/*
 * @file    TestReadSBML.java
 * @brief   Read SBML unit tests
 *
 * @author  Akiya Jouraku (Java conversion)
 * @author  Ben Bornstein 
 *
 * $Id: TestReadSBML.java 11383 2010-07-06 05:14:11Z mhucka $
 * $HeadURL: http://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadSBML.java $
 *
 * ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
 *
 * DO NOT EDIT THIS FILE.
 *
 * This file was generated automatically by converting the file located at
 * src/sbml/test/TestReadSBML.cpp
 * using the conversion program dev/utilities/translateTests/translateTests.pl.
 * Any changes made here will be lost the next time the file is regenerated.
 *
 * -----------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright 2005-2010 California Institute of Technology.
 * Copyright 2002-2005 California Institute of Technology and
 *                     Japan Science and Technology Corporation.
 * 
 * This library 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.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * -----------------------------------------------------------------------------
 */

package org.sbml.libsbml.test.sbml;

import org.sbml.libsbml.*;

import java.io.File;
import java.lang.AssertionError;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.io.BufferedReader;


public class TestReadSBML {

  static void assertTrue(boolean condition) throws AssertionError
  {
    if (condition == true)
    {
      return;
    }
    throw new AssertionError();
  }

  static void assertEquals(Object a, Object b) throws AssertionError
  {
    if ( (a == null) && (b == null) )
    {
      return;
    }
    else if ( (a == null) || (b == null) )
    {
      throw new AssertionError();
    }
    else if (a.equals(b))
    {
      return;
    }

    throw new AssertionError();
  }

  static void assertNotEquals(Object a, Object b) throws AssertionError
  {
    if ( (a == null) && (b == null) )
    {
      throw new AssertionError();
    }
    else if ( (a == null) || (b == null) )
    {
      return;
    }
    else if (a.equals(b))
    {
      throw new AssertionError();
    }
  }

  static void assertEquals(boolean a, boolean b) throws AssertionError
  {
    if ( a == b )
    {
      return;
    }
    throw new AssertionError();
  }

  static void assertNotEquals(boolean a, boolean b) throws AssertionError
  {
    if ( a != b )
    {
      return;
    }
    throw new AssertionError();
  }

  static void assertEquals(int a, int b) throws AssertionError
  {
    if ( a == b )
    {
      return;
    }
    throw new AssertionError();
  }

  static void assertNotEquals(int a, int b) throws AssertionError
  {
    if ( a != b )
    {
      return;
    }
    throw new AssertionError();
  }
  private SBMLDocument D;
  private Model M;

  public String SBML_FOOTER()
  {
    return "</model> </sbml>";
  }

  public String SBML_HEADER_L1v1()
  {
    return "<sbml xmlns='http://www.sbml.org/sbml/level1' level='1' version='1'> <model name='m'>\n";
  }

  public String SBML_HEADER_L1v2()
  {
    return "<sbml xmlns='http://www.sbml.org/sbml/level1' level='1' version='2'> <model name='m'>\n";
  }

  public String SBML_HEADER_L2v1()
  {
    return "<sbml xmlns='http://www.sbml.org/sbml/level2' level='2' version='1'> <model name='m'>\n";
  }

  public String SBML_HEADER_L2v2()
  {
    return "<sbml xmlns='http://www.sbml.org/sbml/level2/version2' level='2' version='2'> <model name='m'>\n";
  }

  public String SBML_HEADER_L2v3()
  {
    return "<sbml xmlns='http://www.sbml.org/sbml/level2/version3' level='2' version='3'> <model name='m'>\n";
  }

  public String XML_HEADER()
  {
    return "<?xml version='1.0' encoding='UTF-8'?>\n";
  }

  public String wrapSBML_L1v1(String s)
  {
    String r = XML_HEADER();
    r += SBML_HEADER_L1v1();
    r += s;
    r += SBML_FOOTER();
    return r;
  }

  public String wrapSBML_L1v2(String s)
  {
    String r = XML_HEADER();
    r += SBML_HEADER_L1v2();
    r += s;
    r += SBML_FOOTER();
    return r;
  }

  public String wrapSBML_L2v1(String s)
  {
    String r = XML_HEADER();
    r += SBML_HEADER_L2v1();
    r += s;
    r += SBML_FOOTER();
    return r;
  }

  public String wrapSBML_L2v2(String s)
  {
    String r = XML_HEADER();
    r += SBML_HEADER_L2v2();
    r += s;
    r += SBML_FOOTER();
    return r;
  }

  public String wrapSBML_L2v3(String s)
  {
    String r = XML_HEADER();
    r += SBML_HEADER_L2v3();
    r += s;
    r += SBML_FOOTER();
    return r;
  }

  public String wrapXML(String s)
  {
    String r = XML_HEADER();
    r += s;
    return r;
  }


  private int USE_LIBXML = 0;
  private int USE_EXPAT  = 0;
  private int USE_XERCES = 0;

  public void setXMLParser() 
  {
    String make_config = "../../../config/makefile-common-vars.mk";

    Pattern pt_expat  = Pattern.compile("^USE_EXPAT\\s*=\\s*1");
    Pattern pt_libxml = Pattern.compile("^USE_LIBXML\\s*=\\s*1");
    Pattern pt_xerces = Pattern.compile("^USE_XERCES\\s*=\\s*1");

    try
    {
      FileInputStream fis = new FileInputStream(make_config);
      InputStreamReader ir = new InputStreamReader(fis);
      BufferedReader br = new BufferedReader(ir);

      String line;
      while( (line = br.readLine()) != null)
      {
        Matcher m; 

        m = pt_libxml.matcher(line);
        if ( m.matches() )
        {
          USE_LIBXML = 1;
        }
  
        m = pt_expat.matcher(line);
        if ( m.matches() )
        {
          USE_EXPAT = 1;
        }

        m = pt_xerces.matcher(line);
        if ( m.matches() )
        {
          USE_XERCES = 1;
        }
      }
    }
    catch (Exception e)
    {
      System.exit(1);    
    }
  }

  protected void setUp() throws Exception
  {
    D = null;
  }

  protected void tearDown() throws Exception
  {
    D = null;
  }

  public void test_ReadSBML_AlgebraicRule()
  {
    Rule ar;
    String s = wrapSBML_L1v2("<listOfRules>" + 
    "  <algebraicRule formula='x + 1'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    ar = M.getRule(0);
    assertTrue(ar.getFormula().equals( "x + 1"));
  }

  public void test_ReadSBML_AlgebraicRule_L2()
  {
    Rule ar;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfRules>" + 
    "  <algebraicRule>" + 
    "    <math>" + 
    "      <apply>" + 
    "        <minus/>" + 
    "        <apply>" + 
    "          <plus/>" + 
    "            <ci> S1 </ci>" + 
    "            <ci> S2 </ci>" + 
    "        </apply>" + 
    "        <ci> T </ci>" + 
    "      </apply>" + 
    "    </math>" + 
    "  </algebraicRule>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    ar = M.getRule(0);
    assertTrue( ar != null );
    assertEquals( true, ar.isSetMath() );
    math = ar.getMath();
    formula = ar.getFormula();
    assertTrue( formula != null );
    assertTrue(formula.equals( "S1 + S2 - T"));
  }

