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Merge pull request #30 from vivo-project/feature/1245-resolve-duplication

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[VIVO-1245] Reduce code duplication and class overwriting in VIVO
This commit is contained in:
grahamtriggs 2016-05-26 19:23:34 +01:00
commit 4643a2a118
27 changed files with 410 additions and 786 deletions
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7
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ExportQrCodeController.java
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@ -3,17 +3,16 @@
package edu.cornell.mannlib.vitro.webapp.controller; package edu.cornell.mannlib.vitro.webapp.controller;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModelBuilder;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution; import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
@ -25,7 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestA
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestAnalyzer; import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestAnalyzer;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestInfo; import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestInfo;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils; import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel; import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.VIVOIndividualTemplateModel;
import freemarker.ext.beans.BeansWrapper; import freemarker.ext.beans.BeansWrapper;
import freemarker.template.DefaultObjectWrapper; import freemarker.template.DefaultObjectWrapper;
@ -67,7 +66,7 @@ public class ExportQrCodeController extends FreemarkerHttpServlet {
wrapper.setExposureLevel(BeansWrapper.EXPOSE_SAFE); wrapper.setExposureLevel(BeansWrapper.EXPOSE_SAFE);
Map<String, Object> body = new HashMap<String, Object>(); Map<String, Object> body = new HashMap<String, Object>();
body.put("individual", wrapper.wrap(new IndividualTemplateModel(individual, vreq))); body.put("individual", wrapper.wrap(IndividualTemplateModelBuilder.build(individual, vreq)));
body.put("qrData", qrData); body.put("qrData", qrData);
return new TemplateResponseValues(TEMPLATE_DEFAULT, body); return new TemplateResponseValues(TEMPLATE_DEFAULT, body);
} catch (Throwable e) { } catch (Throwable e) {

12
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/ajax/QrCodeDetails.java
View file

@ -2,16 +2,12 @@
package edu.cornell.mannlib.vitro.webapp.controller.ajax; package edu.cornell.mannlib.vitro.webapp.controller.ajax;
import java.io.IOException; import java.io.IOException;
import java.lang.Integer;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet; import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
@ -19,21 +15,13 @@ import org.json.JSONException;
import com.hp.hpl.jena.query.QuerySolution; import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
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.ResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestAnalysisContextImpl; 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.IndividualRequestAnalyzer;
import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestInfo; import edu.cornell.mannlib.vitro.webapp.controller.individual.IndividualRequestInfo;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils; import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
public class QrCodeDetails extends AbstractAjaxResponder { public class QrCodeDetails extends AbstractAjaxResponder {

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/SiteAdminController.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/VIVOSiteAdminController.java
View file

@ -11,10 +11,10 @@ import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.visualization.tools.ToolsRequestHandler; import edu.cornell.mannlib.vitro.webapp.visualization.tools.ToolsRequestHandler;
public class SiteAdminController extends BaseSiteAdminController { public class VIVOSiteAdminController extends BaseSiteAdminController {
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
private static final Log log = LogFactory.getLog(SiteAdminController.class); private static final Log log = LogFactory.getLog(VIVOSiteAdminController.class);
@Override @Override
protected Map<String, Object> getSiteMaintenanceUrls(VitroRequest vreq) { protected Map<String, Object> getSiteMaintenanceUrls(VitroRequest vreq) {

87
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/individuallist/IndividualJsonWrapper.java
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@ -1,87 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.individuallist;
import java.util.Collection;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import org.json.JSONObject;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
/**
* Wrap an Individual in a JSON object for display by the script.
*
* This overrides the Vitro version so we can have more info in the display.
*/
public class IndividualJsonWrapper {
private static final Log log = LogFactory
.getLog(IndividualJsonWrapper.class);
private static String VCARD_DATA_QUERY = ""
+ "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
+ "PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> \n"
+ "SELECT DISTINCT ?title \n" + "WHERE { \n"
+ " ?subject obo:ARG_2000028 ?vIndividual . \n"
+ " ?vIndividual vcard:hasTitle ?vTitle . \n"
+ " ?vTitle vcard:title ?title . \n" + "} ";
static JSONObject packageIndividualAsJson(VitroRequest vreq, Individual ind)
throws JSONException {
// need an unfiltered dao to get firstnames and lastnames
WebappDaoFactory fullWdf = vreq.getUnfilteredWebappDaoFactory();
JSONObject jo = new JSONObject();
jo.put("URI", ind.getURI());
jo.put("label", ind.getRdfsLabel());
jo.put("name", ind.getName());
jo.put("thumbUrl", ind.getThumbUrl());
jo.put("imageUrl", ind.getImageUrl());
jo.put("profileUrl", UrlBuilder.getIndividualProfileUrl(ind, vreq));
jo.put("mostSpecificTypes", getMostSpecificTypes(ind, fullWdf));
jo.put("preferredTitle", findPreferredTitle(vreq, ind));
return jo;
}
private static String findPreferredTitle(VitroRequest vreq, Individual ind) {
String queryStr = QueryUtils.subUriForQueryVar(VCARD_DATA_QUERY,
"subject", ind.getURI());
log.debug("queryStr = " + queryStr);
String value = "";
try {
ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
while (results.hasNext()) {
QuerySolution soln = results.nextSolution();
String t = QueryUtils.nodeToString(soln.get("title"));
if (StringUtils.isNotBlank(t)) {
value = t;
}
}
} catch (Exception e) {
log.error(e, e);
}
return value;
}
public static Collection<String> getMostSpecificTypes(
Individual individual, WebappDaoFactory wdf) {
ObjectPropertyStatementDao opsDao = wdf.getObjectPropertyStatementDao();
Map<String, String> mostSpecificTypes = opsDao
.getMostSpecificTypesInClassgroupsForIndividual(individual
.getURI());
return mostSpecificTypes.values();
}
}

9
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/N3TransitionToV2Mapping.java
View file

