implemented the methods in SBMLDocument that are dealing with validat…

…ing the SBML model. Anyway, the overall checkConsistency is not working anymore but the code in SBMLDocument should be fine now + added a test to easily try to validate a model

src/org/sbml/jsbml/SBMLDocument.java

@@ -20,14 +20,18 @@
 
 package org.sbml.jsbml;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.HashMap;
 import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
 import java.util.Map;
 
+import javax.xml.stream.XMLStreamException;
+
 import org.sbml.jsbml.util.NotImplementedException;
 import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.validator.SBMLValidator;
 
 /**
  * Represents the 'sbml' root node of a SBML file.
@@ -76,7 +80,13 @@ public class SBMLDocument extends AbstractSBase {
 	 * Memorizes all {@link SBMLError} when parsing the file containing this
 	 * document.
 	 */
-	private List<SBMLError> listOfErrors;
+	private SBMLErrorLog listOfErrors;
+
+	/**
+	 * Contains all the parameter to validate the SBML document
+	 */
+	private HashMap<String, String> checkConsistencyParameters = new HashMap<String, String>();
+
 	/**
 	 * Represents the 'model' XML subnode of a SBML file.
 	 */
@@ -155,25 +165,58 @@ public void addNamespace(String namespaceName, String prefix, String URI) {
 	}
 
 	/**
-	 * Not yet implemented!
-	 * 
-	 * It is supposed to fill this {@link SBMLDocument}'s {@link #listOfErrors}
+	 * Validates the {@link SBMLDocument} using the
+	 * SBML.org online validator (http://sbml.org/validator/).
+	 * <p>
+	 * It will fill this {@link SBMLDocument}'s {@link #listOfErrors}
 	 * with {@link SBMLError}s for each problem within this whole data
 	 * structure. You will then be able to obtain this list by calling
 	 * {@link #getError(int)} or {@link #getListOfErrors()}.
 	 * 
-	 * @return
-	 * @throws NotImplementedException
-	 *             Currently, this method is not implemented, so please catch a
-	 *             {@link NotImplementedException} in your program until we
-	 *             remove this error.
+	 * @return the number of errors found
 	 */
 	public int checkConsistency() {
-		listOfErrors = getListOfErrors();
-		// TODO: IMPLEMENT!
-		throw new NotImplementedException();
+
+		File tmpFile = null;
+
+		try {
+			tmpFile = File.createTempFile("jsbml-", ".xml");
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		try {
+			new SBMLWriter().writeSBML(this, tmpFile);
+		} catch (FileNotFoundException e) { // TODO : log the errors. Send an exception ??
+			e.printStackTrace();
+			return -1;
+		} catch (XMLStreamException e) {
+			e.printStackTrace();
+			return -1;
+		} catch (SBMLException e) {
+			e.printStackTrace();
+			return -1;
+		}
+
+		HashMap<String, String> parameters = new HashMap<String, String>();
+
+		// System.out.println("SBMLDocument.checkConsistency : tmp file = " + tmpFile.getAbsolutePath());
+
+		listOfErrors = SBMLValidator.checkConsistency(tmpFile.getAbsolutePath(), parameters); 
+
+		return listOfErrors.getNumErrors();
 	}
 
+	public void printErrors() {
+		int nbErrors = listOfErrors.getNumErrors();
+
+		for (int i = 0; i < nbErrors; i++) {
+			System.out.println(listOfErrors.getError(i));
+		}
+	}
+
+
+
 	/*
 	 * (non-Javadoc)
 	 * 
@@ -306,16 +349,15 @@ public String getElementName() {
 	}
 
 	/**
-	 * Not yet implemented!
 	 * 
 	 * @param i
-	 * @return
+	 * @return 
 	 */
 	public SBMLError getError(int i) {
 		if (isSetListOfErrors()) {
-			return listOfErrors.get(i);
+			return listOfErrors.getError(i);
 		}
-		throw new IndexOutOfBoundsException(Integer.toString(i));
+		throw new IndexOutOfBoundsException(Integer.toString(i)); // TODO : test if the number is too low or too big
 	}
 