  public void test_ReadSBML_AssignmentRule()
  {
    Rule ar;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfRules>" + 
    "  <assignmentRule variable='k'>" + 
    "    <math>" + 
    "      <apply>" + 
    "        <divide/>" + 
    "        <ci> k3 </ci>" + 
    "        <ci> k2 </ci>" + 
    "      </apply>" + 
    "    </math>" + 
    "  </assignmentRule>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    ar = M.getRule(0);
    assertTrue( ar != null );
    assertEquals( true, ar.isSetMath() );
    math = ar.getMath();
    formula = ar.getFormula();
    assertTrue( formula != null );
    assertTrue(formula.equals( "k3 / k2"));
  }

  public void test_ReadSBML_Compartment()
  {
    Compartment c;
    String s = wrapSBML_L1v2("<listOfCompartments>" + 
    "  <compartment name='mitochondria' volume='.0001' units='milliliters'" + 
    "               outside='cell'/>" + 
    "</listOfCompartments>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumCompartments() == 1 );
    c = M.getCompartment(0);
    assertTrue(c.getId().equals( "mitochondria" ));
    assertTrue(c.getUnits().equals( "milliliters"  ));
    assertTrue(c.getOutside().equals( "cell"         ));
    assertTrue( c.getVolume() == .0001 );
    assertEquals( true, c.isSetVolume() );
    assertEquals( true, c.isSetSize() );
  }

  public void test_ReadSBML_CompartmentVolumeRule()
  {
    Rule cvr;
    String s = wrapSBML_L1v2("<listOfRules>" + 
    "  <compartmentVolumeRule compartment='A' formula='0.10 * t'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    cvr = M.getRule(0);
    assertEquals( true, cvr.isCompartmentVolume() );
    assertTrue(cvr.getVariable().equals( "A"));
    assertTrue(cvr.getFormula().equals( "0.10 * t" ));
    assertTrue( cvr.getType() == libsbml.RULE_TYPE_SCALAR );
  }

  public void test_ReadSBML_Compartment_L2()
  {
    Compartment c;
    String s = wrapSBML_L2v1("<listOfCompartments>" + 
    "  <compartment id='membrane' size='.3' spatialDimensions='2'" + 
    "               units='area' outside='tissue' constant='false'/>" + 
    "</listOfCompartments>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumCompartments() == 1 );
    c = M.getCompartment(0);
    assertEquals( true, c.isSetId() );
    assertEquals( false, c.isSetName() );
    assertEquals( true, c.isSetVolume() );
    assertEquals( true, c.isSetSize() );
    assertEquals( true, c.isSetUnits() );
    assertEquals( true, c.isSetOutside() );
    assertTrue(c.getId().equals( "membrane" ));
    assertTrue(c.getUnits().equals( "area"     ));
    assertTrue(c.getOutside().equals( "tissue"   ));
    assertTrue( c.getSpatialDimensions() == 2 );
    assertTrue( c.getSize() == .3 );
  }

  public void test_ReadSBML_Compartment_defaults()
  {
    Compartment c;
    String s = wrapSBML_L1v2("<listOfCompartments> <compartment name='cell'/> </listOfCompartments>"  
    );
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumCompartments() == 1 );
    c = M.getCompartment(0);
    assertEquals( true, c.isSetId() );
    assertEquals( true, c.isSetVolume() );
    assertEquals( false, c.isSetSize() );
    assertEquals( false, c.isSetUnits() );
    assertEquals( false, c.isSetOutside() );
    assertTrue(c.getId().equals( "cell" ));
    assertTrue( c.getVolume() == 1.0 );
  }

  public void test_ReadSBML_Compartment_defaults_L2()
  {
    Compartment c;
    String s = wrapSBML_L2v1("<listOfCompartments> <compartment id='cell'/> </listOfCompartments>"  
    );
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumCompartments() == 1 );
    c = M.getCompartment(0);
    assertEquals( true, c.isSetId() );
    assertEquals( false, c.isSetName() );
    assertEquals( false, c.isSetSize() );
    assertEquals( false, c.isSetUnits() );
    assertEquals( false, c.isSetOutside() );
    assertTrue(c.getId().equals( "cell" ));
    assertTrue( c.getSpatialDimensions() == 3 );
    assertTrue( c.getConstant() == true );
  }

  public void test_ReadSBML_Event()
  {
    Event e;
    String s = wrapSBML_L2v2("<listOfEvents>" + 
    "  <event id='e1' name='MyEvent' timeUnits='time'/>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumEvents() == 1 );
    e = M.getEvent(0);
    assertTrue( e != null );
    assertEquals( true, e.isSetId() );
    assertEquals( true, e.isSetName() );
    assertEquals( true, e.isSetTimeUnits() );
    assertEquals( false, e.isSetTrigger() );
    assertEquals( false, e.isSetDelay() );
    assertTrue(e.getId().equals( "e1"      ));
    assertTrue(e.getName().equals( "MyEvent" ));
    assertTrue(e.getTimeUnits().equals( "time"    ));
  }

  public void test_ReadSBML_EventAssignment()
  {
    Event e;
    EventAssignment ea;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfEvents>" + 
    "  <event>" + 
    "    <listOfEventAssignments>" + 
    "      <eventAssignment variable='k2'>" + 
    "        <math> <cn> 0 </cn> </math>" + 
    "      </eventAssignment>" + 
    "    </listOfEventAssignments>" + 
    "  </event>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumEvents() == 1 );
    e = M.getEvent(0);
    assertTrue( e != null );
    assertTrue( e.getNumEventAssignments() == 1 );
    ea = e.getEventAssignment(0);
    assertTrue( ea != null );
    assertEquals( true, ea.isSetVariable() );
    assertTrue(ea.getVariable().equals( "k2"));
    assertEquals( true, ea.isSetMath() );
    math = ea.getMath();
    formula = libsbml.formulaToString(math);
    assertTrue( formula != null );
    assertTrue(formula.equals( "0"));
  }

  public void test_ReadSBML_Event_delay()
  {
    Event e;
    Delay delay;
    String formula;
    String s = wrapSBML_L2v1("<listOfEvents>" + 
    "  <event> <delay> <math> <cn> 5 </cn> </math> </delay> </event>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumEvents() == 1 );
    e = M.getEvent(0);
    assertTrue( e != null );
    assertEquals( true, e.isSetDelay() );
    assertEquals( false, e.isSetTrigger() );
    delay = e.getDelay();
    formula = libsbml.formulaToString(delay.getMath());
    assertTrue( formula != null );
    assertTrue(formula.equals( "5"));
  }

  public void test_ReadSBML_Event_trigger()
  {
    Event e;
    Trigger trigger;
    String formula;
    String s = wrapSBML_L2v1("<listOfEvents>" + 
    "  <event>" + 
    "    <trigger>" + 
    "      <math>" + 
    "        <apply>" + 
    "          <leq/>" + 
    "          <ci> P1 </ci>" + 
    "          <ci> t  </ci>" + 
    "        </apply>" + 
    "      </math>" + 
    "   </trigger>" + 
    "  </event>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumEvents() == 1 );
    e = M.getEvent(0);
    assertTrue( e != null );
    assertEquals( false, e.isSetDelay() );
    assertEquals( true, e.isSetTrigger() );
    trigger = e.getTrigger();
    formula = libsbml.formulaToString(trigger.getMath());
    assertTrue( formula != null );
    assertTrue(formula.equals( "leq(P1, t)"));
  }

