Merge branch 'develop' into feature/fauxEditing

build.xml

@@ -75,6 +75,7 @@
 			<include name="languages/**/*" />
 			<include name="config/*.properties" />
 			<include name="config/*.txt" />
+			<include name="config/*.n3" />
 			<include name="config/jarlist/*.txt" />
 			<include name="config/solr/*" />
 			<include name="context.xml" />

config/applicationSetup.n3

@@ -0,0 +1,35 @@
+@prefix : <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#> .
+
+:application 
+    a   <java:edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.Application> ;
+    :hasSearchEngine              :searchEngineWrapper ;
+    :hasImageProcessor            :imageProcessor ;
+    :hasFileStorage               :fileStorage ;
+    :hasContentTripleSource       :contentTripleSource ;
+    :hasConfigurationTripleSource :configurationTripleSource .
+
+:imageProcessor 
+    a   <java:edu.cornell.mannlib.vitro.webapp.imageprocessor.jai.JaiImageProcessor> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.imageProcessor.ImageProcessor> .
+
+:fileStorage 
+    a   <java:edu.cornell.mannlib.vitro.webapp.filestorage.impl.FileStorageImplWrapper> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.fileStorage.FileStorage> .
+               
+:searchEngineWrapper 
+    a   <java:edu.cornell.mannlib.vitro.webapp.searchengine.InstrumentedSearchEngineWrapper> , 
+        <java:edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine> ;
+    :wraps :searchEngine .
+
+:searchEngine
+    a   <java:edu.cornell.mannlib.vitro.webapp.searchengine.solr.SolrSearchEngine> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngine> .
+
+:contentTripleSource
+    a   <java:edu.cornell.mannlib.vitro.webapp.triplesource.impl.sdb.ContentTripleSourceSDB> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ContentTripleSource> .
+
+:configurationTripleSource
+    a   <java:edu.cornell.mannlib.vitro.webapp.triplesource.impl.tdb.ConfigurationTripleSourceTDB> ,
+        <java:edu.cornell.mannlib.vitro.webapp.modules.tripleSource.ConfigurationTripleSource> .

doc/README.txt

@@ -8,9 +8,9 @@ find these files in this directory:
               Instructions for installing VIVO on your machine, including 
               a simple installation and several options.
 
-    Upgrade Instructions for VIVO release 1.7.pdf
+    Upgrade Instructions for VIVO release 1.8.pdf
               Instructions for migrating a VIVO installation from release
-              1.6 to release 1.7
+              1.7 to release 1.8
               
 If these files are not present, or to obtain the latest version of the 
 instructions, go to:

productMods/WEB-INF/resources/startup_listeners.txt

@@ -7,6 +7,8 @@
 
 edu.cornell.mannlib.vitro.webapp.servlet.setup.JvmSmokeTests
 
+edu.cornell.mannlib.vitro.webapp.application.ApplicationSetup
+
 edu.cornell.mannlib.vitro.webapp.config.ConfigurationPropertiesSetup
 
 edu.cornell.mannlib.vitro.webapp.config.ConfigurationPropertiesSmokeTests
@@ -16,15 +18,12 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.GuardAgainstUnmigratedRDB
 
 edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings$Setup
 
-edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl$Setup
+edu.cornell.mannlib.vitro.webapp.application.ApplicationImpl$ComponentsSetup
 
 edu.cornell.mannlib.vitro.webapp.config.RevisionInfoSetup
 
 edu.cornell.mannlib.vitro.webapp.email.FreemarkerEmailFactory$Setup
 
-# In 1.8, this should replace JenaPersistentDataSourceSetup, RDFServiceSetup, and maybe more.
-edu.cornell.mannlib.vitro.webapp.servlet.setup.rdfsetup.RDFSetup
-
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ConfigurationModelsSetup
 edu.cornell.mannlib.vitro.webapp.servlet.setup.ContentModelSetup
 