@ -1,13 +1,18 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */ /* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing; package edu.cornell.mannlib.vitro.webapp.edit.n3editing;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.JspToGeneratorMapping;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
public class N3TransitionToV2Mapping extends HashMap<String, String>{ public class N3TransitionToV2Mapping extends HashMap<String, String>{
public N3TransitionToV2Mapping(){ public N3TransitionToV2Mapping(){
Map<String,String> map = this; Map<String,String> map = this;
map.put("defaultAddMissingIndividualForm.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVODefaultAddMissingIndividualFormGenerator.class.getName());
// vivo forms: // vivo forms:
map.put("addAuthorsToInformationResource.jsp", map.put("addAuthorsToInformationResource.jsp",
@ -15,7 +20,7 @@ public class N3TransitionToV2Mapping extends HashMap<String, String>{
map.put("manageWebpagesForIndividual.jsp", map.put("manageWebpagesForIndividual.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManageWebpagesForIndividualGenerator.class.getName()); edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManageWebpagesForIndividualGenerator.class.getName());
map.put("newIndividualForm.jsp", map.put("newIndividualForm.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.NewIndividualFormGenerator.class.getName()); edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVONewIndividualFormGenerator.class.getName());
map.put("organizationHasPositionHistory.jsp", map.put("organizationHasPositionHistory.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.OrganizationHasPositionHistoryGenerator.class.getName()); edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.OrganizationHasPositionHistoryGenerator.class.getName());
map.put("personHasEducationalTraining.jsp", map.put("personHasEducationalTraining.jsp",

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddConceptThroughObjectPropertyGenerator.java
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@ -36,7 +36,7 @@ public class AddConceptThroughObjectPropertyGenerator extends DefaultObjectPrope
HttpSession session) throws Exception { HttpSession session) throws Exception {
EditConfigurationVTwo editConfig = super.getEditConfiguration(vreq, session); EditConfigurationVTwo editConfig = super.getEditConfiguration(vreq, session);
//If this isn't adding a new individual, then override template/types //If this isn't adding a new individual, then override template/types
if(!DefaultAddMissingIndividualFormGenerator.isCreateNewIndividual(vreq, session)) { if(!VIVODefaultAddMissingIndividualFormGenerator.isCreateNewIndividual(vreq, session)) {
//return rangetypes in form specific data //return rangetypes in form specific data
editConfig.addFormSpecificData("createNewTypes", getCreateNewTypesOptions(vreq)); editConfig.addFormSpecificData("createNewTypes", getCreateNewTypesOptions(vreq));
//override templates with ones that will override create new types portion //override templates with ones that will override create new types portion

