test000092 Class Reference

#include <test000092.h>

Inheritance diagram for test000092:

Collaboration diagram for test000092:

Public Member Functions
void	setUp ()
void	tearDown ()
void	test_miriam_export_1 ()
void	test_miriam_export_2 ()
void	test_miriam_export_3 ()
void	test_miriam_export_4 ()
void	test_miriam_export_5 ()
void	test_miriam_export_6 ()
void	test_miriam_export_7 ()
void	test_miriam_export_8 ()
void	test_miriam_export_9 ()
void	test_miriam_import_1 ()

Static Protected Attributes
static const char *	MODEL_STRING1
static const char *	MODEL_STRING10
static const char *	MODEL_STRING2
static const char *	MODEL_STRING3
static const char *	MODEL_STRING4
static const char *	MODEL_STRING5
static const char *	MODEL_STRING6
static const char *	MODEL_STRING7
static const char *	MODEL_STRING8
static const char *	MODEL_STRING9
static CCopasiDataModel *	pCOPASIDATAMODEL = NULL

Private Member Functions
	CPPUNIT_TEST (test_miriam_export_1)
	CPPUNIT_TEST (test_miriam_export_2)
	CPPUNIT_TEST (test_miriam_export_3)
	CPPUNIT_TEST (test_miriam_export_4)
	CPPUNIT_TEST (test_miriam_export_5)
	CPPUNIT_TEST (test_miriam_export_6)
	CPPUNIT_TEST (test_miriam_export_7)
	CPPUNIT_TEST (test_miriam_export_8)
	CPPUNIT_TEST (test_miriam_export_9)
	CPPUNIT_TEST (test_miriam_import_1)
	CPPUNIT_TEST_SUITE (test000092)
	CPPUNIT_TEST_SUITE_END ()

Detailed Description

Definition at line 24 of file test000092.h.

Member Function Documentation

test000092::CPPUNIT_TEST ( test_miriam_export_1  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_2  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_3  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_4  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_5  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_6  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_7  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_8  )

private

test000092::CPPUNIT_TEST ( test_miriam_export_9  )

private

test000092::CPPUNIT_TEST ( test_miriam_import_1  )

private

test000092::CPPUNIT_TEST_SUITE ( test000092  )

private

test000092::CPPUNIT_TEST_SUITE_END ( )

private

void test000092::setUp

(

)

Definition at line 38 of file test000092.cpp.

References CCopasiRootContainer::addDatamodel(), CCopasiRootContainer::init(), and pCOPASIDATAMODEL.

{
  // Create the root container.
  CCopasiRootContainer::init(0, NULL, false);
  // Create the global data model.
  pCOPASIDATAMODEL = CCopasiRootContainer::addDatamodel();
}

void test000092::tearDown

(

)

Definition at line 46 of file test000092.cpp.

References CCopasiRootContainer::destroy().

{
  CCopasiRootContainer::destroy();
}

void test000092::test_miriam_export_1

(

)

Definition at line 51 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING1, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING1);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL;
  pMIRIAM1 = &pModelAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = &pModelAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
    }
  else
    {
      pMIRIAM2 = &pModelAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM2 != NULL);
      CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  //
  // Right now, we don't care about the content of the annotations as long as they are there
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartment->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2);
  pMIRIAM1 = &pAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
    }
  else
    {
      pMIRIAM2 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM2 != NULL);
      CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_2

(

)

Definition at line 232 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING2, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING2);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is incomplete , we should have one or two children
  // depending on the version of libsbml we are using
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1 || iMax == 2);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL;
  pMIRIAM1 = &pModelAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = NULL;

      if (iMax == 2)
        {
          pMIRIAM1 = &pModelAnnotation->getChild(1);
          CPPUNIT_ASSERT(pMIRIAM1 != NULL);
          CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
        }
    }
  else
    {
      if (iMax == 2)
        {
          pMIRIAM2 = &pModelAnnotation->getChild(1);
          CPPUNIT_ASSERT(pMIRIAM2 != NULL);
          CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
        }
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");

  // same checks for the libsbml MIRIAM annotation
  if (pMIRIAM1 != NULL)
    {
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
      CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
      ns = &pMIRIAM1->getNamespaces();
      CPPUNIT_ASSERT(ns != NULL);
      index = ns->getIndex("http://purl.org/dc/terms/");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
      index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
      index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
    }

