Elaborating export of RDF for Crop records in GENESYS (crop table).

src/main/java/org/genesys2/server/model/impl/Crop.java

@@ -18,8 +18,12 @@ package org.genesys2.server.model.impl;
 
 import java.io.IOException;
 
+import java.util.HashMap;
+import java.util.Iterator;
+//import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
+import java.util.Map;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -32,7 +36,6 @@ import javax.persistence.Transient;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-
 import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Indexed;
 import org.hibernate.search.annotations.Store;
@@ -127,10 +130,10 @@ public class Crop extends GlobalVersionedAuditedModel {
 	}
 
 	@Transient
-	private JsonNode i18nJO ;
-	
+	private JsonNode i18nJO;
+
 	@Transient
-	private JsonNode i18nJU ;
+	private JsonNode i18nJU;
 
 	/*
 	 * This is meant to be a complex language tag merge operation... is there an easier way?
@@ -146,35 +149,28 @@ public class Crop extends GlobalVersionedAuditedModel {
 			System.err.println("I18n = " + i18n);
 			e.printStackTrace();
 		}
-		if(this.i18nJU != null) {
-			Iterator<String> jui = this.i18nJU.fieldNames() ;
-			while(jui.hasNext()) {
-				String uField = jui.next() ;
-				if(this.i18nJO.has(uField)) {
-					JsonNode juf = this.i18nJU.get(uField) ;					
-					JsonNode jof = this.i18nJO.get(uField) ;
-					 Iterator<String> ulocales = juf.fieldNames() ;
-					 while(ulocales.hasNext()) {
-						 String locale = ulocales.next() ;
-						 // TODO - append/overwrite jof.ufield.locale with juf.ufield.locale
-					 }
+		if (this.i18nJU != null) {
+			Iterator<String> jui = this.i18nJU.fieldNames();
+			while (jui.hasNext()) {
+				String uField = jui.next();
+				if (this.i18nJO.has(uField)) {
+					JsonNode juf = this.i18nJU.get(uField);
+					JsonNode jof = this.i18nJO.get(uField);
+					Iterator<String> ulocales = juf.fieldNames();
+					while (ulocales.hasNext()) {
+						String locale = ulocales.next();
+						// TODO - append/overwrite jof.ufield.locale with
+						// juf.ufield.locale
+					}
 				}
 			}
-			this.i18n = this.i18nJO.asText() ;
+			this.i18n = this.i18nJO.asText();
 		}
 		*/
 	}
 
-	public String getName(Locale locale) {
-		return StringUtils.defaultIfBlank(translate("name", locale), this.name);
-	}
-
-	public String getDescription(Locale locale) {
-		return StringUtils.defaultIfBlank(translate("description", locale), this.name);
-	}
-
-	private synchronized String translate(String field, Locale locale) {
-		if (this.i18nJ == null && !StringUtils.isBlank(this.i18n)) {
+	private synchronized void getI18nJson() {
+		if (this.i18nJ == null && ! StringUtils.isBlank(this.i18n)) {
 			ObjectMapper mapper = new ObjectMapper();
 			try {
 				this.i18nJ = mapper.readTree(this.i18n);
@@ -183,7 +179,58 @@ public class Crop extends GlobalVersionedAuditedModel {
 				e.printStackTrace();
 			}
 		}
+	}
+
+	private synchronized String translate(String field, Locale locale) {
+		getI18nJson() ;
 		return this.i18nJ != null && this.i18nJ.has(field) && this.i18nJ.get(field).has(locale.getLanguage()) ? this.i18nJ.get(field).get(locale.getLanguage())
 				.textValue() : null;
 	}
+	
+	@Transient
+	private Map<String,Map<String,String>> i18nMap = new HashMap<String,Map<String,String>>();
+	
+	private synchronized Map<String,String> buildVernacularMap(String field) {
+		getI18nJson() ;		
+		if(! this.i18nMap.containsKey(field) && this.i18nJ.has(field)) {
+			this.i18nMap.put(field, new HashMap<String,String>() ) ;
+			JsonNode fieldMap = this.i18nJ.get(field) ;	
+			Iterator<String> languages = fieldMap.fieldNames() ;
+			while(languages.hasNext()) {
+				String language = languages.next() ;
+				String vernacular = fieldMap.get(language).textValue() ;
+				this.i18nMap.get(field).put(language, vernacular) ;
+			}
+
+		}
+		return i18nMap.get(field) ;
+	}
+	
+	public String getName(Locale locale) {
+		return StringUtils.defaultIfBlank(translate("name", locale), this.name);
+	}
+
+	public String getDescription(Locale locale) {
+		return StringUtils.defaultIfBlank(translate("description", locale), this.name);
+	}
+
+	/**
+	 * Method to return the map of available vernacular names of crops
+	 * @return Map<String,String> with language code as the key and the vernacular string as the value.
+	 */
+	public Map<String,String> getLocalNameMap() {
+		return buildVernacularMap("name") ;
+	}
+		
+	/**
+	 * Method to return the map of available vernacular definitions of crops
+	 * @return Map<String,String> with language code as the key and the vernacular string as the value.
+	 */
+	public Map<String,String> getLocalDefinitionMap() {
+		return buildVernacularMap("description") ;
+	}
+		
+
+		
+
 }

