Skip to content
GitLab
Commit 0a7b4ecf authored by Matija Obreza's avatar Matija Obreza
Browse files

RDF crop, descriptor controllers updated for production

parent 04980747
Expand all Hide whitespace changes
Inline Side-by-side
pom.xml
View file @ 0a7b4ecf
......@@ -497,9 +497,8 @@
<dependency>
<groupId>org.bioversityinternational</groupId>
<artifactId>org.bioversityinternational.ontology</artifactId>
<version>0.0.6</version>
<version>0.6.2</version>
</dependency>
</dependencies>
<build>
......
src/main/java/org/genesys2/server/servlet/controller/rdf/CropControllerRdf.java
View file @ 0a7b4ecf
......@@ -19,6 +19,12 @@ package org.genesys2.server.servlet.controller.rdf;
import java.util.List;
import java.util.Map;
import org.bioversityinternational.model.germplasm.CCO;
import org.bioversityinternational.model.rdf.dwc.DarwinCore;
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.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.PathVariable;
......@@ -33,19 +39,12 @@ import com.hp.hpl.jena.vocabulary.DC;
import com.hp.hpl.jena.vocabulary.RDF;
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;
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 {
public static final String CROPS_NS = getBaseUri()+"/crops/";;
public static final String SPECIES_NS = CROPS_NS+"species/" ;
private final String CROPS_NS = "/crops/";
private final String SPECIES_NS = CROPS_NS + "species/";
@Autowired
private CropService cropService;
......@@ -71,44 +70,41 @@ public class CropControllerRdf extends RdfBaseController {
.
*/
private void wrapCrop(Model model, Crop crop) {
Resource cropSubj = createSubject(model, crop, CROPS_NS+crop.getId(), crop.getShortName()+" Taxon") ;
cropSubj.addProperty(DarwinCore.scientificName, crop.getShortName()) ;
String seeAlso = crop.getRdfUri() ;
if(seeAlso!=null)
cropSubj.addProperty(
RDFS.seeAlso,
model.createResource(seeAlso)
) ;
Resource cropSubj = createSubject(model, crop, CROPS_NS + crop.getShortName(), crop.getShortName() + " Taxon");
// FIXME That's probably not right
cropSubj.addProperty(DarwinCore.scientificName, crop.getShortName());
String seeAlso = crop.getRdfUri();
if (seeAlso != null)
cropSubj.addProperty(RDFS.seeAlso, model.createResource(seeAlso));
/*
* vernacular names & descriptions in i18n
*/
Map<String,String> vernacularNameMap = crop.getLocalNameMap() ;
if(vernacularNameMap!=null)
for( String language : vernacularNameMap.keySet() ) {
Literal vernacularNameLiteral =
model.createLiteral(vernacularNameMap.get(language), language) ;
cropSubj.addLiteral(DarwinCore.vernacularName,vernacularNameLiteral) ;
*/
Map<String, String> vernacularNameMap = crop.getLocalNameMap();
if (vernacularNameMap != null)
for (String language : vernacularNameMap.keySet()) {
Literal vernacularNameLiteral = model.createLiteral(vernacularNameMap.get(language), language);
cropSubj.addLiteral(DarwinCore.vernacularName, vernacularNameLiteral);
}
else
this._logger.warn("Empty vernacular crop name map for crop "+crop.getShortName());
Map<String,String> vernacularDefinitionMap = crop.getLocalDefinitionMap() ;
if(vernacularDefinitionMap!=null)
for( String language : vernacularDefinitionMap.keySet() ) {
Literal vernacularDefinitionLiteral =
model.createLiteral(vernacularDefinitionMap.get(language), language) ;
cropSubj.addLiteral(DC.description,vernacularDefinitionLiteral) ;
this._logger.warn("Empty vernacular crop name map for crop " + crop.getShortName());
Map<String, String> vernacularDefinitionMap = crop.getLocalDefinitionMap();
if (vernacularDefinitionMap != null)
for (String language : vernacularDefinitionMap.keySet()) {
Literal vernacularDefinitionLiteral = model.createLiteral(vernacularDefinitionMap.get(language), language);
cropSubj.addLiteral(DC.description, vernacularDefinitionLiteral);
}
else
this._logger.warn("Empty vernacular crop description map for crop "+crop.getShortName());
this._logger.warn("Empty vernacular crop description map for crop " + crop.getShortName());
/* Exemplar for CropRule species...