 	/**
@@ -324,13 +366,23 @@ public SBMLError getError(int i) {
 	 * 
 	 * @return
 	 */
-	public List<SBMLError> getListOfErrors() {
+	public SBMLErrorLog getListOfErrors() {
 		if (listOfErrors == null) {
-			listOfErrors = new LinkedList<SBMLError>();
+			listOfErrors = new SBMLErrorLog();
 		}
 		return listOfErrors;
 	}
 
+	/**
+	 * This method returns a collection of all {@link SBMLError}s reflecting
+	 * problems in the overall data structure of this {@link SBMLDocument}.
+	 * 
+	 * @return
+	 */
+	public SBMLErrorLog getErrorLog() {
+		return getListOfErrors();
+	}
+
 	/**
 	 * Returns the model of this {@link SBMLDocument}.
 	 * 
@@ -345,7 +397,7 @@ public Model getModel() {
 	 * @return
 	 */
 	public int getNumErrors() {
-		return isSetListOfErrors() ? listOfErrors.size() : 0;
+		return isSetListOfErrors() ? listOfErrors.getNumErrors() : 0;
 	}
 
 	/**
@@ -369,7 +421,7 @@ public Map<String, String> getSBMLDocumentNamespaces() {
 	 * @return
 	 */
 	private boolean isSetListOfErrors() {
-		return (listOfErrors != null) && (listOfErrors.size() > 0);
+		return (listOfErrors != null) && (listOfErrors.getNumErrors() > 0);
 	}
 
 	/**

src/org/sbml/jsbml/validator/SBMLValidator.java

@@ -341,13 +341,15 @@ public static SBMLErrorLog checkConsistency(String fileName,
 			String output = "xml";
 
 			parameters.put("output", output);
+			parameters.put("offcheck", "u");
 
 			// getting an XML output of the error log
 			// describe there :
 			// http://sbml.org/Facilities/Validator/Validator_Web_API
 			result = Validator.validateSBML(fileName, parameters);
 
-			// print(result, System.out);
+			// DEBUG 
+			print(result, System.out);
 
 			XStream xstream = new XStream(new DomDriver()); // To parse XML
 															// using DOM

test/org/sbml/jsbml/test/ValidateSBML.java

@@ -0,0 +1,66 @@
+package org.sbml.jsbml.test;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLReader;
+
+public class ValidateSBML {
+
+	public static void main (String[] args) throws FileNotFoundException, XMLStreamException
+	{
+		if (args.length < 1)
+		{
+			System.out.println("Usage: java validateSBML filename");
+			System.exit(1);
+		}
+
+		String filename       = args[0];
+		SBMLReader reader     = new SBMLReader();
+		SBMLDocument document;
+		long start, stop;
+
+		start    = System.currentTimeMillis();
+		document = reader.readSBML(filename);
+		stop     = System.currentTimeMillis();
+
+		if (document.getNumErrors() > 0)
+		{
+			print("Encountered the following errors while reading the SBML file:\n");
+			document.printErrors();
+			print("\nFurther consistency checking and validation aborted.\n");
+			System.exit(1);
+		}
+		else
+		{
+			long errors = document.checkConsistency();
+			long size   = new File(filename).length();
+
+			println("            filename: " + filename);
+			println("           file size: " + size);
+			println("      read time (ms): " + (stop - start));
+			println(" validation error(s): " + errors);
+
+			if (errors > 0)
+			{
+				document.printErrors();
+				System.exit(1);
+			}
+		}
+	}
+
+
+	static void print (String msg)
+	{
+		System.out.print(msg);
+	}
+
+	static void println (String msg)
+	{
+		System.out.println(msg);
+	}
+
+}