text: /**
   * \file    TestReadFromFile3.c
   * \brief   Reads tests/l1v1-rules.xml into memory and tests it.
   * \author  Ben Bornstein
   * 
   * <!--------------------------------------------------------------------------
   * This file is part of libSBML.  Please visit http://sbml.org for more
   * information about SBML, and the latest version of libSBML.
   *
   * Copyright (C) 2020 jointly by the following organizations:
   *     1. California Institute of Technology, Pasadena, CA, USA
   *     2. University of Heidelberg, Heidelberg, Germany
   *     3. University College London, London, UK
   *
   * Copyright (C) 2019 jointly by the following organizations:
   *     1. California Institute of Technology, Pasadena, CA, USA
   *     2. University of Heidelberg, Heidelberg, Germany
   *
   * Copyright (C) 2013-2018 jointly by the following organizations:
   *     1. California Institute of Technology, Pasadena, CA, USA
   *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
   *     3. University of Heidelberg, Heidelberg, Germany
   *
   * Copyright (C) 2009-2013 jointly by the following organizations: 
   *     1. California Institute of Technology, Pasadena, CA, USA
   *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
   *  
   * Copyright (C) 2006-2008 by the California Institute of Technology,
   *     Pasadena, CA, USA 
   *  
   * Copyright (C) 2002-2005 jointly by the following organizations: 
   *     1. California Institute of Technology, Pasadena, CA, USA
   *     2. Japan Science and Technology Agency, Japan
   * 
   * 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
   * ---------------------------------------------------------------------- -->*/
  
  #include <sbml/common/common.h>
  #include <sbml/SBMLReader.h>
  #include <sbml/SBMLTypes.h>
  
  #include <check.h>
  
  
  
  #include <sbml/common/extern.h>
  
  LIBSBML_CPP_NAMESPACE_USE
  
  
  BEGIN_C_DECLS
  
  extern char *TestDataDirectory;
  
  
  START_TEST (test_read_l1v1_rules)
  {
    SBMLDocument_t             *d;
    Model_t                    *m;
    Compartment_t              *c;
    KineticLaw_t               *kl;
    Parameter_t                *p;
    Rule_t                     *pr;
    Reaction_t                 *r;
    Species_t                  *s;
    Rule_t                     *scr;
    SpeciesReference_t         *sr;
    UnitDefinition_t           *ud;
  
    char *filename = safe_strcat(TestDataDirectory, "l1v1-rules.xml");
  
  
    d = readSBML(filename);
  
    if (d == NULL)
    {
      fail("readSBML(\"l1v1-rules.xml\") returned a NULL pointer.");
    }
  
    safe_free(filename);
  
  
    /**
     * <sbml level="1" version="1" ...>
     */
    fail_unless( SBMLDocument_getLevel  (d) == 1, NULL );
    fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
  
  
    /**
     * <model>
     */
    m = SBMLDocument_getModel(d);
  
    /**
     * <listOfCompartments>
     *  <compartment name="cell" volume="1"/>
     * </listOfCompartments>
     */
    fail_unless( Model_getNumCompartments(m) == 1, NULL );
  
    c = Model_getCompartment(m, 0);
    fail_unless( !strcmp(Compartment_getName(c), "cell"), NULL );
    fail_unless( Compartment_getVolume(c) == 1, NULL );
  
  
    /**
     * <listOfSpecies>
     *   <specie name="s1" compartment="cell" initialAmount="4"/>
     *   <specie name="s2" compartment="cell" initialAmount="2"/>
     *   <specie name="x0" compartment="cell" initialAmount="1"/>
     *   <specie name="x1" compartment="cell" initialAmount="0"/>
     *   <specie name="x2" compartment="cell" initialAmount="1"/>
     *   <specie name="x3" compartment="cell" initialAmount="0"/>
     * </listOfSpecies>
     */
    fail_unless( Model_getNumSpecies(m) == 6, NULL );
  