/*
* Exemplar for CropRule species...
*
genesys:MusaAcuminata a cco:Species;
dwc:scientificName "Musa acuminata" ;
......@@ -122,55 +118,53 @@ public class CropControllerRdf extends RdfBaseController {
Note: current GENESYS data model does NOT track the description of a species...
*/
List<CropRule> rules = cropService.getCropRules(crop) ;
for(CropRule cr : rules) {
String species = cr.getSpecies() ;
String genus = cr.getGenus() ;
Boolean isIncluded = cr.isIncluded() ;
Resource speciesSubj =
createSubject(
model,
crop,
SPECIES_NS+canonicalID(species,true),
species
) ;
speciesSubj.addProperty(RDF.type, CCO.Species ) ;
speciesSubj.addProperty(DarwinCore.scientificName, species ) ;
speciesSubj.addProperty(DarwinCore.genus, genus ) ;
speciesSubj.addProperty(CCO.speciesIncluded, isIncluded.toString() ) ;
List<CropRule> rules = cropService.getCropRules(crop);
for (CropRule cr : rules) {
String species = cr.getSpecies();
String genus = cr.getGenus();
Boolean isIncluded = cr.isIncluded();
// FIXME in CropRule the Genus is required, species is not.
if (species != null) {
Resource speciesSubj = createSubject(model, crop, SPECIES_NS + canonicalID(species, true), species);
speciesSubj.addProperty(RDF.type, CCO.Species);
speciesSubj.addProperty(DarwinCore.scientificName, species);
speciesSubj.addProperty(DarwinCore.genus, genus);
speciesSubj.addProperty(CCO.speciesIncluded, isIncluded.toString());
}
}
}
@RequestMapping
public @ResponseBody
String dumpCrops() {
Model model = startModel() ;
List<Crop> crops = cropService.listCrops() ;
for(Crop crop : crops) wrapCrop( model, crop) ;
Model model = startModel();
List<Crop> crops = cropService.listCrops();
for (Crop crop : crops)
wrapCrop(model, crop);
return endModel(model) ;
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() ;
Model model = startModel();
Crop crop = cropService.getCrop(shortName);
if (crop == null) {
throw new ResourceNotFoundException();
}
wrapCrop(model,crop) ;
return endModel(model) ;
wrapCrop(model, crop);
return endModel(model);
}
}
src/main/java/org/genesys2/server/servlet/controller/rdf/RdfBaseController.java
View file @ 0a7b4ecf
......@@ -21,6 +21,15 @@ import java.io.PrintStream;
import java.io.UnsupportedEncodingException;
import java.util.Date;
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;
import org.genesys2.server.exception.UserException;
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.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
......@@ -31,25 +40,14 @@ import com.hp.hpl.jena.vocabulary.DC;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import org.genesys2.server.exception.UserException;
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;
/**
* Controller which simply handles RDF requests
*/
public abstract class RdfBaseController extends BaseController {
@Autowired
private UserService userService;
/**
* A String equivalent of {@link RdfBaseController#RDF_MEDIATYPE_XML}.
*/
......@@ -60,203 +58,209 @@ public abstract class RdfBaseController extends BaseController {
*/
public final static String RDF_MEDIATYPE_TURTLE = "text/turtle";
protected static final String GCDT = "Global Crop Diversity Trust" ;
protected static final String RDF_MODEL_VERSION = "Revision: 0.1" ;
// TODO: the @Value initialization with the Spring set Property base.url
// here doesn't seem to work (even if I set the variable to a non-static private
protected static final String GCDT = "Global Crop Diversity Trust";
protected static final String RDF_MODEL_VERSION = "Revision: 0.1";
@Value("${base.url}")
private static String baseUrl = "http://genesys-pgr.org" ;
protected static String getBaseUri() {
if(baseUrl==null)
throw new NullPointerException("Base URI not set in RdfBaseController?") ;
return baseUrl ;
}
private String baseUrl;
protected String getBaseUri() {
if (baseUrl == null)
throw new NullPointerException("Base URI not set in RdfBaseController?");
return baseUrl;
}
protected static String modelVersion() {
return RDF_MODEL_VERSION ;
return RDF_MODEL_VERSION;
}
/*
* Method to set up the RDF model with basic global annotation.