@@ -64,9 +63,6 @@ edu.ucsf.vitro.opensocial.OpenSocialSmokeTests
 # For multiple language support
 edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionSetup
 
-# Add VIVO specific DocumentModifers, this must come before SearchIndexerSetup
-edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoDocumentModifiers
-
 # The search indexer uses a "public" permission, so the PropertyRestrictionPolicyHelper 
 #   and the PermissionRegistry must already be set up.
 edu.cornell.mannlib.vitro.webapp.searchindex.SearchIndexerSetup

rdf/display/everytime/VivoSearchIndexerConfiguration.n3

@@ -0,0 +1,46 @@
+@prefix : <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationSetup#> .
+
+#
+# Specify the SearchIndexExcluders and DocumentModifiers for VIVO. 
+# These are in addition to the ones specified for VIVO.
+#
+
+:vivoSearchExcluder_namespaceExcluder
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ExcludeBasedOnNamespace> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.SearchIndexExcluder> ;
+    :excludes
+        "http://purl.obolibrary.org/obo/" .
+
+# ------------------------------------
+
+:vivodocumentModifier_calculateParameters
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.CalculateParameters> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_valuesFromVcards
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VIVOValuesFromVcards> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_ISFBasicFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoISFBasicFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_ISFAdvisingFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoISFAdvisingFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_ISFEducationFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoISFEducationFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_ISFGrantFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoISFGrantFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_ISFMemberFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoISFMemberFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .
+
+:vivodocumentModifier_informationResourceContextNodeFields
+    a   <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.VivoInformationResourceContextNodeFields> ,
+        <java:edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier> .

src/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java

@@ -34,6 +34,7 @@ import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 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;
@@ -213,13 +214,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
      */
     private static String getUploadPathBase(ServletContext context) throws Exception
     {
-        String vitroHomeDirectoryName = ConfigurationProperties.getBean(context).getProperty(FileStorageImplWrapper.PROPERTY_VITRO_HOME_DIR);
+        String vitroHomeDirectoryName = ApplicationUtils.instance().getHomeDirectory().getPath().toString(); 
-        if (vitroHomeDirectoryName == null) {
+        return vitroHomeDirectoryName + "/" + FileStorageImplWrapper.FILE_STORAGE_SUBDIRECTORY + "/" + PATH_TO_UPLOADS;
-            throw new Exception("Vitro home directory name could not be found.");
-        }
-
-        String pathBase = vitroHomeDirectoryName + "/" + FileStorageImplWrapper.FILE_STORAGE_SUBDIRECTORY + "/" + PATH_TO_UPLOADS;
-        return pathBase;
     }
 
     /**

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/CalculateParameters.java

@@ -12,6 +12,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 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;
@@ -26,12 +27,13 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.shared.Lock;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchInputDocument;
 import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.ContextModelsUser;
 
 
-public class CalculateParameters implements DocumentModifier {
+public class CalculateParameters implements DocumentModifier, ContextModelsUser {
 
     private boolean shutdown = false;
 	private Dataset dataset;
@@ -60,15 +62,11 @@ public class CalculateParameters implements DocumentModifier {
      
     private static Log log = LogFactory.getLog(CalculateParameters.class);
     
-	public CalculateParameters(Dataset dataset){
+	@Override
-		 this.dataset =dataset;
+	public void setContextModels(ContextModelAccess models) {
-		// new Thread(new TotalInd(this.dataset,totalCountQuery)).start();
+		 this.dataset = DatasetFactory.create(models.getOntModel());
 	}
-	
+
-	public CalculateParameters(){
-		super();
-	}
-	
 	public float calculateBeta(String uri){
 		float beta=0;
 		int Conn=0; 

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VIVOValuesFromVcards.java

@@ -15,11 +15,11 @@ 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.modelaccess.ContextModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchInputDocument;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier;
+import edu.cornell.mannlib.vitro.webapp.utils.configuration.ContextModelsUser;
 
