/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.tools.rdf;
import static org.openbel.framework.common.BELUtilities.hasItems;
import static org.openbel.framework.common.BELUtilities.nulls;
import static org.openbel.framework.tools.rdf.KAMVocabulary.AnnotationDefinition;
import static org.openbel.framework.tools.rdf.KAMVocabulary.BelDocument;
import static org.openbel.framework.tools.rdf.KAMVocabulary.KAM;
import static org.openbel.framework.tools.rdf.KAMVocabulary.KAMEdge;
import static org.openbel.framework.tools.rdf.KAMVocabulary.KAMNode;
import static org.openbel.framework.tools.rdf.KAMVocabulary.Namespace;
import static org.openbel.framework.tools.rdf.KAMVocabulary.Parameter;
import static org.openbel.framework.tools.rdf.KAMVocabulary.Statement;
import static org.openbel.framework.tools.rdf.KAMVocabulary.Term;
import static org.openbel.framework.tools.rdf.KAMVocabulary.composedOf;
import static org.openbel.framework.tools.rdf.KAMVocabulary.definedBy;
import static org.openbel.framework.tools.rdf.KAMVocabulary.defines;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasAnnotation;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasArguments;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasAuthor;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasContactInfo;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasCopyright;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasDescription;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasDisclaimer;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasFunction;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasId;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasLabel;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasLicense;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasList;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasName;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasNamespace;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasObjectNode;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasObjectTerm;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasPattern;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasPrefix;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasRelationship;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasResourceLocation;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasSubjectNode;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasSubjectTerm;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasType;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasURL;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasUsage;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasValue;
import static org.openbel.framework.tools.rdf.KAMVocabulary.hasVersion;
import static org.openbel.framework.tools.rdf.KAMVocabulary.isRepresentedBy;
import static org.openbel.framework.tools.rdf.KAMVocabulary.resourceForFunction;
import static org.openbel.framework.tools.rdf.KAMVocabulary.resourceForRelationship;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import org.openbel.framework.api.Kam;
import org.openbel.framework.api.Kam.KamEdge;
import org.openbel.framework.api.Kam.KamNode;
import org.openbel.framework.api.internal.KAMCatalogDao.KamInfo;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.Annotation;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.AnnotationType;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.BelDocumentInfo;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.BelStatement;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.Namespace;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.TermParameter;
import org.openbel.framework.api.KAMStore;
import org.openbel.framework.api.KAMStoreException;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.enums.FunctionEnum;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.AnonId;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFList;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.RDF;
/**
* RDFExporter builds an RDF object model from the KAM data using the
* Jena framework and then serializes it to RDF in N3 format.
*
* Data left to capture:
* TODO Support nested terms in a Term's arguments. Currently only support Parameter resources.
* TODO Support nested statement as a statement's object. Currently only support object Term.
*
* @see <a href="http://jena.sourceforge.net/">http://jena.sourceforge.net/</a>
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public final class RDFExporter {
/**
* Jena format {@link String} for N3 notation.
*/
private static final String N3_FORMAT = "N3";
private static final InputStream kvis;
static {
kvis = RDFExporter.class.getResourceAsStream("kam.rdf");
}
/**
* Private constructor to prevent instantiation.
*/
private RDFExporter() {
}
/**
* Exports an rdf {@link Model} from the KAM data.
*
* @param kam {@link Kam} the kam, which cannot be null
* @param kamInfo {@link KamInfo} the kam info, which cannot be null
* @param kAMStore {@link KAMStore} the kamstore, which cannot be null
* @param outPath {@link String} the output path to write XGMML file to,
* which can be null, in which case the kam's name will be used and it will
* be written to the current directory (user.dir).
