text: /**
   * @file    TestReadGroupsExtension.cpp
   * @brief   Unit tests of writing GroupsExtension 
   * @author  Akiya Jouraku
   *
   * $Id: $
   * $HeadURL: $
   *
   * <!--------------------------------------------------------------------------
   * 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) 2009-2011 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 <limits>
  
  #include <iostream>
  #include <check.h>
  #include <sbml/SBMLTypes.h>
  #include <sbml/common/extern.h>
  #include <sbml/extension/SBMLExtensionRegistry.h>
  #include <sbml/packages/groups/common/GroupsExtensionTypes.h>
  #include <string>
  
  /** @cond doxygenIgnored */
  
  using namespace std;
  LIBSBML_CPP_NAMESPACE_USE
  
  /** @endcond doxygenIgnored */
  
  
  CK_CPPSTART
  
  extern char *TestDataDirectory;
  
  START_TEST (test_GroupsExtension_read_L3V1V1)
  {
    char *filename = safe_strcat(TestDataDirectory, "groups-example1.xml");
    SBMLDocument *document = readSBMLFromFile(filename);
    fail_unless(document->getPackageName() == "core");
  
    Model *model = document->getModel();
  
    fail_unless(model != NULL);
    fail_unless(model->getPackageName() == "core");
    fail_unless(document->getNumErrors() == 0);
  
    // get the Group
  
    GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
    fail_unless(mplugin != NULL);
  
    fail_unless(mplugin->getNumGroups() == 1);
    fail_unless(mplugin->getListOfGroups()->getPackageName() == "groups");
  
    Group* group = mplugin->getGroup(0);
    fail_unless(group->getId()          == "ATP");
    fail_unless(group->getSBOTermID()   == "SBO:0000252");
    fail_unless(group->getKind()        == GROUP_KIND_CLASSIFICATION);
    fail_unless(group->getNumMembers()  == 2);
    fail_unless(group->getPackageName() == "groups");
  
    fail_unless(group->getListOfMembers()->getPackageName() == "groups");
  
    Member* member = group->getMember(0);
    fail_unless(member->getIdRef()      == "ATPc");
    fail_unless(member->getPackageName() == "groups");
  
    member = group->getMember(1);
    fail_unless(member->getIdRef()      == "ATPm");
    fail_unless(member->getPackageName() == "groups");
  
    delete document; 
    safe_free(filename);
  }
  END_TEST
  
  
  START_TEST (test_GroupsExtension_read_L3V1V1_defaultNS)
  {
    char *filename = safe_strcat(TestDataDirectory, "groups-example1-defaultNS.xml");
    SBMLDocument *document = readSBMLFromFile(filename);
    
    fail_unless(document->getPackageName() == "core");
  
    Model *model = document->getModel();
  
    document->printErrors();
  
    fail_unless(model != NULL);
    fail_unless(document->getNumErrors() == 0);
  
    // get the Group
  
    GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
    fail_unless(mplugin != NULL);
  
    fail_unless(mplugin->getNumGroups() == 1);
    fail_unless(mplugin->getListOfGroups()->getPackageName() == "groups");
  
    Group* group = mplugin->getGroup(0);
    fail_unless(group->getId()          == "ATP");
    fail_unless(group->getSBOTermID()   == "SBO:0000252");
    fail_unless(group->getKind()        == GROUP_KIND_CLASSIFICATION);
    fail_unless(group->isSetKind()      == true);
    fail_unless(!strcmp(GroupKind_toString(group->getKind()), "classification"));
    fail_unless(group->getNumMembers()  == 2);
    fail_unless(group->getPackageName() == "groups");
  
    fail_unless(group->getListOfMembers()->getPackageName() == "groups");
  
    Member* member = group->getMember(0);
    fail_unless(member->getIdRef()      == "ATPc");
    fail_unless(member->getPackageName() == "groups");
  
    member = group->getMember(1);
    fail_unless(member->getIdRef()      == "ATPm");
    fail_unless(member->getPackageName() == "groups");
  
    delete document;  
    safe_free(filename);
  }
  END_TEST
  
  
  START_TEST (test_GroupsExtension_read_L3V1V1_unknown_elements)
  {
    const char* s1 =
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
      "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:groups=\"http://www.sbml.org/sbml/level3/version1/groups/version1\" level=\"3\" version=\"1\" groups:required=\"false\">\n"
      "  <model>\n"
      "    <listOfCompartments>\n"
      "      <compartment id=\"cytosol\" constant=\"true\"/>\n"
      "      <compartment id=\"mitochon\" constant=\"true\"/>\n"
      "    </listOfCompartments>\n"
      "    <listOfSpecies>\n"
      "      <species id=\"ATPc\" compartment=\"cytosol\" initialConcentration=\"1\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
      "      <species id=\"ATPm\" compartment=\"mitochon\" initialConcentration=\"2\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
      "    </listOfSpecies>\n"
      "    <groups:listOfGroups>\n"
      "      <groups:group sboTerm=\"SBO:0000252\" groups:kind=\"partonomy\" groups:id=\"ATP\" groups:unknown=\"unknown\" >\n"
      "        <groups:listOfMembers>\n"
      "          <groups:member groups:idRef=\"ATPc\" groups:unknown=\"unknown\"/>\n"
      "          <groups:member groups:idRef=\"ATPm\"/>\n"
      "        </groups:listOfMembers>\n"
      "        <groups:unknown>\n"
      "        </groups:unknown>\n"
      "      </groups:group>\n"
      "    </groups:listOfGroups>\n"
      "  </model>\n"
      "</sbml>\n"
      ;
  
    SBMLDocument *document = readSBMLFromString(s1);
    Model *model = document->getModel();
   
    fail_unless(model != NULL);
    fail_unless(document->getNumErrors() == 3);
  
    delete document;
  }
  END_TEST
  
  
  Suite *
  create_suite_ReadGroupsExtension (void)
  {
    Suite *suite = suite_create("ReadGroupsExtension");
    TCase *tcase = tcase_create("ReadGroupsExtension");
  
    tcase_add_test( tcase, test_GroupsExtension_read_L3V1V1);
    tcase_add_test( tcase, test_GroupsExtension_read_L3V1V1_defaultNS);
    tcase_add_test( tcase, test_GroupsExtension_read_L3V1V1_unknown_elements);
    
    
    suite_add_tcase(suite, tcase);
  
    return suite;
  }
  
  
  CK_CPPEND
  