src/main/java/org/genesys2/server/servlet/controller/rdf/CropControllerRdf.java

@@ -17,6 +17,7 @@
 package org.genesys2.server.servlet.controller.rdf;
 
 import java.util.List;
+import java.util.Map;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
@@ -25,11 +26,14 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseBody;
 
+import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.DC;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.service.CropService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.bioversityinternational.model.germplasm.CCO;
@@ -75,7 +79,7 @@ public class CropControllerRdf extends RdfBaseController {
 
 	private void wrapCrop(Model model, Crop crop) {
 		
-		Resource subject = createSubject(model, crop, CCO.getURI(), crop.getShortName()+" Taxon") ;
+		Resource subject = createSubject(model, crop, CCO.getURI()+crop.getId(), crop.getShortName()+" Taxon") ;
 		subject.addProperty(DarwinCore.scientificName, crop.getShortName()) ;
 
 		String seeAlso = crop.getRdfUri() ;
@@ -87,29 +91,37 @@ public class CropControllerRdf extends RdfBaseController {
 
 		/*
 		 * vernacular names & descriptions in i18n
-		 * 
-		Map<String,String> vernacularNameMap = trait.getLocalNameMap() ;
+		 */ 
+		Map<String,String> vernacularNameMap = crop.getLocalNameMap() ;
+
+		if(vernacularNameMap!=null)
+			for( String language : vernacularNameMap.keySet() ) {
+				Literal vernacularNameLiteral = 
+						model.createLiteral(vernacularNameMap.get(language), language) ;
+				subject.addLiteral(DarwinCore.vernacularName,vernacularNameLiteral) ;
+			}
+		else
+			this._logger.warn("Empty vernacular crop name map for crop "+crop.getShortName());
+
+		Map<String,String> vernacularDefinitionMap = crop.getLocalDefinitionMap() ;
 		
-		for( String language : vernacularNameMap.keySet() ) {
-			Literal vernacularNameLiteral = 
-					model.createLiteral(vernacularNameMap.get(language), language) ;
-			traitSubject.addLiteral(DarwinCore.vernacularName,vernacularNameLiteral) ;
+		if(vernacularDefinitionMap!=null)
+			for( String language : vernacularDefinitionMap.keySet() ) {
+				Literal vernacularDefinitionLiteral = 
+						model.createLiteral(vernacularDefinitionMap.get(language), language) ;
+				subject.addLiteral(DC.description,vernacularDefinitionLiteral) ;
+			}
+		else
+			this._logger.warn("Empty vernacular crop description map for crop "+crop.getShortName());
+
+
+		List<CropRule> rules = cropService.getCropRules(crop) ;
+		for(CropRule cr : rules) {
+			String species = cr.getSpecies() ;
+			String genus   = cr.getGenus() ;
+			Boolean isIncluded = cr.isIncluded() ; 
 		}
 
-		Map<String,String> vernacularDefinitionMap = trait.getLocalDefinitionMap() ;
-		
-		for( String language : vernacularDefinitionMap.keySet() ) {
-			Literal vernacularDefinitionLiteral = 
-					model.createLiteral(vernacularDefinitionMap.get(language), language) ;
-			traitSubject.addLiteral(DC.description,vernacularDefinitionLiteral) ;
-		}
-
-		 */
-		
-		/*
-		model.addAttribute("cropTaxonomies", cropService.getCropTaxonomies(crop, new PageRequest(0, 20, new Sort("taxonomy.genus", "taxonomy.species"))));
-		 */
-
 	}
 	
 	@RequestMapping

src/main/java/org/genesys2/server/servlet/controller/rdf/DescriptorControllerRdf.java

@@ -19,6 +19,8 @@ package org.genesys2.server.servlet.controller.rdf;
 import java.util.List;
 import java.util.Map;
 
+import javax.servlet.http.HttpServletResponse;
+
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -30,7 +32,6 @@ import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseBody;
-
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.ParameterCategory;
@@ -50,30 +51,66 @@ import org.bioversityinternational.model.rdf.skos.SKOS;
 @RequestMapping(value = "/descriptors", method = RequestMethod.GET, headers = "accept=text/turtle", produces = RdfBaseController.RDF_MEDIATYPE_TURTLE)
 public class DescriptorControllerRdf extends RdfBaseController {
 	
