/**
* Checks that the arguments to eq or neq are consistent
* i.e. have same type both boolean or both numeric
*
* If an inconsistency is found, an error message is logged.
*/
void
EqualityArgsMathCheck::checkArgs (const Model& m,
const ASTNode& node,
const SBase & sb)
{
/* check that node has two children */
if (node.getNumChildren() != 2)
{
return;
}
/* arguments must return consistent value types */
if (returnsNumeric(m, node.getLeftChild()) &&
!returnsNumeric(m, node.getRightChild()))
{
logMathConflict(node, sb);
}
else if (node.getLeftChild()->isBoolean() &&
!node.getRightChild()->isBoolean())
{
logMathConflict(node, sb);
}
}
/*
* Checks that the units of the delay function are consistent
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheck::checkUnitsFromDelay (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has two children */
if (node.getNumChildren() != 2)
{
return;
}
if (!m.getSBMLNamespaces()->getNamespaces())
{
#if 0
cout << "[DEBUG] XMLNS IS NULL" << endl;
#endif
}
/* delay(x, t)
* no restrictions on units of x
* but t must have units of time
*/
UnitDefinition *time = new UnitDefinition(m.getSBMLNamespaces());
Unit *unit = new Unit(m.getSBMLNamespaces());
unit->setKind(UNIT_KIND_SECOND);
unit->initDefaults();
UnitDefinition * tempUD;
time->addUnit(unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
tempUD = unitFormat->getUnitDefinition(node.getRightChild(), inKL, reactNo);
if (!unitFormat->getContainsUndeclaredUnits())
{
if (!UnitDefinition::areEquivalent(time, tempUD))
{
logInconsistentDelay(node, sb);
}
}
delete time;
delete tempUD;
delete unit;
delete unitFormat;
checkUnits(m, *node.getLeftChild(), sb, inKL, reactNo);
}
/**
*
* Creates an SBML model represented in "7.2 Example involving units"
* in the SBML Level 2 Version 4 Specification.
*
*/
SBMLDocument* createExampleInvolvingUnits()
{
const unsigned int level = Level;
const unsigned int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument* sbmlDoc = new SBMLDocument(level,version);
// Adds the namespace for XHTML to the SBMLDocument object. We need this
// because we will add notes to the model. (By default, the SBML document
// created by SBMLDocument only declares the SBML XML namespace.)
sbmlDoc->getNamespaces()->add("http://www.w3.org/1999/xhtml", "xhtml");
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model* model = sbmlDoc->createModel();
model->setId("unitsExample");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition* unitdef;
Unit *unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("substance").
//
// This has the effect of redefining the default unit of subtance for the
// whole model.
//---------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("substance");
// Creates an Unit inside the UnitDefinition object
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("mmls")
//--------------------------------------------------------------------------------
// Note that we can reuse the pointers 'unitdef' and 'unit' because the
// actual UnitDefinition object (along with the Unit objects within it)
// is already attached to the Model object.
unitdef = model->createUnitDefinition();
unitdef->setId("mmls");
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_SECOND);
unit->setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition3) Creates an UnitDefinition object ("mml")
//--------------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("mml");
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment* comp;
const string compName = "cell";
// Creates a Compartment object ("cell")
comp = model->createCompartment();
comp->setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp->setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species *sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("x0")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x0");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp->setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimensions" attribute of the Compartment object ("cytosol") in which
// this species object is located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is moles/liters .
//
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("x1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x1");
sp->setCompartment(compName);
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("s1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s1");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("s2")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s2");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
//
// Creates global Parameter objects inside the Model object.
//
//---------------------------------------------------------------------------
Parameter* para;
// Creates a Parameter ("vm")
para = model->createParameter();
para->setId("vm");
para->setValue(2);
para->setUnits("mmls");
// Creates a Parameter ("km")
para = model->createParameter();
para->setId("km");
para->setValue(2);
para->setUnits("mml");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction* reaction;
SpeciesReference* spr;
KineticLaw* kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("v1").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v1");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "x0"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("x0");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s1" in the model.
spr = reaction->createProduct();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Creates a <notes> element in the KineticLaw object.
// Here we illustrate how to do it using a literal string. This requires
// known the required syntax of XHTML and the requirements for SBML <notes>
// elements. Later below, we show how to create notes using objects instead
// of strings.
string notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following KineticLaw object.
//
// <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
// <apply>
// <times/>
// <apply>
// <divide/>
// <apply>
// <times/>
// <ci> vm </ci>
// <ci> s1 </ci>
// </apply>
// <apply>
// <plus/>
// <ci> km </ci>
// <ci> s1 </ci>
// </apply>
// </apply>
// <ci> cell </ci>
// </apply>
// </math>
//---------------------------------------------------------------------------
//
// In the following code, ASTNode objects, which construct an ASTNode tree
// of the above math, are created and added in the order of preorder traversal
// of the tree (i.e. the order corresponds to the nested structure of the above
// MathML elements), and thus the following code maybe a bit more efficient but
// maybe a bit difficult to read.