    s = Model_getSpecies(m, 0);
    fail_unless( !strcmp( Species_getName(s)       , "s1"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 4, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
    s = Model_getSpecies(m, 1);
    fail_unless( !strcmp( Species_getName(s)       , "s2"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 2, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
    s = Model_getSpecies(m, 2);
    fail_unless( !strcmp( Species_getName(s)       , "x0"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 1, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
    s = Model_getSpecies(m, 3);
    fail_unless( !strcmp( Species_getName(s)       , "x1"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 0, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
    s = Model_getSpecies(m, 4);
    fail_unless( !strcmp( Species_getName(s)       , "x2"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 1, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
    s = Model_getSpecies(m, 5);
    fail_unless( !strcmp( Species_getName(s)       , "x3"   ), NULL );
    fail_unless( !strcmp( Species_getCompartment(s), "cell" ), NULL );
    fail_unless( Species_getInitialAmount    (s) == 0, NULL );
    fail_unless( Species_getBoundaryCondition(s) == 0, NULL );
  
  
    /**
     * <listOfParameters>
     *   <parameter name="k1" value="1.2"/>
     *   <parameter name="k2" value="1000"/>
     *   <parameter name="k3" value="3000"/>
     *   <parameter name="k4" value="4.5"/>
     * </listOfParameters>
     */
    fail_unless( Model_getNumParameters(m) == 7, NULL );
  
    p = Model_getParameter(m, 0);
    fail_unless( !strcmp(Parameter_getName(p), "k1"), NULL );
    fail_unless( Parameter_getValue(p) == 1.2, NULL );
  
    p = Model_getParameter(m, 1);
    fail_unless( !strcmp(Parameter_getName(p), "k2"), NULL );
    fail_unless( Parameter_getValue(p) == 1000, NULL );
  
    p = Model_getParameter(m, 2);
    fail_unless( !strcmp(Parameter_getName(p), "k3"), NULL );
    fail_unless( Parameter_getValue(p) == 3000, NULL );
  
    p = Model_getParameter(m, 3);
    fail_unless( !strcmp(Parameter_getName(p), "k4"), NULL );
    fail_unless( Parameter_getValue(p) == 4.5, NULL );
  
  
    /**
     * <listOfRules>
     *   <parameterRule name="t" formula="s1 + s2"/>
     *   <parameterRule name="k" formula="k3/k2"/>
     *   <specieConcentrationRule specie="s2" formula="k * t/(1 + k)"/>
     *   <specieConcentrationRule specie="s1" formula="t - s2"/>
     * </listOfRules>
     */
    fail_unless( Model_getNumRules(m) == 4, NULL );
  
    pr = Model_getRule(m, 0);
    fail_unless( !strcmp(Rule_getVariable(pr), "t"), NULL );
    fail_unless( !strcmp(Rule_getFormula( pr), "s1 + s2"), NULL );
  
    /**
     * tests for the unit API functions
     */
    ud = Rule_getDerivedUnitDefinition(pr);
    fail_unless (UnitDefinition_getNumUnits(ud) == 2, NULL);
    fail_unless( Unit_getKind (UnitDefinition_getUnit(ud, 0)) == UNIT_KIND_MOLE, NULL );
    fail_unless( Unit_getExponent(UnitDefinition_getUnit(ud, 0)) ==  1, NULL );
    fail_unless( Unit_getKind (UnitDefinition_getUnit(ud, 1)) == UNIT_KIND_LITRE, NULL );
    fail_unless( Unit_getExponent(UnitDefinition_getUnit(ud, 1)) ==  -1, NULL );
  
    fail_unless( Rule_containsUndeclaredUnits(pr) == 0, NULL);
  
    pr = Model_getRule(m, 1);
    fail_unless( !strcmp(Rule_getVariable(pr), "k"), NULL );
    fail_unless( !strcmp(Rule_getFormula( pr), "k3/k2"), NULL );
  
    /**
     * tests for the unit API functions
     */
    ud = Rule_getDerivedUnitDefinition(pr);
    fail_unless (UnitDefinition_getNumUnits(ud) == 0, NULL);
  
    fail_unless( Rule_containsUndeclaredUnits(pr) == 1, NULL);
  
    scr = Model_getRule(m, 2);
    fail_unless( !strcmp(Rule_getVariable(scr), "x2"), NULL );
    fail_unless( !strcmp(Rule_getFormula( scr), "k * (s1+s2)/(1 + k)"),
                 NULL );
  
    scr = Model_getRule(m, 3);
    fail_unless( !strcmp(Rule_getVariable(scr), "x3"), NULL );
    fail_unless( !strcmp(Rule_getFormula((Rule_t *) scr), "p*(t - s2)"), NULL );
  