-	public final static String DESCRIPTOR_NS = GENESYS_BASEURI+"/descriptors/";
-	public final static String CATEGORY_NS   = DESCRIPTOR_NS+"categories/" ;
-	public final static String TRAIT_NS      = DESCRIPTOR_NS+"trait/" ;
-	public final static String METHOD_NS     = DESCRIPTOR_NS+"method/" ;
-	public final static String SCALE_NS      = DESCRIPTOR_NS+"scale/" ;
+	public static final String DESCRIPTOR_NS = getBaseUri()+"/descriptors/";;
+	public static final String CATEGORY_NS   = DESCRIPTOR_NS+"categories/" ;
+	public static final String TRAIT_NS      = DESCRIPTOR_NS+"trait/" ;
+	public static final String METHOD_NS     = DESCRIPTOR_NS+"method/" ;
+	public static final String SCALE_NS      = DESCRIPTOR_NS+"scale/" ;
 
 	@Autowired
 	private TraitService traitService;
 	
-	@Override
-	protected Model startModel() {
-		Model model = super.startModel();
-		model.setNsPrefix("cat",   CATEGORY_NS );
-		model.setNsPrefix("trait", TRAIT_NS );
-		model.setNsPrefix("method",METHOD_NS );
-		model.setNsPrefix("scale", SCALE_NS );	
-		return model ;
+	/**
+	 * Method to retrieve list of all descriptor meta-data 
+	 * recorded in the database, formatted as Turtle RDF.
+	 * 
+	 * @return List of RDF Turtle formatted trait properties
+	 */
+	@RequestMapping
+	public @ResponseBody
+	Object dumpAll() {
+		
+		Model model = startModel() ;
+
+		wrapCategories(model) ;
+		
+		for(Parameter trait : traitService.listTraits()) 
+			wrapTrait(model, trait) ;
+		
+		for(Method method : traitService.listMethods()) {
+			Parameter trait = method.getParameter() ;
+			wrapMethod(model, trait, method) ;
+		}
+ 		return endModel(model) ;
 	}
 
 	/*
 	 * Creates and annotates a Method subject
 	 */
 	private Resource categorySubject(Model model, ParameterCategory category) {
-		return createSubject(model, category, CATEGORY_NS, category.getName() ) ;
+		return createSubject(model, category, CATEGORY_NS+category.getId(), category.getName() ) ;
+	}
+	
+	/*
+	 * Method generates RDF for one trait category record as RDF.
+	 */
+	private void wrapCategories(Model model) {
+		List<ParameterCategory> categories = traitService.listCategories() ;
+		for(ParameterCategory category:categories) {
+			// Insert category record into RDF model
+
+			Resource subject = categorySubject(model, category) ;
+			
+			CCO.Vocabulary.set(model, subject, CCO.Vocabulary.CATEGORY, "Plant") ;
+			subject.addProperty(SKOS.broader, CCO.TraitCategory) ;
+			
+			Map<String,String> vernacularNameMap = category.getLocalNameMap() ;
+			for(String language:vernacularNameMap.keySet()) {
+				Literal vernacularNameLiteral = 
+						model.createLiteral(vernacularNameMap.get(language), language) ;
+				subject.addLiteral(SKOS.prefLabel, vernacularNameLiteral) ;
+			}
+		}
 	}
 
 	/**
@@ -100,22 +137,8 @@ public class DescriptorControllerRdf extends RdfBaseController {
 		
 		Model model = startModel() ;		
 		
-		List<ParameterCategory> categories = traitService.listCategories() ;
-		for(ParameterCategory category:categories) {
-			// Insert category record into RDF model
-
-			Resource subject = createSubject(model, category, CCO.getURI(), category.getName()) ;
-			
-			CCO.Vocabulary.set(model, subject, CCO.Vocabulary.CATEGORY, "Plant") ;
-			subject.addProperty(SKOS.broader, CCO.TraitCategory) ;
-			
-			Map<String,String> vernacularNameMap = category.getLocalNameMap() ;
-			for(String language:vernacularNameMap.keySet()) {
-				Literal vernacularNameLiteral = 
-						model.createLiteral(vernacularNameMap.get(language), language) ;
-				subject.addLiteral(SKOS.prefLabel, vernacularNameLiteral) ;
-			}
-		}
+		wrapCategories(model) ;
+		
  		return endModel(model) ;
 	}
 	
@@ -140,7 +163,7 @@ public class DescriptorControllerRdf extends RdfBaseController {
 	 * Creates and annotates a Method subject
 	 */
 	private Resource traitSubject(Model model, Parameter trait) {
-		return createProperty(model, trait, TRAIT_NS, trait.getTitle() ) ;
+		return createProperty(model, trait, DESCRIPTOR_NS+trait.getId(), trait.getTitle() ) ;
 	}
 	