547
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/DefaultAddMissingIndividualFormGenerator.java
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@ -1,547 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpSession;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.DefaultAddMissingIndividualFormModelPreprocessor;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.validators.AntiXssValidation;
import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
/**
* Generates the edit configuration for a default property form.
*
*/
public class DefaultAddMissingIndividualFormGenerator implements EditConfigurationGenerator {
private Log log = LogFactory.getLog(DefaultAddMissingIndividualFormGenerator.class);
private boolean isObjectPropForm = false;
private String subjectUri = null;
private String predicateUri = null;
private String objectUri = null;
private String template = "defaultAddMissingIndividualForm.ftl";
private static String createCommand = "create";
private static String objectVarName = "newIndividual";
private static HashMap<String,String> defaultsForXSDtypes ;
static {
defaultsForXSDtypes = new HashMap<String,String>();
//defaultsForXSDtypes.put("http://www.w3.org/2001/XMLSchema#dateTime","2001-01-01T12:00:00");
defaultsForXSDtypes.put("http://www.w3.org/2001/XMLSchema#dateTime","#Unparseable datetime defaults to now");
}
//Method which checks whether this particular generator should be employed
public static boolean isCreateNewIndividual(VitroRequest vreq, HttpSession session) {
String command = vreq.getParameter("cmd");
String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
//This method also looks at domain and range uris and so is different than just getting the
//object property based on predicate uri alone
ObjectProperty objProp = EditConfigurationUtils.getObjectPropertyForPredicate(vreq,
predicateUri);
if(objProp != null) {
return(objProp.getOfferCreateNewOption() &&
(
(command != null && command.equals(createCommand)) ||
objProp.getSelectFromExisting() == false
)
);
}
return false;
}
@Override
public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
EditConfigurationVTwo editConfiguration = new EditConfigurationVTwo();
//process subject, predicate, object parameters
this.initProcessParameters(vreq, session, editConfiguration);
//Assumes this is a simple case of subject predicate var
editConfiguration.setN3Required(this.generateN3Required(vreq));
//n3 optional
editConfiguration.setN3Optional(this.generateN3Optional(vreq));
editConfiguration.setNewResources(this.generateNewResources(vreq));
//In scope
this.setUrisAndLiteralsInScope(editConfiguration);
//on Form
this.setUrisAndLiteralsOnForm(editConfiguration, vreq);
editConfiguration.setFilesOnForm(new ArrayList<String>());
//Sparql queries
this.setSparqlQueries(editConfiguration);
//set fields
setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq));
//form specific data
addFormSpecificData(editConfiguration, vreq);
//add preprocesoors
addPreprocessors(vreq, editConfiguration);
prepareForUpdate(vreq, session, editConfiguration);
//Form title and submit label now moved to edit configuration template
//TODO: check if edit configuration template correct place to set those or whether
//additional methods here should be used and reference instead, e.g. edit configuration template could call
//default obj property form.populateTemplate or some such method
//Select from existing also set within template itself
setTemplate(editConfiguration, vreq);
editConfiguration.addValidator(new AntiXssValidation());
//edit key now set in the edit request dispatch controller
return editConfiguration;
}
private Map<String, String> generateNewResources(VitroRequest vreq) {
HashMap<String, String> newResources = new HashMap<String, String>();
//Null triggers default namespace
newResources.put(objectVarName, null);
newResources.put("newVcardInd", null);
newResources.put("newVcardName", null);
return newResources;
}
//Need to replace edit key
//TODO:Check if we need to recheck forward to create new or assume that is the case since
//we're using this generator
//In this case we always set a new edit key as the original jsp checked 'isForwardToCreateNew'
//which condition would require that an entirely new edit key be created
private void setEditKey(HttpSession session, EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
String editKey = EditConfigurationVTwo.newEditKey(session);
editConfiguration.setEditKey(editKey);
}
private void setTemplate(EditConfigurationVTwo editConfiguration,
VitroRequest vreq) {
editConfiguration.setTemplate(template);
}
//Initialize setup: process parameters
//Doesn't look like we need to set up separate processing for data property form
private void initProcessParameters(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
String formUrl = EditConfigurationUtils.getFormUrlWithoutContext(vreq);
subjectUri = EditConfigurationUtils.getSubjectUri(vreq);
predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
editConfiguration.setFormUrl(formUrl);
editConfiguration.setUrlPatternToReturnTo("/individual");
editConfiguration.setVarNameForSubject("subject");
editConfiguration.setSubjectUri(subjectUri);
editConfiguration.setEntityToReturnTo(subjectUri);
editConfiguration.setVarNameForPredicate("predicate");
editConfiguration.setPredicateUri(predicateUri);
//this needs to be set for the editing to be triggered properly, otherwise the 'prepare' method
//pretends this is a data property editing statement and throws an error
//"object" : [ "newIndividual" , "${objectUriJson}" , "URI"],
if(EditConfigurationUtils.isObjectProperty(predicateUri, vreq)) {
//not concerned about remainder, can move into default obj prop form if required
this.isObjectPropForm = true;
this.initObjectParameters(vreq);
this.processObjectPropForm(vreq, editConfiguration);
} else {
log.error("Add missing individual called for a data property instead of object property");
}
}
private void initObjectParameters(VitroRequest vreq) {
//in case of object property
String thisObjectUri = EditConfigurationUtils.getObjectUri(vreq);
if(thisObjectUri != null && !thisObjectUri.isEmpty()) {
objectUri = EditConfigurationUtils.getObjectUri(vreq);
}
//otherwise object uri will stay null - since don't want to set it to empty string
}
//this particular form uses a different var name for object "newIndividual"
private void processObjectPropForm(VitroRequest vreq, EditConfigurationVTwo editConfiguration) {
editConfiguration.setVarNameForObject(objectVarName);
//If is replace with new, set Object resource to null
if(isReplaceWithNew(vreq)) {
editConfiguration.setObject(null);
} else {
editConfiguration.setObject(objectUri);
}
//this needs to be set for the editing to be triggered properly, otherwise the 'prepare' method
//pretends this is a data property editing statement and throws an error
//TODO: Check if null in case no object uri exists but this is still an object property
}
//Get N3 required
//Handles both object and data property
private List<String> generateN3Required(VitroRequest vreq) {
List<String> n3ForEdit = new ArrayList<String>();
n3ForEdit.add(getN3PrefixesAsString() + "\n" + getN3ForName());
n3ForEdit.add("?subject ?predicate ?" + objectVarName + " .");
n3ForEdit.add(getN3PrefixesAsString() + "\n" + "?" + objectVarName + " rdf:type <" + getRangeClassUri(vreq) + "> . ");
return n3ForEdit;
}
private List<String> getN3Prefixes() {
List<String> prefixStrings = new ArrayList<String>();
prefixStrings.add("@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .");
prefixStrings.add("@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .");
prefixStrings.add("@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .");
return prefixStrings;
}
private String getN3PrefixesAsString() {
String prefixes = StringUtils.join(getN3Prefixes(), "\n");
return prefixes;
}
private String getN3ForName() {
return "?" + objectVarName + " rdfs:label ?label .";
}
private List<String> generateN3Optional(VitroRequest vreq) {
//flag uri and asserted types need to be added here
List<String> n3Optional = new ArrayList<String>();
n3Optional.add("?" + objectVarName + " ?inverseProp ?subject .");
//asserted types string buffer is empty in the original jsp
//TODO: Review original comments in jsp to see what could go here
//n3Optional.add(getN3AssertedTypes(vreq));
n3Optional.add(getN3PrefixesAsString() + "\n" + "?" + objectVarName + " rdf:type <" + getFlagURI(vreq) + "> . ");
n3Optional.add(getN3PrefixesAsString()
+ "?" + objectVarName + "<http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd <http://purl.obolibrary.org/obo/ARG_2000029> ?" + objectVarName + " . \n"
+ " ?newVcardInd a vcard:Individual . \n"
+ " ?newVcardInd vcard:hasName ?newVcardName . \n"
+ " ?newVcardName a vcard:Name . \n"
+ " ?newVcardName vcard:givenName ?firstName . \n"
+ " ?newVcardName vcard:familyName ?lastName . \n");
n3Optional.add(getN3PrefixesAsString()
+ "?" + objectVarName + "<http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd a vcard:Individual . \n"
+ " ?newVcardInd vcard:hasName ?newVcardName . \n"
+ " ?newVcardName a vcard:Name . \n"
+ " ?newVcardName <http://vivoweb.org/ontology/core#middleName> ?middleName .");
return n3Optional;
}
private String getFlagURI(VitroRequest vreq) {
WebappDaoFactory wdf = vreq.getWebappDaoFactory();
String flagURI = wdf.getVClassDao().getTopConcept().getURI();
return flagURI;
}
private String getN3AssertedTypes(VitroRequest vreq) {
