/**
* 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.parser;
import org.junit.Test;
import org.openbel.framework.common.bel.parser.BELParser;
import org.openbel.framework.common.model.Term;
public class BELStatementParserTest {
@Test
public void testOneParam() {
Term term = BELParser.parseTerm("proteinAbundance(HGNC:AKT1)");
System.out.println(term.toBELLongForm());
}
@Test
public void testMultipleParams() {
Term term =
BELParser
.parseTerm("list(HGNC:AKT1,HGNC:AKT2,GO:\"mito moto\")");
System.out.println(term.toBELLongForm());
}
@Test
public void testMultipleInnerTerms() {
Term term =
BELParser
.parseTerm("complexAbundance(proteinAbundance(HGNC:AKT1),proteinAbundance(HGNC:AKT2),abundance(CHEBI:TLH21))");
System.out.println(term.toBELLongForm());
}
@Test
public void testFunctionThenParams() {
Term term =
BELParser
.parseTerm("translocation(proteinAbundance(HGNC:DIABLO),GO:mitochondrion,GO:cytoplasm)");
System.out.println(term.toBELLongForm());
}
@Test
public void testEmptyModifcation() {
Term term =
BELParser
.parseTerm("proteinAbundance(HGNC:MAP3K1,modification())");
System.out.println(term.toBELLongForm());
}
@Test
public void testAminoAcidModifcation() {
Term term =
BELParser
.parseTerm("proteinAbundance(HGNC:MAP3K1,modification(P))");
System.out.println(term.toBELLongForm());
}
@Test
public void testThreeLevelNesting() {
Term term =
BELParser
.parseTerm("complexAbundance(complexAbundance(proteinAbundance(HGNC:GABPA),proteinAbundance(HGNC:GABPB1)),complexAbundance(proteinAbundance(HGNC:GABPA),proteinAbundance(HGNC:GABPB1)))");
System.out.println(term.toBELLongForm());
}
@Test
public void testNestedReaction() {
Term term =
BELParser
.parseTerm("reaction(reactants(complexAbundance(proteinAbundance(HGNC:ESR1),proteinAbundance(PFAM:\"Ncor Family\"))),products(complexAbundance(proteinAbundance(PFAM:\"Ncoa Family\"),proteinAbundance(HGNC:ESR1))))");
System.out.println(term.toBELLongForm());
}
@Test
public void testModificationTwoParams() {
Term term =
BELParser
.parseTerm("reaction(reactants(proteinAbundance(HGNC:AR)),products(proteinAbundance(HGNC:AR,proteinModification(A,K632))))");
System.out.println(term.toBELLongForm());
}
@Test
public void testCollidingParamWithFunction() {
Term term = BELParser.parseTerm("proteinAbundance(MGI:t)");
System.out.println(term.toBELLongForm());
}
}