  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  //
  // Right now, we don't care about the content of the annotations as long as they are there
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartment->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2);
  pMIRIAM1 = &pAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
    }
  else
    {
      pMIRIAM2 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM2 != NULL);
      CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_3

(

)

Definition at line 426 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING3, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING3);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  // So since we don't expect any annotations for this model,
  // the first node should not be an annotation node
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() != "annotation");
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  // there should be no annotation to the compartment
  CPPUNIT_ASSERT(iMax == 0);
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_4

(

)

Definition at line 481 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING4, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING4);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL, *pLayout = NULL;

  // make sure the libsbml annotation is stored in pMIRIAM1
  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pModelAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "listOfLayouts")
        {
          pLayout = &pModelAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pLayout != NULL);
  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  //
  // Right now, we don't care about the content of the annotations as long as they are there
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartment->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2);
  pMIRIAM1 = NULL;
  pMIRIAM2 = NULL;
  pMIRIAM1 = &pAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
    }
  else
    {
      pMIRIAM2 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM2 != NULL);
      CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_5

(

)

Definition at line 667 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING5, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING5);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is incomplete , we should have one or two children
  // depending on the version of libsbml we are using
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2 || iMax == 3);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL, *pLayout;

  for (unsigned i = 0; i < iMax; ++i)
    {
      if (pModelAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "listOfLayouts")
        {
          pLayout = &pModelAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pLayout != NULL);

  if (iMax == 3)
    {
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");

  // same checks for the libsbml MIRIAM annotation
  if (pMIRIAM1 != NULL)
    {
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
      CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
      ns = &pMIRIAM1->getNamespaces();
      CPPUNIT_ASSERT(ns != NULL);
      index = ns->getIndex("http://purl.org/dc/terms/");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
      index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
      index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
      CPPUNIT_ASSERT(index != -1);
      CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
    }

  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  //
  // Right now, we don't care about the content of the annotations as long as they are there
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartment->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 2);
  pMIRIAM1 = NULL;
  pMIRIAM2 = NULL;
  pMIRIAM1 = &pAnnotation->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);

  // make sure the libsbml annotation is stored in pMIRIAM1
  if (pMIRIAM1->getName() != "RDF")
    {
      pMIRIAM2 = pMIRIAM1;
      pMIRIAM1 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM1 != NULL);
      CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
    }
  else
    {
      pMIRIAM2 = &pAnnotation->getChild(1);
      CPPUNIT_ASSERT(pMIRIAM2 != NULL);
      CPPUNIT_ASSERT(pMIRIAM2->getName() == "COPASI");
    }

  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_6

(

)

Definition at line 862 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), load_cps_model_from_stream(), MODEL_STRING6, and pCOPASIDATAMODEL.

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000092::MODEL_STRING6);
  bool result = load_cps_model_from_stream(iss, *pDataModel);
  CPPUNIT_ASSERT(result == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  CPPUNIT_ASSERT(pModelAnnotation->getNumChildren() == 1);
  CPPUNIT_ASSERT(pModelAnnotation->getChild(0).getName() == "listOfLayouts");
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartment = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pCompartment->getName() == "compartment");
  iMax = pCompartment->getNumChildren();
  // there should be no annotation to the compartment
  CPPUNIT_ASSERT(iMax == 0);
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_7

(

)

Definition at line 916 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CModel::getCompartments(), CCopasiDataModel::getCurrentSBMLDocument(), CModel::getKey(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), MODEL_STRING7, pCOPASIDATAMODEL, CRDFGraphConverter::SBML2Copasi(), CAnnotation::setMiriamAnnotation(), and CCopasiVector< T >::size().