* @throws IOException Thrown if an IO error occurred while writing the RDF
* @throws KAMStoreException Thrown if an error occurred pulling data from
* the kam store
* @throws InvalidArgument Thrown if either the kam, kamInfo, kamStore, or
* outputPath arguments were null
*/
public static void exportRdf(final Kam kam, KamInfo kamInfo,
final KAMStore kAMStore,
String outputPath) throws IOException, InvalidArgument,
KAMStoreException {
if (nulls(kam, kamInfo, kAMStore, outputPath)) {
throw new InvalidArgument("argument(s) were null");
}
// create new ontology model and read in KAM Vocabulary model
OntModel model = ModelFactory.createOntologyModel();
model.read(kvis, null, "RDF/XML");
// add kam resource
Resource kamResource =
model.createResource(new AnonId(UUID.randomUUID().toString()));
// kam type KAM
kamResource.addProperty(RDF.type, KAM);
// kam hasName "kam"^^xsd:string
kamResource.addProperty(hasName,
model.createTypedLiteral(kamInfo.getName()));
// kam hasDescription "kam"^^xsd:string
kamResource.addProperty(hasDescription,
model.createTypedLiteral(kamInfo.getDescription()));
Map<Integer, Resource> documents = new HashMap<Integer, Resource>();
Map<Integer, Resource> annotationDefinitions =
new HashMap<Integer, Resource>();
Map<Integer, Resource> annotations = new HashMap<Integer, Resource>();
List<BelDocumentInfo> docs = kAMStore.getBelDocumentInfos(kamInfo);
for (BelDocumentInfo doc : docs) {
Resource docResource =
model.createResource(new AnonId(UUID.randomUUID()
.toString()));
docResource.addProperty(RDF.type, BelDocument);
// handle document fields
if (doc.getAuthors() != null) {
docResource.addProperty(hasAuthor,
model.createTypedLiteral(doc.getAuthors()));
}
if (doc.getContactInfo() != null) {
docResource.addProperty(hasContactInfo,
model.createTypedLiteral(doc.getContactInfo()));
}
if (doc.getCopyright() != null) {
docResource.addProperty(hasCopyright,
model.createTypedLiteral(doc.getCopyright()));
}
if (doc.getDescription() != null) {
docResource.addProperty(hasDescription,
model.createTypedLiteral(doc.getDescription()));
}
if (doc.getDisclaimer() != null) {
docResource.addProperty(hasDisclaimer,
model.createTypedLiteral(doc.getDisclaimer()));
}
if (doc.getLicenseInfo() != null) {
docResource.addProperty(hasLicense,
model.createTypedLiteral(doc.getLicenseInfo()));
}
if (doc.getName() != null) {
docResource.addProperty(hasName,
model.createTypedLiteral(doc.getName()));
}
if (doc.getVersion() != null) {
docResource.addProperty(hasVersion,
model.createTypedLiteral(doc.getVersion()));
}
List<Namespace> namespaces = doc.getNamespaces();
for (Namespace namespace : namespaces) {
// add namespace resource by it's URL
Resource namespaceResource = model.createResource(namespace
.getResourceLocation());
namespaceResource.addProperty(RDF.type, Namespace);
// associate prefix and resource location
namespaceResource.addProperty(hasPrefix,
model.createTypedLiteral(namespace.getPrefix()));
namespaceResource.addProperty(hasResourceLocation,
model.createTypedLiteral(namespace
.getResourceLocation()));
// associate document with namespace as a defines relationship
docResource.addProperty(defines, namespaceResource);
}
List<AnnotationType> annotationTypes = doc.getAnnotationTypes();
for (AnnotationType annotationType : annotationTypes) {
final Resource annotationDefResource;
switch (annotationType.getAnnotationDefinitionType()) {
case ENUMERATION:
annotationDefResource =
model
.createResource(new AnonId(UUID
.randomUUID().toString()));
// associate metadata of annotation type
annotationDefResource.addProperty(hasName,
model.createTypedLiteral(annotationType.getName()));
if (StringUtils.isNotBlank(annotationType.getDescription())) {
annotationDefResource.addProperty(hasDescription, model
.createTypedLiteral(annotationType
.getDescription()));
}
annotationDefResource.addProperty(hasType, model
.createTypedLiteral(annotationType
.getAnnotationDefinitionType()
.getDisplayValue()));
if (StringUtils.isNotBlank(annotationType.getDescription())) {
