annotation data migration

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java

@@ -12,6 +12,8 @@ public class VitroVocabulary {
     public static final String VITRO_AUTH = "http://vitro.mannlib.cornell.edu/ns/vitro/authorization#";
     public static final String VITRO_PUBLIC = "http://vitro.mannlib.cornell.edu/ns/vitro/public#";
     public static final String VITRO_PUBLIC_ONTOLOGY = "http://vitro.mannlib.cornell.edu/ns/vitro/public";
+    // TODO change the following before 1.6 release
+    public static final String PROPERTY_CONFIG_DATA = "http://example.org/appConfig/";
     
     
     /** BJL23 2008-02-25:

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/ObjectPropertyDaoJena.java

@@ -949,7 +949,6 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         "    { ?property display:listViewConfigFile ?filename \n" +
         "    } UNION { \n" +
         "        ?configuration config:listViewConfigFile ?filename . \n " +
-//        "        ?configuration config:hasListView ?lv . " +
         "        ?context config:hasConfiguration ?configuration . \n" +
         "        ?context config:configContextFor ?property . \n" +
         "        ?context config:qualifiedBy ?range . \n" +

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -44,6 +44,7 @@ public class ABoxUpdater {
 	private Dataset dataset;
 	private RDFService rdfService;
 	private OntModel newTBoxAnnotationsModel;
+	private TBoxUpdater tboxUpdater;
 	private ChangeLogger logger;  
 	private ChangeRecord record;
 	private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
@@ -61,20 +62,19 @@ public class ABoxUpdater {
 	 *                         and the retractions model.
 	 *                    
 	 */
-	public ABoxUpdater(OntModel oldTboxModel,
+	public ABoxUpdater(UpdateSettings settings,
-			           OntModel newTboxModel,
-			           RDFService rdfService,
-			           OntModel newAnnotationsModel,
 		               ChangeLogger logger,
 		               ChangeRecord record) {
 		
-		this.oldTboxModel = oldTboxModel;
+	    this.oldTboxModel = settings.getOldTBoxModel();
-		this.newTboxModel = newTboxModel;
+        this.newTboxModel = settings.getNewTBoxModel();
+        RDFService rdfService = settings.getRDFService();
 		this.dataset = new RDFServiceDataset(rdfService);
 		this.rdfService = rdfService;
-		this.newTBoxAnnotationsModel = newAnnotationsModel;
+		this.newTBoxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
 		this.logger = logger;
 		this.record = record;
+		this.tboxUpdater = new TBoxUpdater(settings, logger, record);
 	}
 	
 	/**
@@ -632,6 +632,8 @@ public class ABoxUpdater {
     					propObj.getDestinationURI() + " instead");		
     		}
         }
+        
+        tboxUpdater.renameProperty(propObj);
 	}
 	
 	public void logChanges(Statement oldStatement, Statement newStatement) throws IOException {

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

@@ -64,7 +64,6 @@ public class KnowledgeBaseUpdater {
 		}
 			
 		long startTime = System.currentTimeMillis();
-        System.out.println("Migrating the knowledge base");
         log.info("Migrating the knowledge base");
         logger.log("Started knowledge base migration");
 		
@@ -84,7 +83,6 @@ public class KnowledgeBaseUpdater {
 		logger.closeLogs();
 
 		long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;		
-		System.out.println("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		
 		return;
@@ -111,20 +109,15 @@ public class KnowledgeBaseUpdater {
 	    	log.error("unable to migrate migration metadata " + e.getMessage());
 	    }
 	        	
-	    log.warn("KnowledgeBaseUpdater needs to be modified to work on all graphs!");
-	    OntModel readModel = settings.getUnionOntModelSelector().getABoxModel();
-	    OntModel writeModel = settings.getAssertionOntModelSelector().getABoxModel();
-	    // TODO make sure the ABox update applies to all graphs
-	    
-		log.info("\tupdating the abox");
-    	updateABox(changes);
-    	
     	log.info("performing SPARQL CONSTRUCT additions");
     	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
     	
         log.info("performing SPARQL CONSTRUCT retractions");
         performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
         