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  bool result = pDataModel->importSBMLFromString(test000092::MODEL_STRING7);
  CPPUNIT_ASSERT(result == true);
  CModel *pModel = pDataModel->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // now we have to add some miriam annotation to the model
  std::string miriamString = \
                             "    <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
                             "      <rdf:Description rdf:about=\"#COPASI1\">\n"
                             "        <dc:creator rdf:parseType=\"Resource\">\n"
                             "          <rdf:Bag>\n"
                             "            <rdf:li rdf:parseType=\"Resource\">\n"
                             "              <vCard:N rdf:parseType=\"Resource\">\n"
                             "                <vCard:Family>Gauges</vCard:Family>\n"
                             "                <vCard:Given>Ralph</vCard:Given>\n"
                             "              </vCard:N>\n"
                             "            </rdf:li>\n"
                             "          </rdf:Bag>\n"
                             "        </dc:creator>\n"
                             "        <dcterms:created rdf:parseType=\"Resource\">\n"
                             "          <dcterms:W3CDTF>2005-02-02T14:56:11Z</dcterms:W3CDTF>\n"
                             "        </dcterms:created>\n"
                             "        <dcterms:modified rdf:parseType=\"Resource\">\n"
                             "          <dcterms:W3CDTF>2009-06-05T11:40:04Z</dcterms:W3CDTF>\n"
                             "        </dcterms:modified>\n"
                             "      </rdf:Description>\n"
                             "    </rdf:RDF>\n";
  const SBMLDocument* pSBMLDocument = pDataModel->getCurrentSBMLDocument();
  CPPUNIT_ASSERT(pSBMLDocument != NULL);
  const Model* pSBMLModel = pDataModel->getCurrentSBMLDocument()->getModel();
  CPPUNIT_ASSERT(pSBMLModel != NULL);
  CPPUNIT_ASSERT(pSBMLModel->isSetMetaId() == true);
  CRDFGraphConverter::SBML2Copasi(miriamString);
  pModel->setMiriamAnnotation(miriamString, pModel->getKey(), pSBMLModel->getMetaId());
  // set some MIRIAM annotation on the compartment as well
  miriamString = \
                 "        <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
                 "          <rdf:Description rdf:about=\"#COPASI2\">\n"
                 "            <bqbiol:is>\n"
                 "              <rdf:Bag>\n"
                 "                <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0031594\"/>\n"
                 "              </rdf:Bag>\n"
                 "            </bqbiol:is>\n"
                 "          </rdf:Description>\n"
                 "        </rdf:RDF>\n";
  CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
  CCompartment* pCompartment = pModel->getCompartments()[0];
  CPPUNIT_ASSERT(pCompartment != NULL);
  CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
  const Compartment* pSBMLCompartment = pSBMLModel->getCompartment(0);
  CPPUNIT_ASSERT(pSBMLCompartment != NULL);
  CPPUNIT_ASSERT(pSBMLCompartment->isSetMetaId() == true);
  CRDFGraphConverter::SBML2Copasi(miriamString);
  pCompartment->setMiriamAnnotation(miriamString, pCompartment->getKey(), pSBMLCompartment->getMetaId());
  //
  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL, *pOther = NULL;

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pModelAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pModelAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  //
  // Right now, we don't care about the content of the annotations as long as they are there
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartmentNode = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartmentNode != NULL);
  CPPUNIT_ASSERT(pCompartmentNode->getName() == "compartment");
  iMax = pCompartmentNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartmentNode->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  pMIRIAM1 = NULL;
  pMIRIAM2 = NULL;
  pOther = NULL;

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the COPASI annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_8

(

)

Definition at line 1148 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CModel::getCompartments(), CModification::getDate(), CBiologicalDescription::getId(), CModel::getKey(), CAnnotation::getMiriamAnnotation(), CCopasiDataModel::getModel(), CBiologicalDescription::getPredicate(), CBiologicalDescription::getResource(), CCopasiDataModel::importSBMLFromString(), CMIRIAMInfo::load(), MODEL_STRING8, pCOPASIDATAMODEL, CBiologicalDescription::setId(), CBiologicalDescription::setPredicate(), CBiologicalDescription::setResource(), and CCopasiVector< T >::size().