  
    /**
     * <listOfReactions>
     *   <reaction name="j1" > ... </reaction>
     *   <reaction name="j3" > ... </reaction>
     * </listOfReactions>
     */
    fail_unless( Model_getNumReactions(m) == 2, NULL );
  
    r = Model_getReaction(m, 0);
    fail_unless( !strcmp(Reaction_getName(r), "j1"), NULL );
    fail_unless( Reaction_getReversible(r) != 0, NULL );
    fail_unless( Reaction_getFast(r)       == 0, NULL );
  
    r = Model_getReaction(m, 1);
    fail_unless( !strcmp(Reaction_getName(r), "j3"), NULL );
    fail_unless( Reaction_getReversible(r) != 0, NULL );
    fail_unless( Reaction_getFast(r)       == 0, NULL );
  
  
    /**
     * <reaction name="j1">
     *   <listOfReactants>
     *     <specieReference specie="x0"/>
     *   </listOfReactants>
     *   <listOfProducts>
     *     <specieReference specie="s1"/>
     *   </listOfProducts>
     *   <kineticLaw formula="k1 * x0"/>
     * </reaction>
     */
    r = Model_getReaction(m, 0);
  
    fail_unless( Reaction_getNumReactants(r) == 1, NULL );
    fail_unless( Reaction_getNumProducts(r)  == 1, NULL );
  
    sr = Reaction_getReactant(r, 0);
    fail_unless( !strcmp(SpeciesReference_getSpecies(sr), "x0"), NULL );
    fail_unless( SpeciesReference_getStoichiometry(sr) == 1, NULL );
    fail_unless( SpeciesReference_getDenominator  (sr) == 1, NULL );
  
    sr = Reaction_getProduct(r, 0);
    fail_unless( !strcmp(SpeciesReference_getSpecies(sr), "s1"), NULL );
    fail_unless( SpeciesReference_getStoichiometry(sr) == 1, NULL );
    fail_unless( SpeciesReference_getDenominator  (sr) == 1, NULL );
  
    kl = Reaction_getKineticLaw(r);
    fail_unless( !strcmp(KineticLaw_getFormula(kl), "k1 * x0"), NULL );
  
  
    /**
     * <reaction name="j3">
     *   <listOfReactants>
     *     <specieReference specie="s2"/>
     *   </listOfReactants>
     *   <listOfProducts>
     *     <specieReference specie="x1"/>
     *   </listOfProducts>
     *   <kineticLaw formula="k4 * s2"/>
     * </reaction>
     */
    r = Model_getReaction(m, 1);
  
    fail_unless( Reaction_getNumReactants(r) == 1, NULL );
    fail_unless( Reaction_getNumProducts(r)  == 1, NULL );
  
    sr = Reaction_getReactant(r, 0);
    fail_unless( !strcmp(SpeciesReference_getSpecies(sr), "s2"), NULL );
    fail_unless( SpeciesReference_getStoichiometry(sr) == 1, NULL );
    fail_unless( SpeciesReference_getDenominator  (sr) == 1, NULL );
  
    sr = Reaction_getProduct(r, 0);
    fail_unless( !strcmp(SpeciesReference_getSpecies(sr), "x1"), NULL );
    fail_unless( SpeciesReference_getStoichiometry(sr) == 1, NULL );
    fail_unless( SpeciesReference_getDenominator  (sr) == 1, NULL );
  
    kl = Reaction_getKineticLaw(r);
    fail_unless( !strcmp(KineticLaw_getFormula(kl), "k4 * s2"), NULL );
  
    SBMLDocument_free(d);
  }
  END_TEST
  
  
  Suite *
  create_suite_TestReadFromFile3 (void)
  { 
    Suite *suite = suite_create("test-data/l1v1-rules.xml");
    TCase *tcase = tcase_create("test-data/l1v1-rules.xml");
  
  
    tcase_add_test(tcase, test_read_l1v1_rules);
  
    suite_add_tcase(suite, tcase);
  
    return suite;
  }
  
  END_C_DECLS
  
  
  