return null;
}
//Set queries
private String retrieveQueryForInverse () {
String queryForInverse = "PREFIX owl: <http://www.w3.org/2002/07/owl#>"
+ " SELECT ?inverse_property "
+ " WHERE { ?inverse_property owl:inverseOf ?predicate } ";
return queryForInverse;
}
private void setUrisAndLiteralsInScope(EditConfigurationVTwo editConfiguration) {
HashMap<String, List<String>> urisInScope = new HashMap<String, List<String>>();
//Add subject uri and predicate turo to uris in scope
urisInScope.put(editConfiguration.getVarNameForSubject(),
Arrays.asList(new String[]{editConfiguration.getSubjectUri()}));
urisInScope.put(editConfiguration.getVarNameForPredicate(),
Arrays.asList(new String[]{editConfiguration.getPredicateUri()}));
editConfiguration.setUrisInScope(urisInScope);
editConfiguration.setLiteralsInScope(new HashMap<String, List<Literal>>());
}
//n3 should look as follows
//?subject ?predicate ?objectVar
private void setUrisAndLiteralsOnForm(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
List<String> urisOnForm = new ArrayList<String>();
List<String> literalsOnForm = new ArrayList<String>();
literalsOnForm.add("label");
literalsOnForm.add("firstName");
literalsOnForm.add("middleName");
literalsOnForm.add("lastName");
editConfiguration.setUrisOnform(urisOnForm);
editConfiguration.setLiteralsOnForm(literalsOnForm);
}
//This is for various items
private void setSparqlQueries(EditConfigurationVTwo editConfiguration) {
//Sparql queries defining retrieval of literals etc.
editConfiguration.setSparqlForAdditionalLiteralsInScope(new HashMap<String, String>());
Map<String, String> urisInScope = new HashMap<String, String>();
urisInScope.put("inverseProp", this.retrieveQueryForInverse());
editConfiguration.setSparqlForAdditionalUrisInScope(urisInScope);
editConfiguration.setSparqlForExistingLiterals(generateSparqlForExistingLiterals());
editConfiguration.setSparqlForExistingUris(generateSparqlForExistingUris());
}
//Sparql queries
private HashMap<String, String> generateSparqlForExistingUris() {
HashMap<String, String> map = new HashMap<String, String>();
return map;
}
private HashMap<String, String> generateSparqlForExistingLiterals() {
HashMap<String, String> map = new HashMap<String, String>();
String query = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> ";
query += "SELECT ?existingName WHERE { ?" + objectVarName + " rdfs:label ?existingName . }";
map.put("name", query);
return map;
}
private void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri) {
Map<String, FieldVTwo> fields = new HashMap<String, FieldVTwo>();
if(EditConfigurationUtils.isObjectProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)) {
//make name field
FieldVTwo labelField = new FieldVTwo();
labelField.setName("label");
FieldVTwo firstNameField = new FieldVTwo();
firstNameField.setName("firstName");
FieldVTwo middleNameField = new FieldVTwo();
middleNameField.setName("middleName");
FieldVTwo lastNameField = new FieldVTwo();
lastNameField.setName("lastName");
List<String> validators = new ArrayList<String>();
validators.add("nonempty");
if(!isPersonType(vreq)) {
labelField.setValidators(validators);
}
if(isPersonType(vreq)) {
firstNameField.setValidators(validators);
lastNameField.setValidators(validators);
}
fields.put(labelField.getName(), labelField);
fields.put(firstNameField.getName(), firstNameField);
fields.put(middleNameField.getName(), middleNameField);
fields.put(lastNameField.getName(), lastNameField);
} else {
log.error("Is not object property so fields not set");
}
editConfiguration.setFields(fields);
}
private String getRangeClassUri(VitroRequest vreq) {
Individual subject = EditConfigurationUtils.getSubjectIndividual(vreq);
ObjectProperty prop = EditConfigurationUtils.getObjectProperty(vreq);
WebappDaoFactory wdf = vreq.getWebappDaoFactory();
if( prop.getRangeVClassURI() == null ) {
// If property has no explicit range, we will use e.g. owl:Thing.
// Typically an allValuesFrom restriction will come into play later.
VClass top = wdf.getVClassDao().getTopConcept();
prop.setRangeVClassURI(top.getURI());
}
VClass rangeClass = null;
String typeOfNew = getTypeOfNew(vreq);
if(typeOfNew != null )
rangeClass = wdf.getVClassDao().getVClassByURI( typeOfNew );
if( rangeClass == null ){
rangeClass = wdf.getVClassDao().getVClassByURI(prop.getRangeVClassURI());
if( rangeClass == null ) throw new Error ("Cannot find class for range for property. Looking for " + prop.getRangeVClassURI() );
}
return rangeClass.getURI();
}
private void prepareForUpdate(VitroRequest vreq, HttpSession session, EditConfigurationVTwo editConfiguration) {
//Here, retrieve model from
OntModel model = ModelAccess.on(session.getServletContext()).getOntModel();
//if object property
if(EditConfigurationUtils.isObjectProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)){
Individual objectIndividual = EditConfigurationUtils.getObjectIndividual(vreq);
if(!isReplaceWithNew(vreq) &&
(isForwardToCreateButEdit(vreq) ||
objectIndividual != null)
) {
editConfiguration.prepareForObjPropUpdate(model);
} else {
//new object to be created
editConfiguration.prepareForNonUpdate( model );
}
} else {
log.error("Data property not object property so update can't be done correctly");
}
}
private void addPreprocessors(VitroRequest vreq, EditConfigurationVTwo editConfiguration) {
if(isReplaceWithNew(vreq)) {
//String subjectUri = EditConfigurationUtils.getSubjectUri(vreq);
//String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
//String objectUri = EditConfigurationUtils.getObjectUri(vreq);
editConfiguration.addModelChangePreprocessor(
new DefaultAddMissingIndividualFormModelPreprocessor(
subjectUri, predicateUri, objectUri));
}
}
//Command processing
private boolean isTypeOfNew(VitroRequest vreq) {
String typeOfNew = getTypeOfNew(vreq);
return (typeOfNew != null && !typeOfNew.isEmpty());
}
private String getTypeOfNew(VitroRequest vreq) {
return vreq.getParameter("typeOfNew");
}
// The default object proepty form offers the option to create a new item
// instead of selecting from existing individuals in the system.
// This is where the request to create a new indivdiual is handled.
//We don't really need this again b/c we wouldn't be using this generator unless we want
//to create a new individual so commenting out for now
/*
private boolean isForwardToCreateNew(VitroRequest vreq) {
String command = vreq.getParameter("cmd");
ObjectProperty objectProp = EditConfigurationUtils.getObjectProperty(vreq);
if(hasCustomForm(objectProp)) {
return false;
}
boolean isForwardToCreateNew =
( objectProp != null && objectProp.getOfferCreateNewOption() )
&& ( objectProp.getSelectFromExisting() == false
|| "create".equals(command));
return isForwardToCreateNew;
}
private boolean hasCustomForm(ObjectProperty objectProp) {
return( objectProp != null &&
objectProp.getCustomEntryForm() != null &&
!objectProp.getCustomEntryForm().isEmpty());
}*/
private boolean isReplaceWithNew(VitroRequest vreq) {
ObjectProperty objectProp = EditConfigurationUtils.getObjectProperty(vreq);
boolean isEditOfExistingStmt = isEditOfExistingStatement(vreq);
String command = vreq.getParameter("cmd");
return (isEditOfExistingStmt
&& "create".equals(command))
&& (objectProp != null)
&& (objectProp.getOfferCreateNewOption() == true);
}
private boolean isForwardToCreateButEdit(VitroRequest vreq) {
boolean isEditOfExistingStmt = isEditOfExistingStatement(vreq);
ObjectProperty objectProp = EditConfigurationUtils.getObjectProperty(vreq);
String command = vreq.getParameter("cmd");
return (isEditOfExistingStmt
&& (! "create".equals(command))
&& (objectProp != null)
&& (objectProp.getOfferCreateNewOption() == true)
&& (objectProp.getSelectFromExisting() == false)
);
}
//Form specific data
public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
formSpecificData.put("typeName", getTypeName(vreq));
//Put in whether or not person type
if(isPersonType(vreq)) {
//Doing this b/c unsure how freemarker will handle boolean value from JAVA
formSpecificData.put("isPersonType", "true");
} else {
formSpecificData.put("isPersonType", "false");
}
editConfiguration.setFormSpecificData(formSpecificData);
}
private String getTypeName(VitroRequest vreq) {
String typeOfNew = getTypeOfNew(vreq);
VClass type = vreq.getWebappDaoFactory().getVClassDao().getVClassByURI(typeOfNew);
return type.getName();
}
public String getFOAFPersonClassURI() {
return "http://xmlns.com/foaf/0.1/Person";
}
public boolean isPersonType(VitroRequest vreq) {
WebappDaoFactory wdf = vreq.getWebappDaoFactory();
Boolean isPersonType = Boolean.FALSE;
String foafPersonType = getFOAFPersonClassURI();
String typeOfNew = getTypeOfNew(vreq);
List<String> superTypes = wdf.getVClassDao().getAllSuperClassURIs(typeOfNew);
//add the actual type as well so we can add that for the list to be checked
superTypes.add(typeOfNew);
if( superTypes != null ){
for( String typeUri : superTypes){
if( foafPersonType.equals(typeUri)) {
isPersonType = Boolean.TRUE;
break;
}
}
}
return isPersonType;
}
//Is edit of existing statement only applicable to object properties
private boolean isEditOfExistingStatement(VitroRequest vreq) {
//TODO: Check if also applicable to data property, currently returning false
if(EditConfigurationUtils.isDataProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)) {
return false;
}
Individual object = EditConfigurationUtils.getObjectIndividual(vreq);
return (object != null);
}
}