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  bool result = pDataModel->importSBMLFromString(test000092::MODEL_STRING8);
  CPPUNIT_ASSERT(result == true);
  CModel* pModel = pDataModel->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // we need to modify the imported MIRIAM annotation,
  // e.g. the add a modified date
  std::string miriamString = pModel->getMiriamAnnotation();
  CPPUNIT_ASSERT(!miriamString.empty());
  CMIRIAMInfo miriamInfo;
  miriamInfo.load(pModel->getKey());
  // check the modified date
  const CCopasiVector<CModification>* pModifications = &miriamInfo.getModifications();
  CPPUNIT_ASSERT(pModifications != NULL);
  // there should be only one modification date
  CPPUNIT_ASSERT(pModifications->size() == 1);
  const CModification* pModification = (*pModifications)[0];
  CPPUNIT_ASSERT(pModification != NULL);
  std::string dateTime = pModification->getDate();
  CPPUNIT_ASSERT(dateTime == "2007-06-05T11:40:04Z");
  // now we add a new modification date
  dateTime = "2008-06-05T11:40:04Z";
  CModification* pNewModification = miriamInfo.createModification(dateTime);
  CPPUNIT_ASSERT(pNewModification != NULL);
  CPPUNIT_ASSERT(pNewModification->getDate() == dateTime);
  CPPUNIT_ASSERT(miriamInfo.save() == true);

  // now we do the same for the compartment
  CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
  CCompartment* pCompartment = pModel->getCompartments()[0];
  CPPUNIT_ASSERT(pCompartment != NULL);
  miriamInfo.load(pCompartment->getKey());
  const CCopasiVector<CBiologicalDescription>* pDescriptions = &miriamInfo.getBiologicalDescriptions();
  CPPUNIT_ASSERT(pDescriptions != NULL);
  CPPUNIT_ASSERT(pDescriptions->size() == 1);
  CBiologicalDescription* pDescription = (*pDescriptions)[0];
  CPPUNIT_ASSERT(pDescription != NULL);
  std::string predicate = pDescription->getPredicate();
  CPPUNIT_ASSERT(predicate == "is version of");
  std::string resource = pDescription->getResource();
  CPPUNIT_ASSERT(resource == "Gene Ontology");
  std::string id = pDescription->getId();
  CPPUNIT_ASSERT(id == "GO:0005623");
  id = "GO:0001111";
  CBiologicalDescription* pNewDescription = miriamInfo.createBiologicalDescription();
  pNewDescription->setPredicate(predicate);
  pNewDescription->setResource(resource);
  pNewDescription->setId(id);
  CPPUNIT_ASSERT(pNewDescription != NULL);
  CPPUNIT_ASSERT(pNewDescription->getPredicate() == "is version of");
  CPPUNIT_ASSERT(pNewDescription->getResource() == "Gene Ontology");
  CPPUNIT_ASSERT(pNewDescription->getId() == "GO:0001111");
  CPPUNIT_ASSERT(miriamInfo.save() == true);

  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have three children
  // depending on the version of libsbml we are using
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL, *pOther = NULL;

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pModelAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pModelAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // make sure the there are two modification dates
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Description");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pMIRIAM2->getChild(i).getName() == "modified")
        {
          pMIRIAM2 = &pMIRIAM2->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM2->getName() == "modified");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 2);

  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");

  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Description");
  iMax = pMIRIAM1->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pMIRIAM1->getChild(i).getName() == "modified")
        {
          pMIRIAM1 = &pMIRIAM1->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1->getName() == "modified");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "W3CDTF");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getCharacters() == "2008-06-05T11:40:04Z");

  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartmentNode = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartmentNode != NULL);
  CPPUNIT_ASSERT(pCompartmentNode->getName() == "compartment");
  iMax = pCompartmentNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartmentNode->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  pMIRIAM1 = NULL;
  pMIRIAM2 = NULL;
  pOther = NULL;

  // make sure the libsbml annotation is stored in pMIRIAM1
  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the COPASI annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  // check if there are two biological descriptions
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Description");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "isVersionOf");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMIRIAM2->getChild(0).getName() == "li");
  CPPUNIT_ASSERT(pMIRIAM2->getChild(1).getName() == "li");

  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // check if there are two biological descriptions
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Description");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "isVersionOf");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMIRIAM1->getChild(0).getName() == "li");
  CPPUNIT_ASSERT(pMIRIAM1->getChild(1).getName() == "li");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_export_9

(

)

Definition at line 1461 of file test000092.cpp.

