/**
* 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 static org.junit.Assert.*;
import java.util.List;
import java.util.Set;
import org.junit.Test;
import org.openbel.bel.model.BELAnnotation;
import org.openbel.bel.model.BELAnnotationDefinition;
import org.openbel.bel.model.BELCitation;
import org.openbel.bel.model.BELDocument;
import org.openbel.bel.model.BELDocumentHeader;
import org.openbel.bel.model.BELEvidence;
import org.openbel.bel.model.BELStatement;
import org.openbel.bel.model.BELStatementGroup;
/**
* {@link BELScriptParser} tests.
*/
public class BELScriptParserTest {
/**
* Test BEL Script lexer/parser handling of annotation patterns with escape
* sequences.
*
* @see https://github.com/OpenBEL/openbel-framework/issues/14
*/
@Test
public void testIssue14() {
StringBuilder bldr = new StringBuilder();
bldr.append("SET DOCUMENT Name = \"Name\"\n");
bldr.append("SET DOCUMENT Description = \"Description\"\n");
bldr.append("SET DOCUMENT Version = \"1.0\"\n");
bldr.append("DEFINE ANNOTATION X AS PATTERN ");
// Note the same string would be captured in BEL Script as:
// "0|1|0?\\.[\\d]+|1\\.[0]+"
bldr.append("\"0|1|0?\\\\.[\\\\d]+|1\\\\.[0]+\"\n");
String belscript = bldr.toString();
BELParseResults parse = BELParser.parse(belscript);
assertTrue(parse.getSyntaxWarnings().isEmpty());
assertTrue(parse.getSyntaxErrors().isEmpty());
BELDocument doc = parse.getDocument();
assertNotNull(doc);
Set<BELAnnotationDefinition> annodefs = doc.getAnnotationDefinitions();
assertNotNull(annodefs);
assertTrue(annodefs.size() == 1);
String value = annodefs.iterator().next().getValue();
assertTrue(value.equals("0|1|0?\\.[\\d]+|1\\.[0]+"));
}
/**
* Test BEL Script lexer/parser handling of document properties with escape
* sequences.
*/
@Test
public void testDocumentProperty() {
StringBuilder bldr = new StringBuilder();
bldr.append("SET DOCUMENT Name = \"Tabbed\tname\\t\"\n");
bldr.append("SET DOCUMENT Description = \"Description\"\n");
bldr.append("SET DOCUMENT Version = \"1.0\"\n");
String belscript = bldr.toString();
BELParseResults parse = BELParser.parse(belscript);
assertTrue(parse.getSyntaxWarnings().isEmpty());
assertTrue(parse.getSyntaxErrors().isEmpty());
BELDocument doc = parse.getDocument();
assertNotNull(doc);
BELDocumentHeader header = doc.getDocumentHeader();
assertNotNull(header);
String name = header.getName();
assertNotNull(name);
assertTrue(name.equals("Tabbed\tname\\t"));
}
/**
* Test BEL Script lexer/parser handling of statement groups with escape
* sequences.
*/
@Test
public void testStatementGroup() {
StringBuilder bldr = new StringBuilder();
bldr.append("SET DOCUMENT Name = \"Name\"\n");
bldr.append("SET DOCUMENT Description = \"Description\"\n");
bldr.append("SET DOCUMENT Version = \"1.0\"\n");
bldr.append("SET STATEMENT_GROUP = \"\u03B2-cell study\"\n");
String belscript = bldr.toString();
BELParseResults parse = BELParser.parse(belscript);
assertTrue(parse.getSyntaxWarnings().isEmpty());
assertTrue(parse.getSyntaxErrors().isEmpty());
BELDocument doc = parse.getDocument();
assertNotNull(doc);
List<BELStatementGroup> groups = doc.getBelStatementGroups();
assertTrue(groups.size() == 1);
BELStatementGroup group = groups.get(0);
assertTrue(group.getName().equals("\"β-cell study\""));
}
/**
* Test BEL Script lexer/parser handling of annotations with escape
* sequences.
*
* @see https://github.com/OpenBEL/openbel-framework/issues/14
*/
@Test
public void testAnnotation() {
StringBuilder bldr = new StringBuilder();
bldr.append("SET DOCUMENT Name = \"Name\"\n");
bldr.append("SET DOCUMENT Description = \"Description\"\n");
bldr.append("SET DOCUMENT Version = \"1.0\"\n");
bldr.append("DEFINE ANNOTATION X AS PATTERN ");
// Note the same string would be captured in BEL Script as:
// "0|1|0?\\.[\\d]+|1\\.[0]+"
bldr.append("\"0|1|0?\\\\.[\\\\d]+|1\\\\.[0]+\"\n");
bldr.append("SET STATEMENT_GROUP = \"\u03B2-cell study\"\n");
bldr.append("SET X = \"0.42\"\n");
bldr.append("p(X) -> p(Y)\n");
bldr.append("UNSET STATEMENT_GROUP\n");
String belscript = bldr.toString();
BELParseResults parse = BELParser.parse(belscript);
assertTrue(parse.getSyntaxWarnings().isEmpty());
assertTrue(parse.getSyntaxErrors().isEmpty());
BELDocument doc = parse.getDocument();
assertNotNull(doc);
List<BELStatementGroup> groups = doc.getBelStatementGroups();
BELStatementGroup group = groups.get(0);
List<BELStatement> stmts = group.getStatements();
assertTrue(stmts.size() == 1);
BELStatement stmt = stmts.get(0);
List<BELAnnotation> annos = stmt.getAnnotations();
assertTrue(annos.size() == 1);
BELAnnotation anno = annos.get(0);
assertTrue(anno.getValues().size() == 1);
assertTrue("0.42".equals(anno.getValues().get(0)));
}
/**
* Test BEL Script lexer/parser handling of citations with escape sequences.
*/
@Test
public void testCitation() {
StringBuilder bldr = new StringBuilder();
bldr.append("SET DOCUMENT Name = \"Name\"\n");
bldr.append("SET DOCUMENT Description = \"Description\"\n");
bldr.append("SET DOCUMENT Version = \"1.0\"\n");
bldr.append("SET STATEMENT_GROUP = \"\u03B2-cell study\"\n");
bldr.append("SET Evidence = \"Evidence\nneeded\"\n");
bldr.append("SET Citation = {\"PubMed\", \"X\", \"Y\", \"\", \"\", \"\"}\n");
bldr.append("p(X) -> p(Y)\n");
bldr.append("UNSET STATEMENT_GROUP\n");
String belscript = bldr.toString();
BELParseResults parse = BELParser.parse(belscript);
for (final Object o : parse.getSyntaxWarnings()) {
System.out.println(o);
}
for (final Object o : parse.getSyntaxErrors()) {
System.out.println(o);
}
assertTrue(parse.getSyntaxWarnings().isEmpty());
assertTrue(parse.getSyntaxErrors().isEmpty());
BELDocument doc = parse.getDocument();
assertNotNull(doc);
List<BELStatementGroup> groups = doc.getBelStatementGroups();
BELStatementGroup group = groups.get(0);
List<BELStatement> stmts = group.getStatements();
assertTrue(stmts.size() == 1);
BELStatement stmt = stmts.get(0);
BELEvidence evidence = stmt.getEvidence();
assertNotNull(evidence);
BELCitation citation = stmt.getCitation();
assertNotNull(citation);
assertEquals("Evidence\nneeded", evidence.getEvidenceLine());
assertEquals("PubMed", citation.getType());
assertEquals("X", citation.getName());
assertEquals("Y", citation.getReference());
}
}