158
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/VIVODefaultAddMissingIndividualFormGenerator.java Normal file
View file

@ -0,0 +1,158 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult.VIVOIndividualSearchResult;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
/**
* Generates the edit configuration for a default property form.
*
*/
public class VIVODefaultAddMissingIndividualFormGenerator extends DefaultAddMissingIndividualFormGenerator {
private Log log = LogFactory.getLog(VIVODefaultAddMissingIndividualFormGenerator.class);
protected Map<String, String> generateNewResources(VitroRequest vreq) {
Map<String, String> newResources = super.generateNewResources(vreq);
newResources.put("newVcardInd", null);
newResources.put("newVcardName", null);
return newResources;
}
protected List<String> getN3Prefixes() {
List<String> prefixStrings = super.getN3Prefixes();
prefixStrings.add("@prefix vcard:<http://www.w3.org/2006/vcard/ns#> .");
return prefixStrings;
}
private String getN3ForName() {
return "?" + objectVarName + " rdfs:label ?label .";
}
protected List<String> generateN3Optional(VitroRequest vreq) {
List<String> n3Optional = super.generateN3Optional(vreq);
n3Optional.add(getN3PrefixesAsString()
+ "?" + objectVarName + "<http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd <http://purl.obolibrary.org/obo/ARG_2000029> ?" + objectVarName + " . \n"
+ " ?newVcardInd a vcard:Individual . \n"
+ " ?newVcardInd vcard:hasName ?newVcardName . \n"
+ " ?newVcardName a vcard:Name . \n"
+ " ?newVcardName vcard:givenName ?firstName . \n"
+ " ?newVcardName vcard:familyName ?lastName . \n");
n3Optional.add(getN3PrefixesAsString()
+ "?" + objectVarName + "<http://purl.obolibrary.org/obo/ARG_2000028> ?newVcardInd . \n"
+ " ?newVcardInd a vcard:Individual . \n"
+ " ?newVcardInd vcard:hasName ?newVcardName . \n"
+ " ?newVcardName a vcard:Name . \n"
+ " ?newVcardName <http://vivoweb.org/ontology/core#middleName> ?middleName .");
return n3Optional;
}
protected void setUrisAndLiteralsOnForm(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
List<String> urisOnForm = new ArrayList<String>();
List<String> literalsOnForm = new ArrayList<String>();
literalsOnForm.add("label");
literalsOnForm.add("firstName");
literalsOnForm.add("middleName");
literalsOnForm.add("lastName");
editConfiguration.setUrisOnform(urisOnForm);
editConfiguration.setLiteralsOnForm(literalsOnForm);
}
protected void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri) {
Map<String, FieldVTwo> fields = new HashMap<String, FieldVTwo>();
if(EditConfigurationUtils.isObjectProperty(EditConfigurationUtils.getPredicateUri(vreq), vreq)) {
//make name field
FieldVTwo labelField = new FieldVTwo();
labelField.setName("label");
FieldVTwo firstNameField = new FieldVTwo();
firstNameField.setName("firstName");
FieldVTwo middleNameField = new FieldVTwo();
middleNameField.setName("middleName");
FieldVTwo lastNameField = new FieldVTwo();
lastNameField.setName("lastName");
List<String> validators = new ArrayList<String>();
validators.add("nonempty");
if(!isPersonType(vreq)) {
labelField.setValidators(validators);
}
if(isPersonType(vreq)) {
firstNameField.setValidators(validators);
lastNameField.setValidators(validators);
}
fields.put(labelField.getName(), labelField);
fields.put(firstNameField.getName(), firstNameField);
fields.put(middleNameField.getName(), middleNameField);
fields.put(lastNameField.getName(), lastNameField);
} else {
log.error("Is not object property so fields not set");
}
editConfiguration.setFields(fields);
}
//Form specific data
public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
formSpecificData.put("typeName", getTypeName(vreq));
//Put in whether or not person type
if(isPersonType(vreq)) {
//Doing this b/c unsure how freemarker will handle boolean value from JAVA
formSpecificData.put("isPersonType", "true");
} else {
formSpecificData.put("isPersonType", "false");
}
editConfiguration.setFormSpecificData(formSpecificData);
}
private String getTypeName(VitroRequest vreq) {
String typeOfNew = getTypeOfNew(vreq);
VClass type = vreq.getWebappDaoFactory().getVClassDao().getVClassByURI(typeOfNew);
return type.getName();
}
public String getFOAFPersonClassURI() {
return "http://xmlns.com/foaf/0.1/Person";
}
public boolean isPersonType(VitroRequest vreq) {
WebappDaoFactory wdf = vreq.getWebappDaoFactory();
Boolean isPersonType = Boolean.FALSE;
String foafPersonType = getFOAFPersonClassURI();
String typeOfNew = getTypeOfNew(vreq);
List<String> superTypes = wdf.getVClassDao().getAllSuperClassURIs(typeOfNew);
//add the actual type as well so we can add that for the list to be checked
superTypes.add(typeOfNew);
if( superTypes != null ){
for( String typeUri : superTypes){
if( foafPersonType.equals(typeUri)) {
isPersonType = Boolean.TRUE;
break;
}
}
}
return isPersonType;
}
}