References CCopasiDataModel::exportSBMLToString(), CModel::getCompartments(), CModification::getDate(), CBiologicalDescription::getId(), CModel::getKey(), CAnnotation::getMiriamAnnotation(), CCopasiDataModel::getModel(), CBiologicalDescription::getPredicate(), CBiologicalDescription::getResource(), CCopasiDataModel::importSBMLFromString(), CMIRIAMInfo::load(), MODEL_STRING9, pCOPASIDATAMODEL, CBiologicalDescription::setId(), CBiologicalDescription::setPredicate(), CBiologicalDescription::setResource(), and CCopasiVector< T >::size().

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  bool result = pDataModel->importSBMLFromString(test000092::MODEL_STRING9);
  CPPUNIT_ASSERT(result == true);
  CModel* pModel = pDataModel->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // we need to modify the imported MIRIAM annotation,
  // e.g. the add a modified date
  std::string miriamString = pModel->getMiriamAnnotation();
  CPPUNIT_ASSERT(!miriamString.empty());
  CMIRIAMInfo miriamInfo;
  miriamInfo.load(pModel->getKey());
  // check the modified date
  const CCopasiVector<CModification>* pModifications = &miriamInfo.getModifications();
  CPPUNIT_ASSERT(pModifications != NULL);
  // there should be only one modification date
  CPPUNIT_ASSERT(pModifications->size() == 1);
  const CModification* pModification = (*pModifications)[0];
  CPPUNIT_ASSERT(pModification != NULL);
  std::string dateTime = pModification->getDate();
  CPPUNIT_ASSERT(dateTime == "2007-06-05T11:40:04Z");
  // now we add a new modification date
  dateTime = "2008-06-05T11:40:04Z";
  CModification* pNewModification = miriamInfo.createModification(dateTime);
  CPPUNIT_ASSERT(pNewModification != NULL);
  CPPUNIT_ASSERT(pNewModification->getDate() == dateTime);
  CPPUNIT_ASSERT(miriamInfo.save() == true);

  // now we do the same for the compartment
  CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
  CCompartment* pCompartment = pModel->getCompartments()[0];
  CPPUNIT_ASSERT(pCompartment != NULL);
  miriamInfo.load(pCompartment->getKey());
  const CCopasiVector<CBiologicalDescription>* pDescriptions = &miriamInfo.getBiologicalDescriptions();
  CPPUNIT_ASSERT(pDescriptions != NULL);
  CPPUNIT_ASSERT(pDescriptions->size() == 1);
  CBiologicalDescription* pDescription = (*pDescriptions)[0];
  CPPUNIT_ASSERT(pDescription != NULL);
  std::string predicate = pDescription->getPredicate();
  CPPUNIT_ASSERT(predicate == "is version of");
  std::string resource = pDescription->getResource();
  CPPUNIT_ASSERT(resource == "Gene Ontology");
  std::string id = pDescription->getId();
  CPPUNIT_ASSERT(id == "GO:0005623");
  id = "GO:0001111";
  CBiologicalDescription* pNewDescription = miriamInfo.createBiologicalDescription();
  pNewDescription->setPredicate(predicate);
  pNewDescription->setResource(resource);
  pNewDescription->setId(id);
  CPPUNIT_ASSERT(pNewDescription != NULL);
  CPPUNIT_ASSERT(pNewDescription->getPredicate() == "is version of");
  CPPUNIT_ASSERT(pNewDescription->getResource() == "Gene Ontology");
  CPPUNIT_ASSERT(pNewDescription->getId() == "GO:0001111");
  CPPUNIT_ASSERT(miriamInfo.save() == true);

  std::string content = pDataModel->exportSBMLToString(NULL, 2, 4);
  CPPUNIT_ASSERT(content.empty() == false);
  // now we convert the content into an XMLNode and check if everything is there that needs to be there
  XMLInputStream inputstream(content.c_str(), false);
  XMLNode node(inputstream);
  CPPUNIT_ASSERT(node.getName() == "sbml");
  unsigned int i, iMax = node.getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pModelNode = &node.getChild(0);
  CPPUNIT_ASSERT(pModelNode != NULL);
  CPPUNIT_ASSERT(pModelNode->getName() == "model");
  iMax = pModelNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pModelAnnotation = &pModelNode->getChild(0);
  CPPUNIT_ASSERT(pModelAnnotation != NULL);
  CPPUNIT_ASSERT(pModelAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have three children
  // depending on the version of libsbml we are using
  iMax = pModelAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  const XMLNode* pMIRIAM1 = NULL, *pMIRIAM2 = NULL, *pOther = NULL;

