Updates for n3 editing, fixing bugs in new individual form generator and adding field validators to person has educational training

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java

@@ -0,0 +1,383 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators;
+
+import java.util.Arrays;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import org.apache.commons.lang.StringUtils;
+import javax.servlet.http.HttpSession;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.vivoweb.webapp.util.ModelUtils;
+
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.DateTimeWithPrecisionVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.DateTimeIntervalValidationVTwo;
+
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
+
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.vocabulary.RDFS;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.XSD;
+import com.hp.hpl.jena.ontology.OntModel;
+import edu.cornell.mannlib.vitro.webapp.beans.DataProperty;
+import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
+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.controller.freemarker.responsevalues.ResponseValues;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.Field;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.RoleToActivityPredicatePreprocessor;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.processEdit.RdfLiteralHash;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditN3GeneratorVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.SelectListGeneratorVTwo;
+import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.FieldVTwo;
+import edu.cornell.mannlib.vitro.webapp.web.MiscWebUtils;
+import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
+import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils.EditMode;
+import edu.cornell.mannlib.vitro.webapp.utils.generators.AddRoleUtils;
+/**
+ * Generates the edit configuration for importing concepts from external
+ * search services, e.g. UMLS etc.      
+ * 
+ * The N3 for this is set with the default settinf of 
+ *
+ */
+public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements EditConfigurationGenerator {
+	
+	private Log log = LogFactory.getLog(AddAssociatedConceptGenerator.class);
+	private boolean isObjectPropForm = false;
+	private String subjectUri = null;
+	private String predicateUri = null;
+	private String objectUri = null;
+	private String datapropKeyStr= null;
+	private int dataHash = 0;
+	private DataPropertyStatement dps = null;
+	private String dataLiteral = null;
+	private String template = "addAssociatedConcept.ftl";
+	private static HashMap<String,String> defaultsForXSDtypes ;
+	
+	
+    @Override
+    public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
+    	EditConfigurationVTwo editConfiguration = new EditConfigurationVTwo();
+	  initBasics(editConfiguration, vreq);
+      initPropertyParameters(vreq, session, editConfiguration);
+      initObjectPropForm(editConfiguration, vreq);               
+      
+      editConfiguration.setTemplate(template);
+      
+      setVarNames(editConfiguration);
+    	
+    	//Assumes this is a simple case of subject predicate var
+      editConfiguration.setN3Required(this.generateN3Required(vreq));
+    	    	
+      //n3 optional
+      editConfiguration.setN3Optional(this.generateN3Optional());
+    	
+	//Todo: what do new resources depend on here?
+	//In original form, these variables start off empty
+	editConfiguration.setNewResources(generateNewResources(vreq));
+	//In scope
+	this.setUrisAndLiteralsInScope(editConfiguration, vreq);
+	
+	//on Form
+	this.setUrisAndLiteralsOnForm(editConfiguration, vreq);
+	
+	editConfiguration.setFilesOnForm(new ArrayList<String>());
+    	
+    	//Sparql queries
+    	this.setSparqlQueries(editConfiguration, vreq);
+    	
+    	//set fields
+    	setFields(editConfiguration, vreq, EditConfigurationUtils.getPredicateUri(vreq));
+    	
+    
+    	setTemplate(editConfiguration, vreq);
+    	//No validators required here
+        //Add preprocessors
+        addPreprocessors(editConfiguration, vreq.getWebappDaoFactory());
+        //Adding additional data, specifically edit mode
+        addFormSpecificData(editConfiguration, vreq);
+        //One override for basic functionality, changing url pattern
+        //and entity 
