/**
* 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.common.bel.converters;
import static org.openbel.framework.common.BELUtilities.*;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.openbel.bel.model.BELAnnotation;
import org.openbel.bel.model.BELCitation;
import org.openbel.bel.model.BELEvidence;
import org.openbel.bel.model.BELStatement;
import org.openbel.framework.common.bel.parser.BELParser;
import org.openbel.framework.common.model.Annotation;
import org.openbel.framework.common.model.AnnotationDefinition;
import org.openbel.framework.common.model.AnnotationGroup;
import org.openbel.framework.common.model.CommonModelFactory;
import org.openbel.framework.common.model.Namespace;
import org.openbel.framework.common.model.Parameter;
import org.openbel.framework.common.model.Statement;
public class BELStatementConverter extends
BELConverter<BELStatement, Statement> {
private static final Pattern QUOTED_NS_VALUE = Pattern.compile("\"(.*)\"");
private final BELCitationConverter bcc = new BELCitationConverter();
private final BELEvidenceConverter bec = new BELEvidenceConverter();
private final Map<String, Namespace> ndefs;
private final Map<String, AnnotationDefinition> adefs;
public BELStatementConverter(Map<String, Namespace> ndefs,
Map<String, AnnotationDefinition> adefs) {
this.ndefs = ndefs;
this.adefs = adefs;
}
/**
* {@inheritDoc}
*/
@Override
public Statement convert(BELStatement bs) {
if (bs == null) {
return null;
}
String comment = bs.getComment();
String belSyntax = bs.getStatementSyntax();
Statement s = BELParser.parseStatement(belSyntax);
repopulateNamespaces(s);
s.setComment(comment);
final BELAnnotationConverter bac =
new BELAnnotationConverter(adefs);
List<BELAnnotation> annotations = bs.getAnnotations();
List<Annotation> alist = null;
if (hasItems(annotations)) {
alist = sizedArrayList(annotations.size());
for (BELAnnotation annotation : annotations) {
alist.addAll(bac.convert(annotation));
}
}
BELCitation bc = bs.getCitation();
BELEvidence be = bs.getEvidence();
AnnotationGroup ag = new AnnotationGroup();
boolean hasAnnotation = false;
if (hasItems(alist)) {
ag.setAnnotations(alist);
hasAnnotation = true;
}
if (bc != null) {
ag.setCitation(bcc.convert(bc));
hasAnnotation = true;
}
if (be != null) {
ag.setEvidence(bec.convert(be));
hasAnnotation = true;
}
if (hasAnnotation) {
s.setAnnotationGroup(ag);
}
return s;
}
/**
* {@inheritDoc}
*/
@Override
public BELStatement convert(Statement s) {
throw new UnsupportedOperationException(
"Do not support conversion to BELScript.");
}
protected void repopulateNamespaces(final Statement statement) {
if (hasItems(statement.getAllParameters())) {
for (Parameter p : statement.getAllParameters()) {
Namespace ns = p.getNamespace();
if (ns != null) {
String prefix = ns.getPrefix();
Namespace namespace = ndefs.get(prefix);
if (namespace == null) {
continue;
}
p.setNamespace(namespace);
}
// remove quoted ns value boundary if present.
if (p.getValue() != null) {
Matcher m = QUOTED_NS_VALUE.matcher(p.getValue());
if (m.matches()) {
p.setValue(CommonModelFactory.getInstance()
.resolveValue(m.group(1)));
}
}
}
}
}
}