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pModelAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pModelAnnotation->getChild(i);
        }
      else if (pModelAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pModelAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the libsbml annotation
  // has all necessary namespaces
  const XMLNamespaces* ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  int index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // make sure the there are two modification dates
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Description");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pMIRIAM2->getChild(i).getName() == "modified")
        {
          pMIRIAM2 = &pMIRIAM2->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM2->getName() == "modified");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 2);

  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");

  // there are actually more namespace attributes in the libsbml annotation, but that is enough to make sure
  // that everything should be OK
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Description");
  iMax = pMIRIAM1->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);

  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pMIRIAM1->getChild(i).getName() == "modified")
        {
          pMIRIAM1 = &pMIRIAM1->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1->getName() == "modified");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "W3CDTF");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getCharacters() == "2008-06-05T11:40:04Z");
  //
  // Find the compartment node
  iMax = pModelNode->getNumChildren();
  const XMLNode* pListOfCompartments = NULL;

  for (i = 0; i < iMax; ++i)
    {
      if (pModelNode->getChild(i).getName() == "listOfCompartments")
        {
          pListOfCompartments = &pModelNode->getChild(i);
          break;
        }
    }

  CPPUNIT_ASSERT(pListOfCompartments != NULL);
  iMax = pListOfCompartments->getNumChildren();
  // we have only one compartment
  CPPUNIT_ASSERT(iMax == 1);
  const XMLNode* pCompartmentNode = &pListOfCompartments->getChild(0);
  CPPUNIT_ASSERT(pCompartmentNode != NULL);
  CPPUNIT_ASSERT(pCompartmentNode->getName() == "compartment");
  iMax = pCompartmentNode->getNumChildren();
  CPPUNIT_ASSERT(iMax > 0);
  // the annotation to the model should always be the first child
  const XMLNode* pAnnotation = &pCompartmentNode->getChild(0);
  CPPUNIT_ASSERT(pAnnotation != NULL);
  CPPUNIT_ASSERT(pAnnotation->getName() == "annotation");
  // since the MIRIAM information is complete , we should have two children
  // one with the libsbml MIRIAM annotation and one with the COPASI MIRIAM annotation
  iMax = pAnnotation->getNumChildren();
  CPPUNIT_ASSERT(iMax == 3);
  pMIRIAM1 = NULL;
  pMIRIAM2 = NULL;
  pOther = NULL;

  // make sure the libsbml annotation is stored in pMIRIAM1
  for (unsigned int i = 0; i < iMax; ++i)
    {
      if (pAnnotation->getChild(i).getName() == "RDF")
        {
          pMIRIAM1 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "COPASI")
        {
          pMIRIAM2 = &pAnnotation->getChild(i);
        }
      else if (pAnnotation->getChild(i).getName() == "SOMEANNOTATION")
        {
          pOther = &pAnnotation->getChild(i);
        }
    }

  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pOther != NULL);
  // check if the top level element for the COPASI annotation
  // has all necessary namespaces
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.copasi.org/static/sbml");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "");
  iMax = pMIRIAM2->getNumChildren();
  CPPUNIT_ASSERT(iMax == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM2->getPrefix() == "rdf");
  ns = &pMIRIAM2->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  // check if there are two biological descriptions
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Description");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "isVersionOf");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 1);
  pMIRIAM2 = &pMIRIAM2->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM2 != NULL);
  CPPUNIT_ASSERT(pMIRIAM2->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM2->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMIRIAM2->getChild(0).getName() == "li");
  CPPUNIT_ASSERT(pMIRIAM2->getChild(1).getName() == "li");

