Substantially complete RDF dumping of Trait ("Parameter"),

ParameterCategory and Method (w/ Scale) meta-data.  Considerable
progress on Crop RDF dump (to complete manana).

src/main/java/org/genesys2/server/model/genesys/Method.java

@@ -17,7 +17,10 @@
 package org.genesys2.server.model.genesys;
 
 import java.io.IOException;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.Locale;
+import java.util.Map;
 import java.util.UUID;
 
 import javax.persistence.Column;
@@ -91,11 +94,7 @@ public class Method extends GlobalVersionedAuditedModel implements AclAwareModel
 		return this.method;
 	}
 
-	public String getMethod(Locale locale) {
-		return getMethodLocal(locale);
-	}
-
-	private synchronized String getMethodLocal(Locale locale) {
+	private synchronized void parseMethodLocal() {
 		if (this.methodJ == null && this.i18n != null) {
 			ObjectMapper mapper = new ObjectMapper();
 			try {
@@ -104,6 +103,38 @@ public class Method extends GlobalVersionedAuditedModel implements AclAwareModel
 				e.printStackTrace();
 			}
 		}
+	}
+	
+	@Transient
+	private Map<String,String> methodMap = new HashMap<String,String>();
+	
+	/**
+	 * Method to return the map of available languages keys
+	 * @return Map<String,String> with language code as the key and the vernacular string as the value.
+	 */
+	public Map<String,String> getLocalMethodMap() {
+		return buildLocalMethodMap() ;
+	}
+		
+	private synchronized Map<String,String> buildLocalMethodMap() {
+
+		if (this.methodMap.isEmpty() && this.i18n != null) {		
+			parseMethodLocal() ;
+			Iterator<String> languages = this.methodJ.fieldNames() ;
+			while(languages.hasNext()) {
+				String language = languages.next() ;
+				methodMap.put(language, this.methodJ.get(language).textValue()) ;
+			}
+		}
+		return methodMap ;
+	}
+	
+	public String getMethod(Locale locale) {
+		return getMethodLocal(locale);
+	}
+
+	private synchronized String getMethodLocal(Locale locale) {
+		parseMethodLocal() ;
 		return this.methodJ != null && this.methodJ.has(locale.getLanguage()) ? this.methodJ.get(locale.getLanguage()).textValue() : this.method;
 	}
 

src/main/java/org/genesys2/server/service/CropService.java

@@ -30,6 +30,8 @@ public interface CropService {
 
 	Crop getCrop(String shortName);
 
+	List<Crop> listCrops();
+
 	List<Crop> list(Locale locale);
 
 	List<Crop> getCrops(Taxonomy taxonomy);

src/main/java/org/genesys2/server/service/TraitService.java

@@ -34,10 +34,10 @@ public interface TraitService {
 
 	Page<Parameter> listTraits(Crop crop, Pageable pageable);
 
-	Parameter getTrait(long traitId);
-
 	List<Parameter> listTraits();
 
+	Parameter getTrait(long traitId);
+
 	List<Method> getTraitMethods(Parameter trait);
 
 	Method getMethod(long traitId);
@@ -46,6 +46,8 @@ public interface TraitService {
 
 	Page<Method> listMethods(Pageable pageable);
 
+	List<Method> listMethods();
+
 	/**
 	 * Add new crop descriptor Property Category
 	 * 

src/main/java/org/genesys2/server/service/impl/CropServiceImpl.java

@@ -69,6 +69,12 @@ public class CropServiceImpl implements CropService {
 		return cropRepository.findByShortName(shortName);
 	}
 
+
+	@Override
+	public List<Crop> listCrops() {
+		return cropRepository.findAll();
+	}
+	
 	@Override
 	public List<Crop> list(final Locale locale) {
 		List<Crop> crops = cropRepository.findAll();
@@ -275,4 +281,5 @@ public class CropServiceImpl implements CropService {
 	public List<CropRule> getCropRules(Crop crop) {
 		return crop == null ? null : cropRuleRepository.findByCrop(crop);
 	}
+
 }

