupN3 = this.retrieveN3ForTypeAndClassGroup(counter);
classGroupN3.addAll(this.addIndividualClassesN3(counter));
return classGroupN3;
}
protected List<String> addIndividualClassesN3(int counter) {
List<String> classN3 = new ArrayList<String>();
if(classCount > 0) {
classN3.add(generateIndividualClassN3(counter));
}
return classN3;
}
protected String generateIndividualClassN3(int counter) {
String dataGetterVar = getDataGetterVar(counter);
String n3 = dataGetterVar + " <" + DisplayVocabulary.GETINDIVIDUALS_FOR_CLASS + "> ";
//Consider a multi-valued field - in this case single field with multiple values
n3 += getN3VarName(individualClassVarNameBase, counter);
/*
int i;
for(i = 0; i < classCount; i++) {
if(i != 0) {
n3+= ",";
}
n3 += getN3VarName(individualClassVarNameBase + counter, classCount);
}*/
n3 += " .";
return n3;
}
public List<String> retrieveN3Optional(int counter) {
return null;
}
//These methods will return the literals and uris expected within the n3
//and the counter is used to ensure they are numbered correctly
public List<String> retrieveLiteralsOnForm(int counter) {
//no literals, just the class group URI
List<String> literalsOnForm = new ArrayList<String>();
return literalsOnForm;
}
public List<String> retrieveUrisOnForm(int counter) {
//get class group uris
List<String> urisOnForm = super.retrieveUrisOnForm(counter);
//now get individual classes selected uri
//urisOnForm.addAll(getIndividualClassesVarNames(counter));
//here again,consider multi-valued
urisOnForm.add(getVarName(individualClassVarNameBase, counter));
return urisOnForm;
}
private List<String> getIndividualClassesVarNames(int counter) {
List<String> individualClassUris = new ArrayList<String>();
int i;
for(i = 0; i < classCount; i++) {
individualClassUris.add(getVarName(individualClassVarNameBase + counter, classCount));
}
return individualClassUris;
}
public List<FieldVTwo> retrieveFields(int counter) {
List<FieldVTwo> fields = super.retrieveFields(counter);
fields.add(new FieldVTwo().setName(getVarName(individualClassVarNameBase, counter)));
//Add fields for each class selected
/* List<String> classVarNames = getIndividualClassesVarNames(counter);
for(String v:classVarNames) {
fields.add(new FieldVTwo().setName(v));
}*/
return fields;
}
//These var names match the names of the elements within the json object returned with the info required for the data getter
public List<String> getLiteralVarNamesBase() {
return Arrays.asList();
}
//these are for the fields ON the form
public List<String> getUriVarNamesBase() {
return Arrays.asList("classGroup", individualClassVarNameBase);
}
@Override
public String getClassType() {
return classType;
}
}

28
webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessSparqlDataGetterN3.java
View file

@ -15,7 +15,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import net.sf.json.JSONObject;
import net.sf.json.JSONSerializer;
//Returns the appropriate n3 based on data getter
public class ProcessSparqlDataGetterN3 implements ProcessDataGetterN3 {
public class ProcessSparqlDataGetterN3 extends ProcessDataGetterAbstract {
private static String classType = "java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter";
public ProcessSparqlDataGetterN3(){
@ -39,15 +39,6 @@ public class ProcessSparqlDataGetterN3 implements ProcessDataGetterN3 {
public List<String> retrieveN3Optional(int counter) {
return null;
}
//placeholder so need "?" in front of the variable
public String getDataGetterVar(int counter) {
return "?dataGetter" + counter;
}
private String getPrefixes() {
return "@prefix display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> . \n" +
"@prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> . \n";
}
//Need to add method sfor returning the fields, literals on form, and all that
@ -105,22 +96,7 @@ public class ProcessSparqlDataGetterN3 implements ProcessDataGetterN3 {
return Arrays.asList("queryModel");
}
public String getVarName(String base, int counter) {
return base + counter;
}
//For use within n3 strings, need a "?"
public String getN3VarName(String base, int counter) {
return "?" + getVarName(base, counter);
}
//Return name of new resources
public List<String> getNewResources(int counter) {
//Each data getter requires a new resource
List<String> newResources = new ArrayList<String>();
newResources.add("dataGetter" + counter);
return newResources;
}
}

93
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sdb/RDFServiceSDB.java
View file

@ -13,16 +13,21 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.graph.Triple;
import com.hp.hpl.jena.query.DataSource;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.DatasetFactory;
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.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.listeners.StatementListener;
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.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.sdb.SDBFactory;
@ -30,11 +35,6 @@ import com.hp.hpl.jena.sdb.Store;
import com.hp.hpl.jena.sdb.StoreDesc;
import com.hp.hpl.jena.sdb.sql.SDBConnection;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.update.GraphStore;
import com.hp.hpl.jena.update.GraphStoreFactory;
import com.hp.hpl.jena.update.UpdateAction;
import com.hp.hpl.jena.update.UpdateFactory;
import com.hp.hpl.jena.update.UpdateRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
import edu.cornell.mannlib.vitro.webapp.dao.jena.SparqlGraph;
@ -141,6 +141,7 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
}
private void removeBlankNodesWithSparqlUpdate(Dataset dataset, Model model, String graphURI) {
Model blankNodeModel = ModelFactory.createDefaultModel();
StmtIterator stmtIt = model.listStatements();
while (stmtIt.hasNext()) {
@ -149,7 +150,61 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
blankNodeModel.add(stmt);
}
}
removeUsingSparqlUpdate(dataset, blankNodeModel, graphURI);
String rootFinder = "SELECT ?s WHERE { ?s ?p ?o OPTIONAL { ?ss ?pp ?s } FILTER (!bound(?ss)) }";
Query rootFinderQuery = QueryFactory.create(rootFinder);
QueryExecution qe = QueryExecutionFactory.create(rootFinderQuery, blankNodeModel);
try {
ResultSet rs = qe.execSelect();
while (rs.hasNext()) {
QuerySolution qs = rs.next();
Resource s = qs.getResource("s");
String treeFinder = makeDescribe(s);
Query treeFinderQuery = QueryFactory.create(treeFinder);
QueryExecution qee = QueryExecutionFactory.create(treeFinderQuery, blankNodeModel);
try {
Model tree = qee.execDescribe();
StmtIterator sit = tree.listStatements(s, null, (RDFNode) null);
while (sit.hasNext()) {
Statement stmt = sit.nextStatement();
RDFNode n = stmt.getObject();
Model m2 = ModelFactory.createDefaultModel();
if (n.isResource()) {
Resource s2 = (Resource) n;
// now run yet another describe query
String smallerTree = makeDescribe(s2);
Query smallerTreeQuery = QueryFactory.create(smallerTree);
QueryExecution qe3 = QueryExecutionFactory.create(
smallerTreeQuery, tree);
try {
qe3.execDescribe(m2);
} finally {
qe3.close();
}
}
m2.add(stmt);
DataSource ds = DatasetFactory.create();
ds.addNamedModel(graphURI, dataset.getNamedModel(graphURI));
removeUsingSparqlUpdate(ds, m2, graphURI);
}
} finally {
qee.close();
}
}
} finally {
qe.close();
}
}
private String makeDescribe(Resource s) {
StringBuffer query = new StringBuffer("DESCRIBE <") ;
if (s.isAnon()) {
query.append("_:" + s.getId().toString());
} else {
query.append(s.getURI());
}
query.append(">");
return query.toString();
}
private void removeUsingSparqlUpdate(Dataset dataset, Model model, String graphURI) {
@ -173,11 +228,8 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
}
StringBuffer queryBuff = new StringBuffer();
queryBuff.append("DELETE { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : "" ) + " \n");
queryBuff.append("CONSTRUCT { \n");
queryBuff.append(patternBuff);
if (graphURI != null) {
queryBuff.append(" } \n");
}
queryBuff.append("} WHERE { \n");
if (graphURI != null) {
queryBuff.append(" GRAPH <" + graphURI + "> { \n");
@ -190,10 +242,23 @@ public class RDFServiceSDB extends RDFServiceImpl implements RDFService {
//log.debug(queryBuff.toString());
GraphStore graphStore = GraphStoreFactory.create(dataset);
UpdateRequest request = UpdateFactory.create();
request.add(queryBuff.toString());
UpdateAction.execute(request, graphStore);
Query construct = QueryFactory.create(queryBuff.toString());
// make a plain dataset to force the query to be run in a way that
// won't overwhelm MySQL with too many joins
DataSource ds = DatasetFactory.create();
ds.addNamedModel(graphURI, (graphURI != null)
? dataset.getNamedModel(graphURI) : dataset.getDefaultModel());
QueryExecution qe = QueryExecutionFactory.create(construct, ds);
try {
Model m = qe.execConstruct();
if (graphURI != null) {
dataset.getNamedModel(graphURI).remove(m);
} else {
dataset.getDefaultModel().remove(m);
}
} finally {
qe.close();
}
}
private Model parseModel(ModelChange modelChange) {