 	/*
@@ -209,7 +232,7 @@ public class DescriptorControllerRdf extends RdfBaseController {
 	 */
 	@RequestMapping("/{traitId}")
 	public @ResponseBody
-	Object dumpTrait(@PathVariable long traitId) {
+	Object dumpTrait(@PathVariable long traitId, HttpServletResponse response) {
 		
 		Parameter trait = traitService.getTrait(traitId);
 		
@@ -221,6 +244,8 @@ public class DescriptorControllerRdf extends RdfBaseController {
 		
 		wrapTrait(model, trait) ;
 		
+		response.setDateHeader("Last-Modified", trait.getLastModifiedDate().getTime());
+
 		return endModel(model);
 	}
 	
@@ -313,8 +338,19 @@ public class DescriptorControllerRdf extends RdfBaseController {
 	private Resource[] traitAndMethodSubjects(Model model, Parameter trait, Method method) {
 		Resource[] subjects = new Resource[3] ;
 		subjects[0] = traitSubject(model, trait) ;
-		subjects[1] = createProperty(model, method, METHOD_NS, trait.getTitle()+" Method" ) ;
-		subjects[2] = createProperty(model, method, SCALE_NS,  trait.getTitle()+" Scale" ) ;
+		subjects[1] = createProperty(
+				model, 
+				method, 
+				DESCRIPTOR_NS+trait.getId()+"/"+method.getId(), 
+				trait.getTitle()+" Method" 
+		) ;
+		subjects[2] = createProperty(
+				model, 
+				method, 
+				/* not sure if this is a complete enough specification for a Scale URI...*/
+				SCALE_NS+trait.getId()+"/"+method.getId(),  
+				trait.getTitle()+" Scale" 
+		) ;
 		return subjects ;
 	}
 	
@@ -441,7 +477,14 @@ public class DescriptorControllerRdf extends RdfBaseController {
 			Resource scaleSubj, Resource scaleVocabulary, String units
 		) {
 		
-		Resource scaleValuesSubj = createProperty(model, method, SCALE_NS,  trait.getTitle()+" Scale Values", true) ;
+		Resource scaleValuesSubj = 
+				createProperty(
+						model, 
+						method, 
+						SCALE_NS+trait.getId()+"/"+method.getId(),  
+						trait.getTitle()+" Scale Values", 
+						true  // is a SKOS Collection...
+		) ;
 		scaleSubj.addProperty( CCO.scaleType, "Nominal" ) ;
 		scaleSubj.addProperty( CCO.scaleUnit, scaleValuesSubj ) ;
 		scaleValuesSubj.addProperty(SKOS.inScheme, scaleVocabulary ) ;
@@ -452,7 +495,13 @@ public class DescriptorControllerRdf extends RdfBaseController {
 		Map<String, String> codeMap = TraitCode.parseCodeMap(options);
 		int n = 1 ;
 		for(String code : codeMap.keySet()) {
-			Resource valueSubj = createProperty(model, method, SCALE_NS,  trait.getTitle()+" Scale Value"+n) ;
+			Resource valueSubj = 
+					createProperty(
+							model, 
+							method, 
+							SCALE_NS+trait.getId()+"/"+method.getId()+"/"+n,  
+							trait.getTitle()+" Scale Value"+n
+			) ;
 			scaleValuesSubj.addProperty( SKOS.member, valueSubj ) ;
 			valueSubj.addProperty( SKOS.broader, scaleSubj ) ;
 			valueSubj.addProperty(SKOS.inScheme, scaleVocabulary ) ;
@@ -483,7 +532,6 @@ public class DescriptorControllerRdf extends RdfBaseController {
 			Parameter trait = method.getParameter() ;
 			wrapMethod(model, trait, method) ;
 		}
-		
  		return endModel(model) ;
 	}
 
@@ -497,7 +545,7 @@ public class DescriptorControllerRdf extends RdfBaseController {
 	 */
 	@RequestMapping("/{traitId}/{methodId}")
 	public @ResponseBody
-	Object dumpMethod( @PathVariable long traitId, @PathVariable long methodId) {
+	Object dumpMethod( @PathVariable long traitId, @PathVariable long methodId, HttpServletResponse response) {
 		
 		Parameter trait = traitService.getTrait(traitId);
 		
@@ -520,6 +568,8 @@ public class DescriptorControllerRdf extends RdfBaseController {
 		wrapTrait(model, trait) ;
 		wrapMethod(model, trait, method) ;
 
+		response.setDateHeader("Last-Modified", method.getLastModifiedDate().getTime());
+
 		return endModel(model);
 		
 	}

src/main/java/org/genesys2/server/servlet/controller/rdf/RdfBaseController.java

@@ -22,6 +22,7 @@ import java.io.UnsupportedEncodingException;
 import java.util.Date;
 
 import org.springframework.beans.factory.annotation.Autowired;