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -410,6 +410,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	public List<Parameter> listTraits() {
 		return parameterRepository.findAll(new Sort(new Order(Direction.ASC, "id")));
 	}
+	
 	@Override
 	public Page<Parameter> listTraits(Pageable pageable) {
 		return parameterRepository.findAll(pageable);
@@ -435,6 +436,11 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		return methodRepository.findOne(methodId);
 	}
 
+	@Override
+	public List<Method> listMethods() {
+		return methodRepository.findAll(new Sort(new Order(Direction.ASC, "id")));
+	}
+	
 	@Override
 	public Page<Method> listMethods(Pageable pageable) {
 		return methodRepository.findAll(pageable);

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

+/**
+ * Copyright 2014 Global Crop Diversity Trust
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
+package org.genesys2.server.servlet.controller.rdf;
+
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Controller;
+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 com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.service.CropService;
+import org.genesys2.spring.ResourceNotFoundException;
+import org.bioversityinternational.model.germplasm.CCO;
+import org.bioversityinternational.model.rdf.dwc.DarwinCore;
+
+@Controller
+@RequestMapping(value = "/crops", method = RequestMethod.GET, headers = "accept=text/turtle", produces = RdfBaseController.RDF_MEDIATYPE_TURTLE)
+public class CropControllerRdf extends RdfBaseController {
+
+	@Autowired
+	private CropService cropService;
+
+	/*
+	 * Method generates RDF for one crop record as RDF.
+	 * 
+	 * Crop RDF exemplar:
+	 * 
+ 		cco:MusaTaxon a dwc:Taxon, skos:Collection;
+			dwc:scientificName "Musa" ;
+			dwc:vernacularName "Musa"@en ;
+			dwc:vernacularName "Musa"@es ;
+			dwc:vernacularName "Муса"@ru ;
+			dwc:vernacularName "穆萨" @zh ;
+			dc:description "Bananas and plantains"@en ;
+			dc:description "Los bananos y plátanos"@es ;
+			dc:description "Бананы и бананы"@ru ;
+			dc:description "香蕉和大蕉"@zh ;
+			dc:hasVersion "Revision: 0.1" ;
+			dc:creator "Bioversity International" ;
+			skos:member cco:MusaAcuminata, cco:MusaBalbisiana
+		.
+		
+		cco:MusaAcuminata a cco:Species;
+			dwc:scientificName "Musa acuminata" ;
+			dwc:genus "Musa" ;
+			dc:description "Wild progenitor of domesticated bananas."@en ;
+			dc:description "Progenitor salvaje de plátanos domesticados."@es ;
+			dc:description "Дикий прародителем домашних бананов."@ru ;
+			dc:description "香蕉驯化野生祖。"@zh ;
+			cco:speciesIncluded "true"
+		.
+	 */
+
+	private void wrapCrop(Model model, Crop crop) {
+		
+		Resource subject = createSubject(model, crop, CCO.getURI(), crop.getShortName()+" Taxon") ;
+		subject.addProperty(DarwinCore.scientificName, crop.getShortName()) ;
+
+		String seeAlso = crop.getRdfUri() ;
+		if(seeAlso!=null) 
+			subject.addProperty(
+					RDFS.seeAlso,
+					model.createResource(seeAlso)
+			) ;
+
+		/*
+		 * vernacular names & descriptions in i18n
+		 * 
+		Map<String,String> vernacularNameMap = trait.getLocalNameMap() ;
+		
+		for( String language : vernacularNameMap.keySet() ) {
+			Literal vernacularNameLiteral = 
+					model.createLiteral(vernacularNameMap.get(language), language) ;
+			traitSubject.addLiteral(DarwinCore.vernacularName,vernacularNameLiteral) ;
+		}
+
+		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
+	public @ResponseBody
+	String dumpCrops() {
+
+		Model model = startModel() ;		
+		
+		List<Crop> crops = cropService.listCrops() ;
+		for(Crop crop : crops) wrapCrop( model, crop) ;
+
+ 		return endModel(model) ;
+	}
+	
+	@RequestMapping("/{shortName}")
+	public @ResponseBody
+	String dumpCrop(@PathVariable(value = "shortName") String shortName) {
+		
+		_logger.debug("Dump RDF data for crop: " + shortName);
+		
+		Model model = startModel() ;		
+
+		Crop crop = cropService.getCrop(shortName);
+		if (crop == null) {
+			throw new ResourceNotFoundException();
+		}
+		
+		wrapCrop(model,crop) ;
+
+		return endModel(model) ;
+	}
+
+}