463
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -14,6 +14,7 @@ import com.hp.hpl.jena.ontology.AnnotationProperty;
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.ontology.OntProperty;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
@ -25,6 +26,7 @@ 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.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -32,6 +34,7 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.JenaException;
import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
@ -126,12 +129,13 @@ public class SimpleReasoner extends StatementListener {
*/
@Override
public void addedStatement(Statement stmt) {
try {
if (stmt.getPredicate().equals(RDF.type)) {
addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
}
} else {
addedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.ADD,stmt);
@ -150,8 +154,9 @@ public class SimpleReasoner extends StatementListener {
public void removedStatement(Statement stmt) {
try {
if (!isInterestedInRemovedStatement(stmt)) { return; }
// if (!isInterestedInRemovedStatement(stmt)) { return; }
// interested in all of them now that we are doing inverse
// property reasoning
handleRemovedStatement(stmt);
} catch (Exception e) {
@ -160,7 +165,6 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Synchronized part of removedStatement. Interacts
* with DeltaComputer.
@ -175,7 +179,9 @@ public class SimpleReasoner extends StatementListener {
if (stmt.getPredicate().equals(RDF.type)) {
removedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
}
} else {
removedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.RETRACT,stmt);
}
}
@ -184,29 +190,32 @@ public class SimpleReasoner extends StatementListener {
* Performs incremental ABox reasoning based
* on changes to the class hierarchy.
*
* Handles rdfs:subclassOf, owl:equivalentClass,
* Handles rdfs:subclassOf, owl:equivalentClass, and owl:inverseOf
*/
public void addedTBoxStatement(Statement stmt) {
try {
if (!(stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) || stmt.getPredicate().equals(OWL.inverseOf))) {
return;
}
try {
log.debug("added TBox assertion = " + stmt.toString());
log.debug("added TBox assertion = " + stmt.toString());
if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
if (stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass)) {
// ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return;
}
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
@ -220,13 +229,27 @@ public class SimpleReasoner extends StatementListener {
}
if (stmt.getPredicate().equals(RDFS.subClassOf)) {
addedSubClass(subject,object,inferenceModel);
addedSubClass(subject,object,inferenceModel);
} else {
// equivalent class is the same as subclass in both directions
addedSubClass(subject,object,inferenceModel);
addedSubClass(object,subject,inferenceModel);
// equivalent class is the same as subclass in both directions
addedSubClass(subject,object,inferenceModel);
addedSubClass(object,subject,inferenceModel);
}
} else {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
}
addedInverseProperty(prop1, prop2, inferenceModel);
}
} catch (Exception e) {
// don't stop the edit if there's an exception
log.error("Exception while adding inference(s): " + e.getMessage());
@ -237,29 +260,33 @@ public class SimpleReasoner extends StatementListener {
* Performs incremental ABox reasoning based
* on changes to the class hierarchy.
*
* Handles rdfs:subclassOf, owl:equivalentClass,
* Handles rdfs:subclassOf, owl:equivalentClass, and owl:inverseOf
*/
public void removedTBoxStatement(Statement stmt) {
public void removedTBoxStatement(Statement stmt) {
try {
log.debug("removed TBox assertion = " + stmt.toString());
if (!(stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) || stmt.getPredicate().equals(OWL.inverseOf))) {
return;
}
log.debug("removed TBox assertion = " + stmt.toString());
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
// ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return;
}
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
@ -279,7 +306,21 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(subject,object,inferenceModel);
removedSubClass(object,subject,inferenceModel);
}
}
} else {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
removedInverseProperty(prop1, prop2, inferenceModel);
}
} catch (Exception e) {
// don't stop the edit if there's an exception
log.error("Exception while removing inference(s): " + e.getMessage());
@ -376,6 +417,45 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Performs incremental property-based reasoning.
*
* Materializes inferences based on the owl:inverseOf relationship.
*
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
* then add y prop2 x to the inference graph, if it is not already in
* the assertions graph.
*/
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
Property inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
aboxModel.enterCriticalSection(Lock.READ);
try {
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt) ) {
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
} finally {
aboxModel.leaveCriticalSection();
}
}
}
/*
* If it is removed that B is of type A, then for each superclass of A remove
* the inferred statement that B is of that type UNLESS it is otherwise entailed
@ -386,8 +466,7 @@ public class SimpleReasoner extends StatementListener {
tboxModel.enterCriticalSection(Lock.READ);
try {
try {
OntClass cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
@ -453,13 +532,50 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Performs incremental property-based reasoning.
*
* Retracts inferences based on the owl:inverseOf relationship.
*
* If it is removed that x prop1 y, and prop2 is an inverseOf prop1
* then remove y prop2 x from the inference graph, unless it is
* otherwise entailed by the assertions graph independently of
* this removed statement.
*/
public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
OntProperty inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!entailedInverseStmt(infStmt) && inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
}
// if a statement has been removed that is otherwise entailed,
// add it to the inference graph.
if (entailedInverseStmt(stmt) && !inferenceModel.contains(stmt)) {
inferenceModel.add(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
}
// Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false.
protected boolean entailedType(Resource subject, OntClass cls) {
aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.READ);
try {
try {
List<OntClass> subclasses = null;
subclasses = (cls.listSubClasses(false)).toList();
subclasses.addAll((cls.listEquivalentClasses()).toList());
@ -477,12 +593,101 @@ public class SimpleReasoner extends StatementListener {
} catch (Exception e) {
log.debug("exception in method entailedType: " + e.getMessage());
return false;
} finally {
} finally {
aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
}
}
// Returns true if the triple is entailed by inverse property
// reasoning; otherwise returns false.
protected boolean entailedInverseStmt(Statement stmt) {
ExtendedIterator <? extends OntProperty> iter = null;
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().asResource().getURI());
iter = prop.listInverse();
} finally {
tboxModel.leaveCriticalSection();
}
aboxModel.enterCriticalSection(Lock.READ);
try {
while (iter.hasNext()) {
Property invProp = iter.next();
// not reasoning on properties in the OWL, RDF or RDFS namespace
if ((invProp.getNameSpace()).equals(OWL.NS) ||
(invProp.getNameSpace()).equals(RDFS.getURI()) ||
(invProp.getNameSpace()).equals(RDF.getURI())) {
continue;
}
Statement invStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), invProp, stmt.getSubject());
if (aboxModel.contains(invStmt)) {
return true;
}
}
return false;
} finally {
aboxModel.leaveCriticalSection();
}
}
/*
* Returns a list of properties that are inverses of the property
* in the given statement.
*/
protected List<OntProperty> getInverseProperties(Statement stmt) {
List<OntProperty> inverses = new ArrayList<OntProperty>();
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return inverses;
}
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
if (!prop.isObjectProperty()) {
return inverses;
}
if (!stmt.getObject().isResource()) {
log.warn("The predicate of this statement is an object property, but the object is not a resource.");
return inverses;
}
// not reasoning on properties in the OWL, RDF or RDFS namespace
if ((prop.getNameSpace()).equals(OWL.NS) ||
(prop.getNameSpace()).equals(RDFS.getURI()) ||
(prop.getNameSpace()).equals(RDF.getURI())) {
return inverses;
}
ExtendedIterator <? extends OntProperty> iter = prop.listInverse();
while (iter.hasNext()) {
OntProperty invProp = iter.next();
if ((invProp.getNameSpace()).equals(OWL.NS) ||
(invProp.getNameSpace()).equals(RDFS.getURI()) ||
(invProp.getNameSpace()).equals(RDF.getURI())) {
continue;
}
inverses.add(invProp);
}
}
} finally {
tboxModel.leaveCriticalSection();
}
return inverses;
}
/*
* If it is added that B is a subClass of A, then for each
* individual that is typed as B, either in the ABox or in the
@ -566,6 +771,112 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* If it is added that P is an inverse of Q, then:
* 1. For each statement involving predicate P in
* the assertions model add the inverse statement
* to the inference model if that inverse is
* in the assertions model.
*
* 2. Repeat the same for predicate Q.
*
*/
public void addedInverseProperty(OntProperty prop1, OntProperty prop2, Model inferenceModel) {
if ( !prop1.isObjectProperty() || !prop2.isObjectProperty() ) {
log.warn("The subject and object of the inverseOf statement are not both object properties. No inferencing will be performed. property 1: " + prop1.getURI() + " property 2:" + prop2.getURI());
return;
}
Model inferences = ModelFactory.createDefaultModel();
inferences.add(generateInverseInferences(prop1, prop2));
inferences.add(generateInverseInferences(prop2, prop1));
if (inferences.isEmpty()) return;
aboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator iter = inferences.listStatements();
while (iter.hasNext()) {
Statement infStmt = iter.next();
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} finally {
aboxModel.leaveCriticalSection();
}
}
public Model generateInverseInferences(OntProperty prop, OntProperty inverseProp) {
Model inferences = ModelFactory.createDefaultModel();
aboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator iter = aboxModel.listStatements((Resource) null, prop, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!stmt.getObject().isResource()) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
inferences.add(infStmt);
}
} finally {
aboxModel.leaveCriticalSection();
}
return inferences;
}
/*
* If it is removed that P is an inverse of Q, then:
* 1. For each statement involving predicate P in
* the abox assertions model remove the inverse
* statement from the inference model unless
* that statement is otherwise entailed.
*
* 2. Repeat the same for predicate Q.
*/
public void removedInverseProperty(OntProperty prop1, OntProperty prop2, Model inferenceModel) {
if ( !prop1.isObjectProperty() || !prop2.isObjectProperty() ) {
log.warn("The subject and object of the inverseOf statement are not both object properties. No inferencing will be performed. property 1: " + prop1.getURI() + " property 2:" + prop2.getURI());
return;
}
Model inferences = ModelFactory.createDefaultModel();
inferences.add(generateInverseInferences(prop1, prop2));
inferences.add(generateInverseInferences(prop2, prop1));
if (inferences.isEmpty()) return;
StmtIterator iter = inferences.listStatements();
while (iter.hasNext()) {
Statement infStmt = iter.next();
if (entailedInverseStmt(infStmt)) {
continue;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
}
/*
* Find the most specific types (classes) of an individual and
* indicate them for the individual with the mostSpecificType
@ -740,13 +1051,12 @@ public class SimpleReasoner extends StatementListener {
* inference models.
*/
protected synchronized void recomputeABox() {
HashSet<String> unknownTypes = new HashSet<String>();
// recompute the inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
try {
log.info("Computing class-based ABox inferences.");
log.info("Computing ABox inferences.");
inferenceRebuildModel.removeAll();
int numStmts = 0;
@ -784,6 +1094,57 @@ public class SimpleReasoner extends StatementListener {
log.info("Still computing class-based ABox inferences...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
return;
}
}
log.info("Finished computing class-based ABox inferences");
Iterator<Statement> invStatements = null;
tboxModel.enterCriticalSection(Lock.READ);
try {
invStatements = tboxModel.listStatements((Resource) null, OWL.inverseOf, (Resource) null);
} finally {
tboxModel.leaveCriticalSection();
}
while (invStatements.hasNext()) {
Statement stmt = invStatements.next();
try {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
continue;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
continue;
}
addedInverseProperty(prop1, prop2, inferenceRebuildModel);
} catch (NullPointerException npe) {
log.error("a NullPointerException was received while recomputing the ABox inferences. Halting inference computation.");
return;
} catch (JenaException je) {
if (je.getMessage().equals("Statement models must no be null")) {
log.error("Exception while recomputing ABox inference model. Halting inference computation.", je);
return;
}
log.error("Exception while recomputing ABox inference model: ", je);
} catch (Exception e) {
log.error("Exception while recomputing ABox inference model: ", e);
}
numStmts++;
if ((numStmts % 10000) == 0) {
log.info("Still computing property-based ABox inferences...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
return;
@ -798,7 +1159,7 @@ public class SimpleReasoner extends StatementListener {
inferenceRebuildModel.leaveCriticalSection();
}
log.info("Finished computing class-based ABox inferences");
log.info("Finished computing property-based ABox inferences");
// reflect the recomputed inferences into the application
// inference model.
@ -983,9 +1344,9 @@ public class SimpleReasoner extends StatementListener {
}
break;
}
} catch (Throwable t) {
} catch (Exception e) {
log.error("Exception while processing " + (op == ModelUpdate.Operation.ADD ? "an added" : "a removed") +
" statement in SimpleReasoner plugin:" + plugin.getClass().getName() + " -- " + t.getMessage());
" statement in SimpleReasoner plugin:" + plugin.getClass().getName() + " -- " + e.getMessage());
}
}
}