+        //Adding term should return to this same page, not the subject
+        //Return takes the page back to the individual form
+        editConfiguration.setUrlPatternToReturnTo(EditConfigurationUtils.getFormUrlWithoutContext(vreq));
+    	return editConfiguration;
+    }
+    
+ 
+
+	private void setVarNames(EditConfigurationVTwo editConfiguration) {
+		  editConfiguration.setVarNameForSubject("person");
+	      editConfiguration.setVarNameForPredicate("predicate");
+	      editConfiguration.setVarNameForObject("edTraining");
+	}
+
+	protected void setTemplate(EditConfigurationVTwo editConfiguration,
+			VitroRequest vreq) {
+    	editConfiguration.setTemplate(template);
+		
+	}
+   
+   
+    
+   /*
+    * N3 Required and Optional Generators as well as supporting methods 
+    */
+	
+	private String getPrefixesString() {
+		//TODO: Include dynamic way of including this
+		return "@prefix core: <http://vivoweb.org/ontology/core#> .";
+	}
+	
+	//TODO: Check if single string or multiple strings - check rdfslabel form etc. for prefix
+	//processing
+    private List<String> generateN3Required(VitroRequest vreq) {
+    	return list(    	            	        
+    	        getPrefixesString() + "\n" +
+    	        "?subject ?predicate ?conceptNode .\n" +
+    	        "?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" + 
+    	        "?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?vocabURI ."
+    	);
+    }
+    
+   //Don't think there's any n3 optional here
+	private List<String> generateN3Optional() {
+		return list(    	            	        
+    	);
+    }
+	
+	
+  
+	
+	/*
+	 * Get new resources
+	 */
+	 private Map<String, String> generateNewResources(VitroRequest vreq) {
+			HashMap<String, String> newResources = new HashMap<String, String>();
+			//TODO: Get default namespace
+			String defaultNamespace = vreq.getWebappDaoFactory().getDefaultNamespace();
+			newResources.put("conceptNode", defaultNamespace + "individual");
+			//Only the node itself will be new for a newly created concept node
+			return newResources;
+		}
+    
+
+	
+	
+	/*
+	 * Set URIS and Literals In Scope and on form and supporting methods
+	 */
+    
+    private void setUrisAndLiteralsInScope(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
+    	HashMap<String, List<String>> urisInScope = new HashMap<String, List<String>>();
+    	//note that at this point the subject, predicate, and object var parameters have already been processed
+    	//these two were always set when instantiating an edit configuration object from json,
+    	//although the json itself did not specify subject/predicate as part of uris in scope
+    	urisInScope.put(editConfiguration.getVarNameForSubject(), 
+    			Arrays.asList(new String[]{editConfiguration.getSubjectUri()}));
+    	urisInScope.put(editConfiguration.getVarNameForPredicate(), 
+    			Arrays.asList(new String[]{editConfiguration.getPredicateUri()}));
+    	//Setting inverse role predicate
+    	urisInScope.put("inverseRolePredicate", getInversePredicate(vreq));
+    	
+    	
+    	editConfiguration.setUrisInScope(urisInScope);
+    	//Uris in scope include subject, predicate, and object var
+    	//literals in scope empty initially, usually populated by code in prepare for update
+    	//with existing values for variables
+    	editConfiguration.setLiteralsInScope(new HashMap<String, List<Literal>>());
+    }
+    
+    private List<String> getInversePredicate(VitroRequest vreq) {
+		List<String> inversePredicateArray = new ArrayList<String>();
+		ObjectProperty op = EditConfigurationUtils.getObjectProperty(vreq);
+		if(op != null && op.getURIInverse() != null) {
+			inversePredicateArray.add(op.getURIInverse());
+		}
+		return inversePredicateArray;
+	}
+
+	//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>();
+    	//The URI of the node that defines the concept
+    	urisOnForm.add("vocabURI");
+    	//Also need to add the label of the concept
+    	literalsOnForm.add("conceptLabel");
+    	editConfiguration.setLiteralsOnForm(literalsOnForm);
+    }
+    
+    
+    /**
+     * Set SPARQL Queries and supporting methods
+     */
+    
+    
+    private void setSparqlQueries(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
+    	//Sparql queries defining retrieval of literals etc.
