/**
* 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.ws.service;
import static java.lang.String.format;
import static org.openbel.framework.common.BELUtilities.sizedArrayList;
import static org.openbel.framework.ws.utils.Converter.convert;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.openbel.framework.api.Equivalencer;
import org.openbel.framework.api.KAMStore;
import org.openbel.framework.api.Kam;
import org.openbel.framework.api.Resolver;
import org.openbel.framework.api.ResolverException;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.ws.model.Edge;
import org.openbel.framework.ws.model.KamEdge;
import org.openbel.framework.ws.model.KamNode;
import org.openbel.framework.ws.model.Namespace;
import org.openbel.framework.ws.model.NamespaceDescriptor;
import org.openbel.framework.ws.model.Node;
import org.openbel.framework.ws.model.RelationshipType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
/**
* Implements a resolver service that resolves nodes and edges to a KAM.
*
* <p>
* The namespace values do not have to exist in a specific KAM, but they must be
* discoverable within the current BELFramework instance.
* </p>
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
@Service
public class ResolverServiceImpl implements ResolverService {
private final Resolver resolver;
@Autowired
private KAMStore kAMStore;
@Autowired
private EquivalencerService eqsvc;
@Autowired(required = true)
private NamespaceResourceService nsrsvc;
public ResolverServiceImpl() {
resolver = new Resolver();
}
/**
* {@inheritDoc}
*/
@Override
public List<KamNode> resolveNodes(Kam kam, List<Node> nodes)
throws ResolverServiceException {
final List<KamNode> resolvedKamNodes = sizedArrayList(nodes.size());
final Equivalencer eq = getEquivalencer();
Map<String, String> nsmap = namespaces(kam);
for (final Node node : nodes) {
if (node == null || node.getLabel() == null) {
throw new InvalidArgument("Node is invalid.");
}
String bel = node.getLabel();
try {
resolvedKamNodes.add(convert(kam.getKamInfo(), resolver
.resolve(kam, kAMStore, bel, nsmap, eq)));
} catch (ResolverException e) {
String fmt = "Failed to resolve BEL node %s.";
throw new ResolverServiceException(format(fmt, bel), e);
}
}
return resolvedKamNodes;
}
/**
* {@inheritDoc}
*/
@Override
public List<KamEdge> resolveEdges(Kam kam, List<Edge> edges)
throws ResolverServiceException {
final List<KamEdge> resolvedKamEdges = sizedArrayList(edges.size());
final Equivalencer eq = getEquivalencer();
Map<String, String> nsmap = namespaces(kam);
for (final Edge edge : edges) {
// If relationship type is UNKNOWN then we cannot find it in the
// KAM.
if (edge.getRelationship() == RelationshipType.UNKNOWN) {
continue;
}
final Node subject = edge.getSource();
final Node object = edge.getTarget();
if (subject == null) {
throw new InvalidArgument("Edge subject is invalid.");
}
if (object == null) {
throw new InvalidArgument("Edge object is invalid.");
}
String subLbl = subject.getLabel();
String objLbl = object.getLabel();
final Kam.KamEdge re;
org.openbel.framework.common.enums.RelationshipType rel;
rel = convert(edge.getRelationship());
try {
re = resolver.resolve(kam, kAMStore, subLbl, rel, objLbl,
nsmap, eq);
resolvedKamEdges.add(convert(kam.getKamInfo(), re));
} catch (ResolverException e) {
String fmt = "Failed to resolve BEL edge %s %s %s.";
throw new ResolverServiceException(format(fmt, subLbl,
rel.getAbbreviation(), objLbl), e);
}
}
return resolvedKamEdges;
}
/**
* Assemble all known namespaces from the resource index and {@link Kam}.
*
* @param kam
* {@link Kam}
* @return {@link Map} of namespace {@link String prefix} to {@link String
* resource location}
*/
private Map<String, String> namespaces(Kam kam) {
Map<String, String> nsmap = new HashMap<String, String>();
// find namespaces in resource index
List<NamespaceDescriptor> ns = nsrsvc.getAllNamespaceDescriptors();
for (NamespaceDescriptor n : ns) {
Namespace the_ns = n.getNamespace();
nsmap.put(the_ns.getPrefix(), the_ns.getResourceLocation());
}
// then find namespaces identified by the KAM
List<org.openbel.framework.api.internal.KAMStoreDaoImpl.Namespace> nsl =
kAMStore.getNamespaces(kam);
for (org.openbel.framework.api.internal.KAMStoreDaoImpl.Namespace kam_ns : nsl) {
nsmap.put(kam_ns.getPrefix(), kam_ns.getResourceLocation());
}
return nsmap;
}
private Equivalencer getEquivalencer() {
return ((EquivalencerServiceImpl) eqsvc).leak();
}
}