21
webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java
View file

@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.search.controller;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@ -51,6 +52,7 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.VitroQueryFactory;
import edu.cornell.mannlib.vitro.webapp.search.solr.SolrSetup;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.LinkTemplateModel;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult.IndividualSearchResult;
import edu.ucsf.vitro.opensocial.OpenSocialManager;
/**
* Paged search controller that uses Solr
@ -268,7 +270,24 @@ public class PagedSearchController extends FreemarkerHttpServlet {
vreq.getServletPath(), pagingLinkParams));
}
String template = templateTable.get(format).get(Result.PAGED);
// VIVO OpenSocial Extension by UCSF
try {
OpenSocialManager openSocialManager = new OpenSocialManager(vreq, "search");
// put list of people found onto pubsub channel
List<String> ids = OpenSocialManager.getOpenSocialId(individuals);
openSocialManager.setPubsubData(OpenSocialManager.JSON_PERSONID_CHANNEL,
OpenSocialManager.buildJSONPersonIds(ids, "" + ids.size() + " people found"));
body.put("openSocial", openSocialManager);
if (openSocialManager.isVisible()) {
body.put("bodyOnload", "my.init();");
}
} catch (IOException e) {
log.error("IOException in doTemplate()", e);
} catch (SQLException e) {
log.error("SQLException in doTemplate()", e);
}
String template = templateTable.get(format).get(Result.PAGED);
return new TemplateResponseValues(template, body);
} catch (Throwable e) {

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

@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
*/
public class UserModelSetup extends JenaDataSourceSetupBase
implements ServletContextListener {
protected static String AUTHPATH = BASE + "auth/";
private static final Log log = LogFactory.getLog(
UserModelSetup.class.getName());
@ -55,7 +56,12 @@ public class UserModelSetup extends JenaDataSourceSetupBase
OntModel userAccountsModel =
ModelFactory.createOntologyModel( MEM_ONT_MODEL_SPEC);
userAccountsModel.add(userAccountsDbModel);
// This is used in Selenium testing, when we load user accounts from a file.
if (userAccountsDbModel.isEmpty()) {
readOntologyFilesInPathSet(AUTHPATH, ctx, userAccountsDbModel);
}
userAccountsModel.add(userAccountsDbModel);
userAccountsModel.getBaseModel().register(
new ModelSynchronizer(userAccountsDbModel));
ctx.setAttribute("userAccountsOntModel", userAccountsModel);
@ -65,5 +71,4 @@ public class UserModelSetup extends JenaDataSourceSetupBase
ss.fatal(this, "Unable to load user accounts model from DB", t);
}
}
}

128
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/FixedHTMLDataGetter.java Normal file
View file