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsGenerator.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/VIVOManageLabelsGenerator.java
View file

@ -18,7 +18,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTw
*This generator selects the actual generator to be employed based on whether the individual is a Person *This generator selects the actual generator to be employed based on whether the individual is a Person
*or another individual. Adding a label for a person relies on first/name last name information i.e. object properties. *or another individual. Adding a label for a person relies on first/name last name information i.e. object properties.
*/ */
public class ManageLabelsGenerator extends BaseEditConfigurationGenerator implements EditConfigurationGenerator { public class VIVOManageLabelsGenerator extends BaseEditConfigurationGenerator implements EditConfigurationGenerator {
public static Log log = LogFactory.getLog(ManageLabelsForIndividualGenerator.class); public static Log log = LogFactory.getLog(ManageLabelsForIndividualGenerator.class);
@Override @Override
public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) { public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/NewIndividualFormGenerator.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/VIVONewIndividualFormGenerator.java
View file

@ -27,7 +27,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.validators.
* Generates the edit configuration for a default property form. * Generates the edit configuration for a default property form.
* ModelChangePreprocessor creates the rdfs:label statement. * ModelChangePreprocessor creates the rdfs:label statement.
*/ */
public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator implements EditConfigurationGenerator { public class VIVONewIndividualFormGenerator extends BaseEditConfigurationGenerator implements EditConfigurationGenerator {
@Override @Override
public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) { public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {

25
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/utils/ProcessDataGetterN3Map.java
View file

@ -1,25 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
import java.util.HashMap;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
/*
* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
*/
public class ProcessDataGetterN3Map {
private static final Log log = LogFactory.getLog(ProcessDataGetterN3Map.class);
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.InternalClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessInternalClassDataGetterN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SearchIndividualsDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSearchIndividualsDataGetterN3");
return map;
}
}

74
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/menuManagement/SelectDataGetterUtils.java
View file

@ -1,74 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.utils.menuManagement;
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.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData;
import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter;
/*
* This class includes methods that help in selecting a data getter based on
* parameters, and VIVO will have its own version or extend this
*/
public class SelectDataGetterUtils {
private static final Log log = LogFactory.getLog(SelectDataGetterUtils.class);
/**Get data for an existing page and set variables for the template accordingly**/
public static void processAndRetrieveData(VitroRequest vreq, ServletContext context, Map<String, Object> pageData, String dataGetterClass, Map<String, Object> templateData) {
//The type of the data getter will show how to process the data from the data getter
ProcessDataGetter processor = selectProcessor(dataGetterClass);
processor.populateTemplate(vreq, pageData, templateData);
}
//This will be different in VIVO than in VITRO
private static ProcessDataGetter selectProcessor(String dataGetterClass) {
if(dataGetterClass.equals(ClassGroupPageData.class.getName())) {
return new ProcessClassGroup();
} else if(dataGetterClass.equals(InternalClassesDataGetter.class.getName())) {
return new ProcessInternalClasses();
//below should be for vitro specific version
//return new ProcessIndividualsForClasses();
}
return null;
}
/**Process parameters from form and select appropriate data getter on this basis **/
public static Model createDataGetterModel(VitroRequest vreq, Resource dataGetterResource) {
Model dataGetterModel = null;
if(dataGetterResource != null) {
//If "All selected" then use class group else use individuals for classes
dataGetterModel = ModelFactory.createDefaultModel();
ProcessInternalClasses individualsProcess = new ProcessInternalClasses();
ProcessClassGroup classGroupProcess = new ProcessClassGroup();
if(individualsProcess.useProcessor(vreq)) {
dataGetterModel = individualsProcess.processSubmission(vreq, dataGetterResource);
} else {
dataGetterModel = classGroupProcess.processSubmission(vreq, dataGetterResource);
}
} else {
log.error("Data getter is null ");
}
return dataGetterModel;
}
}

11
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/menuManagement/MenuManagementDataUtils.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/menuManagement/VIVOMenuManagementDataUtils.java
View file

@ -23,18 +23,17 @@ import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
* This class includes methods that help in selecting a data getter based on * This class includes methods that help in selecting a data getter based on
* parameters, and VIVO will have its own version or extend this * parameters, and VIVO will have its own version or extend this
*/ */
public class MenuManagementDataUtils { public class VIVOMenuManagementDataUtils implements MenuManagementDataUtils.IMenuManagementDataUtils {
private static final Log log = LogFactory.getLog(MenuManagementDataUtils.class); private static final Log log = LogFactory.getLog(VIVOMenuManagementDataUtils.class);
//Data that is to be returned to template that does not involve data getters //Data that is to be returned to template that does not involve data getters
//e.g. what are the current class groups, etc. //e.g. what are the current class groups, etc.
public static void includeRequiredSystemData(ServletContext context, Map<String, Object> templateData) { public void includeRequiredSystemData(ServletContext context, Map<String, Object> templateData) {
checkInstitutionalInternalClass(context, templateData); checkInstitutionalInternalClass(context, templateData);
} }
//Check whether any classes exist with internal class restrictions //Check whether any classes exist with internal class restrictions
private static void checkInstitutionalInternalClass(ServletContext context, Map<String, Object> templateData) { private void checkInstitutionalInternalClass(ServletContext context, Map<String, Object> templateData) {
//TODO: replace with more generic ModelContext retrieval method //TODO: replace with more generic ModelContext retrieval method
String internalClass = retrieveInternalClass(context); String internalClass = retrieveInternalClass(context);
if(internalClass != null) { if(internalClass != null) {
@ -47,7 +46,7 @@ public class MenuManagementDataUtils {
} }
private static String retrieveInternalClass(ServletContext context) { private String retrieveInternalClass(ServletContext context) {
OntModel mainModel = ModelAccess.on(context).getOntModel(TBOX_ASSERTIONS); OntModel mainModel = ModelAccess.on(context).getOntModel(TBOX_ASSERTIONS);
StmtIterator internalIt = mainModel.listStatements(null, ResourceFactory.createProperty(VitroVocabulary.IS_INTERNAL_CLASSANNOT), (RDFNode) null); StmtIterator internalIt = mainModel.listStatements(null, ResourceFactory.createProperty(VitroVocabulary.IS_INTERNAL_CLASSANNOT), (RDFNode) null);
if(internalIt.hasNext()) { if(internalIt.hasNext()) {