+    	editConfiguration.setSparqlForAdditionalLiteralsInScope(new HashMap<String, String>());
+    	
+    	Map<String, String> urisInScope = new HashMap<String, String>();
+    	editConfiguration.setSparqlForAdditionalUrisInScope(urisInScope);
+    	
+    	editConfiguration.setSparqlForExistingLiterals(generateSparqlForExistingLiterals(vreq));
+    	editConfiguration.setSparqlForExistingUris(generateSparqlForExistingUris(vreq));
+    }
+    
+    
+    //Get page uri for object
+    private HashMap<String, String> generateSparqlForExistingUris(VitroRequest vreq) {
+    	HashMap<String, String> map = new HashMap<String, String>();
+    	//Existing uris here might include is defined by
+    	map.put("vocabURI", getExistingVocabURIQuery());
+    	return map;
+    }
+    
+    private String getExistingVocabURIQuery() {
+    	String query = "SELECT ?existingVocabURI \n " + 
+		"WHERE { \n" +
+	      "?conceptNode <" + RDFS.isDefinedBy.getURI() + ">  ?existingVocabURI ."
+	      + "}";
+		return query;
+	}
+
+
+
+
+	private HashMap<String, String> generateSparqlForExistingLiterals(VitroRequest vreq) {
+    	HashMap<String, String> map = new HashMap<String, String>();
+    	//Queries for existing concept label 
+    	//Vocab uri label is something that can be retrieved
+    	map.put("conceptLabel", getConceptLabelQuery());
+    	return map;
+    }
+
+    
+   
+	private String getConceptLabelQuery() {
+		String query = "SELECT ?existingConceptLabel \n " + 
+		"WHERE { \n" +
+	      "?conceptNode <" + RDFS.label.getURI() + ">  ?existingConceptLabel ."
+	      + "}";
+		return query;
+	}
+
+
+
+	/**
+	 * 
+	 * Set Fields and supporting methods
+	 */
+	
+	private void setFields(EditConfigurationVTwo editConfiguration, VitroRequest vreq, String predicateUri) {
+    	
+    	setConceptLabelField(editConfiguration, vreq);
+    	setVocabURIField(editConfiguration, vreq);
+    }
+    
+	private void setVocabURIField(EditConfigurationVTwo editConfiguration,
+			VitroRequest vreq) {
+		editConfiguration.addField(new FieldVTwo().
+				setName("vocabURI").
+				setValidators(new ArrayList<String>()).
+				setOptionsType("UNDEFINED"));
+	}
+
+
+
+	private void setConceptLabelField(EditConfigurationVTwo editConfiguration,
+			VitroRequest vreq) {
+		editConfiguration.addField(new FieldVTwo().
+				setName("conceptLabel").
+				setValidators(new ArrayList<String>()).
+				setOptionsType("UNDEFINED").
+				setRangeDatatypeUri(XSD.xstring.toString())
+				);
+	}
+
+
+
+	
+
+	
+    
+   
+    //Add preprocessor
+	
+   private void addPreprocessors(EditConfigurationVTwo editConfiguration, WebappDaoFactory wadf) {
+	   //Will be a completely different type of preprocessor
+	  /*
+	   editConfiguration.addEditSubmissionPreprocessor(
+			   new RoleToActivityPredicatePreprocessor(editConfiguration, wadf));
+	   */
+	}
+     
+   
+	//Form specific data
+	public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
+		HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
+		//Existing concepts should probably be a hash map or a hash map of classes
+		//with URI of concept node to label and information about existing URI
+		//This would be a sparql query and would need to be run here?
+		//For test purposes
+		List<AssociatedConceptInfo> testInfo = new ArrayList<AssociatedConceptInfo>();
+		testInfo.add(new AssociatedConceptInfo("testLabel", "testURI", "testVocabURI", "testVocabLabel"));
+		formSpecificData.put("existingConcepts", testInfo);
+		editConfiguration.setFormSpecificData(formSpecificData);
+	}
+	
+	public class AssociatedConceptInfo {
+		private String conceptLabel;
+		private String conceptURI;
+		private String vocabURI;
+		private String vocabLabel;
+		public AssociatedConceptInfo(String inputLabel, String inputURI, String inputVocabURI, String inputVocabLabel) {
+			this.conceptLabel = inputLabel;
+			this.conceptURI = inputURI;
+			this.vocabURI = inputVocabURI;
+			this.vocabLabel = inputVocabLabel;
+		}
+		
+		//Getters
+		public String getConceptLabel() {
+			return conceptLabel;
+		}
+		
+		public  String getConceptURI() {
+			return conceptURI;
+		}
+		
+		public  String getVocabURI() {
+			return vocabURI;
+		}
+		
+		public  String getVocabLabel(){
+			return vocabLabel;
+		}
+		
+	}
+	
+	
+	
+	
+}