@ -0,0 +1,128 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.utils.dataGetter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
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.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
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.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
public class FixedHTMLDataGetter extends DataGetterBase implements DataGetter{
String dataGetterURI;
String htmlValue;
String saveToVar;
VitroRequest vreq;
ServletContext context;
private final static String defaultTemplate = "menupage--defaultFixedHtml.ftl";
final static Log log = LogFactory.getLog(FixedHTMLDataGetter.class);
/**
* Constructor with display model and data getter URI that will be called by reflection.
*/
public FixedHTMLDataGetter(VitroRequest vreq, Model displayModel, String dataGetterURI){
this.configure(vreq, displayModel,dataGetterURI);
}
@Override
public Map<String, Object> getData(Map<String, Object> pageData) {
Map<String, Object> rmap = new HashMap<String,Object>();
rmap.put("variableName", this.saveToVar);
rmap.put(this.saveToVar, this.htmlValue);
//this is the default template set here - overridden by page level template if there is one
rmap.put("bodyTemplate", defaultTemplate);
return rmap;
}
/**
* Configure this instance based on the URI and display model.
*/
protected void configure(VitroRequest vreq, Model displayModel, String dataGetterURI) {
if( vreq == null )
throw new IllegalArgumentException("VitroRequest may not be null.");
if( displayModel == null )
throw new IllegalArgumentException("Display Model may not be null.");
if( dataGetterURI == null )
throw new IllegalArgumentException("PageUri may not be null.");
this.vreq = vreq;
this.context = vreq.getSession().getServletContext();
this.dataGetterURI = dataGetterURI;
QuerySolutionMap initBindings = new QuerySolutionMap();
initBindings.add("dataGetterURI", ResourceFactory.createResource(this.dataGetterURI));
int count = 0;
Query dataGetterConfigurationQuery = QueryFactory.create(dataGetterQuery) ;
displayModel.enterCriticalSection(Lock.READ);
try{
QueryExecution qexec = QueryExecutionFactory.create(
dataGetterConfigurationQuery, displayModel, initBindings) ;
ResultSet res = qexec.execSelect();
try{
while( res.hasNext() ){
count++;
QuerySolution soln = res.next();
// is NOT OPTIONAL
Literal value = soln.getLiteral("htmlValue");
if( dataGetterConfigurationQuery == null )
log.error("no html value defined for page " + this.dataGetterURI);
else
this.htmlValue = value.getLexicalForm();
//saveToVar is OPTIONAL
Literal saveTo = soln.getLiteral("saveToVar");
if( saveTo != null && saveTo.isLiteral() ){
this.saveToVar = saveTo.asLiteral().getLexicalForm();
}else{
this.saveToVar = defaultVarNameForResults;
}
}
}finally{ qexec.close(); }
}finally{ displayModel.leaveCriticalSection(); }
}
private static final String saveToVarPropertyURI= "<" + DisplayVocabulary.SAVE_TO_VAR+ ">";
private static final String htmlValuePropertyURI= "<" + DisplayVocabulary.FIXED_HTML_VALUE+ ">";
public static final String defaultVarNameForResults = "results";
/**
* Query to get the definition of the SparqlDataGetter for a given URI.
*/
private static final String dataGetterQuery =
"PREFIX display: <" + DisplayVocabulary.DISPLAY_NS +"> \n" +
"SELECT ?saveToVar ?htmlValue WHERE { \n" +
" ?dataGetterURI "+saveToVarPropertyURI+" ?saveToVar . \n" +
" ?dataGetterURI "+htmlValuePropertyURI+" ?htmlValue . \n" +
"}";
}

5
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/IndividualsForClassesDataGetter.java
View file

@ -47,7 +47,8 @@ public class IndividualsForClassesDataGetter extends DataGetterBase implements D
String dataGetterURI;
String classGroupURI;
Map<String, Object> classIntersectionsMap;
private final static String defaultTemplate = "page-classgroup.ftl";
/**
* Constructor with display model and data getter URI that will be called by reflection.
*/
@ -132,6 +133,8 @@ public class IndividualsForClassesDataGetter extends DataGetterBase implements D
data.put("dataServiceUrlIndividualsByVClass", this.getDataServiceUrl());
//this is the class group associated with the data getter utilized for display on menu editing, not the custom one created
data.put("classGroupUri",this.classGroupURI);
//default template, overridden at page level if specified in display model
data.put("bodyTemplate", defaultTemplate);
} catch(Exception ex) {
log.error("An error occurred retrieving Vclass Intersection individuals", ex);
}

8
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/SparqlQueryDataGetter.java
View file

@ -37,9 +37,11 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
String modelURI;
VitroRequest vreq;
ServletContext context;
final static Log log = LogFactory.getLog(SparqlQueryDataGetter.class);
//default template
private final static String defaultTemplate = "menupage--defaultSparql.ftl";
/**
* Constructor with display model and data getter URI that will be called by reflection.
@ -134,7 +136,9 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
//put results in page data, what key to use for results?
Map<String, Object> rmap = new HashMap<String,Object>();
rmap.put(this.saveToVar, results);
rmap.put(this.saveToVar, results);
//This will be overridden at page level in display model if template specified there
rmap.put("bodyTemplate", defaultTemplate);
return rmap;
}

159
webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/customlistview/DataPropertyListConfig.java Normal file
View file

@ -0,0 +1,159 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.customlistview;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.lang.reflect.Constructor;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DataPropertyTemplateModel;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DataPropertyTemplateModel.ConfigError;
import freemarker.cache.TemplateLoader;
import freemarker.template.Configuration;
public class DataPropertyListConfig {
private static final Log log = LogFactory.getLog(DataPropertyListConfig.class);
private static final String CONFIG_FILE_PATH = "/config/";
private static final String DEFAULT_CONFIG_FILE_NAME = "listViewConfig-dataDefault.xml";
/* NB The default post-processor is not the same as the post-processor for the default view. The latter
* actually defines its own post-processor, whereas the default post-processor is used for custom views
* that don't define a post-processor, to ensure that the standard post-processing applies.
*
* edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DefaultObjectPropertyDataPostProcessor
*/
// TODO Lump these together into the PropertyListConfigContext
private final DataPropertyTemplateModel dptm;
private final VitroRequest vreq;
private final TemplateLoader templateLoader;
private boolean isDefaultConfig;
private Set<String> constructQueries;
private String selectQuery;
private String templateName;
public DataPropertyListConfig(DataPropertyTemplateModel dptm, TemplateLoader templateLoader, VitroRequest vreq,
DataProperty dp, boolean editing)
throws InvalidConfigurationException {
this.dptm = dptm;
this.vreq = vreq;
WebappDaoFactory wadf = vreq.getWebappDaoFactory();
this.templateLoader = templateLoader;
// Get the custom config filename
String configFileName = wadf.getDataPropertyDao().getCustomListViewConfigFileName(dp);
if (configFileName == null) { // no custom config; use default config
configFileName = DEFAULT_CONFIG_FILE_NAME;
}
log.debug("Using list view config file " + configFileName + " for data property " + dp.getURI());
String configFilePath = getConfigFilePath(configFileName);
try {
File config = new File(configFilePath);
if ( ! isDefaultConfig(configFileName) && ! config.exists() ) {
log.warn("Can't find config file " + configFilePath + " for data property " + dp.getURI() + "\n" +
". Using default config file instead.");
configFilePath = getConfigFilePath(DEFAULT_CONFIG_FILE_NAME);
// Should we test for the existence of the default, and throw an error if it doesn't exist?
}
setValuesFromConfigFile(configFilePath, wadf, editing);
} catch (Exception e) {
log.error("Error processing config file " + configFilePath + " for data property " + dp.getURI(), e);
// What should we do here?
}
if ( ! isDefaultConfig(configFileName) ) {
ConfigError configError = checkConfiguration();
if ( configError != null ) { // the configuration contains an error
log.warn("Invalid list view config for data property " + dp.getURI() +
" in " + configFilePath + ":\n" +
configError + " Using default config instead.");
configFilePath = getConfigFilePath(DEFAULT_CONFIG_FILE_NAME);
setValuesFromConfigFile(configFilePath, wadf, editing);
}
}
isDefaultConfig = isDefaultConfig(configFileName);
}
private boolean isDefaultConfig(String configFileName) {
return configFileName.equals(DEFAULT_CONFIG_FILE_NAME);
}
private ConfigError checkConfiguration() {
ConfigError error = dptm.checkQuery(selectQuery);
if (error != null) {
return error;
}
if (StringUtils.isBlank(selectQuery)) {
return ConfigError.NO_SELECT_QUERY;
}
if ( StringUtils.isBlank(templateName)) {
return ConfigError.NO_TEMPLATE;
}
try {
if ( templateLoader.findTemplateSource(templateName) == null ) {
return ConfigError.TEMPLATE_NOT_FOUND;
}
} catch (IOException e) {
log.error("Error finding template " + templateName, e);
}
return null;
}
private void setValuesFromConfigFile(String configFilePath, WebappDaoFactory wdf,
boolean editing) {
try {
FileReader reader = new FileReader(configFilePath);
CustomListViewConfigFile configFileContents = new CustomListViewConfigFile(reader);
selectQuery = configFileContents.getSelectQuery(false, editing);
templateName = configFileContents.getTemplateName();
constructQueries = configFileContents.getConstructQueries();
} catch (Exception e) {
log.error("Error processing config file " + configFilePath, e);
}
}
private String getConfigFilePath(String filename) {
return vreq.getSession().getServletContext().getRealPath(CONFIG_FILE_PATH + filename);
}
public String getSelectQuery() {
return this.selectQuery;
}
public Set<String> getConstructQueries() {
return this.constructQueries;
}
public String getTemplateName() {
return this.templateName;
}
public boolean isDefaultListView() {
return this.isDefaultConfig;
}
}