  public void test_ReadSBML_FunctionDefinition()
  {
    FunctionDefinition fd;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfFunctionDefinitions>" + 
    "  <functionDefinition id='pow3' name='cubed'>" + 
    "    <math>" + 
    "      <lambda>" + 
    "        <bvar><ci> x </ci></bvar>" + 
    "        <apply>" + 
    "          <power/>" + 
    "          <ci> x </ci>" + 
    "          <cn> 3 </cn>" + 
    "        </apply>" + 
    "      </lambda>" + 
    "    </math>" + 
    "  </functionDefinition>" + 
    "</listOfFunctionDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumFunctionDefinitions() == 1 );
    fd = M.getFunctionDefinition(0);
    assertTrue( fd != null );
    assertEquals( true, fd.isSetId() );
    assertEquals( true, fd.isSetName() );
    assertTrue(fd.getId().equals( "pow3"  ));
    assertTrue(fd.getName().equals( "cubed" ));
    assertEquals( true, fd.isSetMath() );
    math = fd.getMath();
    formula = libsbml.formulaToString(math);
    assertTrue( formula != null );
    assertTrue(formula.equals( "lambda(x, pow(x, 3))"));
  }

  public void test_ReadSBML_KineticLaw()
  {
    Reaction r;
    KineticLaw kl;
    String s = wrapSBML_L1v2("<listOfReactions>" + 
    "  <reaction name='J1'>" + 
    "    <kineticLaw formula='k1*X0'/>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals( "k1*X0"));
  }

  public void test_ReadSBML_KineticLaw_L2()
  {
    Reaction r;
    KineticLaw kl;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfReactions>" + 
    "  <reaction id='J1'>" + 
    "    <kineticLaw>" + 
    "      <math>" + 
    "        <apply>" + 
    "          <times/>" + 
    "          <ci> k  </ci>" + 
    "          <ci> S2 </ci>" + 
    "          <ci> X0 </ci>" + 
    "        </apply>" + 
    "      </math>" + 
    "    </kineticLaw>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue( r != null );
    kl = r.getKineticLaw();
    assertTrue( kl != null );
    assertEquals( true, kl.isSetMath() );
    math = kl.getMath();
    formula = kl.getFormula();
    assertTrue( formula != null );
    assertTrue(formula.equals( "k * S2 * X0"));
  }

  public void test_ReadSBML_KineticLaw_Parameter()
  {
    Reaction r;
    KineticLaw kl;
    Parameter p;
    String s = wrapSBML_L1v2("<listOfReactions>" + 
    "  <reaction name='J1'>" + 
    "    <kineticLaw formula='k1*X0'>" + 
    "      <listOfParameters>" + 
    "        <parameter name='k1' value='0'/>" + 
    "      </listOfParameters>" + 
    "    </kineticLaw>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals( "k1*X0"));
    assertTrue( kl.getNumParameters() == 1 );
    p = kl.getParameter(0);
    assertTrue(p.getId().equals( "k1"));
    assertTrue( p.getValue() == 0 );
  }

  public void test_ReadSBML_Model()
  {
    String s = wrapXML("<sbml level='1' version='1'>" + 
    "  <model name='testModel'></model>" + 
    "</sbml>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue(M.getId().equals( "testModel"));
  }

  public void test_ReadSBML_Model_L2()
  {
    String s = wrapXML("<sbml level='2' version='1'>" + 
    "  <model id='testModel'> </model>" + 
    "</sbml>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertEquals( true, M.isSetId() );
    assertEquals( false, M.isSetName() );
    assertTrue(M.getId().equals( "testModel"));
  }

  public void test_ReadSBML_Parameter()
  {
    Parameter p;
    String s = wrapSBML_L1v2("<listOfParameters>" + 
    "  <parameter name='Km1' value='2.3' units='second'/>" + 
    "</listOfParameters>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumParameters() == 1 );
    p = M.getParameter(0);
    assertTrue(p.getId().equals( "Km1"    ));
    assertTrue(p.getUnits().equals( "second" ));
    assertTrue( p.getValue() == 2.3 );
    assertTrue( p.isSetValue() == true );
  }

  public void test_ReadSBML_ParameterRule()
  {
    Rule pr;
    String s = wrapSBML_L1v2("<listOfRules>" + 
    "  <parameterRule name='k' formula='k3/k2'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    pr = M.getRule(0);
    assertEquals( true, pr.isParameter() );
    assertTrue(pr.getVariable().equals( "k"));
    assertTrue(pr.getFormula().equals( "k3/k2" ));
    assertTrue( pr.getType() == libsbml.RULE_TYPE_SCALAR );
  }

  public void test_ReadSBML_Parameter_L2()
  {
    Parameter p;
    String s = wrapSBML_L2v1("<listOfParameters>" + 
    "  <parameter id='T' value='4.6' units='Celsius' constant='false'/>" + 
    "</listOfParameters>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumParameters() == 1 );
    p = M.getParameter(0);
    assertEquals( true, p.isSetId() );
    assertEquals( false, p.isSetName() );
    assertEquals( true, p.isSetValue() );
    assertEquals( true, p.isSetUnits() );
    assertTrue(p.getId().equals( "T"       ));
    assertTrue(p.getUnits().equals( "Celsius" ));
    assertTrue( p.getValue() == 4.6 );
    assertTrue( p.getConstant() == false );
  }

  public void test_ReadSBML_Parameter_L2_defaults()
  {
    Parameter p;
    String s = wrapSBML_L2v1("<listOfParameters> <parameter id='x'/> </listOfParameters>"  
    );
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumParameters() == 1 );
    p = M.getParameter(0);
    assertEquals( true, p.isSetId() );
    assertEquals( false, p.isSetName() );
    assertEquals( false, p.isSetValue() );
    assertEquals( false, p.isSetUnits() );
    assertTrue(p.getId().equals( "x"));
    assertTrue( p.getConstant() == true );
  }

  public void test_ReadSBML_RateRule()
  {
    Rule rr;
    ASTNode math;
    String formula;
    String s = wrapSBML_L2v1("<listOfRules>" + 
    "  <rateRule variable='x'>" + 
    "    <math>" + 
    "      <apply>" + 
    "        <times/>" + 
    "        <apply>" + 
    "          <minus/>" + 
    "          <cn> 1 </cn>" + 
    "          <ci> x </ci>" + 
    "        </apply>" + 
    "        <apply>" + 
    "          <ln/>" + 
    "          <ci> x </ci>" + 
    "        </apply>" + 
    "      </apply>" + 
    "    </math>" + 
    "  </rateRule>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    rr = M.getRule(0);
    assertTrue( rr != null );
    assertEquals( true, rr.isSetMath() );
    math = rr.getMath();
    formula = rr.getFormula();
    assertTrue( formula != null );
    assertTrue(formula.equals( "(1 - x) * log(x)"));
  }

