/**
* 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.openbel.framework.common.BELUtilities.hasItems;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.List;
import org.openbel.bel.model.*;
/**
* TODO Convert to true unit test and remove hardcoded paths.
*
* @author Anthony Bargnesi {@code <abargnesi@selventa.com>}
*/
public class BELScriptWalkerTest {
public static void main(String[] args) throws IOException {
parseBELScript(new File(
"/home/abargnesi/projects-bel/docs/BEL Script/example1.bel"));
parseBELScript(new File(
"/home/abargnesi/projects-bel/docs/BEL Script/fullabstract1.bel"));
parseBELScript(new File(
"/home/abargnesi/projects-bel/docs/BEL Script/fullabstract2.bel"));
parseBELScript(new File(
"/home/abargnesi/projects-bel/docs/BEL Script/fullabstract3.bel"));
}
private static void parseBELScript(File belscriptFile) throws IOException {
BufferedReader reader =
new BufferedReader(new FileReader(belscriptFile));
StringBuilder sb = new StringBuilder();
String line;
while ((line = reader.readLine()) != null) {
sb.append(line + "\n");
}
reader.close();
parseBELScript(sb.toString());
}
private static void parseBELScript(String belscript) {
BELParseResults results = BELParser.parse(belscript);
if (!results.getSyntaxWarnings().isEmpty()) {
for (BELParseWarningException syntaxWarning : results
.getSyntaxWarnings()) {
System.out.println(syntaxWarning.getMessage());
}
}
if (!results.getSyntaxErrors().isEmpty()) {
for (BELParseErrorException syntaxError : results.getSyntaxErrors()) {
System.out.println(syntaxError.getMessage());
}
} else {
report(results.getDocument());
}
}
private static void report(BELDocument doc) {
// header
System.out.println("\n-header-");
BELDocumentHeader docheader = doc.getDocumentHeader();
System.out.println("Authors are: " + docheader.getAuthor());
System.out.println("Copyright is: " + docheader.getCopyright());
System.out.println("ContactInfo is: " + docheader.getContactInfo());
System.out.println("Description is: " + docheader.getDescription());
System.out.println("Disclaimer is: " + docheader.getDisclaimer());
System.out.println("Licenses are: " + docheader.getLicense());
System.out.println("Name is: " + docheader.getName());
System.out.println("Version is: " + docheader.getVersion());
// annotation definitions
System.out.println("\n-annotations-");
for (BELAnnotationDefinition anndef : doc.getAnnotationDefinitions()) {
switch (anndef.getAnnotationType()) {
case PATTERN:
case URL:
System.out.println(anndef.getName() + "("
+ anndef.getAnnotationType() + "), Domain: "
+ anndef.getValue());
break;
case LIST:
System.out.println(anndef.getName() + "("
+ anndef.getAnnotationType() + "), Domain: "
+ anndef.getList());
break;
}
}
System.out.println("\n-namespaces-");
// namespace definitions
for (BELNamespaceDefinition nsdef : doc.getNamespaceDefinitions()) {
if (nsdef.isNsDefault()) {
System.out.println("DEFAULT NAMESPACE, Location: "
+ nsdef.getResourceLocation());
} else {
System.out.println(nsdef.getPrefix() + ", Location: "
+ nsdef.getResourceLocation());
}
}
System.out.println("\n-statements-");
// statements
for (BELStatementGroup stmtGroup : doc.getBelStatementGroups()) {
for (BELStatement stmt : stmtGroup.getStatements()) {
if (stmt.getComment() != null) {
System.out.println("\n" + stmt.getStatementSyntax());
System.out.println("Comment: " + stmt.getComment());
} else {
System.out.println("\n" + stmt.getStatementSyntax());
}
final BELCitation citation = stmt.getCitation();
if (citation != null) {
System.out.println("Citation: " + citation.getName());
}
final BELEvidence evidence = stmt.getEvidence();
if (evidence != null) {
System.out.println("Evidence: "
+ evidence.getEvidenceLine());
}
List<BELAnnotation> annotations = stmt.getAnnotations();
if (hasItems(annotations)) {
for (BELAnnotation annotation : annotations) {
System.out.print("Annotation ("
+ annotation.getAnnotationDefinition()
.getName()
+ "): ");
int i = 0;
for (String value : annotation.getValues()) {
if (i++ != 0) {
System.out.print(", ");
}
System.out.print(value);
}
System.out.println();
}
}
}
}
}
}