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/NewIndividualFormGenerator.java

@@ -2,11 +2,15 @@
 
 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 javax.servlet.http.HttpSession;
 
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.vocabulary.RDFS;
 import com.hp.hpl.jena.vocabulary.XSD;
 
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
@@ -32,29 +36,36 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	config.setTemplate( "newIndividualForm.ftl" );
     	
     	config.setN3Required( list(
-    	        "?newInd ?rdfType ?typeOfNew .",
+    	        "?newInd ?rdfType ?typeOfNew ."
-    	        N3_PREFIX + "?newInd foaf:firstName ?firstName .",             
-                N3_PREFIX + "?newInd foaf:lastName  ?lastName ."
     	));    
+    	//Optional because user may have selected either person or individual of another kind
+    	//Person uses first name and last name whereas individual of other class would use label 
+    	config.setN3Optional(list(
+    	        N3_PREFIX + "?newInd foaf:firstName ?firstName ; foaf:lastName ?lastName .",             
+                N3_PREFIX + "?newInd <" + RDFS.label.getURI() + "> ?label ."
+    	));
     	                    
-    	config.addNewResource("newInd", null);
+    	config.addNewResource("newInd", vreq.getWebappDaoFactory().getDefaultNamespace());
-    	
-    	config.addUrisInScope("typeOfNew",list( getTypeOfNew(vreq) ) )
-    	      .addUrisInScope("rdfType",  list( VitroVocabulary.RDF_TYPE ));
     	    	
-        config.setLiteralsOnForm( list( "firstName", "lastName" ));            	
+    	config.setUrisOnform(list ());
-    	
+        config.setLiteralsOnForm( list( "label", "firstName", "lastName" ));            	
+    	setUrisAndLiteralsInScope(config);
     	//No SPARQL queries for existing since this is only used to create new, never for edit    	
     	    	
     	config.addField(new FieldVTwo().
     	        setName("firstName").
     	        setRangeDatatypeUri(XSD.xstring.getURI()).
-    	        setValidators(list("nonempty")));
+    	        setValidators(getFirstNameValidators(vreq)));
     	
     	config.addField(new FieldVTwo().
                 setName("lastName").
     	        setRangeDatatypeUri(XSD.xstring.getURI()).
-                setValidators(list("nonempty")));    	    	        
+                setValidators(getLastNameValidators(vreq)));    	
+    
+    	config.addField(new FieldVTwo().
+                setName("label").
+    	        setRangeDatatypeUri(XSD.xstring.getURI()).
+                setValidators(getLabelValidators(vreq)));    	  
     	    	
         addFormSpecificData(config, vreq);        
         
@@ -71,7 +82,33 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
     	return config;
     }
     