  public void test_ReadSBML_Reaction()
  {
    Reaction r;
    String s = wrapSBML_L1v2("<listOfReactions>" + 
    "  <reaction name='reaction_1' reversible='false'/>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getFast() == false );
  }

  public void test_ReadSBML_Reaction_L2()
  {
    Reaction r;
    String s = wrapSBML_L2v1("<listOfReactions>" + 
    "  <reaction id='r1' reversible='false' fast='false'/>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertEquals( true, r.isSetId() );
    assertEquals( false, r.isSetName() );
    assertEquals( true, r.isSetFast() );
    assertTrue(r.getId().equals( "r1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getFast() == false );
  }

  public void test_ReadSBML_Reaction_L2_defaults()
  {
    Reaction r;
    String s = wrapSBML_L2v1("<listOfReactions> <reaction id='r1'/> </listOfReactions>"  
    );
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertEquals( true, r.isSetId() );
    assertEquals( false, r.isSetName() );
    assertEquals( false, r.isSetFast() );
    assertTrue(r.getId().equals( "r1"));
    assertTrue( r.getReversible() == true );
  }

  public void test_ReadSBML_Reaction_defaults()
  {
    Reaction r;
    String s = wrapSBML_L1v2("<listOfReactions>" + 
    "  <reaction name='reaction_1'/>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() != false );
    assertTrue( r.getFast() == false );
  }

  public void test_ReadSBML_SBML()
  {
    String s = wrapXML("<sbml level='1' version='1'> </sbml>");
    D = libsbml.readSBMLFromString(s);
    assertTrue( D.getLevel() == 1 );
    assertTrue( D.getVersion() == 1 );
  }

  public void test_ReadSBML_Specie()
  {
    Species sp;
    String s = wrapSBML_L1v1("<listOfSpecie>" + 
    "  <specie name='Glucose' compartment='cell' initialAmount='4.1'" + 
    "          units='volume' boundaryCondition='false' charge='6'/>" + 
    "</listOfSpecie>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertTrue(sp.getId().equals( "Glucose" ));
    assertTrue(sp.getCompartment().equals( "cell"    ));
    assertTrue(sp.getUnits().equals( "volume"  ));
    assertTrue( sp.getInitialAmount() == 4.1 );
    assertTrue( sp.getBoundaryCondition() == false );
    assertTrue( sp.getCharge() == 6 );
    assertTrue( sp.isSetInitialAmount() == true );
    assertTrue( sp.isSetCharge() == true );
  }

  public void test_ReadSBML_SpecieConcentrationRule()
  {
    Rule scr;
    String s = wrapSBML_L1v1("<listOfRules>" + 
    "  <specieConcentrationRule specie='s2' formula='k * t/(1 + k)'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    scr = M.getRule(0);
    assertEquals( true, scr.isSpeciesConcentration() );
    assertTrue(scr.getVariable().equals( "s2"));
    assertTrue(scr.getFormula().equals( "k * t/(1 + k)" ));
    assertTrue( scr.getType() == libsbml.RULE_TYPE_SCALAR );
  }

  public void test_ReadSBML_SpecieConcentrationRule_rate()
  {
    Rule scr;
    String s = wrapSBML_L1v1("<listOfRules>" + 
    "  <specieConcentrationRule specie='s2' formula='k * t/(1 + k)' " + 
    "                           type='rate'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    scr = M.getRule(0);
    assertEquals( true, scr.isSpeciesConcentration() );
    assertTrue(scr.getVariable().equals( "s2"));
    assertTrue(scr.getFormula().equals( "k * t/(1 + k)" ));
    assertTrue( scr.getType() == libsbml.RULE_TYPE_RATE );
  }

  public void test_ReadSBML_SpecieReference_Product()
  {
    Reaction r;
    SpeciesReference sr;
    String s = wrapSBML_L1v1("<listOfReactions>" + 
    "  <reaction name='reaction_1' reversible='false'>" + 
    "    <listOfProducts>" + 
    "      <specieReference specie='S1' stoichiometry='1'/>" + 
    "    </listOfProducts>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getNumProducts() == 1 );
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals( "S1"));
    assertTrue( sr.getStoichiometry() == 1 );
    assertTrue( sr.getDenominator() == 1 );
  }

  public void test_ReadSBML_SpecieReference_Reactant()
  {
    Reaction r;
    SpeciesReference sr;
    String s = wrapSBML_L1v1("<listOfReactions>" + 
    "  <reaction name='reaction_1' reversible='false'>" + 
    "    <listOfReactants>" + 
    "      <specieReference specie='X0' stoichiometry='1'/>" + 
    "    </listOfReactants>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getNumReactants() == 1 );
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals( "X0"));
    assertTrue( sr.getStoichiometry() == 1 );
    assertTrue( sr.getDenominator() == 1 );
  }

  public void test_ReadSBML_SpecieReference_defaults()
  {
    Reaction r;
    SpeciesReference sr;
    String s = wrapSBML_L1v1("<listOfReactions>" + 
    "  <reaction name='reaction_1' reversible='false'>" + 
    "    <listOfReactants>" + 
    "      <specieReference specie='X0'/>" + 
    "    </listOfReactants>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getNumReactants() == 1 );
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals( "X0"));
    assertTrue( sr.getStoichiometry() == 1 );
    assertTrue( sr.getDenominator() == 1 );
  }

  public void test_ReadSBML_Specie_defaults()
  {
    Species sp;
    String s = wrapSBML_L1v1("<listOfSpecie>" + 
    "  <specie name='Glucose' compartment='cell' initialAmount='1.0'/>" + 
    "</listOfSpecie>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertTrue(sp.getId().equals( "Glucose" ));
    assertTrue(sp.getCompartment().equals( "cell"    ));
    assertTrue( sp.getInitialAmount() == 1.0 );
    assertTrue( sp.getBoundaryCondition() == false );
    assertTrue( sp.isSetInitialAmount() == true );
    assertTrue( sp.isSetCharge() == false );
  }

  public void test_ReadSBML_Species()
  {
    Species sp;
    String s = wrapSBML_L1v2("<listOfSpecies>" + 
    "  <species name='Glucose' compartment='cell' initialAmount='4.1'" + 
    "           units='volume' boundaryCondition='false' charge='6'/>" + 
    "</listOfSpecies>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertTrue(sp.getId().equals( "Glucose" ));
    assertTrue(sp.getCompartment().equals( "cell"    ));
    assertTrue(sp.getUnits().equals( "volume"  ));
    assertTrue( sp.getInitialAmount() == 4.1 );
    assertTrue( sp.getBoundaryCondition() == false );
    assertTrue( sp.getCharge() == 6 );
    assertTrue( sp.isSetInitialAmount() == true );
    assertTrue( sp.isSetCharge() == true );
  }