21
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/IndividualTemplateModel.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/VIVOIndividualTemplateModel.java
View file

@ -2,32 +2,19 @@
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual; package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.RDFNode;
import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.beans.Individual; import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder; 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.ParamMap;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Route; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Route;
import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationFrameworkConstants; import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationFrameworkConstants;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
public class IndividualTemplateModel extends BaseIndividualTemplateModel { public class VIVOIndividualTemplateModel extends IndividualTemplateModel {
private static final Log log = LogFactory.getLog(IndividualTemplateModel.class); private static final Log log = LogFactory.getLog(VIVOIndividualTemplateModel.class);
private static final String FOAF = "http://xmlns.com/foaf/0.1/"; private static final String FOAF = "http://xmlns.com/foaf/0.1/";
private static final String PERSON_CLASS = FOAF + "Person"; private static final String PERSON_CLASS = FOAF + "Person";
@ -42,10 +29,10 @@ public class IndividualTemplateModel extends BaseIndividualTemplateModel {
private static final String BASE_VISUALIZATION_URL = private static final String BASE_VISUALIZATION_URL =
UrlBuilder.getUrl(Route.VISUALIZATION_SHORT.path()); UrlBuilder.getUrl(Route.VISUALIZATION_SHORT.path());
public IndividualTemplateModel(Individual individual, VitroRequest vreq) { VIVOIndividualTemplateModel(Individual individual, VitroRequest vreq) {
super(individual, vreq); super(individual, vreq);
} }
private String getVisUrl(String visPath) { private String getVisUrl(String visPath) {
String visUrl; String visUrl;
boolean isUsingDefaultNameSpace = UrlBuilder.isUriInDefaultNamespace( boolean isUsingDefaultNameSpace = UrlBuilder.isUriInDefaultNamespace(

11
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/VIVOIndividualTemplateModelBuilder.java Normal file
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@ -0,0 +1,11 @@
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
public class VIVOIndividualTemplateModelBuilder implements IndividualTemplateModelBuilder.IIndividualTemplateModelBuilder {
@Override
public VIVOIndividualTemplateModel build(Individual individual, VitroRequest vreq) {
return new VIVOIndividualTemplateModel(individual, vreq);
}
}

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/ListedIndividual.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividual.java
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@ -13,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils; import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
public class ListedIndividual extends BaseListedIndividual { public class VIVOListedIndividual extends ListedIndividual {
private static final Log log = LogFactory.getLog(ListedIndividual.class); private static final Log log = LogFactory.getLog(VIVOListedIndividual.class);
private static String VCARD_DATA_QUERY = "" private static String VCARD_DATA_QUERY = ""
+ "PREFIX obo: <http://purl.obolibrary.org/obo/> \n" + "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
@ -28,7 +28,7 @@ public class ListedIndividual extends BaseListedIndividual {
private final String title; private final String title;
public ListedIndividual(Individual individual, VitroRequest vreq) { VIVOListedIndividual(Individual individual, VitroRequest vreq) {
super(individual, vreq); super(individual, vreq);
title = findPreferredTitle(); title = findPreferredTitle();
} }

11
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individuallist/VIVOListedIndividualBuilder.java Normal file
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@ -0,0 +1,11 @@
package edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
public class VIVOListedIndividualBuilder implements ListedIndividualBuilder.ILIstedIndividualBuilder {
@Override
public ListedIndividual build(Individual individual, VitroRequest vreq) {
return new VIVOListedIndividual(individual, vreq);
}
}

9
api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/IndividualSearchResult.java → api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/searchresult/VIVOIndividualSearchResult.java
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@ -13,8 +13,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils; import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
public class IndividualSearchResult extends BaseIndividualSearchResult { public class VIVOIndividualSearchResult extends IndividualSearchResult {
private static final Log log = LogFactory.getLog(IndividualSearchResult.class); private static final Log log = LogFactory.getLog(VIVOIndividualSearchResult.class);
private static String VCARD_DATA_QUERY = "" private static String VCARD_DATA_QUERY = ""
+ "PREFIX obo: <http://purl.obolibrary.org/obo/> \n" + "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
@ -33,7 +33,7 @@ public class IndividualSearchResult extends BaseIndividualSearchResult {
private String email = ""; private String email = "";
private String title = ""; private String title = "";
public IndividualSearchResult(Individual individual, VitroRequest vreq) { public VIVOIndividualSearchResult(Individual individual, VitroRequest vreq) {
super(individual, vreq); super(individual, vreq);
log.debug("Called Individual Search Result"); log.debug("Called Individual Search Result");
findVcardInfo(); findVcardInfo();
@ -71,4 +71,7 @@ public class IndividualSearchResult extends BaseIndividualSearchResult {
return email; return email;
} }
public static void register() {
IndividualSearchResult.registerResultClass(VIVOIndividualSearchResult.class);
}
} }

27
api/src/main/java/org/vivoweb/webapp/startup/DataGetterN3Setup.java Normal file
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@ -0,0 +1,27 @@
package org.vivoweb.webapp.startup;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVODefaultAddMissingIndividualFormGenerator;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3Map;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import java.util.HashMap;
public class DataGetterN3Setup implements ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
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.InternalClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessInternalClassDataGetterN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SearchIndividualsDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSearchIndividualsDataGetterN3");
ProcessDataGetterN3Map.replaceDataGetterMap(map);
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