annotationDefResource.addProperty(hasUsage, model
.createTypedLiteral(annotationType.getUsage()));
}
// read list domain for internal list annotation
List<String> domain =
kAMStore.getAnnotationTypeDomainValues(kamInfo,
annotationType);
if (hasItems(domain)) {
RDFList enumres = model.createList();
enumres.setStrict(true);
// iterate domain to pre-build RDF resources and associate domain value
Resource[] itemResources = new Resource[domain.size()];
String[] domainValues =
domain.toArray(new String[domain.size()]);
for (int i = 0; i < domainValues.length; i++) {
itemResources[i] = model
.createResource(new AnonId(UUID
.randomUUID().toString()));
itemResources[i].addProperty(RDF.type, RDF.List);
itemResources[i].addProperty(RDF.first,
model.createTypedLiteral(domainValues[i]));
}
// iterate item resources to link them
for (int i = 0; i < itemResources.length; i++) {
if ((i + 1) < itemResources.length) {
// link to next domain value
itemResources[i].addProperty(RDF.rest,
itemResources[i + 1]);
} else {
// link to RDF.nil indicating end of list
itemResources[i].addProperty(RDF.rest, RDF.nil);
}
enumres = enumres.with(itemResources[i]);
}
// associate annotation to the domain list
annotationDefResource.addProperty(hasList, enumres);
}
break;
case REGULAR_EXPRESSION:
// read list domain for internal pattern annotation
domain =
kAMStore.getAnnotationTypeDomainValues(kamInfo,
annotationType);
if (domain.size() != 1) {
throw new IllegalStateException(
"Expecting a single, Regular Expression pattern, but received: "
+ domain);
}
annotationDefResource =
model
.createResource(new AnonId(UUID
.randomUUID().toString()));
// associate metadata of annotation type
annotationDefResource.addProperty(hasName,
model.createTypedLiteral(annotationType.getName()));
annotationDefResource.addProperty(hasDescription,
model.createTypedLiteral(annotationType
.getDescription()));
annotationDefResource.addProperty(hasType, model
.createTypedLiteral(annotationType
.getAnnotationDefinitionType()
.getDisplayValue()));
annotationDefResource
.addProperty(hasUsage, model
.createTypedLiteral(annotationType
.getUsage()));
String patternDomain = domain.get(0);
// associate annotation to the domain pattern
annotationDefResource.addProperty(hasPattern,
model.createTypedLiteral(patternDomain));
break;
case URL:
if (annotationType.getUrl() == null) {
throw new IllegalStateException(
"Expecting non-null URL for external annotation");
}
// associate annotation to the URL where the domain is defined
annotationDefResource =
model.createResource(annotationType.getUrl());
annotationDefResource.addProperty(hasName,
model.createTypedLiteral(annotationType.getName()));
annotationDefResource.addProperty(hasURL,
model.createTypedLiteral(annotationType.getUrl()));
break;
default:
throw new UnsupportedOperationException(
"Annotation definition type not supported: "
+ annotationType
.getAnnotationDefinitionType());
}
annotationDefResource.addProperty(RDF.type,
AnnotationDefinition);
// associate document with annotation definition as a defines relationship
docResource.addProperty(defines, annotationDefResource);
annotationDefinitions.put(annotationType.getId(),
annotationDefResource);
}
kamResource.addProperty(composedOf, docResource);
documents.put(doc.getId(), docResource);
}
Map<KamNode, Resource> kamNodeResources =
new HashMap<Kam.KamNode, Resource>();
Map<Integer, Resource> termResources = new HashMap<Integer, Resource>();
// handle kam nodes first
Iterator<KamNode> kamNodes = kam.getNodes().iterator();
while (kamNodes.hasNext()) {
KamNode kamNode = kamNodes.next();
// TODO: This is a sanity check that should be removed as LIST is not a KAM function type
if (FunctionEnum.LIST == kamNode.getFunctionType()) {
System.err.println("Invalid KAM node type found: "
+ kamNode.getFunctionType().getDisplayValue());
continue;
}
Resource functionResource = model.getResource(KAMVocabulary
.resourceForFunction(kamNode.getFunctionType()).getURI());
// Retrieve seen KAMNode Resource or create a new Blank Node for it.