  public void test_ReadSBML_SpeciesConcentrationRule()
  {
    Rule scr;
    String s = wrapSBML_L1v2("<listOfRules>" + 
    "  <speciesConcentrationRule species='s2' formula='k * t/(1 + k)'/>" + 
    "</listOfRules>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumRules() == 1 );
    scr = M.getRule(0);
    assertEquals( true, scr.isSpeciesConcentration() );
    assertTrue(scr.getVariable().equals( "s2"));
    assertTrue(scr.getFormula().equals( "k * t/(1 + k)" ));
    assertTrue( scr.getType() == libsbml.RULE_TYPE_SCALAR );
  }

  public void test_ReadSBML_SpeciesReference_StoichiometryMath_1()
  {
    Reaction r;
    SpeciesReference sr;
    StoichiometryMath math;
    String formula;
    String s = wrapSBML_L2v1("<listOfReactions>" + 
    "  <reaction name='r1'>" + 
    "    <listOfReactants>" + 
    "      <speciesReference species='X0'>" + 
    "        <stoichiometryMath>" + 
    "          <math> <ci> x </ci> </math>" + 
    "        </stoichiometryMath>" + 
    "      </speciesReference>" + 
    "    </listOfReactants>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue( r != null );
    assertTrue( r.getNumReactants() == 1 );
    sr = r.getReactant(0);
    assertTrue( sr != null );
    assertEquals( true, sr.isSetStoichiometryMath() );
    math = sr.getStoichiometryMath();
    formula = libsbml.formulaToString(math.getMath());
    assertTrue( formula != null );
    assertTrue(formula.equals( "x"));
  }

  public void test_ReadSBML_SpeciesReference_StoichiometryMath_2()
  {
    Reaction r;
    SpeciesReference sr;
    String s = wrapSBML_L2v1("<listOfReactions>" + 
    "  <reaction name='r1'>" + 
    "    <listOfReactants>" + 
    "      <speciesReference species='X0'>" + 
    "        <stoichiometryMath>" + 
    "          <math> <cn type='rational'> 3 <sep/> 2 </cn> </math>" + 
    "        </stoichiometryMath>" + 
    "      </speciesReference>" + 
    "    </listOfReactants>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue( r != null );
    assertTrue( r.getNumReactants() == 1 );
    sr = r.getReactant(0);
    assertTrue( sr != null );
    assertEquals( false, sr.isSetStoichiometryMath() );
    assertTrue( sr.getStoichiometry() == 3 );
    assertTrue( sr.getDenominator() == 2 );
  }

  public void test_ReadSBML_SpeciesReference_defaults()
  {
    Reaction r;
    SpeciesReference sr;
    String s = wrapSBML_L1v2("<listOfReactions>" + 
    "  <reaction name='reaction_1' reversible='false'>" + 
    "    <listOfReactants>" + 
    "      <speciesReference species='X0'/>" + 
    "    </listOfReactants>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumReactions() == 1 );
    r = M.getReaction(0);
    assertTrue(r.getId().equals( "reaction_1"));
    assertTrue( r.getReversible() == false );
    assertTrue( r.getNumReactants() == 1 );
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals( "X0"));
    assertTrue( sr.getStoichiometry() == 1 );
    assertTrue( sr.getDenominator() == 1 );
  }

  public void test_ReadSBML_Species_L2_1()
  {
    Species sp;
    String s = wrapSBML_L2v1("<listOfSpecies>" + 
    "  <species id='Glucose' compartment='cell' initialConcentration='4.1'" + 
    "           substanceUnits='item' spatialSizeUnits='volume'" + 
    "           boundaryCondition='true' charge='6' constant='true'/>" + 
    "</listOfSpecies>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertEquals( true, sp.isSetId() );
    assertEquals( false, sp.isSetName() );
    assertEquals( true, sp.isSetCompartment() );
    assertEquals( false, sp.isSetInitialAmount() );
    assertEquals( true, sp.isSetInitialConcentration() );
    assertEquals( true, sp.isSetSubstanceUnits() );
    assertEquals( true, sp.isSetSpatialSizeUnits() );
    assertEquals( true, sp.isSetCharge() );
    assertTrue(sp.getId().equals( "Glucose" ));
    assertTrue(sp.getCompartment().equals( "cell"    ));
    assertTrue(sp.getSubstanceUnits().equals( "item"    ));
    assertTrue(sp.getSpatialSizeUnits().equals( "volume"  ));
    assertTrue( sp.getInitialConcentration() == 4.1 );
    assertTrue( sp.getHasOnlySubstanceUnits() == false );
    assertTrue( sp.getBoundaryCondition() == true );
    assertTrue( sp.getCharge() == 6 );
    assertTrue( sp.getConstant() == true );
  }

  public void test_ReadSBML_Species_L2_2()
  {
    Species sp;
    String s = wrapSBML_L2v1("<listOfSpecies>" + 
    "  <species id='s' compartment='c' hasOnlySubstanceUnits='true'/>" + 
    "</listOfSpecies>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertEquals( true, sp.isSetId() );
    assertEquals( false, sp.isSetName() );
    assertEquals( true, sp.isSetCompartment() );
    assertEquals( false, sp.isSetInitialAmount() );
    assertEquals( false, sp.isSetInitialConcentration() );
    assertEquals( false, sp.isSetSubstanceUnits() );
    assertEquals( false, sp.isSetSpatialSizeUnits() );
    assertEquals( false, sp.isSetCharge() );
    assertTrue(sp.getId().equals( "s" ));
    assertTrue(sp.getCompartment().equals( "c" ));
    assertTrue( sp.getHasOnlySubstanceUnits() == true );
    assertTrue( sp.getBoundaryCondition() == false );
    assertTrue( sp.getConstant() == false );
  }

  public void test_ReadSBML_Species_L2_defaults()
  {
    Species sp;
    String s = wrapSBML_L2v1("<listOfSpecies>" + 
    "  <species id='Glucose_6_P' compartment='cell'/>" + 
    "</listOfSpecies>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumSpecies() == 1 );
    sp = M.getSpecies(0);
    assertEquals( true, sp.isSetId() );
    assertEquals( false, sp.isSetName() );
    assertEquals( true, sp.isSetCompartment() );
    assertEquals( false, sp.isSetInitialAmount() );
    assertEquals( false, sp.isSetInitialConcentration() );
    assertEquals( false, sp.isSetSubstanceUnits() );
    assertEquals( false, sp.isSetSpatialSizeUnits() );
    assertEquals( false, sp.isSetCharge() );
    assertTrue(sp.getId().equals( "Glucose_6_P" ));
    assertTrue(sp.getCompartment().equals( "cell"        ));
    assertTrue( sp.getHasOnlySubstanceUnits() == false );
    assertTrue( sp.getBoundaryCondition() == false );
    assertTrue( sp.getConstant() == false );
  }

  public void test_ReadSBML_Unit()
  {
    Unit u;
    UnitDefinition ud;
    String s = wrapSBML_L1v2("<listOfUnitDefinitions>" + 
    "  <unitDefinition name='substance'>" + 
    "    <listOfUnits> <unit kind='mole' scale='-3'/> </listOfUnits>" + 
    "  </unitDefinition>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumUnitDefinitions() == 1 );
    ud = M.getUnitDefinition(0);
    assertTrue(ud.getId().equals( "substance"));
    assertTrue( ud.getNumUnits() == 1 );
    u = ud.getUnit(0);
    assertTrue( u.getKind() == libsbml.UNIT_KIND_MOLE );
    assertTrue( u.getExponent() == 1 );
    assertTrue( u.getScale() == -3 );
  }