24
api/src/main/java/org/vivoweb/webapp/startup/GeneratorSetup.java Normal file
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@ -0,0 +1,24 @@
package org.vivoweb.webapp.startup;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.JspToGeneratorMapping;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVODefaultAddMissingIndividualFormGenerator;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult.VIVOIndividualSearchResult;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
public class GeneratorSetup implements ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
JspToGeneratorMapping.jspsToGenerators.put("defaultAddMissingIndividualForm.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVODefaultAddMissingIndividualFormGenerator.class.getName());
JspToGeneratorMapping.jspsToGenerators.put("newIndividualForm.jsp",
edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVONewIndividualFormGenerator.class.getName());
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

70
api/src/main/java/org/vivoweb/webapp/startup/JSONWrapperSetup.java Normal file
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@ -0,0 +1,70 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package org.vivoweb.webapp.startup;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.controller.individuallist.IndividualJsonWrapper;
import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyStatementDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONException;
import org.json.JSONObject;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import java.util.Collection;
import java.util.Map;
public class JSONWrapperSetup implements ServletContextListener {
private static final Log log = LogFactory.getLog(JSONWrapperSetup.class);
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
IndividualJsonWrapper.setAddJSONFields(new IndividualJsonWrapper.AddJSONFields() {
@Override
public void add(JSONObject jo, VitroRequest vreq, Individual ind) throws JSONException {
jo.put("preferredTitle", findPreferredTitle(vreq, ind));
}
private String VCARD_DATA_QUERY = ""
+ "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
+ "PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> \n"
+ "SELECT DISTINCT ?title \n" + "WHERE { \n"
+ " ?subject obo:ARG_2000028 ?vIndividual . \n"
+ " ?vIndividual vcard:hasTitle ?vTitle . \n"
+ " ?vTitle vcard:title ?title . \n" + "} ";
private String findPreferredTitle(VitroRequest vreq, Individual ind) {
String queryStr = QueryUtils.subUriForQueryVar(VCARD_DATA_QUERY,
"subject", ind.getURI());
log.debug("queryStr = " + queryStr);
String value = "";
try {
ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
while (results.hasNext()) {
QuerySolution soln = results.nextSolution();
String t = QueryUtils.nodeToString(soln.get("title"));
if (StringUtils.isNotBlank(t)) {
value = t;
}
}
} catch (Exception e) {
log.error(e, e);
}
return value;
}
});
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

19
api/src/main/java/org/vivoweb/webapp/startup/MenuManagementSetup.java Normal file
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@ -0,0 +1,19 @@
package org.vivoweb.webapp.startup;
import edu.cornell.mannlib.vitro.webapp.utils.menuManagement.MenuManagementDataUtils;
import edu.cornell.mannlib.vitro.webapp.utils.menuManagement.VIVOMenuManagementDataUtils;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
public class MenuManagementSetup implements ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
MenuManagementDataUtils.setImplementation(new VIVOMenuManagementDataUtils());
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

18
api/src/main/java/org/vivoweb/webapp/startup/SearchResultTemplateModelSetup.java Normal file
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@ -0,0 +1,18 @@
package org.vivoweb.webapp.startup;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.searchresult.VIVOIndividualSearchResult;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
public class SearchResultTemplateModelSetup implements ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
VIVOIndividualSearchResult.register();
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

27
api/src/main/java/org/vivoweb/webapp/startup/TemplateModelSetup.java Normal file
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@ -0,0 +1,27 @@
package org.vivoweb.webapp.startup;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.VIVOIndividualTemplateModel;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModelBuilder;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.VIVOIndividualTemplateModelBuilder;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividual;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.ListedIndividualBuilder;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.VIVOListedIndividual;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individuallist.VIVOListedIndividualBuilder;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
public class TemplateModelSetup implements ServletContextListener {
@Override
public void contextInitialized(ServletContextEvent servletContextEvent) {
IndividualTemplateModelBuilder.setCustomBuilder(new VIVOIndividualTemplateModelBuilder());
ListedIndividualBuilder.setCustomBuilder(new VIVOListedIndividualBuilder());
}
@Override
public void contextDestroyed(ServletContextEvent servletContextEvent) {
}
}

7
webapp/src/main/webapp/WEB-INF/resources/startup_listeners.txt
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@ -57,6 +57,13 @@ edu.cornell.mannlib.vitro.webapp.services.shortview.ShortViewServiceSetup
edu.cornell.mannlib.vitro.webapp.visualization.setup.VisualizationSetup edu.cornell.mannlib.vitro.webapp.visualization.setup.VisualizationSetup
org.vivoweb.webapp.startup.DataGetterN3Setup
org.vivoweb.webapp.startup.GeneratorSetup
org.vivoweb.webapp.startup.JSONWrapperSetup
org.vivoweb.webapp.startup.MenuManagementSetup
org.vivoweb.webapp.startup.TemplateModelSetup
org.vivoweb.webapp.startup.SearchResultTemplateModelSetup
edu.ucsf.vitro.opensocial.OpenSocialSmokeTests edu.ucsf.vitro.opensocial.OpenSocialSmokeTests
# For multiple language support # For multiple language support

2
webapp/src/main/webapp/WEB-INF/web.xml
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@ -326,7 +326,7 @@
<servlet> <servlet>
<servlet-name>SiteAdminController</servlet-name> <servlet-name>SiteAdminController</servlet-name>
<servlet-class>edu.cornell.mannlib.vitro.webapp.controller.freemarker.SiteAdminController</servlet-class> <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.freemarker.VIVOSiteAdminController</servlet-class>
</servlet> </servlet>
<servlet-mapping> <servlet-mapping>
<servlet-name>SiteAdminController</servlet-name> <servlet-name>SiteAdminController</servlet-name>

4
webapp/src/main/webapp/templates/freemarker/lib/lib-generator-classes.ftl Normal file
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@ -0,0 +1,4 @@
<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
<#assign ManageLabelsGenerator = "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVOManageLabelsGenerator" />
<#assign NewIndividualFormGenerator = "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.VIVONewIndividualFormGenerator" />