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

@ -25,13 +25,15 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
private final Literal literalValue;
private final String deleteUrl;
private final String editUrl;
private final String templateName;
//Extended to include vitro request to check for special parameters
public DataPropertyStatementTemplateModel(String subjectUri, String propertyUri,
Literal literal, VitroRequest vreq) {
public DataPropertyStatementTemplateModel(String subjectUri, String propertyUri, Literal literal,
String templateName, VitroRequest vreq) {
super(subjectUri, propertyUri, vreq);
this.literalValue = literal;
this.templateName = templateName;
// Do delete url first, since used in building edit url
this.deleteUrl = makeDeleteUrl();
@ -52,6 +54,7 @@ public class DataPropertyStatementTemplateModel extends PropertyStatementTemplat
"datapropKey", makeHash(dps),
"cmd", "delete");
params.put("templateName", templateName);
params.putAll(UrlBuilder.getModelParams(vreq));
return UrlBuilder.getUrl(EDIT_PATH, params);

88
webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/DataPropertyTemplateModel.java
View file

@ -4,7 +4,11 @@ package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -17,11 +21,15 @@ import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.Property;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerConfigurationLoader;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Route;
import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.customlistview.InvalidConfigurationException;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.customlistview.DataPropertyListConfig;
import freemarker.cache.TemplateLoader;
public class DataPropertyTemplateModel extends PropertyTemplateModel {
@ -31,6 +39,33 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
private static final String EDIT_PATH = "editRequestDispatch";
private final List<DataPropertyStatementTemplateModel> statements;
private static final String KEY_SUBJECT = "subject";
private static final String KEY_PROPERTY = "property";
public static enum ConfigError {
NO_SELECT_QUERY("Missing select query specification"),
NO_TEMPLATE("Missing template specification"),
TEMPLATE_NOT_FOUND("Specified template does not exist");
String message;
ConfigError(String message) {
this.message = message;
}
public String getMessage() {
return message;
}
public String toString() {
return getMessage();
}
}
private DataPropertyListConfig config;
private String objectKey;
private String queryString;
private Set<String> constructQueries;
DataPropertyTemplateModel(DataProperty dp, Individual subject, VitroRequest vreq,
boolean editing, List<DataProperty> populatedDataPropertyList) {
@ -38,15 +73,25 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
super(dp, subject, vreq);
setName(dp.getPublicName());
// Get the config for this data property
try {
config = new DataPropertyListConfig(this, getFreemarkerTemplateLoader(), vreq, dp, editing);
} catch (Exception e) {
log.error(e, e);
}
queryString = getSelectQuery();
constructQueries = getConstructQueries();
statements = new ArrayList<DataPropertyStatementTemplateModel>();
// If the property is populated, get the data property statements via a sparql query
if (populatedDataPropertyList.contains(dp)) {
log.debug("Getting data for populated data property " + getUri());
DataPropertyStatementDao dpDao = vreq.getWebappDaoFactory().getDataPropertyStatementDao();
List<Literal> values = dpDao.getDataPropertyValuesForIndividualByProperty(subject, dp);
List<Literal> values = dpDao.getDataPropertyValuesForIndividualByProperty(subject, dp, queryString, constructQueries);
for (Literal value : values) {
statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, vreq));
statements.add(new DataPropertyStatementTemplateModel(subjectUri, propertyUri, value, getTemplateName(), vreq));
}
} else {
log.debug("Data property " + getUri() + " is unpopulated.");
@ -57,7 +102,6 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
}
}
protected void setAddUrl(Property property) {
DataProperty dp = (DataProperty) property;
@ -91,6 +135,10 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
addUrl = UrlBuilder.getUrl(EDIT_PATH, params);
}
protected TemplateLoader getFreemarkerTemplateLoader() {
return FreemarkerConfigurationLoader.getConfig(vreq).getTemplateLoader();
}
@Override
protected int getPropertyDisplayTier(Property p) {
return ((DataProperty)p).getDisplayTier();
@ -101,6 +149,37 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
return Route.DATA_PROPERTY_EDIT;
}
public ConfigError checkQuery(String queryString) {
if (StringUtils.isBlank(queryString)) {
return ConfigError.NO_SELECT_QUERY;
}
return null;
}
private String getSelectQuery() {
return config.getSelectQuery();
}
private Set<String> getConstructQueries() {
return config.getConstructQueries();
}
protected String getTemplateName() {
return config.getTemplateName();
}
protected boolean hasDefaultListView() {
return config.isDefaultListView();
}
protected String getObjectKey() {
return objectKey;
}
protected boolean isEmpty() {
return statements.isEmpty();
}
/* Template properties */
public String getType() {
@ -111,6 +190,9 @@ public class DataPropertyTemplateModel extends PropertyTemplateModel {
return statements;
}
public String getTemplate() {
return getTemplateName();
}
/* Template methods */

2
webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ObjectPropertyStatementTemplateModel.java
View file

@ -34,7 +34,7 @@ public class ObjectPropertyStatementTemplateModel extends PropertyStatementTempl
public ObjectPropertyStatementTemplateModel(String subjectUri, String propertyUri, String objectKey,
Map<String, String> data, String templateName, VitroRequest vreq) {
super(subjectUri, propertyUri, vreq);
this.data = Collections.unmodifiableMap(new HashMap<String, String>(data));
this.objectUri = data.get(objectKey);
this.templateName = templateName;

100
webapp/src/edu/ucsf/vitro/opensocial/GadgetController.java Normal file
View file

@ -0,0 +1,100 @@
package edu.ucsf.vitro.opensocial;
import java.io.IOException;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ExceptionResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RedirectResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
public class GadgetController extends FreemarkerHttpServlet {
private static final long serialVersionUID = 1L;
private static final Log log = LogFactory.getLog(GadgetController.class);
@Override
protected ResponseValues processRequest(VitroRequest vreq) {
if (vreq.getServletPath().endsWith("/sandbox")) {
boolean sandbox = "True".equalsIgnoreCase(ConfigurationProperties.getBean(vreq.getSession()
.getServletContext()).getProperty("OpenSocial.sandbox"));
if (!sandbox) {
return new ExceptionResponseValues( new Exception("Sandbox not available"));
}
return processGadgetSandbox(vreq);
}
else {
return processGadgetDetails(vreq);
}
}
protected ResponseValues processGadgetDetails(VitroRequest vreq) {
try {
Map<String, Object> body = new HashMap<String, Object>();
body.put("title", "Gadget Details");
// VIVO OpenSocial Extension by UCSF
try {
OpenSocialManager openSocialManager = new OpenSocialManager(vreq, "gadgetDetails");
body.put(OpenSocialManager.TAG_NAME, openSocialManager);
if (openSocialManager.isVisible()) {
body.put("bodyOnload", "my.init();");
}
} catch (IOException e) {
log.error("IOException in doTemplate()", e);
} catch (SQLException e) {
log.error("SQLException in doTemplate()", e);
}
return new TemplateResponseValues("gadgetDetails.ftl", body);
} catch (Throwable e) {
log.error(e, e);
return new ExceptionResponseValues(e);
}
}
@Override
protected String getTitle(String siteName, VitroRequest vreq) {
return "Gadget Details";
}
protected ResponseValues processGadgetSandbox(VitroRequest vreq) {
if ("POST".equalsIgnoreCase(vreq.getMethod())) {
vreq.getSession().setAttribute(OpenSocialManager.OPENSOCIAL_GADGETS, vreq.getParameter("gadgetURLS"));
vreq.getSession().setAttribute(OpenSocialManager.OPENSOCIAL_DEBUG, vreq.getParameter("debug") != null);
vreq.getSession().setAttribute(OpenSocialManager.OPENSOCIAL_NOCACHE, vreq.getParameter("useCache") == null);
return new RedirectResponseValues("/");
}
Map<String, Object> body = new HashMap<String, Object>();
body.put("title", "Gadget Sandbox");
try {
OpenSocialManager openSocialManager = new OpenSocialManager(vreq, "gadgetSandbox");
String gadgetURLS = "";
for (PreparedGadget gadget : openSocialManager.getVisibleGadgets())
{
gadgetURLS += gadget.getGadgetURL() + System.getProperty("line.separator");
}
body.put("gadgetURLS", gadgetURLS);
body.put(OpenSocialManager.TAG_NAME, openSocialManager);
} catch (IOException e) {
log.error("IOException in doTemplate()", e);
} catch (SQLException e) {
log.error("SQLException in doTemplate()", e);
}
return new TemplateResponseValues("gadgetLogin.ftl", body);
}
}

