/**
* 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.core.compiler.expansion;
import static org.junit.Assert.assertThat;
import java.util.List;
import org.antlr.runtime.RecognitionException;
import static org.hamcrest.CoreMatchers.is;
import org.junit.Test;
import org.openbel.framework.common.bel.parser.BELParser;
import org.openbel.framework.common.model.Statement;
import org.openbel.framework.common.model.Term;
import org.openbel.framework.core.compiler.expansion.ModificationExpansionRule;
/**
* {@link TermExpansionTest} defines unit tests for
* {@link TermExpansionRule term expansion rules} classes.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class TermExpansionTest {
/**
* Validate the rule match and expansion of the
* {@link ModificationExpansionRule modification expansion rule}.
*
* @throws RecognitionException Thrown if test BEL expressions are not
* parsed correctly which will result in a test failure
*/
@Test
public void testModificationExpansions()
throws RecognitionException {
final ModificationExpansionRule rule = new ModificationExpansionRule();
Term term;
List<Statement> stmts;
// valid substitution
term = BELParser.parseTerm("p(HGNC:TNF,sub(V,599,E))");
assertThat(rule.match(term), is(true));
stmts = rule.expand(term);
assertThat(stmts.size(), is(1));
assertThat(stmts.get(0).toBELShortForm(),
is("p(HGNC:TNF) hasVariant p(HGNC:TNF,sub(V,599,E))"));
// valid truncation
term = BELParser.parseTerm("p(HGNC:TNF,trunc(S,1099))");
assertThat(rule.match(term), is(true));
stmts = rule.expand(term);
assertThat(stmts.size(), is(1));
assertThat(stmts.get(0).toBELShortForm(),
is("p(HGNC:TNF) hasVariant p(HGNC:TNF,trunc(S,1099))"));
// valid protein modification
term = BELParser.parseTerm("p(HGNC:TNF,pmod(P,Y))");
assertThat(rule.match(term), is(true));
stmts = rule.expand(term);
assertThat(stmts.size(), is(1));
assertThat(stmts.get(0).toBELShortForm(),
is("p(HGNC:TNF) hasModification p(HGNC:TNF,pmod(P,Y))"));
// valid fusion
term = BELParser.parseTerm("p(HGNC:TNF,fus(HGNC:ABL1))");
assertThat(rule.match(term), is(true));
stmts = rule.expand(term);
assertThat(stmts.size(), is(1));
assertThat(stmts.get(0).toBELShortForm(),
is("p(HGNC:TNF) hasVariant p(HGNC:TNF,fus(HGNC:ABL1))"));
// invalid based on outer function
term = BELParser.parseTerm("complex(p(HGNC:TNF),p(HGNC:MAPK1))");
assertThat(rule.match(term), is(false));
// invalid based on missing modification argument
term = BELParser.parseTerm("p(HGNC:TNF)");
assertThat(rule.match(term), is(false));
// invalid based on non-parameter first argument
term = BELParser.parseTerm("p(r(HGNC:TNF),sub(V,599,E))");
assertThat(rule.match(term), is(false));
// invalid based on non-term second argument
term = BELParser.parseTerm("p(HGNC:TNF,\"Substitution at P,Y\")");
assertThat(rule.match(term), is(false));
// invalid protein decorator function for second argument
term = BELParser.parseTerm("p(HGNC:TNF,g(HGNC:AKT1))");
assertThat(rule.match(term), is(false));
}
}