  public void test_ReadSBML_UnitDefinition()
  {
    UnitDefinition ud;
    String s = wrapSBML_L1v2("<listOfUnitDefinitions>" + 
    "  <unitDefinition name='mmls'/>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumUnitDefinitions() == 1 );
    ud = M.getUnitDefinition(0);
    assertTrue(ud.getId().equals( "mmls"));
  }

  public void test_ReadSBML_UnitDefinition_L2()
  {
    UnitDefinition ud;
    String s = wrapSBML_L2v1("<listOfUnitDefinitions>" + 
    "  <unitDefinition id='mmls' name='mmol/ls'/>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumUnitDefinitions() == 1 );
    ud = M.getUnitDefinition(0);
    assertEquals( true, ud.isSetId() );
    assertEquals( true, ud.isSetName() );
    assertTrue(ud.getId().equals( "mmls"));
    assertTrue(ud.getName().equals( "mmol/ls"));
  }

  public void test_ReadSBML_Unit_L2()
  {
    Unit u;
    UnitDefinition ud;
    String s = wrapSBML_L2v1("<listOfUnitDefinitions>" + 
    "  <unitDefinition id='Fahrenheit'>" + 
    "    <listOfUnits>" + 
    "      <unit kind='Celsius' multiplier='1.8' offset='32'/>" + 
    "    </listOfUnits>" + 
    "  </unitDefinition>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumUnitDefinitions() == 1 );
    ud = M.getUnitDefinition(0);
    assertEquals( true, ud.isSetId() );
    assertTrue(ud.getId().equals( "Fahrenheit"));
    assertTrue( ud.getNumUnits() == 1 );
    u = ud.getUnit(0);
    assertTrue( u.getKind() == libsbml.UNIT_KIND_CELSIUS );
    assertTrue( u.getExponent() == 1 );
    assertTrue( u.getScale() == 0 );
    assertTrue( u.getMultiplier() == 1.8 );
    assertTrue( u.getOffset() == 32 );
  }

  public void test_ReadSBML_Unit_defaults_L1_L2()
  {
    Unit u;
    UnitDefinition ud;
    String s = wrapSBML_L1v2("<listOfUnitDefinitions>" + 
    "  <unitDefinition name='bogomips'>" + 
    "    <listOfUnits> <unit kind='second'/> </listOfUnits>" + 
    "  </unitDefinition>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNumUnitDefinitions() == 1 );
    ud = M.getUnitDefinition(0);
    assertTrue(ud.getId().equals( "bogomips"));
    assertTrue( ud.getNumUnits() == 1 );
    u = ud.getUnit(0);
    assertTrue( u.getKind() == libsbml.UNIT_KIND_SECOND );
    assertTrue( u.getExponent() == 1 );
    assertTrue( u.getScale() == 0 );
    assertTrue( u.getMultiplier() == 1.0 );
    assertTrue( u.getOffset() == 0.0 );
  }

  public void test_ReadSBML_annotation()
  {
    String s = wrapSBML_L2v3("<annotation xmlns:mysim=\"http://www.mysim.org/ns\">" + 
    "  <mysim:nodecolors mysim:bgcolor=\"green\" mysim:fgcolor=\"white\">" + 
    "  </mysim:nodecolors>" + 
    "  <mysim:timestamp>2000-12-18 18:31 PST</mysim:timestamp>" + 
    "</annotation>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getAnnotation() != null );
    XMLNode ann = M.getAnnotation();
    assertTrue( ann.getNumChildren() == 2 );
  }

  public void test_ReadSBML_annotation_sbml()
  {
    String s = wrapXML("<sbml level=\"1\" version=\"1\">" + 
    "  <annotation xmlns:jd = \"http://www.sys-bio.org/sbml\">" + 
    "    <jd:header>" + 
    "      <VersionHeader SBMLVersion = \"1.0\"/>" + 
    "    </jd:header>" + 
    "    <jd:display>" + 
    "      <SBMLGraphicsHeader BackGroundColor = \"15728639\"/>" + 
    "    </jd:display>" + 
    "  </annotation>" + 
    "</sbml>");
    D = libsbml.readSBMLFromString(s);
    assertTrue( D.getNumErrors() > 0 );
  }

  public void test_ReadSBML_annotation_sbml_L2()
  {
    String s = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\"> " + 
    "  <annotation>" + 
    "    <rdf xmlns=\"http://www.w3.org/1999/anything\">" + 
    "		 </rdf>" + 
    "	  </annotation>" + 
    "	  <model>" + 
    "   </model>" + 
    " </sbml>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( D.getNumErrors() == 0 );
  }