 /**
  * If there are any VCards on this Individual with Title objects, store the text
@@ -28,7 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.DocumentModifier
  * If there are any VCards on this Individual with EMail objects, store the text
  * in the ALL_TEXT field.
  */
-public class VIVOValuesFromVcards implements DocumentModifier {
+public class VIVOValuesFromVcards implements DocumentModifier, ContextModelsUser {
 	private static final Log log = LogFactory
 			.getLog(VIVOValuesFromVcards.class);
 
@@ -77,11 +77,12 @@ public class VIVOValuesFromVcards implements DocumentModifier {
 			}
 		}};
 
-	private RDFServiceFactory rdfServiceFactory;
+	private RDFService rdfService;
 	private boolean shutdown = false;
 
-	public VIVOValuesFromVcards(RDFServiceFactory rdfServiceFactory) {
+	@Override
-		this.rdfServiceFactory = rdfServiceFactory;
+	public void setContextModels(ContextModelAccess models) {
+		this.rdfService = models.getRDFService();
 	}
 
 	@Override
@@ -100,7 +101,6 @@ public class VIVOValuesFromVcards implements DocumentModifier {
 		String query = queryTemplate.replaceAll("\\?uri", uri);
 
 		try {
-			RDFService rdfService = rdfServiceFactory.getRDFService();
 			ResultSet results = RDFServiceUtils.sparqlSelectQuery(query,
 					rdfService);
 			if (results != null) {

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoAgentContextNodeFields.java

@@ -4,9 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /**
  * Class that adds text from context nodes to Search Documents for 
  * foaf:Agent individuals.
@@ -15,8 +12,8 @@ public class VivoAgentContextNodeFields extends ContextNodeFields{
     
     static List<String> queriesForAgent = new ArrayList<String>();    
     
-    public VivoAgentContextNodeFields(RDFServiceFactory rdfServiceFactory){        
+    public VivoAgentContextNodeFields(){        
-        super(queriesForAgent,rdfServiceFactory);
+        super(queriesForAgent);
     }
       
   protected static final String prefix = 

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoDocumentModifiers.java

@@ -1,72 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.servlet.ServletContext;
-import javax.servlet.ServletContextEvent;
-
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.DatasetFactory;
-
-import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
-
-public class VivoDocumentModifiers implements javax.servlet.ServletContextListener{
-    
-    /** 
-     * Exclude from the search index individuals who's URIs start with these namespaces. 
-     */
-    private static final String[] INDIVIDUAL_NS_EXCLUDES={
-        //bdc34: seems that there are a lot of odd OBO things in the search, exclude them
-        "http://purl.obolibrary.org/obo/"
-    };
-    
-    @SuppressWarnings("unchecked")
-    @Override
-    public void contextInitialized(ServletContextEvent sce) {
-        
-        ServletContext context = sce.getServletContext();
-		RDFServiceFactory rdfServiceFactory = RDFServiceUtils.getRDFServiceFactory(context);
-        
-        Dataset dataset = DatasetFactory.create(ModelAccess.on(context).getOntModel());
-        
-        /* Put DocumentModifiers into servlet context for use later in startup by SearchSetup 
-         * This adds the code for VIVO specific additions to the building
-         * of search input Documents. */        
-        List<DocumentModifier> modifiers = (List<DocumentModifier>)context.getAttribute("DocumentModifiers");
-        if( modifiers == null ){                    
-            modifiers = new ArrayList<DocumentModifier>();
-            context.setAttribute("DocumentModifiers", modifiers);
-        }
-        
-        modifiers.add(new CalculateParameters(dataset));   
-        modifiers.add( new VIVOValuesFromVcards( rdfServiceFactory ));
-        modifiers.add( new VivoISFBasicFields( rdfServiceFactory ));
-        modifiers.add( new VivoISFAdvisingFields( rdfServiceFactory ));
-        modifiers.add( new VivoISFEducationFields( rdfServiceFactory ));
-        modifiers.add( new VivoISFGrantFields( rdfServiceFactory ));
-        modifiers.add( new VivoISFMemberFields( rdfServiceFactory ));        
-        modifiers.add(new VivoInformationResourceContextNodeFields(rdfServiceFactory));                
-        
-        /*
-         * Add VIVO specific code that excludes Individuals from the search index. 
-         */        
-        List<SearchIndexExcluder> excludes = 
-            (List<SearchIndexExcluder>)context.getAttribute("SearchIndexExcludes");
-        
-        if( excludes == null ){
-            excludes = new ArrayList<SearchIndexExcluder>();
-            context.setAttribute("SearchIndexExcludes", excludes);
-        }
-                
-        excludes.add(new ExcludeBasedOnNamespace(INDIVIDUAL_NS_EXCLUDES ));        
-    }
-
-    @Override
-    public void contextDestroyed(ServletContextEvent arg0) {
-        // do nothing.        
-    }    
-}