*/
protected Model startModel() {
Model model = ModelFactory.createDefaultModel();
model.setNsPrefix("rdf", RDF.getURI() );
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", getBaseUri()+"/" );
return model ;
model.setNsPrefix("rdf", RDF.getURI());
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", getBaseUri() + "/");
return model;
}
/**
* Generates a canonical RDF identifier from its input string
* (blanks removed, with title case or camel case words, depending
* on capitalizeFirst being true or false, respectively)
* Generates a canonical RDF identifier from its input string (blanks
* removed, with title case or camel case words, depending on
* capitalizeFirst being true or false, respectively)
*
* @param identifier
* @param capitlizeFirst - if true, then the first letter of the identifier is capitalized
* @param capitlizeFirst
* - if true, then the first letter of the identifier is
* capitalized
* @return
*/
public static String canonicalID(String identifier, Boolean capitalizeFirst) {
String[] words = identifier.split("\\s") ;
identifier = "" ;
for(String word: words) {
if(!capitalizeFirst) {
String[] words = identifier.split("\\s");
identifier = "";
for (String word : words) {
if (!capitalizeFirst) {
// only run once in the loop if false (reset to true...)
identifier += word.toLowerCase() ;
capitalizeFirst = true ;
identifier += word.toLowerCase();
capitalizeFirst = true;
} else {
identifier += word.substring(0,1).toUpperCase() ;
identifier += word.substring(1).toLowerCase() ;
identifier += word.substring(0, 1).toUpperCase();
identifier += word.substring(1).toLowerCase();
}
}
return identifier ;
return identifier;
}
/*
* Method to create a subject Resource initialized with common core annotation.
* Method to create a subject Resource initialized with common core
* annotation.
*/
// Same as following method but defaults to SKOS.Concept ...
private Resource createResource(
Model model,
VersionedAuditedModel entity,
String uri,
String tag,
Boolean isProperty
) {
return createResource( model, entity, uri, tag, isProperty, false ) ;
private Resource createResource(Model model, VersionedAuditedModel entity, String uri, String tag, Boolean isProperty) {
return createResource(model, entity, uri, tag, isProperty, false);
}
// This version checks a flag for SKOS:Collection status
private Resource createResource(
Model model,
VersionedAuditedModel entity,
String uri,
String tag,
Boolean isProperty,
Boolean isCollection // SKOS type - true if isa SKOS:Collection
) {
Resource subject = model.createResource(uri) ;
subject.addProperty(DC.publisher,GCDT) ;
if(isCollection)
subject.addProperty(RDF.type, SKOS.Collection) ;
private Resource createResource(Model model, VersionedAuditedModel entity, String uri, String tag, Boolean isProperty, Boolean isCollection // SKOS
// type
// -
// true
// if
// isa
// SKOS:Collection
) {
Resource subject = model.createResource(getBaseUri() + uri);
subject.addProperty(DC.publisher, GCDT);
if (isCollection)
subject.addProperty(RDF.type, SKOS.Collection);
else
subject.addProperty(RDF.type, SKOS.Concept) ;
subject.addProperty(RDF.type, SKOS.Concept);
if(isProperty)
tag= canonicalID(tag,false) ;
if (isProperty)
tag = canonicalID(tag, false);
else
tag = canonicalID(tag,true) ;
subject.addProperty(SKOS.hiddenLabel,tag) ;
tag = canonicalID(tag, true);
subject.addProperty(SKOS.hiddenLabel, tag);
// dc:creator <user>
long userId = entity.getCreatedBy() ;
try {
User user = userService.getUserById(userId) ;
// just put the user's name for now?