Resource kamNodeResource;
if (kamNodeResources.containsKey(kamNode)) {
kamNodeResource = kamNodeResources.get(kamNode);
} else {
kamNodeResource = model.createResource(new AnonId(UUID
.randomUUID().toString()));
// associate kam node with kam resource
kamResource.addProperty(composedOf, kamNodeResource);
}
// node type KAMNode
kamNodeResource.addProperty(RDF.type, KAMNode);
// node hasFunction Function
kamNodeResource.addProperty(hasFunction, functionResource);
// node hasId "1"^^xsd:int
kamNodeResource.addLiteral(hasId,
model.createTypedLiteral(kamNode.getId()));
// node hasLabel "p(EG:207)"^^xsd:string
kamNodeResource.addLiteral(hasLabel,
model.createTypedLiteral(kamNode.getLabel()));
// hold on to kam node resources
kamNodeResources.put(kamNode, kamNodeResource);
// handle terms for this KAMNode
// TODO Support nested terms instead of just Parameters!
List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
for (BelTerm term : terms) {
Resource termResource = model.createResource(new AnonId(UUID
.randomUUID().toString()));
termResource.addProperty(RDF.type, Term);
termResource.addProperty(hasId,
model.createTypedLiteral(term.getId()));
termResource.addProperty(hasLabel,
model.createTypedLiteral(term.getLabel()));
termResource.addProperty(hasFunction,
resourceForFunction(kamNode.getFunctionType()));
RDFList argumentres = model.createList();
List<TermParameter> termParameters =
kAMStore.getTermParameters(kamInfo, term);
TermParameter[] tparray = termParameters
.toArray(new TermParameter[termParameters.size()]);
Resource[] tpresarray = new Resource[tparray.length];
// iterate term parameters to pre-build RDF resources and associate Parameter
for (int i = 0; i < tparray.length; i++) {
tpresarray[i] = model.createResource(new AnonId(UUID
.randomUUID().toString()));
tpresarray[i].addProperty(RDF.type, RDF.List);
Resource parameterResource =
model
.createResource(new AnonId(UUID
.randomUUID().toString()));
parameterResource.addProperty(RDF.type, Parameter);
parameterResource
.addProperty(hasValue, model
.createTypedLiteral(tparray[i]
.getParameterValue()));
if (tparray[i].getNamespace() != null) {
parameterResource.addProperty(hasNamespace, model
.getResource(tparray[i].getNamespace()
.getResourceLocation()));
}
tpresarray[i].addProperty(RDF.first, parameterResource);
}
// iterate argument resources to link them
for (int i = 0; i < tpresarray.length; i++) {
if ((i + 1) < tpresarray.length) {
// link to next term argument
tpresarray[i].addProperty(RDF.rest, tpresarray[i + 1]);
} else {
// link to RDF.nil indicating end of list
tpresarray[i].addProperty(RDF.rest, RDF.nil);
}
argumentres = argumentres.with(tpresarray[i]);
}
// associate term resource to the arguments list
termResource.addProperty(hasArguments, argumentres);
// node is represented by the term
kamNodeResource.addProperty(isRepresentedBy, termResource);
// hold on to term resources
termResources.put(term.getId(), termResource);
}
}
// handle kam edges second
Iterator<KamEdge> kamEdges = kam.getEdges().iterator();
while (kamEdges.hasNext()) {
KamEdge kamEdge = kamEdges.next();
Resource relationshipResource =
KAMVocabulary.resourceForRelationship(kamEdge
.getRelationshipType());
Resource kamEdgeResource =
model.createResource(new AnonId(UUID.randomUUID()
.toString()));
// associate kam edge with kam resource