  public void test_ReadSBML_invalid_default_namespace()
  {
    String valid = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\"> " + 
    "   <model>" + 
    "     <notes>" + 
    "       <p xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</p>" + 
    "     </notes>" + 
    "     <annotation>" + 
    "       <example xmlns=\"http://www.example.org/\"/>" + 
    "     </annotation>" + 
    "     <listOfCompartments>" + 
    "       <compartment id=\"compartmentOne\" size=\"1\"/>" + 
    "     </listOfCompartments>" + 
    "     <listOfSpecies>" + 
    "       <species id=\"S1\" initialConcentration=\"1\" compartment=\"compartmentOne\"/>" + 
    "       <species id=\"S2\" initialConcentration=\"0\" compartment=\"compartmentOne\"/>" + 
    "     </listOfSpecies>" + 
    "     <listOfParameters>" + 
    "       <parameter id=\"t\" value = \"1\" units=\"second\"/>" + 
    "     </listOfParameters>" + 
    "     <listOfConstraints>" + 
    "       <constraint sboTerm=\"SBO:0000064\">" + 
    "         <math xmlns=\"http://www.w3.org/1998/Math/MathML\">" + 
    "           <apply>" + 
    "             <leq/>" + 
    "             <ci> S1 </ci>" + 
    "             <ci> t </ci>" + 
    "           </apply>" + 
    "         </math>" + 
    "         <message>" + 
    "           <p xmlns=\"http://www.w3.org/1999/xhtml\"> Species S1 is out of range </p>" + 
    "         </message>" + 
    "       </constraint>" + 
    "     </listOfConstraints>" + 
    "     <listOfReactions>" + 
    "       <reaction id=\"reaction_1\" reversible=\"false\">" + 
    "           <listOfReactants>" + 
    "             <speciesReference species=\"S1\"/>" + 
    "           </listOfReactants>" + 
    "           <listOfProducts>" + 
    "             <speciesReference species=\"S2\">" + 
    "             </speciesReference>" + 
    "           </listOfProducts>" + 
    "       </reaction>" + 
    "     </listOfReactions>" + 
    "   </model>" + 
    " </sbml>");
    String invalid = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\"> " + 
    "   <model xmlns=\"http://invalid/custom/default/uri\">" + 
    "     <notes xmlns=\"http://invalid/custom/default/uri/in/notes\">" + 
    "       <p xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</p>" + 
    "     </notes>" + 
    "     <annotation xmlns=\"http://invalid/custom/default/uri/in/annotation\">" + 
    "       <example xmlns=\"http://www.example.org/\"/>" + 
    "     </annotation>" + 
    "     <listOfCompartments>" + 
    "       <compartment id=\"compartmentOne\" size=\"1\"/>" + 
    "     </listOfCompartments>" + 
    "     <listOfSpecies>" + 
    "       <notes xmlns=\"http://invalid/custom/default/uri/in/notes\">" + 
    "         <p xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</p>" + 
    "       </notes>" + 
    "       <annotation xmlns=\"http://invalid/custom/default/uri/in/annotation\">" + 
    "         <example xmlns=\"http://www.example.org/\"/>" + 
    "       </annotation>" + 
    "       <species id=\"S1\" initialConcentration=\"1\" compartment=\"compartmentOne\"/>" + 
    "       <species id=\"S2\" initialConcentration=\"0\" compartment=\"compartmentOne\"/>" + 
    "     </listOfSpecies>" + 
    "     <listOfParameters>" + 
    "       <parameter id=\"t\" value = \"1\" units=\"second\"/>" + 
    "     </listOfParameters>" + 
    "     <listOfConstraints>" + 
    "       <constraint sboTerm=\"SBO:0000064\">" + 
    "         <math xmlns=\"http://www.w3.org/1998/Math/MathML\">" + 
    "           <apply>" + 
    "             <leq/>" + 
    "             <ci> S1 </ci>" + 
    "             <ci> t </ci>" + 
    "           </apply>" + 
    "         </math>" + 
    "         <message xmlns=\"http://invalid/custom/default/uri/in/message\">" + 
    "           <p xmlns=\"http://www.w3.org/1999/xhtml\"> Species S1 is out of range </p>" + 
    "         </message>" + 
    "       </constraint>" + 
    "     </listOfConstraints>" + 
    "     <listOfReactions>" + 
    "       <reaction id=\"reaction_1\" reversible=\"false\">" + 
    "           <listOfReactants>" + 
    "             <speciesReference xmlns=\"http://invalid/custom/default/uri\" species=\"S1\"/>" + 
    "           </listOfReactants>" + 
    "           <listOfProducts>" + 
    "             <speciesReference species=\"S2\">" + 
    "               <notes xmlns=\"http://invalid/custom/default/uri/in/notes\">" + 
    "                 <p xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</p>" + 
    "               </notes>" + 
    "               <annotation xmlns=\"http://invalid/custom/default/uri/in/annotation\">" + 
    "                 <example xmlns=\"http://www.example.org/\"/>" + 
    "               </annotation>" + 
    "             </speciesReference>" + 
    "           </listOfProducts>" + 
    "       </reaction>" + 
    "     </listOfReactions>" + 
    "   </model>" + 
    " </sbml>");
    D = libsbml.readSBMLFromString(valid);
    assertTrue( D.getNumErrors() == 0 );
    D = null;
    D = libsbml.readSBMLFromString(invalid);
    assertTrue( D.getNumErrors() == 9 );
  }

  public void test_ReadSBML_line_col_numbers()
  {
    setXMLParser();


    SBase sb;
    String s = "<?xml version='1.0' encoding='UTF-8'?>\n" + 
    "<sbml xmlns='http://www.sbml.org/sbml/level2' level='2' version='1'>\n" + 
    "  <model id='testModel' name='testModel'>\n" + 
    "    <listOfReactions> <reaction/> </listOfReactions>\n" + 
    "  </model>\n" + 
    "</sbml>\n";
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    sb = M;
    sb = M.getListOfReactions();
    sb = M.getReaction(0);
  }

  public void test_ReadSBML_metaid()
  {
    SBase sb;
    String s = wrapSBML_L2v1("<listOfFunctionDefinitions>" + 
    "  <functionDefinition metaid='fd'/>" + 
    "</listOfFunctionDefinitions>" + 
    "<listOfUnitDefinitions>" + 
    "  <unitDefinition metaid='ud'/>" + 
    "</listOfUnitDefinitions>" + 
    "<listOfCompartments>" + 
    "  <compartment metaid='c'/>" + 
    "</listOfCompartments>" + 
    "<listOfSpecies>" + 
    "  <species metaid='s'/>" + 
    "</listOfSpecies>" + 
    "<listOfParameters>" + 
    "  <parameter metaid='p'/>" + 
    "</listOfParameters>" + 
    "<listOfRules>" + 
    "  <rateRule metaid='rr'/>" + 
    "</listOfRules>" + 
    "<listOfReactions>" + 
    "  <reaction metaid='rx'/>" + 
    "</listOfReactions>" + 
    "<listOfEvents>" + 
    " <event metaid='e'/>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    sb = M.getFunctionDefinition(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "fd"));
    sb = M.getUnitDefinition(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "ud"));
    sb = M.getCompartment(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "c"));
    sb = M.getSpecies(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "s"));
    sb = M.getParameter(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "p"));
    sb = M.getRule(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "rr"));
    sb = M.getReaction(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "rx"));
    sb = M.getEvent(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "e"));
  }

  public void test_ReadSBML_metaid_Event()
  {
    SBase sb;
    Event e;
    String s = wrapSBML_L2v1("<listOfEvents>" + 
    "  <event metaid='e'>" + 
    "    <listOfEventAssignments metaid='loea'>" + 
    "      <eventAssignment metaid='ea'/>" + 
    "    </listOfEventAssignments>" + 
    "  </event>" + 
    "</listOfEvents>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    e = M.getEvent(0);
    sb = e;
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "e"));
    sb = e.getListOfEventAssignments();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "loea"));
    sb = e.getEventAssignment(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "ea"));
  }

  public void test_ReadSBML_metaid_ListOf()
  {
    SBase sb;
    String s = wrapSBML_L2v1("<listOfFunctionDefinitions metaid='lofd'/>" + 
    "<listOfUnitDefinitions     metaid='loud'/>" + 
    "<listOfCompartments        metaid='loc'/>" + 
    "<listOfSpecies             metaid='los'/>" + 
    "<listOfParameters          metaid='lop'/>" + 
    "<listOfRules               metaid='lor'/>" + 
    "<listOfReactions           metaid='lorx'/>" + 
    "<listOfEvents              metaid='loe'/>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    sb = M.getListOfFunctionDefinitions();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lofd"));
    sb = M.getListOfUnitDefinitions();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "loud"));
    sb = M.getListOfCompartments();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "loc"));
    sb = M.getListOfSpecies();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "los"));
    sb = M.getListOfParameters();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lop"));
    sb = M.getListOfRules();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lor"));
    sb = M.getListOfReactions();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lorx"));
    sb = M.getListOfEvents();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "loe"));
  }