+        log.info("\tupdating the abox");
+        updateABox(changes);
+
 	}
 	
     private static final boolean ADD = true;
@@ -249,10 +242,8 @@ public class KnowledgeBaseUpdater {
 	private void updateABox(AtomicOntologyChangeLists changes) 
 			throws IOException {
 		
-		OntModel oldTBoxModel = settings.getOldTBoxModel();
+	
-		OntModel newTBoxModel = settings.getNewTBoxModel();
+		ABoxUpdater aboxUpdater = new ABoxUpdater(settings, logger, record);
-		RDFService rdfService = settings.getRDFService();
-		ABoxUpdater aboxUpdater = new ABoxUpdater(oldTBoxModel, newTBoxModel, rdfService, settings.getNewTBoxAnnotationsModel(), logger, record);
 		aboxUpdater.processPropertyChanges(changes.getAtomicPropertyChanges());
 		aboxUpdater.processClassChanges(changes.getAtomicClassChanges());
 	}
@@ -290,14 +281,18 @@ public class KnowledgeBaseUpdater {
 		rdfService.changeSetUpdate(removeChangeSet);	
 	}
 	
-	private void updateTBoxAnnotations() throws IOException {
+	private void updateTBoxAnnotations() {
-		
+		TBoxUpdater tboxUpdater = new TBoxUpdater(settings, logger, record);         
-		TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
+		try {
-		                                          settings.getNewTBoxAnnotationsModel(),
+		    tboxUpdater.modifyPropertyQualifications();
-                                                  settings.getAssertionOntModelSelector().getTBoxModel(), logger, record);
+		} catch (Exception e) {
-                                                  
+		    log.error("Unable to modify qualified property config file ", e);
+		}
+		try {
             tboxUpdater.updateDefaultAnnotationValues();
-        //tboxUpdater.updateAnnotationModel();
+		} catch (Exception e) {
+		    log.error("Unable to update default annotation values ", e);
+		}
 	}
 	
 	/**

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/TBoxUpdater.java

@@ -2,11 +2,22 @@
 
 package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -14,6 +25,7 @@ import com.hp.hpl.jena.rdf.model.NodeIterator;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
@@ -21,6 +33,8 @@ import com.hp.hpl.jena.vocabulary.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 /**  
  * Performs knowledge base updates to the tbox to align with a new ontology version
@@ -28,6 +42,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
  */ 
 public class TBoxUpdater {
 
+    private static final Log log = LogFactory.getLog(TBoxUpdater.class);
+
+    private UpdateSettings settings;
     private OntModel oldTboxAnnotationsModel;
     private OntModel newTboxAnnotationsModel;
     private OntModel siteModel;
@@ -53,19 +70,33 @@ public class TBoxUpdater {
      *                         and the retractions model.
      *                    
      */
-	public TBoxUpdater(OntModel oldTboxAnnotationsModel,
+    public TBoxUpdater(UpdateSettings settings,
-			           OntModel newTboxAnnotationsModel,
-			           OntModel siteModel,
             ChangeLogger logger,
             ChangeRecord record) {
-		
+        this.settings = settings;
-		this.oldTboxAnnotationsModel = oldTboxAnnotationsModel;
+        this.oldTboxAnnotationsModel = settings.getOldTBoxAnnotationsModel();
-		this.newTboxAnnotationsModel = newTboxAnnotationsModel;
+        this.newTboxAnnotationsModel = settings.getNewTBoxAnnotationsModel();
-		this.siteModel = siteModel;
+        this.siteModel = settings.getAssertionOntModelSelector().getTBoxModel();
         this.logger = logger;
         this.record = record;
     }
 
+    /**
+     * Update application ontology data for domain and range-qualified properties
+     * to use any applicable settings from obsolete subproperties
+     */
+    public void modifyPropertyQualifications() throws IOException {
+ 
+    }
+
+    private Model mergeConfigurations(Model oldConfig, Model newConfig) {
+        return null;
+    }
+    
+    public void updateDefaultAnnotationValues() throws IOException {
+        updateDefaultAnnotationValues(null);
+    }
+
     /**
      * 
      * Update a knowledge base to align with changes to vitro annotation property default 
@@ -91,7 +122,7 @@ public class TBoxUpdater {
      *  Note: as specified, this method for now assumes that no new vitro annotation
      *  properties have been introduced. This should be updated for future versions.
      */
-	public void updateDefaultAnnotationValues() throws IOException {
+    public void updateDefaultAnnotationValues(String subjectURI) throws IOException {
 
         siteModel.enterCriticalSection(Lock.WRITE);
 