204
webapp/src/edu/ucsf/vitro/opensocial/GadgetSpec.java Normal file
View file

@ -0,0 +1,204 @@
package edu.ucsf.vitro.opensocial;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.dbcp.BasicDataSource;
public class GadgetSpec {
private String openSocialGadgetURL;
private String name;
private int appId = 0;
private List<String> channels = new ArrayList<String>();
private boolean unknownGadget = false;
private Map<String, GadgetViewRequirements> viewRequirements = new HashMap<String, GadgetViewRequirements>();
// For preloading
public GadgetSpec(int appId, String name, String openSocialGadgetURL,
List<String> channels) {
this.appId = appId;
this.name = name;
this.openSocialGadgetURL = openSocialGadgetURL;
this.channels.addAll(channels);
}
public GadgetSpec(int appId, String name, String openSocialGadgetURL,
String channelsStr) {
this(appId, name, openSocialGadgetURL, Arrays.asList(channelsStr != null
&& channelsStr.length() > 0 ? channelsStr.split(" ") : new String[0]));
}
public GadgetSpec(int appId, String name, String openSocialGadgetURL,
List<String> channels, boolean unknownGadget, BasicDataSource ds)
throws SQLException {
this(appId, name, openSocialGadgetURL, channels);
this.unknownGadget = unknownGadget;
// Load gadgets from the DB first
if (!unknownGadget) {
Connection conn = null;
Statement stmt = null;
ResultSet rset = null;
try {
String sqlCommand = "select page, viewer_req, owner_req, view, closed_width, open_width, start_closed, chromeId, display_order from shindig_app_views where appId = "
+ appId;
conn = ds.getConnection();
stmt = conn.createStatement();
rset = stmt.executeQuery(sqlCommand);
while (rset.next()) {
viewRequirements.put(
rset.getString(1),
new GadgetViewRequirements(rset.getString(1), rset
.getString(2), rset.getString(3), rset
.getString(4), rset.getInt(5), rset
.getInt(6), rset.getBoolean(7), rset
.getString(8), rset.getInt(9)));
}
} finally {
try {
if (rset != null) {
rset.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (stmt != null) {
stmt.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (conn != null) {
conn.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
public int getAppId() {
return appId;
}
public String getName() {
return name;
}
public String getGadgetURL() {
return openSocialGadgetURL;
}
public List<String> getChannels() {
return channels;
}
public boolean listensTo(String channel) { // if an unknown gadget just say yes,
// we don't care about
// performance in this situation
return unknownGadget || channels.contains(channel);
}
public GadgetViewRequirements getGadgetViewRequirements(String page) {
if (viewRequirements.containsKey(page)) {
return viewRequirements.get(page);
}
return null;
}
public boolean show(String viewerId, String ownerId, String page,
BasicDataSource ds) throws SQLException {
boolean show = true;
// if there are no view requirements, go ahead and show it. We are
// likely testing out a new gadget
// if there are some, turn it off unless this page is
if (viewRequirements.size() > 0) {
show = false;
}
if (viewRequirements.containsKey(page)) {
show = true;
GadgetViewRequirements req = getGadgetViewRequirements(page);
if ('U' == req.getViewerReq() && viewerId != null) {
show = false;
} else if ('R' == req.getViewerReq()) {
show &= isRegisteredTo(viewerId, ds);
}
if ('R' == req.getOwnerReq()) {
show &= isRegisteredTo(ownerId, ds);
} else if ('S' == req.getOwnerReq()) {
show &= (viewerId == ownerId);
}
}
return show;
}
public boolean isRegisteredTo(String personId, BasicDataSource ds)
throws SQLException {
int count = 0;
Connection conn = null;
Statement stmt = null;
ResultSet rset = null;
try {
String sqlCommand = "select count(*) from shindig_app_registry where appId = "
+ getAppId() + " and personId = '" + personId + "';";
conn = ds.getConnection();
stmt = conn.createStatement();
rset = stmt.executeQuery(sqlCommand);
while (rset.next()) {
count = rset.getInt(1);
}
} finally {
try {
if (rset != null) {
rset.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (stmt != null) {
stmt.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (conn != null) {
conn.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
return (count == 1);
}
public boolean fromSandbox() {
return unknownGadget;
}
// who sees it? Return the viewerReq for the ProfileDetails page
public char getVisibleScope() {
GadgetViewRequirements req = getGadgetViewRequirements("/display");
return req != null ? req.getViewerReq() : ' ';
}
public String toString() {
return "" + this.appId + ":" + this.name + ":" + this.openSocialGadgetURL;
}
}

67
webapp/src/edu/ucsf/vitro/opensocial/GadgetViewRequirements.java Normal file
View file

@ -0,0 +1,67 @@
package edu.ucsf.vitro.opensocial;
public class GadgetViewRequirements {
private String page;
private char viewerReq; // U for User or null for no requirement
private char ownerReq; // R for Registered or null for no requirement
private String view;
private int closedWidth;
private int openWidth;
private boolean startClosed;
private String chromeId;
private int display_order;
public GadgetViewRequirements(String page, char viewerReq, char ownerReq,
String view, int closedWidth, int openWidth, boolean startClosed,
String chromeId, int display_order) {
this.page = page;
this.viewerReq = viewerReq;
this.ownerReq = ownerReq;
this.view = view;
this.closedWidth = closedWidth;
this.openWidth = openWidth;
this.startClosed = startClosed;
this.chromeId = chromeId;
this.display_order = display_order;
}
public GadgetViewRequirements(String page, String viewerReq,
String ownerReq, String view, int closedWidth, int openWidth,
boolean startClosed, String chromeId, int display_order) {
this(page, viewerReq != null ? viewerReq.charAt(0) : ' ',
ownerReq != null ? ownerReq.charAt(0) : ' ', view, closedWidth,
openWidth, startClosed, chromeId, display_order);
}
public char getViewerReq() {
return viewerReq;
}
public char getOwnerReq() {
return ownerReq;
}
public String getView() {
return view;
}
public int getClosedWidth() {
return closedWidth;
}
public int getOpenWidth() {
return openWidth;
}
public boolean getStartClosed() {
return startClosed;
}
public String getChromeId() {
return chromeId;
}
int getDisplayOrder() {
return display_order;
}
}

483
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialManager.java Normal file
View file