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoISFAdvisingFields.java

@@ -5,9 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /**
  * DocumentModifier for adding rdfs:labels of individuals related via
  * a advising relationship.
@@ -31,8 +28,8 @@ public class VivoISFAdvisingFields extends ContextNodeFields {
         queries.add( makeQueryForPeople() );
     }
     
-    public VivoISFAdvisingFields(RDFServiceFactory rdfServiceFactory){                
+    public VivoISFAdvisingFields(){                
-        super(queries,rdfServiceFactory);        
+        super(queries);        
     }
     
     /**

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoISFBasicFields.java

@@ -5,9 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /**
  * DocumentModifier to populate Search index fields for the basic ISF relationships. 
  * 
@@ -23,8 +20,7 @@ public class VivoISFBasicFields extends ContextNodeFields {
      * Subtypes of vivo:Relationship that get handled by this class.
      */
     private static String[] RELATIONSHIP_TYPES = {
-        //VIVONS + "Relationship",
+        VIVONS + "Position",
-        VIVONS + "Postion",
         VIVONS + "Authorship",
         VIVONS + "Collaboration",
         VIVONS + "Affiliation"
@@ -32,8 +28,8 @@ public class VivoISFBasicFields extends ContextNodeFields {
     
     static List<String> queries = new ArrayList<String>();    
     
-    public VivoISFBasicFields(RDFServiceFactory rdfServiceFactory){        
+    public VivoISFBasicFields(){        
-        super(queries,rdfServiceFactory);
+        super(queries);
     }
       
     protected static final String prefix =               

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoISFEducationFields.java

@@ -5,9 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 public class VivoISFEducationFields extends ContextNodeFields {
     private static String VIVONS = "http://vivoweb.org/ontology/core#";
     
@@ -18,8 +15,8 @@ public class VivoISFEducationFields extends ContextNodeFields {
           + " prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> \n" 
           + " prefix obo: <http://purl.obolibrary.org/obo/> \n" ;
     
-    public VivoISFEducationFields(RDFServiceFactory rdfServiceFactory){                
+    public VivoISFEducationFields(){                
-        super(queries,rdfServiceFactory);        
+        super(queries);        
     }
     
     /**

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoISFGrantFields.java

@@ -5,9 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /*
  * This DocumentModifier is for the ISF style grants.
  * It will 
@@ -30,8 +27,8 @@ public class VivoISFGrantFields extends ContextNodeFields {
           + " prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> \n" 
           + " prefix obo: <http://purl.obolibrary.org/obo/> \n" ;
     
-    public VivoISFGrantFields(RDFServiceFactory rdfServiceFactory){                
+    public VivoISFGrantFields(){                
-        super(queries,rdfServiceFactory);        
+        super(queries);        
     }
     
     /**

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoISFMemberFields.java

@@ -5,9 +5,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /**
  * This class will:
  *   add people's names to organization's search Documents.
@@ -26,8 +23,8 @@ public class VivoISFMemberFields extends ContextNodeFields {
           + " prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> \n" 
           + " prefix obo: <http://purl.obolibrary.org/obo/> \n" ;
     