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

@@ -35,9 +35,9 @@ import org.genesys2.server.model.VersionedAuditedModel;
 import org.genesys2.server.model.impl.User;
 import org.genesys2.server.service.UserService;
 import org.genesys2.server.servlet.controller.BaseController;
-
 import org.bioversityinternational.model.germplasm.CCO;
 import org.bioversityinternational.model.rdf.dc.DublinCore;
+import org.bioversityinternational.model.rdf.dwc.DarwinCore;
 import org.bioversityinternational.model.rdf.skos.SKOS;
 
 /**
@@ -77,6 +77,7 @@ public abstract class RdfBaseController extends BaseController {
 		model.setNsPrefix("rdfs", RDFS.getURI() );
 		model.setNsPrefix("dc", DC.getURI() );
 		model.setNsPrefix("dcterms", DublinCore.getURI() );
+		model.setNsPrefix("dwc", DarwinCore.getURI() );
 		model.setNsPrefix("skos", SKOS.getURI() );
 		model.setNsPrefix("cco",  CCO.getURI() );
 		model.setNsPrefix("genesys",  GENESYS_BASEURI+"/" );
@@ -108,8 +109,28 @@ public abstract class RdfBaseController extends BaseController {
 	/*
 	 * Method to create a subject Resource initialized with common core annotation.
 	 */
-	private Resource createResource(Model model, VersionedAuditedModel entity, String uri, String id, Boolean isProperty) {
-		
+	
+	// Same as following method but defaults to SKOS.Concept ...
+	private Resource createResource(
+			Model model, 
+			VersionedAuditedModel entity, 
+			String uri, 
+			String id, 
+			Boolean isProperty
+		) {
+		return createResource( model, entity, uri, id, isProperty, false ) ;
+	}
+
+	// This version checks a flag for SKOS:Collection status
+	private Resource createResource(
+				Model model, 
+				VersionedAuditedModel entity, 
+				String uri, 
+				String id, 
+				Boolean isProperty,
+				Boolean isCollection  // SKOS type - true if isa SKOS:Collection
+			) {
+			
 		if(isProperty)
 			id= TitleCase(id,false) ; 
 		else
@@ -120,7 +141,10 @@ public abstract class RdfBaseController extends BaseController {
 		Resource subject = model.createResource(uri) ;
 		
 		subject.addProperty(DC.publisher,GCDT) ;
-		subject.addProperty(RDF.type, SKOS.Concept) ;
+		if(isCollection) 
+			subject.addProperty(RDF.type, SKOS.Collection) ;
+		else
+			subject.addProperty(RDF.type, SKOS.Concept) ;
 		
 		// dc:creator <user>
 		long userId = entity.getCreatedBy() ;
@@ -145,7 +169,7 @@ public abstract class RdfBaseController extends BaseController {
 		return subject ;
 	}
 	
-	/*
+	/**
 	 * Method to create a Subject Resource initialized with common core annotation.
 	 */
 	protected Resource createSubject(Model model, VersionedAuditedModel entity, String uri, String id) {
@@ -153,7 +177,7 @@ public abstract class RdfBaseController extends BaseController {
 		
 	}
 	
-	/*
+	/**
 	 * Method to create a Property Resource initialized with common core annotation.
 	 */
 	protected Resource createProperty(Model model, VersionedAuditedModel entity, String uri, String id) {
@@ -161,6 +185,15 @@ public abstract class RdfBaseController extends BaseController {
 		
 	}
 	
+	/**
+	 * Method to create a Property Resource initialized with common core annotation.
+	 * This version checks if the Resource is meant to be a SKOS Collection
+	 */
+	protected Resource createProperty(Model model, VersionedAuditedModel entity, String uri, String id, Boolean isCollection) {
+		return createResource(model, entity, uri, id, true, isCollection) ;
+		
+	}
+	
 	/*
 	 * Method to create an Object Resource initialized with common core annotation.
 	 */