@@ -109,7 +140,9 @@ public class TBoxUpdater {
                 return;
             }
             
-		  StmtIterator iter = oldTboxAnnotationsModel.listStatements();
+            Resource subj = (subjectURI == null) ? null : ResourceFactory.createResource(subjectURI);
+
+            StmtIterator iter = oldTboxAnnotationsModel.listStatements(subj, null, (RDFNode) null);
 
             while (iter.hasNext()) {
 
@@ -420,4 +453,119 @@ public void removeObsoleteAnnotations() throws IOException {
         }
     }
     
+    public void renameProperty(AtomicOntologyChange changeObj) throws IOException {
+        if(changeObj.getNotes() != null && changeObj.getNotes().startsWith("cc:")) {
+            mergePropertyAnnotationsToPropertyConfig(changeObj);
+        }        
+        
+    }
+    
+    private void mergePropertyAnnotationsToPropertyConfig(AtomicOntologyChange changeObj) throws IOException {
+        String contextURI = VitroVocabulary.PROPERTY_CONFIG_DATA + changeObj.getNotes().substring(3);
+        String oldPropertyURI = changeObj.getSourceURI();
+        
+        Model oldAnnotationsModel = settings.getOldTBoxAnnotationsModel();
+        Dataset dataset = new RDFServiceDataset(settings.getRDFService());
+        Model userAnnotationsModel = dataset.getNamedModel(
+                JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
+        
+        String propertyAnnotationsQuery = 
+                "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "    <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "    <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "    <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "    <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "    <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "} WHERE { \n" +
+                "    { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                "    UNION { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                "    UNION { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                "} \n" ; 
+        
+        Model userChangesModel = construct(
+                propertyAnnotationsQuery, userAnnotationsModel).difference(
+                        construct(propertyAnnotationsQuery, oldAnnotationsModel));
+        
+        String addQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                          "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                          "CONSTRUCT { \n" +
+                          "    ?configuration config:propertyGroup ?group . \n" +
+                          "    ?configuration config:displayName ?label . \n" +
+                          "    ?configuration vitro:displayRankAnnot ?displayRank . \n" +
+                          "    ?configuration vitro:customEntryFormAnnot ?customForm . \n" +
+                          "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                          "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +                              
+                          "} WHERE { \n" +
+                          "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel } \n" +
+                          "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } \n " +
+                          "} \n" ;
+        
+        String retractQuery = "PREFIX config: <" + VitroVocabulary.configURI + "> \n" +
+                "PREFIX vitro: <" + VitroVocabulary.vitroURI  + "> \n" +
+                "CONSTRUCT { \n" +
+                "    <" + oldPropertyURI + "> config:propertyGroup ?rgroup . \n" +
+                "    ?configuration config:displayName ?rlabel . \n" +
+                "    ?configuration vitro:displayRankAnnot ?rdisplayRank . \n" +
+                "    ?configuration vitro:customEntryFormAnnot ?rcustomForm . \n" +
+                "    ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel . \n" +
+                "    ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?rupdateLevel . \n " +                              
+                "} WHERE { \n" +
+                "    <" + contextURI + "> config:hasConfiguration ?configuration . \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:inPropertyGroupAnnot ?group . \n" +
+                "               ?configuration config:propertyGroup ?rgroup } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> <" + RDFS.label.getURI() + "> ?label . \n" +
+                "               ?configuration config:displayName ?rlabel } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:displayRankAnnot ?displayRank . \n" +
+                "               ?configuration vitro:displayRantAnnot ?rdisplayRank } \n " +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:customEntryFormAnnot ?customForm . \n" +
+                "               ?configuration vitro:customEntryFormAnnot ?rcustomForm } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:hiddenFromDisplayBelowRoleLevelAnnot ?displayLevel . \n" +
+                "               ?configuration vitro:hiddenFromDisplayBelowRoleLevelAnnot ?rdisplayLevel } \n" +
+                "    OPTIONAL { <" + oldPropertyURI + "> vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel . \n " +
+                "               ?configuration vitro:prohibitedFromUpdateBelowRoleLevelAnnot ?updateLevel } " +
+                "} \n" ;
+        
+        Model configModel = ModelFactory.createDefaultModel();
+        String configFileName = settings.getQualifiedPropertyConfigFile();
+        File file = new File(configFileName);
+        FileInputStream fis = new FileInputStream(file);
+        configModel.read(fis, null, "N3");
+
+        Model union = ModelFactory.createUnion(configModel, 
+                userChangesModel);
+
+        Model additions = construct(addQuery, union);
+        Model retractions = construct(retractQuery, union);
+        
+        if (additions.size() > 0 || retractions.size() > 0) {
+            configModel.remove(retractions);
+            log.info("Removing " + retractions.size() + " statements from " + contextURI);
+            configModel.add(additions);
+            log.info("Adding " + additions.size() + " statements from " + contextURI);
+            FileOutputStream fos = new FileOutputStream(file);
+            configModel.write(fos, "N3");
+        }
+    }
+    
+    private Model construct(String queryStr, Model model) {    
+        Query query = QueryFactory.create(queryStr);
+        QueryExecution qe = QueryExecutionFactory.create(query, model);
+        try {
+            return qe.execConstruct();
+        } finally {
+            qe.close();
+        }
+    }
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/UpdateSettings.java

