/**
* 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 java.lang.String.format;
import static org.openbel.framework.common.BELUtilities.noLength;
import static org.openbel.framework.common.BELUtilities.sizedHashMap;
import java.util.List;
import java.util.Map;
import org.openbel.framework.common.InvalidArgument;
import org.openbel.framework.common.model.Namespace;
import org.openbel.framework.common.model.Parameter;
import org.openbel.framework.common.protonetwork.model.SkinnyUUID;
import org.openbel.framework.core.equivalence.DefaultParameterEquivalencer;
import org.openbel.framework.core.equivalence.ParameterEquivalencer;
/**
* Equivalencer defines a utility to equivalencing namespace values.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class Equivalencer {
private ParameterEquivalencer paramEquivalencer;
/**
* Finds a parameter, equivalent to the <tt>sourceParameter</tt>, and found
* in the {@link Namespace} identified by <tt>targetNamespace</tt>.
* <p>
* Note: The first time any method in {@link Equivalencer} is called the
* equivalencing engine is instantiated, but only once. The equivalencing
* engine loads the BEL equivalence files associated with the framework and
* uses them do perform equivalencing.
* </p>
*
* @param sourceNamespace {@link Namespace}, the namespace of the source
* parameter
* @param sourceValue {@link String}, the source parameter value
* @param targetNamespace {@link Namespace}, the namespace of the equivalent
* parameter to find
* @return the equivalent parameter found in <tt>targetNamespace</tt>, or
* null if no equivalent parameter is found in that namespace
* @throw InvalidArgument Thrown if <tt>sourceNamespace</tt>,
* <tt>sourceParameter</tt>, or <tt>targetNamespace</tt> is null
* @throws EquivalencerException Thrown if an exception occurs finding the
* equivalent parameter
*/
public String equivalence(final Namespace sourceNamespace,
final String sourceValue, final Namespace targetNamespace)
throws EquivalencerException {
if (sourceNamespace == null) {
throw new InvalidArgument("sourceNamespace", sourceNamespace);
}
if (noLength(sourceValue)) {
throw new InvalidArgument("sourceValue", sourceValue);
}
if (targetNamespace == null) {
throw new InvalidArgument("targetNamespace", targetNamespace);
}
loadEquivalencingEngine();
// convert namespace and value to parameter (common model).
final Parameter sp = new Parameter(sourceNamespace, sourceValue);
try {
Parameter parameter = this.paramEquivalencer.findEquivalence(sp,
targetNamespace);
return parameter == null ? null : parameter.getValue();
} catch (InvalidArgument e) {
//TODO change exception when paramEquivalencer is changed
return null;
} catch (Exception e) {
final String fmt = "Unable to find equivalences for '%s'";
final String msg = format(fmt, sp.toBELShortForm());
throw new EquivalencerException(msg, e);
}
}
/**
* Finds all parameters equivalent to the <tt>sourceParameter</tt>.
* <p>
* Note: The first time any method in {@link Equivalencer} is called the
* equivalencing engine is instantiated, but only once. The equivalencing
* engine loads the BEL equivalence files associated with the framework and
* uses them do perform equivalencing.
* </p>
*
* @param sourceNamespace {@link Namespace}, the namespace of the source
* parameter
* @param sourceValue {@link String}, the source parameter value
* @return the equivalent parameters or an empty map if no equivalent
* parameter is found
* @throws EquivalencerException Thrown if an exception occurs finding all
* equivalences
*/
public Map<Namespace, String> equivalence(final Namespace sourceNamespace,
final String sourceValue) throws EquivalencerException {
if (sourceNamespace == null) {
throw new InvalidArgument("sourceNamespace", sourceNamespace);
}
if (noLength(sourceValue)) {
throw new InvalidArgument("sourceValue", sourceValue);
}
loadEquivalencingEngine();
final Parameter sp = new Parameter(sourceNamespace, sourceValue);
try {
final List<Parameter> equivalences = this.paramEquivalencer
.findEquivalences(sp);
Map<Namespace, String> equivalenceMap = sizedHashMap(equivalences
.size());
for (final Parameter equivalence : equivalences) {
equivalenceMap.put(equivalence.getNamespace(),
equivalence.getValue());
}
return equivalenceMap;
} catch (InvalidArgument e) {
//TODO change exception when paramEquivalencer is changed
return null;
} catch (Exception e) {
final String fmt = "Unable to find equivalences for '%s'";
final String msg = format(fmt, sp.toBELShortForm());
throw new EquivalencerException(msg, e);
}
}
/**
* Finds a parameter, equivalent to the <tt>sourceUUID</tt>, and found in
* the {@link Namespace} identified by <tt>targetNamespace</tt>.