-    public VivoISFMemberFields(RDFServiceFactory rdfServiceFactory){                
+    public VivoISFMemberFields(){                
-        super(queries,rdfServiceFactory);        
+        super(queries);        
     }
     
     /**
@@ -37,7 +34,7 @@ public class VivoISFMemberFields extends ContextNodeFields {
             prefix +
             "SELECT (str(?rawresult) as ?result) WHERE {\n" +              
             " ?uri    rdf:type               foaf:Organization . \n" +
-            " ?role   core:roleContrigutesTo ?uri . \n" +
+            " ?role   core:roleContributesTo ?uri . \n" +
             " ?person obo:RO_0000053         ?role . \n" +
             " ?person rdfs:label             ?rawresult .\n" +                       
             "}";
@@ -49,7 +46,7 @@ public class VivoISFMemberFields extends ContextNodeFields {
             prefix +
             "SELECT (str(?rawresult) as ?result) WHERE {\n" +              
             " ?uri    rdf:type               foaf:Person . \n" +
-            " ?uri obo:RO_0000053 / core:roleContrigutesTo / rdfs:label ?rawresult . \n" +                        
+            " ?uri obo:RO_0000053 / core:roleContributesTo / rdfs:label ?rawresult . \n" +                        
             "}";
     
         

src/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoInformationResourceContextNodeFields.java

@@ -4,9 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.search.documentBuilding;
 import java.util.ArrayList;
 import java.util.List;
 
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.search.documentBuilding.ContextNodeFields;
-
 /**
  * Class that adds text from context nodes to search index Documents for 
  * obo:IAO_0000030 individuals.
@@ -18,8 +15,8 @@ public class VivoInformationResourceContextNodeFields extends ContextNodeFields{
     
     static List<String> queriesForInformationResource = new ArrayList<String>();
     
-    public VivoInformationResourceContextNodeFields(RDFServiceFactory rdfServiceFactory){        
+    public VivoInformationResourceContextNodeFields(){        
-        super(queriesForInformationResource, rdfServiceFactory);
+        super(queriesForInformationResource);
     }
       
   protected static final String prefix = 

test/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoAgentContextNodeFieldsTest.java

@@ -9,6 +9,8 @@ import java.io.InputStream;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccessStub;
+
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
@@ -18,17 +20,14 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
 
 
 public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
         
         static String SPCA = "http://vivo.mydomain.edu/individual/n8087";
-        
+        static ContextModelAccessStub contextModels;
-        static RDFServiceFactory rdfServiceFactory;
         
         @BeforeClass
         public static void setup(){
@@ -44,8 +43,8 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
                 assertTrue("expect statements about SPCA",
                                 m.contains(ResourceFactory.createResource(SPCA),(Property) null,(RDFNode) null));
                 
-        RDFService rdfService = new RDFServiceModel(m);
+        contextModels = new ContextModelAccessStub();
-        rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
+        contextModels.setRDFService(WhichService.CONTENT, new RDFServiceModel(m));
         }
         
         @Test
@@ -53,7 +52,8 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
                 Individual ind = new IndividualImpl();
         ind.setURI(SPCA);
         
-        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
+        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields();
+        vacnf.setContextModels(contextModels);
         StringBuffer sb = vacnf.getValues( ind );
         
         assertNotNull( sb );
@@ -68,7 +68,8 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
                 Individual ind = new IndividualImpl();
         ind.setURI(SPCA);
         
-        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
+        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields();
+        vacnf.setContextModels(contextModels);
         StringBuffer sb = vacnf.getValues( ind );
         
         assertNotNull( sb );
@@ -83,7 +84,8 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
                 Individual ind = new IndividualImpl();
         ind.setURI(SPCA);
         
-        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
+        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields();
+        vacnf.setContextModels(contextModels);
         StringBuffer sb = vacnf.getValues( ind );
         
         assertNotNull( sb );

test/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoAgentContextNodeFieldsTest2.java

