/**
* 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.api;
import static org.openbel.framework.common.BELUtilities.nulls;
import java.util.List;
import java.util.Map;
import org.openbel.framework.api.Kam.KamEdge;
import org.openbel.framework.api.Kam.KamNode;
import org.openbel.framework.api.internal.KAMStoreDaoImpl.BelTerm;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.bel.parser.BELParser;
import org.openbel.framework.common.enums.RelationshipType;
import org.openbel.framework.common.model.Namespace;
import org.openbel.framework.common.model.Parameter;
import org.openbel.framework.common.model.Term;
import org.openbel.framework.common.protonetwork.model.SkinnyUUID;
/**
* Resolver defines a utility to resolve BEL expressions to elements within
* a specific {@link Kam}.
* <p>
* BelTerm expressions can be resolved to {@link KamNode} elements within a
* specific {@link Kam}.
* </p>
*
* <p>
* Edges in the form (subject BelTerm, Relationship, object BelTerm) can also
* be resolved to {@link KamEdge} elements within a specific {@link Kam}. This
* implementation relies on resolving both the subject and object BelTerm to
* {@link KamNode} elements.
* </p>
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class Resolver {
/**
* Resolves a BelTerm, as a {@link String}, to an equivalent
* {@link KamNode} in the {@link Kam}.
*
* @param kam {@link Kam}, the KAM to resolve against
* @param kAMStore {@link KAMStore}, the KAM store to use in resolving the
* bel term expression
* @param belTerm {@link String}, the BelTerm string, which cannot be null
* or the empty string
* @return the resolved {@link KamNode} for the BelTerm, or null if one
* could not be found
* @throws InvalidArgument Thrown when a parameter is {@code null}
* @throws ResolverException Thrown if an error occurred resolving the
* BelTerm; exceptions will be wrapped
*/
public KamNode resolve(final Kam kam, final KAMStore kAMStore,
final String belTerm, Map<String, String> nsmap,
Equivalencer equivalencer) throws ResolverException {
if (nulls(kam, kAMStore, belTerm, nsmap, equivalencer)) {
throw new InvalidArgument(
"null parameter(s) provided to resolve API.");
}
try {
// algorithm:
// - parse the bel term
// - get all parameters; remap to kam namespace by prefix
// - convert bel term to string replacing each parameter with '#'
// - get uuid for each parameter; ordered by sequence (l to r)
// - (x) if no match, attempt non-equivalence query
// - find kam node by term signature / uuids
// parse the bel term
Term term = null;
try {
term = BELParser.parseTerm(belTerm);
if (term == null) return null;
} catch (Exception e) {
// unrecognized BEL structure
return null;
}
// get all parameters; remap to kam namespace by prefix
List<Parameter> params = term.getAllParametersLeftToRight();
remapNamespace(params, nsmap);
// convert bel term to signature
String termSignature = term.toTermSignature();
// find uuids for all parameters; bucket both the mapped and
// unmapped namespace values
SkinnyUUID[] uuids = new SkinnyUUID[params.size()];
Parameter[] parray = params.toArray(new Parameter[params.size()]);
boolean missing = false;
for (int i = 0; i < parray.length; i++) {
Parameter param = parray[i];
Namespace ns = param.getNamespace();
if (ns == null) {
missing = true;
break;
}
String value = clean(param.getValue());
SkinnyUUID uuid = null;
try {
uuid = equivalencer.getUUID(ns, value);
} catch (EquivalencerException e) {
throw new ResolverException(e);
}
if (uuid != null && !kAMStore.getKamNodes(kam, uuid).isEmpty()) {
uuids[i] = uuid;
} else {
missing = true;
break;
}
}
// TODO Handle terms that may not have UUID parameters!
if (missing) {
KamNode kamNode = kAMStore.getKamNode(kam, belTerm);
return kamNode;
}
// find kam node by term signature / uuids
return kAMStore.getKamNodeForTerm(kam, termSignature,
term.getFunctionEnum(), uuids);
} catch (KAMStoreException e) {
throw new ResolverException(e);
}
}
/**
* Resolves a BelTerm to an equivalent {@link KamNode} in the {@link Kam}.
*
* @param kam {@link Kam}, the KAM to resolve against
* @param kAMStore {@link KAMStore}, the KAM store to use in resolving the
* bel term expression
* @param belTerm {@link BelTerm}, the BelTerm which cannot be null
* @return the resolved {@link KamNode} for the BelTerm, or null if one
* could not be found
* @throws InvalidArgument Thrown when a parameter is {@code null}
* @throws ResolverException Thrown if an error occurred resolving the
* BelTerm; exceptions will be wrapped
*/
public KamNode resolve(final Kam kam, final KAMStore kAMStore,
final BelTerm belTerm) throws ResolverException {
if (nulls(kam, kAMStore, belTerm)) {
throw new InvalidArgument(
"null parameter(s) provided to resolve API.");
}
if (null == belTerm) {
throw new InvalidArgument("belTerm", belTerm);
}
KamNode kamNode = null;
try {
// If we parsed Ok we can go ahead and lookup the string in the KAMStore
kamNode = kAMStore.getKamNode(kam, belTerm);
} catch (KAMStoreException e) {
throw new ResolverException(e);
}
return kamNode;
}
/**
* Resolves a subject BelTerm, relationship type, and object BelTerm to a
* {@link KamEdge}, if it exists within the {@link Kam}. If it does not
* exist then a <tt>null</tt> is returned.
