package org.molgenis.fair.controller;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Model;
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.impl.LinkedHashModel;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.molgenis.data.Entity;
import org.molgenis.data.meta.model.Attribute;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.semantic.LabeledResource;
import org.molgenis.data.semantic.Relation;
import org.molgenis.data.semanticsearch.service.TagService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import javax.xml.datatype.DatatypeConfigurationException;
import static com.google.common.collect.Iterables.contains;
import static java.util.Arrays.stream;
import static java.util.Objects.requireNonNull;
@Component
public class EntityModelWriter
{
private static final String KEYWORD = "http://www.w3.org/ns/dcat#keyword";
private final SimpleValueFactory valueFactory;
private final TagService<LabeledResource, LabeledResource> tagService;
@Autowired
public EntityModelWriter(TagService<LabeledResource, LabeledResource> tagService, SimpleValueFactory valueFactory)
throws DatatypeConfigurationException
{
this.valueFactory = requireNonNull(valueFactory);
this.tagService = requireNonNull(tagService);
}
private void setNamespacePrefixes(Model model)
{
model.setNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
model.setNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
model.setNamespace("dcat", "http://www.w3.org/ns/dcat#");
model.setNamespace("xsd", "http://www.w3.org/2001/XMLSchema#");
model.setNamespace("owl", "http://www.w3.org/2002/07/owl#");
model.setNamespace("dct", "http://purl.org/dc/terms/");
model.setNamespace("lang", "http://id.loc.gov/vocabulary/iso639-1/");
model.setNamespace("fdpo", "http://rdf.biosemantics.org/ontologies/fdp-o#");
model.setNamespace("ldp", "http://www.w3.org/ns/ldp#");
model.setNamespace("foaf", "http://xmlns.com/foaf/0.1/");
model.setNamespace("orcid", "http://orcid.org/");
}
public Model createRdfModel(String subjectIRI, Entity objectEntity)
{
Resource subject = valueFactory.createIRI(subjectIRI);
Model model = new LinkedHashModel();
setNamespacePrefixes(model);
EntityType entityType = objectEntity.getEntityType();
for (Attribute objectAttribute : entityType.getAtomicAttributes())
{
Object value = objectEntity.get(objectAttribute.getName());
if (value == null)
{
continue;
}
for (LabeledResource tag : tagService.getTagsForAttribute(entityType, objectAttribute)
.get(Relation.isAssociatedWith))
{
IRI predicate = valueFactory.createIRI(tag.getIri());
addRelationForAttribute(model, subject, predicate, objectEntity, objectAttribute);
}
}
return model;
}
private void addRelationForAttribute(Model model, Resource subject, IRI predicate, Entity objectEntity,
Attribute objectAttribute)
{
String name = objectAttribute.getName();
switch (objectAttribute.getDataType())
{
case MREF:
case CATEGORICAL_MREF:
addRelationForMrefTypeAttribute(model, subject, predicate, objectEntity.getEntities(name));
break;
case BOOL:
model.add(subject, predicate, valueFactory.createLiteral(objectEntity.getBoolean(name)));
break;
case DATE:
case DATE_TIME:
model.add(subject, predicate, valueFactory.createLiteral(objectEntity.getUtilDate(name)));
break;
case DECIMAL:
model.add(subject, predicate, valueFactory.createLiteral(objectEntity.getDouble(name)));
break;
case LONG:
model.add(subject, predicate, valueFactory.createLiteral(objectEntity.getLong(name)));
break;
case INT:
model.add(subject, predicate, valueFactory.createLiteral(objectEntity.getInt(name)));
break;
case ENUM:
case EMAIL:
case HTML:
case TEXT:
case SCRIPT:
case STRING:
addRelationForStringTypeAttribute(model, subject, predicate, objectEntity.getString(name));
break;
case HYPERLINK:
model.add(subject, predicate, valueFactory.createIRI(objectEntity.getString(name)));
break;
case XREF:
case CATEGORICAL:
case FILE:
addRelationForXrefTypeAttribute(model, subject, predicate, objectEntity.getEntity(name));
break;
default:
throw new RuntimeException("DataType " + objectAttribute.getDataType() + "is not supported");
}
}
private void addRelationForXrefTypeAttribute(Model model, Resource subject, IRI predicate, Entity objectEntity)
{
if (contains(objectEntity.getEntityType().getAttributeNames(), "IRI"))
{
model.add(subject, predicate, valueFactory.createIRI(objectEntity.getString("IRI")));
}
else
{
model.add(subject, predicate,
valueFactory.createIRI(subject.stringValue() + '/' + objectEntity.getIdValue()));
}
}
private void addRelationForStringTypeAttribute(Model model, Resource subject, IRI predicate, String value)
{
if (predicate.stringValue().equals(KEYWORD))
{
stream(value.split(",")).map(String::trim)
.forEach(keyword -> model.add(subject, predicate, valueFactory.createLiteral(keyword)));
}
else
{
model.add(subject, predicate, valueFactory.createLiteral(value));
}
}
private void addRelationForMrefTypeAttribute(Model model, Resource subject, IRI predicate,
Iterable<Entity> objectEntities)
{
for (Entity objectEntity : objectEntities)
{
model.add(subject, predicate,
valueFactory.createIRI(subject.stringValue() + '/' + objectEntity.getIdValue()));
}
}
}