kamResource.addProperty(composedOf, kamEdgeResource);
// edge type KAMEdge
kamEdgeResource.addProperty(RDF.type, KAMEdge);
// edge hasRelationship Relationship
kamEdgeResource.addProperty(hasRelationship, relationshipResource);
// edge hasId "1"^^xsd:int
kamEdgeResource.addLiteral(hasId,
model.createTypedLiteral(kamEdge.getId()));
Resource sourceResource =
kamNodeResources.get(kamEdge.getSourceNode());
Resource targetResource =
kamNodeResources.get(kamEdge.getTargetNode());
// TODO: This is a sanity check that should be removed
if (null == sourceResource || null == targetResource) {
System.err
.println("Can't locate source or target node resource for edge: "
+ kamEdge.toString());
continue;
}
// edge hasSubjectNode KAMNode
kamEdgeResource.addProperty(hasSubjectNode, sourceResource);
// edge hasObjectNode KAMNode
kamEdgeResource.addProperty(hasObjectNode, targetResource);
// TODO Handle object statements
// TODO Handle statement annotation associations
List<BelStatement> statements =
kAMStore.getSupportingEvidence(kamEdge);
for (BelStatement statement : statements) {
if (null == statement.getObject()) {
continue;
}
if (!BelTerm.class.isAssignableFrom(statement.getObject()
.getClass())) {
continue;
}
Resource statementResource =
model.createResource(new AnonId(UUID.randomUUID()
.toString()));
statementResource.addProperty(RDF.type, Statement);
statementResource.addProperty(hasId,
model.createTypedLiteral(statement.getId()));
// associate statement with document
Resource docres =
documents.get(statement.getBelDocumentInfo().getId());
docres.addProperty(defines, statementResource);
Resource subjectTermResource =
termResources.get(statement.getSubject().getId());
if (subjectTermResource == null) {
throw new IllegalStateException(
"subject term for statement is not known.");
}
statementResource.addProperty(hasSubjectTerm,
subjectTermResource);
if (statement.getObject() != null) {
Resource objectTermResource =
termResources.get(statement.getObject().getId());
if (objectTermResource == null) {
throw new IllegalStateException(
"object term for statement is not known.");
}
// associate to relationship and object term
statementResource.addProperty(hasRelationship,
resourceForRelationship(statement
.getRelationshipType()));
statementResource.addProperty(hasObjectTerm,
objectTermResource);
// associate edge to this subject,rel,object statement
kamEdgeResource.addProperty(isRepresentedBy,
statementResource);
}
// associate annotations to statement
List<Annotation> statementAnnotations =
statement.getAnnotationList();
for (Annotation statementAnnotation : statementAnnotations) {
Resource ares =
annotations.get(statementAnnotation.getId());
if (ares == null) {
ares =
model.createResource(new AnonId(UUID
.randomUUID().toString()));
annotations.put(statementAnnotation.getId(), ares);
}
// associate annotation value to annotation
ares.addProperty(hasValue, model
.createTypedLiteral(statementAnnotation.getValue()));
Integer adefId =
statementAnnotation.getAnnotationType().getId();
Resource adefResource = annotationDefinitions.get(adefId);
// associate annotation with the annotation definition it is defined by
ares.addProperty(definedBy, adefResource);
// associate statement with its annotation
statementResource.addProperty(hasAnnotation, ares);
}
}
}
model.write(new FileWriter(outputPath), N3_FORMAT);
}
}