@ -0,0 +1,483 @@
package edu.ucsf.vitro.opensocial;
import java.io.IOException;
import java.net.Socket;
import java.net.URLEncoder;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.dbcp.BasicDataSource;
import org.json.JSONException;
import org.json.JSONObject;
import edu.cornell.mannlib.vedit.beans.LoginStatusBean;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.UserAccount;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestAnalysisContextImpl;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestAnalyzer;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestInfo;
public class OpenSocialManager {
public static final String SHINDIG_URL_PROP = "OpenSocial.shindigURL";
public static final String OPENSOCIAL_DEBUG = "OPENSOCIAL_DEBUG";
public static final String OPENSOCIAL_NOCACHE = "OPENSOCIAL_NOCACHE";
public static final String OPENSOCIAL_GADGETS = "OPENSOCIAL_GADGETS";
public static final String JSON_PERSONID_CHANNEL = "JSONPersonIds";
public static final String JSON_PMID_CHANNEL = "JSONPubMedIds";
public static final String TAG_NAME = "openSocial";
private static final String DEFAULT_DRIVER = "com.mysql.jdbc.Driver";
private List<PreparedGadget> gadgets = new ArrayList<PreparedGadget>();
private Map<String, String> pubsubdata = new HashMap<String, String>();
private String viewerId = null;
private String ownerId = null;
private boolean isDebug = false;
private boolean noCache = false;
private String pageName;
private ConfigurationProperties configuration;
private BasicDataSource dataSource;
public OpenSocialManager(VitroRequest vreq, String pageName) throws SQLException, IOException {
this(vreq, pageName, false);
}
public OpenSocialManager(VitroRequest vreq, String pageName, boolean editMode) throws SQLException, IOException {
this.isDebug = vreq.getSession() != null
&& Boolean.TRUE.equals(vreq.getSession().getAttribute(OPENSOCIAL_DEBUG));
this.noCache = vreq.getSession() != null
&& Boolean.TRUE.equals(vreq.getSession().getAttribute(OPENSOCIAL_NOCACHE));
this.pageName = pageName;
configuration = ConfigurationProperties.getBean(vreq.getSession()
.getServletContext());
if (configuration.getProperty(SHINDIG_URL_PROP) == null) {
// do nothing
return;
}
// Analyze the request to figure out whose page we are viewing.
this.ownerId = figureOwnerId(vreq);
// in editMode we need to set the viewer to be the same as the owner
// otherwise, the gadget will not be able to save appData correctly
if (editMode) {
this.viewerId = ownerId;
}
else {
UserAccount viewer = LoginStatusBean.getCurrentUser(vreq);
this.viewerId = viewer != null ? viewer.getUri() : null;
}
boolean gadgetSandbox = "gadgetSandbox".equals(pageName);
String requestAppId = vreq.getParameter("appId");
Map<String, GadgetSpec> dbApps = new HashMap<String, GadgetSpec>();
Map<String, GadgetSpec> officialApps = new HashMap<String, GadgetSpec>();
dataSource = new BasicDataSource();
dataSource.setDriverClassName(DEFAULT_DRIVER);
dataSource.setUsername(configuration
.getProperty("VitroConnection.DataSource.username"));
dataSource.setPassword(configuration
.getProperty("VitroConnection.DataSource.password"));
dataSource.setUrl(configuration
.getProperty("VitroConnection.DataSource.url"));
// Load gadgets from the DB first
Connection conn = null;
Statement stmt = null;
ResultSet rset = null;
try {
String sqlCommand = "select appId, name, url, channels, enabled from shindig_apps";
// if a specific app is requested, only grab it
if (requestAppId != null) {
sqlCommand += " where appId = " + requestAppId;
}
conn = dataSource.getConnection();
stmt = conn.createStatement();
rset = stmt.executeQuery(sqlCommand);
while (rset.next()) {
GadgetSpec spec = new GadgetSpec(rset.getInt(1),
rset.getString(2), rset.getString(3), rset.getString(4));
String gadgetFileName = getGadgetFileNameFromURL(rset
.getString(3));
dbApps.put(gadgetFileName, spec);
if (requestAppId != null || rset.getBoolean(5)) {
officialApps.put(gadgetFileName, spec);
}
}
} finally {
try {
if (rset != null) {
rset.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (stmt != null) {
stmt.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (conn != null) {
conn.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
// Add manual gadgets if there are any
// Note that this block of code only gets executed after someone fills in the
// gadget/sandbox form!
int moduleId = 0;
if (vreq.getSession() != null
&& vreq.getSession().getAttribute(OPENSOCIAL_GADGETS) != null) {
String openSocialGadgetURLS = (String) vreq.getSession()
.getAttribute(OPENSOCIAL_GADGETS);
String[] urls = openSocialGadgetURLS.split(System.getProperty("line.separator"));
for (String openSocialGadgetURL : urls) {
if (openSocialGadgetURL.length() == 0)
continue;
int appId = 0; // if URL matches one in the DB, use DB provided
// appId, otherwise generate one
String gadgetFileName = getGadgetFileNameFromURL(openSocialGadgetURL);
String name = gadgetFileName;
List<String> channels = new ArrayList<String>();
boolean unknownGadget = true;
if (dbApps.containsKey(gadgetFileName)) {
appId = dbApps.get(gadgetFileName).getAppId();
name = dbApps.get(gadgetFileName).getName();
channels = dbApps.get(gadgetFileName).getChannels();
unknownGadget = false;
} else {
appId = openSocialGadgetURL.hashCode();
}
// if they asked for a specific one, only let it in
if (requestAppId != null
&& Integer.getInteger(requestAppId) != appId) {
continue;
}
GadgetSpec gadget = new GadgetSpec(appId, name,
openSocialGadgetURL, channels, unknownGadget, dataSource);
// only add ones that are visible in this context!
if (unknownGadget
|| gadget.show(viewerId, ownerId, pageName, dataSource)) {
String securityToken = socketSendReceive(viewerId, ownerId,
"" + gadget.getAppId());
gadgets.add(new PreparedGadget(gadget, this, moduleId++,
securityToken));
}
}
}
// if no manual one were added, use the ones from the DB
if (gadgets.size() == 0) {
// Load DB gadgets
if (gadgetSandbox) {
officialApps = dbApps;
}
for (GadgetSpec spec : officialApps.values()) {
GadgetSpec gadget = new GadgetSpec(spec.getAppId(),
spec.getName(), spec.getGadgetURL(),
spec.getChannels(), false, dataSource);
// only add ones that are visible in this context!
if (gadgetSandbox
|| gadget.show(viewerId, ownerId, pageName, dataSource)) {
String securityToken = socketSendReceive(viewerId, ownerId,
"" + gadget.getAppId());
gadgets.add(new PreparedGadget(gadget, this, moduleId++,
securityToken));
}
}
}
// sort the gadgets
Collections.sort(gadgets);
}
private String figureOwnerId(VitroRequest vreq) {
IndividualRequestAnalyzer requestAnalyzer = new IndividualRequestAnalyzer(vreq,
new IndividualRequestAnalysisContextImpl(vreq));
IndividualRequestInfo requestInfo = requestAnalyzer.analyze();
Individual owner = requestInfo.getIndividual();
return owner != null ? owner.getURI() : null;
}
private String getGadgetFileNameFromURL(String url) {
String[] urlbits = url.split("/");
return urlbits[urlbits.length - 1];
}
public boolean isDebug() {
return isDebug;
}
public boolean noCache() {
return noCache;
}
public String getOwnerId() {
return ownerId;
}
public boolean hasGadgetListeningTo(String channel) {
for (PreparedGadget gadget : getVisibleGadgets()) {
if (gadget.getGadgetSpec().listensTo(channel)) {
return true;
}
}
return false;
}
public static List<String> getOpenSocialId(List<Individual> individuals) {
List<String> personIds = new ArrayList<String>();
for (Individual ind : individuals) {
personIds.add(ind.getURI());
}
return personIds;
}
// JSON Helper Functions
public static String buildJSONPersonIds(List<String> personIds,
String message) throws JSONException {
JSONObject json = new JSONObject();
json.put("message", message);
json.put("personIds", personIds);
return json.toString();
}
public static String buildJSONPersonIds(String personId, String message) throws JSONException {
List<String> personIds = new ArrayList<String>();
personIds.add(personId);
return buildJSONPersonIds(personIds, message);
}
public static String buildJSONPersonIds(Individual ind, String message) throws JSONException {
List<String> personIds = new ArrayList<String>();
personIds.add(ind.getURI());
return buildJSONPersonIds(personIds, message);
}
/****
* public static String BuildJSONPubMedIds(Person person) { List<Int32>
* pubIds = new List<Int32>(); foreach (Publication pub in
* person.PublicationList) { foreach (PublicationSource pubSource in
* pub.PublicationSourceList) { if ("PubMed".Equals(pubSource.Name)) {
* pubIds.Add(Int32.Parse(pubSource.ID)); } } } Dictionary<string, Object>
* foundPubs = new Dictionary<string, object>(); foundPubs.Add("pubIds",
* pubIds); foundPubs.Add("message", "PubMedIDs for " +
* person.Name.FullName); JavaScriptSerializer serializer = new
* JavaScriptSerializer(); return serializer.Serialize(foundPubs); }
***/
public void setPubsubData(String key, String value) {
if (pubsubdata.containsKey(key)) {
pubsubdata.remove(key);
}
if (value != null && !value.isEmpty()) {
pubsubdata.put(key, value);
}
}
public Map<String, String> getPubsubData() {
return pubsubdata;
}
public void removePubsubGadgetsWithoutData() {
// if any visible gadgets depend on pubsub data that isn't present,
// throw them out
List<PreparedGadget> removedGadgets = new ArrayList<PreparedGadget>();
for (PreparedGadget gadget : gadgets) {
for (String channel : gadget.getGadgetSpec().getChannels()) {
if (!pubsubdata.containsKey(channel)) {
removedGadgets.add(gadget);
break;
}
}
}
for (PreparedGadget gadget : removedGadgets) {
gadgets.remove(gadget);
}
}
public void removeGadget(String name) {
// if any visible gadgets depend on pubsub data that isn't present,
// throw them out
PreparedGadget gadgetToRemove = null;
for (PreparedGadget gadget : gadgets) {
if (name.equals(gadget.getName())) {
gadgetToRemove = gadget;
break;
}
}
gadgets.remove(gadgetToRemove);
}
public String getPageName() {
return pageName;
}
public String getIdToUrlMapJavascript() {
String retval = "var idToUrlMap = {";
for (PreparedGadget gadget : gadgets) {
// retval += gadget.GetAppId() + ":'" + gadget.GetGadgetURL() +
// "', ";
retval += "'remote_iframe_" + gadget.getAppId() + "':'"
+ gadget.getGadgetURL() + "', ";
}
return retval.substring(0, retval.length() - 2) + "};";
}
public boolean isVisible() {
// always have turned on for ProfileDetails.aspx because we want to
// generate the "profile was viewed" in Javascript (bot proof)
// regardless of any gadgets being visible, and we need this to be True
// for the shindig javascript libraries to load
return (configuration.getProperty(SHINDIG_URL_PROP) != null
&& (getVisibleGadgets().size() > 0) || getPageName().equals(
"/display"));
}
public List<PreparedGadget> getVisibleGadgets() {
return gadgets;
}
public void postActivity(int userId, String title) throws SQLException {
postActivity(userId, title, null, null, null);
}
public void postActivity(int userId, String title, String body) throws SQLException {
postActivity(userId, title, body, null, null);
}
public void postActivity(int userId, String title, String body,
String xtraId1Type, String xtraId1Value) throws SQLException {
Connection conn = null;
Statement stmt = null;
String sqlCommand = "INSERT INTO shindig_activity (userId, activity, xtraId1Type, xtraId1Value) VALUES ('"
+ userId + "','<activity xmlns=\"http://ns.opensocial.org/2008/opensocial\"><postedTime>"
+ System.currentTimeMillis() + "</postedTime><title>" + title + "</title>"
+ (body != null ? "<body>" + body + "</body>" : "") + "</activity>','"
+ xtraId1Type + "','" + xtraId1Value + "');";
try {
conn = dataSource.getConnection();
stmt = conn.createStatement();
stmt.executeUpdate(sqlCommand);
} finally {
try {
if (stmt != null) {
stmt.close();
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (conn != null) {
conn.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
private String socketSendReceive(String viewer, String owner, String gadget)
throws IOException {
// These keys need to match what you see in
// edu.ucsf.orng.shindig.service.SecureTokenGeneratorService in
// Shindig
String[] tokenService = configuration.getProperty(
"OpenSocial.tokenService").split(":");
String request = "c=default" + (viewer != null ? "&v=" + URLEncoder.encode(viewer, "UTF-8") : "") +
(owner != null ? "&o=" + URLEncoder.encode(owner, "UTF-8") : "") + "&g=" + gadget + "\r\n";
// Create a socket connection with the specified server and port.
Socket s = new Socket(tokenService[0],
Integer.parseInt(tokenService[1]));
// Send request to the server.
s.getOutputStream().write(request.getBytes());
// Receive the encoded content.
int bytes = 0;
String page = "";
byte[] bytesReceived = new byte[256];
// The following will block until the page is transmitted.
while ((bytes = s.getInputStream().read(bytesReceived)) > 0) {
page += new String(bytesReceived, 0, bytes);
}
return page;
}
public String getContainerJavascriptSrc() {
return configuration.getProperty(SHINDIG_URL_PROP)
+ "/gadgets/js/core:dynamic-height:osapi:pubsub:rpc:views:shindig-container.js?c=1"
+ (isDebug ? "&debug=1" : "");
}
public String getGadgetJavascript() {
String lineSeparator = System.getProperty("line.separator");
String gadgetScriptText = lineSeparator
+ "var my = {};"
+ lineSeparator
+ "my.gadgetSpec = function(appId, name, url, secureToken, view, closed_width, open_width, start_closed, chrome_id, visible_scope) {"
+ lineSeparator + "this.appId = appId;" + lineSeparator
+ "this.name = name;" + lineSeparator + "this.url = url;"
+ lineSeparator + "this.secureToken = secureToken;"
+ lineSeparator + "this.view = view || 'default';"
+ lineSeparator + "this.closed_width = closed_width;"
+ lineSeparator + "this.open_width = open_width;"
+ lineSeparator + "this.start_closed = start_closed;"
+ lineSeparator + "this.chrome_id = chrome_id;" + lineSeparator
+ "this.visible_scope = visible_scope;" + lineSeparator + "};"
+ lineSeparator + "my.pubsubData = {};" + lineSeparator;
for (String key : getPubsubData().keySet()) {
gadgetScriptText += "my.pubsubData['" + key + "'] = '"
+ getPubsubData().get(key) + "';" + lineSeparator;
}
gadgetScriptText += "my.openSocialURL = '"
+ configuration.getProperty(SHINDIG_URL_PROP) + "';"
+ lineSeparator + "my.debug = " + (isDebug() ? "1" : "0") + ";"
+ lineSeparator + "my.noCache = " + (noCache() ? "1" : "0")
+ ";" + lineSeparator + "my.gadgets = [";
for (PreparedGadget gadget : getVisibleGadgets()) {
gadgetScriptText += "new my.gadgetSpec(" + gadget.getAppId() + ",'"
+ gadget.getName() + "','" + gadget.getGadgetURL() + "','"
+ gadget.getSecurityToken() + "','" + gadget.getView()
+ "'," + gadget.getClosedWidth() + ","
+ gadget.getOpenWidth() + ","
+ (gadget.getStartClosed() ? "1" : "0") + ",'"
+ gadget.getChromeId() + "','"
+ gadget.getGadgetSpec().getVisibleScope() + "'), ";
}
gadgetScriptText = gadgetScriptText.substring(0,
gadgetScriptText.length() - 2)
+ "];"
+ lineSeparator;
return gadgetScriptText;
}
}