* <p>
* Note: The first time any method in {@link Equivalencer} is called the
* equivalencing engine is instantiated, but only once. The equivalencing
* engine loads the BEL equivalence files associated with the framework and
* uses them do perform equivalencing.
* </p>
*
* @param sourceUUID
* @param targetNamespace
* @return the equivalent parameters or an empty map if no equivalent
* parameter is found
* @throws EquivalencerException Thrown if an exception occurs finding all
* equivalences
*/
public String equivalence(SkinnyUUID sourceUUID, Namespace targetNamespace)
throws EquivalencerException {
if (sourceUUID == null) {
throw new InvalidArgument("sourceUUID", sourceUUID);
}
if (targetNamespace == null) {
throw new InvalidArgument("targetNamespace", targetNamespace);
}
loadEquivalencingEngine();
try {
Parameter parameter = this.paramEquivalencer.findEquivalence(
sourceUUID, targetNamespace);
return parameter == null ? null : parameter.getValue();
} catch (InvalidArgument e) {
//TODO change exception when paramEquivalencer is changed
return null;
} catch (Exception e) {
final String fmt = "Unable to find equivalences for '%s'";
final String msg = format(fmt, sourceUUID.toString());
throw new EquivalencerException(msg, e);
}
}
/**
* Finds all parameters equivalent to the <tt>sourceParameter</tt>.
* <p>
* Note: The first time any method in {@link Equivalencer} is called the
* equivalencing engine is instantiated, but only once. The equivalencing
* engine loads the BEL equivalence files associated with the framework and
* uses them do perform equivalencing.
* </p>
*
* @param sourceUUID
* @return the equivalent parameters or an empty map if no equivalent
* parameter is found
* @throws EquivalencerException Thrown if an exception occurs finding all
* equivalences
*/
public Map<Namespace, String> equivalence(SkinnyUUID sourceUUID)
throws EquivalencerException {
if (sourceUUID == null) {
throw new InvalidArgument("sourceUUID", sourceUUID);
}
loadEquivalencingEngine();
try {
final List<Parameter> equivalences = this.paramEquivalencer
.findEquivalences(sourceUUID);
Map<Namespace, String> equivalenceMap = sizedHashMap(equivalences
.size());
for (final Parameter equivalence : equivalences) {
equivalenceMap.put(equivalence.getNamespace(),
equivalence.getValue());
}
return equivalenceMap;
} catch (InvalidArgument e) {
//TODO change exception when paramEquivalencer is changed
return null;
} catch (Exception e) {
final String fmt = "Unable to find equivalences for '%s'";
final String msg = format(fmt, sourceUUID.toString());
throw new EquivalencerException(msg, e);
}
}
/**
* Obtain the equivalence UUID for the given {@link Namespace namespace} and value.
* @param namespace {@link Namespace namespace}, must not be null
* @param value {@link String value}, must not be null
* @return {@link SkinnyUUID UUID} representing the value or <code>null</code> if the
* namespace/value combination has no equivalents. null is also returned if the
* namespace has no equivalences defined.
* @throws EquivalencerException Thrown if an exception occurs finding all
* equivalences
*/
public SkinnyUUID getUUID(Namespace namespace, String value)
throws EquivalencerException {
loadEquivalencingEngine();
final Parameter p = new Parameter(namespace, value);
try {
return paramEquivalencer.getUUID(p);
} catch (InvalidArgument e) {
//TODO change when paramEquivalencer exception is changed
return null;
} catch (Exception e) {
final String fmt = "Unable to find UUID for '%s'";
final String msg = format(fmt, p.toBELShortForm());
throw new EquivalencerException(msg, e);
}
}
/**
* Loads the {@link ParameterEquivalencer} if it has not already been
* loaded.
*
* @throws EquivalencerException Thrown if an error occurred loading the
* equivalencing engine.
*/
private void loadEquivalencingEngine() throws EquivalencerException {
if (paramEquivalencer == null) {
try {
paramEquivalencer = DefaultParameterEquivalencer.getInstance();
} catch (Exception e) {
throw new EquivalencerException(
"Unable to load equivalencing engine.", e);
}
}
}
}