  // same checks for the libsbml MIRIAM annotation
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "RDF");
  CPPUNIT_ASSERT(pMIRIAM1->getPrefix() == "rdf");
  ns = &pMIRIAM1->getNamespaces();
  CPPUNIT_ASSERT(ns != NULL);
  index = ns->getIndex("http://purl.org/dc/terms/");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "dcterms");
  index = ns->getIndex("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "rdf");
  index = ns->getIndex("http://www.w3.org/2001/vcard-rdf/3.0#");
  CPPUNIT_ASSERT(index != -1);
  CPPUNIT_ASSERT(ns->getPrefix(index) == "vCard");
  // check if there are two biological descriptions
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Description");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "isVersionOf");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 1);
  pMIRIAM1 = &pMIRIAM1->getChild(0);
  CPPUNIT_ASSERT(pMIRIAM1 != NULL);
  CPPUNIT_ASSERT(pMIRIAM1->getName() == "Bag");
  CPPUNIT_ASSERT(pMIRIAM1->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMIRIAM1->getChild(0).getName() == "li");
  CPPUNIT_ASSERT(pMIRIAM1->getChild(1).getName() == "li");
  // try to reimport the stuff to make sure it is valid SBML
  result = pDataModel->importSBMLFromString(content);
  CPPUNIT_ASSERT(result == true);
}

void test000092::test_miriam_import_1

(

)

This test will most likely fail until we have a workaround for the SBML one modification limit.

Definition at line 1776 of file test000092.cpp.

References CModification::getDate(), CModel::getKey(), CAnnotation::getMiriamAnnotation(), CCopasiDataModel::getModel(), CCopasiDataModel::importSBMLFromString(), CMIRIAMInfo::load(), MODEL_STRING10, pCOPASIDATAMODEL, and CCopasiVector< T >::size().

{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  bool result = pDataModel->importSBMLFromString(test000092::MODEL_STRING10);
  CPPUNIT_ASSERT(result == true);
  CModel* pModel = pDataModel->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // we need to modify the imported MIRIAM annotation,
  // e.g. the add a modified date
  std::string miriamString = pModel->getMiriamAnnotation();
  CPPUNIT_ASSERT(!miriamString.empty());
  CMIRIAMInfo miriamInfo;
  miriamInfo.load(pModel->getKey());
  // check the modified date
  const CCopasiVector<CModification>* pModifications = &miriamInfo.getModifications();
  CPPUNIT_ASSERT(pModifications != NULL);
  // there should be only one modification date
  CPPUNIT_ASSERT_MESSAGE("This test will fail until we have a workaround for the one modification date limit in SBML.", pModifications->size() == 2);
  const CModification* pModification = (*pModifications)[0];
  CPPUNIT_ASSERT(pModification != NULL);
  std::string dateTime = pModification->getDate();
  CPPUNIT_ASSERT(dateTime == "2007-06-05T11:40:04Z" || dateTime == "2008-06-05T11:40:04Z");
  const CModification* pModification2 = (*pModifications)[1];
  CPPUNIT_ASSERT(pModification2 != NULL);
  std::string dateTime2 = pModification2->getDate();
  CPPUNIT_ASSERT(dateTime2 == "2007-06-05T11:40:04Z" || dateTime2 == "2008-06-05T11:40:04Z");
  // make sure both dates are not the same
  CPPUNIT_ASSERT(dateTime != dateTime2);
}

Member Data Documentation

const char * test000092::MODEL_STRING1

staticprotected

This model has complete MIRIAM compliant annotation, so of of it should be exported by libsbml and in addition to that as annotation in the COPASI namespace.

Definition at line 40 of file test000092.h.

Referenced by test_miriam_export_1().

const char * test000092::MODEL_STRING10

staticprotected

Definition at line 49 of file test000092.h.

Referenced by test_miriam_import_1().

const char * test000092::MODEL_STRING2

staticprotected

In this model the Model history is incomplete because there is no creator and no modified date so libsbml 4 will no longer write the model history. Nevertheless the annotation should be written in the COPASI namespace.

Definition at line 41 of file test000092.h.

Referenced by test_miriam_export_2().

const char * test000092::MODEL_STRING3

staticprotected

Initial value:

= 
                                        "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
                                        "<!-- generated with COPASI 4.5.31 (Debug) (http://www.copasi.org) at 2010-04-21 14:00:12 UTC -->\n"
                                        "<?oxygen RNGSchema=\"http://www.copasi.org/static/schema/CopasiML.rng\" type=\"xml\"?>\n"
                                        "<COPASI xmlns=\"http://www.copasi.org/static/schema\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"31\">\n"
                                        "  <Model key=\"Model_0\" name=\"New Model\" simulationType=\"time\" timeUnit=\"s\" volumeUnit=\"ml\" areaUnit=\"m²\" lengthUnit=\"m\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
                                        "    <ListOfCompartments>\n"
                                        "      <Compartment key=\"Compartment_0\" name=\"Compartment\" simulationType=\"fixed\" dimensionality=\"3\"/>\n"
                                        "    </ListOfCompartments>\n"
                                        "    <StateTemplate>\n"
                                        "      <StateTemplateVariable objectReference=\"Model_0\"/>\n"
                                        "      <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
                                        "    </StateTemplate>\n"
                                        "    <InitialState type=\"initialState\">\n"
                                        "      0 1 \n"
                                        "    </InitialState>\n"
                                        "  </Model>\n"
                                        "</COPASI>\n"

In this model the Model there is no MIRIAM annotation. There should be no annotation in the exported SBML model.

Definition at line 42 of file test000092.h.

Referenced by test_miriam_export_3().

const char * test000092::MODEL_STRING4

staticprotected

This model has complete MIRIAM compliant annotation, so of of it should be exported by libsbml and in addition to that as annotation in the COPASI namespace. In addition there is layout information that should also end up in the annotation to the SBML model

Definition at line 43 of file test000092.h.

Referenced by test_miriam_export_4().

const char * test000092::MODEL_STRING5

staticprotected

In this model the Model history is incomplete because there is no creator and no modified date so libsbml 4 will no longer write the model history. Nevertheless the annotation should be written in the COPASI namespace. In addition there is layout information that should also end up in the annotation to the SBML model

Definition at line 44 of file test000092.h.

Referenced by test_miriam_export_5().

const char * test000092::MODEL_STRING6

staticprotected

In this model the Model there is no MIRIAM annotation. But the model has a layout, that should be exported as an annotation to the SBML Model,

Definition at line 45 of file test000092.h.

Referenced by test_miriam_export_6().

const char * test000092::MODEL_STRING7

staticprotected

Initial value:

= 
                                        "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
                                        "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\">\n"
                                        "  <model metaid=\"COPASI1\" id=\"Model_1\" name=\"New Model\">\n"
                                        "    <annotation>\n"
                                        "      <SOMEANNOTATION xmlns=\"http://www.SOMEORGANISATION.org/\" />\n"
                                        "    </annotation>\n"
                                        "    <listOfCompartments>\n"
                                        "     <compartment metaid=\"COPASI2\" id=\"compartment_1\" name=\"Compartment\" size=\"1\">\n"
                                        "       <annotation>\n"
                                        "         <SOMEANNOTATION xmlns=\"http://www.SOMEORGANISATION.org/\" />\n"
                                        "       </annotation>\n"
                                        "     </compartment>\n"
                                        "    </listOfCompartments>\n"
                                        "  </model>\n"
                                        "</sbml>\n"

This SBML model already contains an annotation. We load it and add some MIRIAM annotation and write it out again to check if MIRIAM annotation is correctly written even if another annotation exists.

Definition at line 46 of file test000092.h.

Referenced by test_miriam_export_7().

const char * test000092::MODEL_STRING8

staticprotected

This SBML model already contains RDF annotation and other annotation. We load it and modify the MIRIAM annotation and write it out again to check if MIRIAM annotation is correctly updated

Definition at line 47 of file test000092.h.

Referenced by test_miriam_export_8().

const char * test000092::MODEL_STRING9

staticprotected

This SBML model already contains RDF annotation and other annotation. It also contains COPASI RDF annotation. We load it and modify the MIRIAM annotation and write it out again to check if MIRIAM annotation is correctly updated and COPASI annotation is correctly replaced.

Definition at line 48 of file test000092.h.

Referenced by test_miriam_export_9().

CCopasiDataModel * test000092::pCOPASIDATAMODEL = NULL

staticprotected

Definition at line 50 of file test000092.h.

Referenced by setUp(), test_miriam_export_1(), test_miriam_export_2(), test_miriam_export_3(), test_miriam_export_4(), test_miriam_export_5(), test_miriam_export_6(), test_miriam_export_7(), test_miriam_export_8(), test_miriam_export_9(), and test_miriam_import_1().

---

The documentation for this class was generated from the following files:

• test000092.h
• test000092.cpp