-    //Get parameter from HTTP request for type of new individual
+    //first and last name have validators if is person is true
+    private List<String> getFirstNameValidators(VitroRequest vreq) {
+		List<String> validators = new ArrayList<String>();
+		if(isPersonType(vreq)) {
+			validators.add("nonempty");
+		}
+		return validators;
+	}
+
+	private List<String> getLastNameValidators(VitroRequest vreq) {
+		List<String> validators = new ArrayList<String>();
+		if(isPersonType(vreq)) {
+			validators.add("nonempty");
+		}
+		return validators;
+	}
+
+	//validate label if person is not true
+	private List<String> getLabelValidators(VitroRequest vreq) {
+		List<String> validators = new ArrayList<String>();
+		if(!isPersonType(vreq)) {
+			validators.add("nonempty");
+		}
+		return validators;
+	}
+
+	//Get parameter from HTTP request for type of new individual
     private String getTypeOfNew(VitroRequest vreq) {
         String typeUri = vreq.getParameter("typeOfNew");
         if( typeUri == null || typeUri.trim().isEmpty() )
@@ -120,6 +157,18 @@ public class NewIndividualFormGenerator extends BaseEditConfigurationGenerator i
 	    }
 	    return isPersonType;
 	}
+	 private void setUrisAndLiteralsInScope(EditConfigurationVTwo editConfiguration) {
+	    	HashMap<String, List<String>> urisInScope = new HashMap<String, List<String>>();
+	    	//note that at this point the subject, predicate, and object var parameters have already been processed
+	    	urisInScope.put(editConfiguration.getVarNameForSubject(), 
+	    			Arrays.asList(new String[]{editConfiguration.getSubjectUri()}));
+	    	urisInScope.put(editConfiguration.getVarNameForPredicate(), 
+	    			Arrays.asList(new String[]{editConfiguration.getPredicateUri()}));
+	    	editConfiguration.setUrisInScope(urisInScope);
+	    	//Uris in scope include subject, predicate, and object var
+	    	
+	    	editConfiguration.setLiteralsInScope(new HashMap<String, List<Literal>>());
+	    }
 	
 	private String N3_PREFIX = "@prefix foaf:<http://xmlns.com/foaf/0.1/> .\n";
 }

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/PersonHasEducationalTraining.java

@@ -127,8 +127,8 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
 
         conf.addField( new FieldVTwo().
                 setName("majorField").
-                setRangeDatatypeUri( XSD.xstring.toString() ));
+                setRangeDatatypeUri( XSD.xstring.toString() ).
-                //setValidators( ) datatype:stringDatatypeUriJson                        
+                setValidators(list("datatype:" + XSD.xstring.toString())));
         
         conf.addField( new FieldVTwo().
                 setName("org").
@@ -138,23 +138,25 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         
         conf.addField( new FieldVTwo().
                 setName("orgLabel").
-                setRangeDatatypeUri(XSD.xstring.toString() ));
+                setRangeDatatypeUri(XSD.xstring.toString() ).
-                //setValidators( ["nonempty"] )
+                setValidators( list("nonempty") ));
                 
         conf.addField( new FieldVTwo().
                 setName("orgType").
                 setOptionsType(FieldVTwo.OptionsType.CHILD_VCLASSES).
-                setObjectClassUri( orgClass ));
+                setObjectClassUri( orgClass ).
-                //setValidators( ["nonempty"])
+                setValidators( list("nonempty")));
                 //setLiteralOptions( [ "Select one" ] )
                 
         conf.addField( new FieldVTwo().
                 setName("dept").
-                setRangeDatatypeUri( XSD.xstring.toString() ));
+                setRangeDatatypeUri( XSD.xstring.toString() ).
+                setValidators(list("datatype:" + XSD.xstring.toString())));
                 
         conf.addField( new FieldVTwo().
                 setName("info").
-                setRangeDatatypeUri( XSD.xstring.toString() ));
+                setRangeDatatypeUri( XSD.xstring.toString() ).
+                setValidators(list("datatype:" + XSD.xstring.toString())));
 
         FieldVTwo startField = new FieldVTwo().
         						setName("startField");

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/VivoBaseGenerator.java

@@ -35,4 +35,8 @@ public abstract class VivoBaseGenerator extends BaseEditConfigurationGenerator i
     final static String intervalToEnd =vivoCore+"end";
 
     final static String orgClass ="http://xmlns.com/foaf/0.1/Organization" ;
+    
+    //TODO: Define these elsewhere
+    final static String UMLSClass = vivoCore + "UMLS";
+    final static String AgrovocClass = vivoCore + "Agrovoc";
 }