  public void test_ReadSBML_metaid_Reaction()
  {
    SBase sb;
    Reaction r;
    String s = wrapSBML_L2v1("<listOfReactions>" + 
    "  <reaction metaid='r'>" + 
    "    <listOfReactants metaid='lor'>" + 
    "      <speciesReference metaid='sr1'/>" + 
    "    </listOfReactants>" + 
    "    <listOfProducts metaid='lop'>" + 
    "      <speciesReference metaid='sr2'/>" + 
    "    </listOfProducts>" + 
    "    <listOfModifiers metaid='lom'>" + 
    "      <modifierSpeciesReference metaid='msr'/>" + 
    "    </listOfModifiers>" + 
    "    <kineticLaw metaid='kl'/>" + 
    "  </reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    r = M.getReaction(0);
    sb = r;
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "r"));
    sb = r.getListOfReactants();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lor"));
    sb = r.getReactant(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "sr1"));
    sb = r.getListOfProducts();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lop"));
    sb = r.getProduct(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "sr2"));
    sb = r.getListOfModifiers();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lom"));
    sb = r.getModifier(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "msr"));
    sb = r.getKineticLaw();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "kl"));
  }

  public void test_ReadSBML_metaid_Unit()
  {
    SBase sb;
    UnitDefinition ud;
    String s = wrapSBML_L2v1("<listOfUnitDefinitions>" + 
    "  <unitDefinition metaid='ud'>" + 
    "    <listOfUnits metaid='lou'>" + 
    "      <unit metaid='u'/>" + 
    "    </listOfUnits>" + 
    "  </unitDefinition>" + 
    "</listOfUnitDefinitions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    ud = M.getUnitDefinition(0);
    sb = ud;
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "ud"));
    sb = ud.getListOfUnits();
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "lou"));
    sb = ud.getUnit(0);
    assertEquals( true, sb.isSetMetaId() );
    assertTrue(sb.getMetaId().equals( "u"));
  }

  public void test_ReadSBML_notes()
  {
    Reaction r;
    KineticLaw kl;
    String s = wrapSBML_L2v3("<listOfReactions>" + 
    "<reaction name='J1'>" + 
    "  <kineticLaw formula='k1*X0'>" + 
    "    <notes>This is a test note.</notes>" + 
    "    <listOfParameters>" + 
    "      <parameter name='k1' value='0'/>" + 
    "    </listOfParameters>" + 
    "  </kineticLaw>" + 
    "</reaction>" + 
    "</listOfReactions>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    r = M.getReaction(0);
    kl = r.getKineticLaw();
    assertTrue( kl.getNotes() != null );
    String notes = kl.getNotes().getChild(0).getCharacters();
    assertTrue( !notes.equals( "This is a test note.") == false );
  }

  public void test_ReadSBML_notes_ListOf()
  {
    SBase sb;
    String s = wrapSBML_L2v1("<listOfFunctionDefinitions>" + 
    "  <notes>My Functions</notes>" + 
    "  <functionDefinition/>" + 
    "</listOfFunctionDefinitions>" + 
    "<listOfUnitDefinitions>" + 
    "  <notes>My Units</notes>" + 
    "  <unitDefinition/>" + 
    "</listOfUnitDefinitions>" + 
    "<listOfCompartments>" + 
    "  <notes>My Compartments</notes>" + 
    "  <compartment/>" + 
    "</listOfCompartments>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M != null );
    sb = M.getListOfFunctionDefinitions();
    assertEquals( true, sb.isSetNotes() );
    String notes = sb.getNotes().getChild(0).getCharacters();
    assertTrue( !notes.equals( "My Functions") == false );
    sb = M.getListOfUnitDefinitions();
    assertEquals( true, sb.isSetNotes() );
    notes = sb.getNotes().getChild(0).getCharacters();
    assertTrue( !notes.equals( "My Units") == false );
    sb = M.getListOfCompartments();
    assertEquals( true, sb.isSetNotes() );
    notes = sb.getNotes().getChild(0).getCharacters();
    assertTrue( !notes.equals( "My Compartments") == false );
  }

  public void test_ReadSBML_notes_sbml()
  {
    String s = wrapXML("<sbml level='1' version='1'>" + 
    "  <notes>Notes are not allowed as part of the SBML element.</notes>" + 
    "</sbml>");
    D = libsbml.readSBMLFromString(s);
    assertTrue( D.getNotes() != null );
    String notes = D.getNotes().getChild(0).getCharacters();
    assertTrue( !notes.equals( "Notes are not allowed as part of the SBML element.") == false );
    assertTrue( D.getNumErrors() > 0 );
  }

  public void test_ReadSBML_notes_sbml_L2()
  {
    String s = wrapXML("<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\"> " + 
    "  <notes>" + 
    "    <html xmlns=\"http://www.w3.org/1999/xhtml\">" + 
    "		 </html>" + 
    "	  </notes>" + 
    "	  <model>" + 
    "   </model>" + 
    " </sbml>");
    D = libsbml.readSBMLFromString(s);
    assertTrue( D.getNotes() != null );
    assertTrue( D.getNumErrors() == 0 );
  }

  public void test_ReadSBML_notes_xmlns()
  {
    String s = wrapSBML_L2v3("<notes>" + 
    "  <body xmlns=\"http://www.w3.org/1999/xhtml\">Some text.</body>" + 
    "</notes>");
    D = libsbml.readSBMLFromString(s);
    M = D.getModel();
    assertTrue( M.getNotes() != null );
    XMLNamespaces ns = M.getNotes().getChild(0).getNamespaces();
    assertTrue( ns.getLength() == 1 );
    assertTrue(ns.getURI(0).equals( "http://www.w3.org/1999/xhtml"));
    String notes = M.getNotes().getChild(0).getChild(0).getCharacters();
    assertTrue( !notes.equals( "Some text.") == false );
  }

  /**
   * Loads the SWIG-generated libSBML Java module when this class is
   * loaded, or reports a sensible diagnostic message about why it failed.
   */
  static
  {
    String varname;
    String shlibname;

    if (System.getProperty("mrj.version") != null)
    {
      varname = "DYLD_LIBRARY_PATH";    // We're on a Mac.
      shlibname = "libsbmlj.jnilib and/or libsbml.dylib";
    }
    else
    {
      varname = "LD_LIBRARY_PATH";      // We're not on a Mac.
      shlibname = "libsbmlj.so and/or libsbml.so";
    }

    try
    {
      System.loadLibrary("sbmlj");
      // For extra safety, check that the jar file is in the classpath.
      Class.forName("org.sbml.libsbml.libsbml");
    }
    catch (SecurityException e)
    {
      e.printStackTrace();
      System.err.println("Could not load the libSBML library files due to a"+
                         " security exception.\n");
      System.exit(1);
    }
    catch (UnsatisfiedLinkError e)
    {
      e.printStackTrace();
      System.err.println("Error: could not link with the libSBML library files."+
                         " It is likely\nyour " + varname +
                         " environment variable does not include the directories\n"+
                         "containing the " + shlibname + " library files.\n");
      System.exit(1);
    }
    catch (ClassNotFoundException e)
    {
      e.printStackTrace();
      System.err.println("Error: unable to load the file libsbmlj.jar."+
                         " It is likely\nyour -classpath option and CLASSPATH" +
                         " environment variable\n"+
                         "do not include the path to libsbmlj.jar.\n");
      System.exit(1);
    }
  }
}