@@ -21,6 +21,7 @@ public class UpdateSettings {
 	private String errorLogFile;
 	private String addedDataFile;
 	private String removedDataFile;
+	private String qualifiedPropertyConfigFile;
 	private String defaultNamespace;
 	private OntModelSelector assertionOntModelSelector;
 	private OntModelSelector inferenceOntModelSelector;
@@ -121,6 +122,12 @@ public class UpdateSettings {
 	public void setRemovedDataFile(String removedDataFile) {
 		this.removedDataFile = removedDataFile;
 	}
+	public String getQualifiedPropertyConfigFile() {
+	    return qualifiedPropertyConfigFile;
+	}
+	public void setQualifiedPropertyConfigFile(String qualifiedPropertyConfigFile) {
+	    this.qualifiedPropertyConfigFile = qualifiedPropertyConfigFile;
+	}
  	public String getDefaultNamespace() {
 		return defaultNamespace;
 	}

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

@@ -96,7 +96,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 			settings.setNewTBoxModel(newTBoxModel);
 			OntModel oldTBoxAnnotationsModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
 			settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
-			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "everytime").toString());
+			OntModel newTBoxAnnotationsModel = loadModelFromDirectory(createDirectory(homeDir, "rdf", "tbox", "firsttime").toString());
 			settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
 			settings.setRDFService(RDFServiceUtils.getRDFServiceFactory(ctx).getRDFService());
 				
@@ -145,6 +145,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 							   log.warn("unable to successfully update display model: " + e.getMessage());
 						  }
 					  }
+					  // reload the display model since the TBoxUpdater may have 
+					  // modified it
+					  new ApplicationModelSetup().contextInitialized(sce);
 				  }
 			   } catch (Exception ioe) {
 					ss.fatal(this, "Exception updating knowledge base for ontology changes: ", ioe);
@@ -189,6 +192,17 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		Path logDir = createDirectory(dataDir, "logs");
 		settings.setLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate", "log")).toString());
 		settings.setErrorLogFile(logDir.resolve(timestampedFileName("knowledgeBaseUpdate.error", "log")).toString());
+		
+		Path qualifiedPropertyConfigFile = getFilePath(homeDir, "rdf", "display", "everytime", "PropertyConfig.n3");
+		settings.setQualifiedPropertyConfigFile(qualifiedPropertyConfigFile.toString());
+	}
+
+	private Path getFilePath(Path parent, String... children) throws IOException {
+        Path path = parent;
+        for (String child : children) {
+            path = path.resolve(child);
+        }
+        return path;	    
 	}
 	
 	private Path createDirectory(Path parent, String... children) throws IOException {