@@ -10,6 +10,8 @@ import org.apache.commons.lang.StringUtils;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccessStub;
+
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
@@ -19,9 +21,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
 
 /**
@@ -32,9 +32,8 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceMod
 public class VivoAgentContextNodeFieldsTest2  extends AbstractTestClass{
 	    	
 	static String HISTORY_DEPT = "http://vivo.colorado.edu/deptid_10238" ;
-	
+    static ContextModelAccessStub contextModels;
-	static RDFServiceFactory rdfServiceFactory;
+
-	
 	@BeforeClass
 	public static void setup(){
 		Model m = ModelFactory.createDefaultModel();
@@ -52,8 +51,8 @@ public class VivoAgentContextNodeFieldsTest2  extends AbstractTestClass{
 		assertTrue("expect statements about HISTORY_DEPT", 
 				m.contains(ResourceFactory.createResource(HISTORY_DEPT),(Property) null,(RDFNode) null));
 		
-        RDFService rdfService = new RDFServiceModel(m);
+        contextModels = new ContextModelAccessStub();
-        rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
+        contextModels.setRDFService(WhichService.CONTENT, new RDFServiceModel(m));
 	}
 	
 	/**
@@ -65,7 +64,8 @@ public class VivoAgentContextNodeFieldsTest2  extends AbstractTestClass{
 		Individual ind = new IndividualImpl();
         ind.setURI(HISTORY_DEPT);
         
-        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
+        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields();
+        vacnf.setContextModels(contextModels);
         StringBuffer sb = vacnf.getValues( ind );
         
         assertNotNull( sb );        

test/edu/cornell/mannlib/vitro/webapp/search/documentBuilding/VivoInformationResourceContextNodeFieldsTest.java

@@ -9,6 +9,7 @@ import java.util.Collection;
 import org.junit.Assert;
 import org.junit.Test;
 
+import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccessStub;
 import stubs.edu.cornell.mannlib.vitro.webapp.modules.ApplicationStub;
 import stubs.edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchEngineStub;
 import stubs.javax.servlet.ServletContextStub;
@@ -23,10 +24,8 @@ import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.WebappDaoFactoryJena;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess.WhichService;
 import edu.cornell.mannlib.vitro.webapp.modules.searchEngine.SearchInputDocument;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
 
 public class VivoInformationResourceContextNodeFieldsTest extends AbstractTestClass {
@@ -54,13 +53,15 @@ public class VivoInformationResourceContextNodeFieldsTest extends AbstractTestCl
         WebappDaoFactory wadf = new WebappDaoFactoryJena(ontModel);        
         Individual ind = wadf.getIndividualDao().getIndividualByURI(DOCUMENT_URI);
         Assert.assertNotNull(ind);
-        
+
-        RDFService rdfService = new RDFServiceModel(ontModel);
+        ContextModelAccessStub contextModels = new ContextModelAccessStub();
-        RDFServiceFactory rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
+        contextModels.setRDFService(WhichService.CONTENT, new RDFServiceModel(ontModel));
+
         SearchInputDocument doc = ApplicationUtils.instance().getSearchEngine().createInputDocument();
         doc.addField("ALLTEXT", "");                
         
-        VivoInformationResourceContextNodeFields vircnf = new VivoInformationResourceContextNodeFields(rdfServiceFactory);
+        VivoInformationResourceContextNodeFields vircnf = new VivoInformationResourceContextNodeFields();
+        vircnf.setContextModels(contextModels);
         vircnf.modifyDocument(ind, doc);                
         
         Collection<Object> values = doc.getField("ALLTEXT").getValues();
@@ -68,7 +69,8 @@ public class VivoInformationResourceContextNodeFieldsTest extends AbstractTestCl
             Assert.assertFalse("rdf:label erroneously added by document modifier:", value.toString().contains(RDFS_LABEL_VALUE));
         }
         
-        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
+        VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields();
+        vacnf.setContextModels(contextModels);
         vacnf.modifyDocument(ind, doc);
         
      }