123
webapp/src/edu/ucsf/vitro/opensocial/PreparedGadget.java Normal file
View file

@ -0,0 +1,123 @@
package edu.ucsf.vitro.opensocial;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
public class PreparedGadget implements Comparable<PreparedGadget> {
private GadgetSpec gadgetSpec;
private OpenSocialManager helper;
private int moduleId;
private String securityToken;
public PreparedGadget(GadgetSpec gadgetSpec, OpenSocialManager helper,
int moduleId, String securityToken) {
this.gadgetSpec = gadgetSpec;
this.helper = helper;
this.moduleId = moduleId;
this.securityToken = securityToken;
}
public int compareTo(PreparedGadget other) {
GadgetViewRequirements gvr1 = this.getGadgetViewRequirements();
GadgetViewRequirements gvr2 = other.getGadgetViewRequirements();
return ("" + this.getView() + (gvr1 != null ? gvr1.getDisplayOrder()
: Integer.MAX_VALUE)).compareTo("" + other.getView()
+ (gvr2 != null ? gvr2.getDisplayOrder() : Integer.MAX_VALUE));
}
public GadgetSpec getGadgetSpec() {
return gadgetSpec;
}
public String getSecurityToken() {
return securityToken;
}
public int getAppId() {
return gadgetSpec.getAppId();
}
public String getName() {
return gadgetSpec.getName();
}
public int getModuleId() {
return moduleId;
}
public String getGadgetURL() {
return gadgetSpec.getGadgetURL();
}
GadgetViewRequirements getGadgetViewRequirements() {
return gadgetSpec.getGadgetViewRequirements(helper.getPageName());
}
public String getView() {
GadgetViewRequirements reqs = getGadgetViewRequirements();
if (reqs != null) {
return reqs.getView();
}
// default behavior that will get invoked when there is no reqs. Useful
// for sandbox gadgets
else if (helper.getPageName().equals("individual-EDIT-MODE")) {
return "home";
} else if (helper.getPageName().equals("individual")) {
return "profile";
} else if (helper.getPageName().equals("gadgetDetails")) {
return "canvas";
} else if (gadgetSpec.getGadgetURL().contains("Tool")) {
return "small";
} else {
return null;
}
}
public int getOpenWidth() {
GadgetViewRequirements reqs = getGadgetViewRequirements();
return reqs != null ? reqs.getOpenWidth() : 0;
}
public int getClosedWidth() {
GadgetViewRequirements reqs = getGadgetViewRequirements();
return reqs != null ? reqs.getClosedWidth() : 0;
}
public boolean getStartClosed() {
GadgetViewRequirements reqs = getGadgetViewRequirements();
// if the page specific reqs are present, honor those. Otherwise defaut
// to true for regular gadgets, false for sandbox gadgets
return reqs != null ? reqs.getStartClosed() : !gadgetSpec.fromSandbox();
}
public String getChromeId() {
GadgetViewRequirements reqs = getGadgetViewRequirements();
if (reqs != null) {
return reqs.getChromeId();
}
// default behavior that will get invoked when there is no reqs. Useful
// for sandbox gadgets
else if (gadgetSpec.getGadgetURL().contains("Tool")) {
return "gadgets-tools";
} else if (helper.getPageName().equals("individual-EDIT-MODE")) {
return "gadgets-edit";
} else if (helper.getPageName().equals("individual")) {
return "gadgets-view";
} else if (helper.getPageName().equals("gadgetDetails")) {
return "gadgets-detail";
} else if (helper.getPageName().equals("search")) {
return "gadgets-search";
} else {
return null;
}
}
public String getCanvasURL() throws UnsupportedEncodingException {
return "~/gadget?appId=" + getAppId() + "&Person="
+ URLEncoder.encode(helper.getOwnerId(), "UTF-8");
}
public String toString() {
return "" + this.moduleId + ", (" + this.gadgetSpec.toString() + ")";
}
}