* <p>
* This resolve operation must resolve both the <tt>subjectBelTerm</tt> and
* <tt>objectBelTerm</tt> to a {@link KamNode} in order to find a
* {@link KamEdge}.
* </p>
*
* @param kam {@link Kam}, the kam to resolve into, which cannot be null
* @param kAMStore {@link KAMStore}, the KAM store to use in resolving
* the BelTerms and Edge, which cannot be null
* @param subject {@link String}, the subject BelTerm to resolve to
* a {@link KamNode}, which cannot be null
* @param r {@link RelationshipType}, the relationship type of the
* edge to resolve, which cannot be null
* @param object {@link String}, the object BelTerm to resolve to a
* {@link KamNode}, which cannot be null
* @return the resolved {@link KamEdge} in <tt>kam</tt>, or <tt>null</tt>
* if the edge does not exist
* @throws InvalidArgument Thrown when a parameter is {@code null}
* @throws ResolverException Thrown if an error occurred resolving the
* BelTerm; exceptions will be wrapped
*/
public KamEdge resolve(final Kam kam, final KAMStore kAMStore,
final String subject, final RelationshipType r,
final String object, Map<String, String> nsmap, Equivalencer eq)
throws ResolverException {
if (nulls(kam, kAMStore, subject, r, object, eq)) {
throw new InvalidArgument(
"null parameter(s) provided to resolve API.");
}
// resolve subject bel term to kam node.
final KamNode subjectKamNode = resolve(kam, kAMStore, subject, nsmap, eq);
if (subjectKamNode == null) return null;
// resolve object bel term to kam node.
final KamNode objectKamNode = resolve(kam, kAMStore, object, nsmap, eq);
if (objectKamNode == null) return null;
// only resolve edge if kam nodes resolved
return resolveEdge(kam, subjectKamNode, r, objectKamNode);
}
/**
* Resolves a subject {@link BelTerm}, relationship type, and object
* {@link BelTerm} to a {@link KamEdge}, if it exists within the
* {@link Kam}. If it does not exist then a <tt>null</tt> is returned.
* <p>
* This resolve operation must resolve both the <tt>subjectBelTerm</tt> and
* <tt>objectBelTerm</tt> to a {@link KamNode} in order to find a
* {@link KamEdge}.
* </p>
*
* @param kam {@link Kam}, the kam to resolve into, which cannot be null
* @param kAMStore {@link KAMStore}, the KAM store to use in resolving
* the BelTerms and Edge, which cannot be null
* @param subjectBelTerm {@link BelTerm}, the subject BelTerm to resolve to
* a {@link KamNode}, which cannot be null
* @param rtype {@link RelationshipType}, the relationship type of the
* edge to resolve, which cannot be null
* @param objectBelTerm {@link BelTerm}, the object BelTerm to resolve to a
* {@link KamNode}, which cannot be null
* @return the resolved {@link KamEdge} in <tt>kam</tt>, or <tt>null</tt>
* if the edge does not exist
* @throws InvalidArgument Thrown when a parameter is {@code null}
* @throws ResolverException Thrown if an error occurred resolving the
* BelTerm using the {@link KAMStore}
*/
public KamEdge resolve(final Kam kam, final KAMStore kAMStore,
final BelTerm subjectBelTerm, final RelationshipType rtype,
final BelTerm objectBelTerm) throws ResolverException {
if (nulls(kam, kAMStore, subjectBelTerm, rtype, objectBelTerm)) {
throw new InvalidArgument(
"null parameter(s) provided to resolve API.");
}
// resolve subject bel term to kam node.
final KamNode subjectKamNode = resolve(kam, kAMStore, subjectBelTerm);
if (subjectKamNode == null) {
return null;
}
// resolve object bel term to kam node.
final KamNode objectKamNode = resolve(kam, kAMStore, objectBelTerm);
return resolveEdge(kam, subjectKamNode, rtype, objectKamNode);
}
/**
* Resolve edge based on a subject {@link KamNode},
* {@link RelationshipType}, and an object {@link KamNode}.
*
* @param kam {@link Kam}, the kam to resolve into
* @param subjectKamNode {@link KamNode}, the subject kam node
* @param rtype {@link RelationshipType}, the relationship type
* @param objectKamNode {@link KamNode}, the object kam node
* @return the resolved {@link KamEdge}, or null if it does not exist in
* the {@link Kam}
*/
private KamEdge resolveEdge(final Kam kam, final KamNode subjectKamNode,
final RelationshipType rtype, final KamNode objectKamNode) {
final KamEdge resolvedEdge = kam.findEdge(subjectKamNode, rtype,
objectKamNode);
return resolvedEdge;
}
private static void remapNamespace(List<Parameter> params,
Map<String, String> nsmap) {
for (Parameter p : params) {
Namespace ns = p.getNamespace();
if (ns != null) {
String prefix = ns.getPrefix();
String rloc = nsmap.get(prefix);
if (rloc == null) {
// namespace not supported; remove it
p.setNamespace(null);
} else {
p.setNamespace(new Namespace(prefix, rloc));
}
}
}
}
private static String clean(String value) {
value = value.trim();
int len = value.length();
if (value.charAt(0) == '"' && value.charAt(len - 1) == '"')
value = value.substring(1, len - 1); // exclude 0th and nth-1 char
return value;
}
}