subject.addProperty(DC.creator, user.getName()) ;
} catch (UserException e) {
this._logger.debug("Invalid user access?", e);
Long userId = entity.getCreatedBy();
if (userId != null) {
try {
User user = userService.getUserById(userId);
// just put the user's name for now?
subject.addProperty(DC.creator, user.getName());
} catch (UserException e) {
this._logger.debug("Invalid user access?", e);
}
}
// dc:date <createdData>
Date createdDate = entity.getCreatedDate() ;
subject.addProperty(DC.date, createdDate.toString()) ;
Date createdDate = entity.getCreatedDate();
if (createdDate != null)
subject.addProperty(DC.date, createdDate.toString());
// dc:hasVersion <createdData>
String version = String.valueOf(entity.getVersion()) ;
subject.addProperty(DublinCore.hasVersion, version ) ;
return subject ;
String version = String.valueOf(entity.getVersion());
subject.addProperty(DublinCore.hasVersion, version);
return subject;
}
/**
* Method to create a Subject Resource initialized with common core annotation.
* Method to create a Subject Resource initialized with common core
* annotation.
*/
protected Resource createSubject(Model model, VersionedAuditedModel entity, String uri, String tag) {
return createResource(model, entity, uri, tag, false) ;
return createResource(model, entity, uri, tag, false);
}
/**
* Method to create a Property Resource initialized with common core annotation.
* Method to create a Property Resource initialized with common core
* annotation.
*/
protected Resource createProperty(Model model, VersionedAuditedModel entity, String uri, String tag) {
return createResource(model, entity, uri, tag, true) ;
return createResource(model, entity, uri, tag, true);
}
/**
* Method to create a Property Resource initialized with common core annotation.
* This version checks if the Resource is meant to be a SKOS Collection
* 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 tag, Boolean isCollection) {
return createResource(model, entity, uri, tag, true, isCollection) ;
return createResource(model, entity, uri, tag, true, isCollection);
}
/*
* Method to create an Object Resource initialized with common core annotation.
* Method to create an Object Resource initialized with common core
* annotation.
*/
protected Resource createObject(Model model, VersionedAuditedModel entity, String uri, String tag) {
return createResource(model, entity, uri, tag, false) ;
return createResource(model, entity, uri, tag, false);
}
protected void seeAlso(Model model, Resource subject, String seeAlso) {
if(seeAlso!=null)
subject.addProperty(RDFS.seeAlso,model.createResource(seeAlso)) ;
if (seeAlso != null)
subject.addProperty(RDFS.seeAlso, model.createResource(seeAlso));
}
/**
* Method to write out the model as a Turtle RDF string
*
* @param model - Apache Jena RDF Model class object of current model being rendered
* @param format Predefined values are "RDF/XML", "RDF/XML-ABBREV", "N-TRIPLE", "TURTLE", (and "TTL") and "N3".
* @param model
* - Apache Jena RDF Model class object of current model being
* rendered
* @param format
* Predefined values are "RDF/XML", "RDF/XML-ABBREV", "N-TRIPLE",
* "TURTLE", (and "TTL") and "N3".
* @return
*/
/*
* TODO: maybe convert this to an HTTP Converter (which can handle diverse RDF formats?)
* TODO: maybe convert this to an HTTP Converter (which can handle diverse
* RDF formats?)
*/
protected String endModel(Model model, String format) {
ByteArrayOutputStream os = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(os);
if(format==null)//model.write(ps, "RDF/XML-ABBREV") ;
model.write(ps, "TURTLE") ;
if (format == null)// model.write(ps, "RDF/XML-ABBREV") ;
model.write(ps, "TURTLE");
else
model.write(ps,format) ;
String output = "" ;
model.write(ps, format);
String output = "";
try {
output = os.toString("UTF8");
} catch (UnsupportedEncodingException e) {
_logger.debug("os.toString(\"UTF8\") failed while to write out parameter categories as Turtle RDF");
}
_logger.trace("RdfBaseController.endModel() returning RDF text: "+output);
return output ;
_logger.trace("RdfBaseController.endModel() returning RDF text: " + output);
return output;
}
/*
* Method to write out the model as a Turtle RDF string
* (TODO: maybe convert this to an HTTP Converter which can
* handle other RDF formats?)