//
ASTNode* astMath = new ASTNode(AST_TIMES);
astMath->addChild(new ASTNode(AST_DIVIDE));
ASTNode* astDivide = astMath->getLeftChild();
astDivide->addChild(new ASTNode(AST_TIMES));
ASTNode* astTimes = astDivide->getLeftChild();
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getLeftChild()->setName("vm");
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getRightChild()->setName("s1");
astDivide->addChild(new ASTNode(AST_PLUS));
ASTNode* astPlus = astDivide->getRightChild();
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getLeftChild()->setName("km");
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getRightChild()->setName("s1");
astMath->addChild(new ASTNode(AST_NAME));
astMath->getRightChild()->setName("cell");
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("v2").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v2");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s1"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s2" in the model.
spr = reaction->createProduct();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by XMLNode) to the KineticLaw object.
//
// The following code is an alternative to using setNotes(const string&).
// The equivalent code would be like this:
//
// notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
// kl->setNotes(notesString);
// Creates an XMLNode of start element (<xhtml:p>) without attributes.
XMLNode notesXMLNode(XMLTriple("p", "", "xhtml"), XMLAttributes());
// Adds a text element to the start element.
notesXMLNode.addChild(XMLNode(" ((vm * s2)/(km + s2)) * cell "));
// Adds it to the kineticLaw object.
kl->setNotes(¬esXMLNode);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
// To create mathematical expressions, one would typically construct
// an ASTNode tree as the above example code which creates a math of another
// KineticLaw object. Here, to save some space and illustrate another approach
// of doing it, we will write out the formula in MathML form and then use a
// libSBML convenience function to create the ASTNode tree for us.
// (This is a bit dangerous; it's very easy to make mistakes when writing MathML
// by hand, so in a real program, we would not really want to do it this way.)
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> s2 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> s2 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction3) Creates a Reaction object ("v3").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v3");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s2"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "x1" in the model.
spr = reaction->createProduct();
spr->setSpecies("x1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by string) to the KineticLaw object.
notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> x1 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> x1 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
/**
* Checks that the units of the power function are consistent
*
* If inconsistent units are found, an error message is logged.
*
* The two arguments to power, which are of the form power(a, b)
* with the meaning a^b, should be as follows:
* (1) if the second argument is an integer,
* then the first argument can have any units;
* (2) if the second argument b is a rational number n/m,
* it must be possible to derive the m-th root of (a{unit})n,
* where {unit} signifies the units associated with a;
* otherwise, (3) the units of the first argument must be “dimensionless”.
* The second argument (b) should always have units of “dimensionless”.
*
*/
void
PowerUnitsCheck::checkUnitsFromPower (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has 2 children */
if (node.getNumChildren() != 2)
{
return;
}
double value;
UnitDefinition dim(m.getSBMLNamespaces());
Unit unit(m.getSBMLNamespaces());
unit.setKind(UNIT_KIND_DIMENSIONLESS);
unit.initDefaults();
dim.addUnit(&unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
UnitDefinition *tempUD = NULL;
UnitDefinition *unitsArg1, *unitsArgPower;
unitsArg1 = unitFormat->getUnitDefinition(node.getLeftChild(), inKL, reactNo);
unsigned int undeclaredUnits =
unitFormat->getContainsUndeclaredUnits();
ASTNode *child = node.getRightChild();
unitFormat->resetFlags();
unitsArgPower = unitFormat->getUnitDefinition(child, inKL, reactNo);
unsigned int undeclaredUnitsPower =
unitFormat->getContainsUndeclaredUnits();
// The second argument (b) should always have units of “dimensionless”.
// or it has undeclared units that we assume are correct
if (undeclaredUnitsPower == 0 && !UnitDefinition::areEquivalent(&dim, unitsArgPower))
{
logNonDimensionlessPowerConflict(node, sb);
}
// The first argument is dimensionless then it doesnt matter
// what the power is
if (undeclaredUnits == 0 && !UnitDefinition::areEquivalent(&dim, unitsArg1))
{
// if not argument needs to be an integer or a rational
unsigned int isInteger = 0;
unsigned int isRational = 0;
unsigned int isExpression = 0;
/* power must be an integer
* but need to check that it is not a real
* number that is integral
* i.e. mathml <cn> 2 </cn> will record a "real"
*/
if (child->isRational())
{
isRational = 1;
}
else if (child->isInteger())
{
isInteger = 1;
}
else if (child->isReal())
{
if (ceil(child->getReal()) == child->getReal())
{
isInteger = 1;
}
}
else if (child->getNumChildren() > 0)
{
// power might itself be an expression
tempUD = unitFormat->getUnitDefinition(child, inKL, reactNo);
UnitDefinition::simplify(tempUD);
if (tempUD->isVariantOfDimensionless())
{
SBMLTransforms::mapComponentValues(&m);
double value = SBMLTransforms::evaluateASTNode(child);
SBMLTransforms::clearComponentValues();
#if defined(__linux)
if (!std::isnan(value))
#else
if (!isnan(value))
#endif
{
if (floor(value) != value)
isExpression = 1;
else
isInteger = 1;
}
else
{
isExpression = 1;
}
}
else
{
/* here the child is an expression with units
* flag the expression as not checked
*/
isExpression = 1;
}
}
else
{
// power could be a parameter or a speciesReference in l3
const Parameter *param = NULL;
const SpeciesReference *sr = NULL;
if (child->isName())
{
/* Parameters may be declared in two places (the model and the
* kinetic law's local parameter list), so we have to check both.
*/
if (sb.getTypeCode() == SBML_KINETIC_LAW)
{
const KineticLaw* kl = dynamic_cast<const KineticLaw*>(&sb);
/* First try local parameters and if null is returned, try
* the global parameters */
if (kl != NULL)
{
param = kl->getParameter(child->getName());
}
}
if (param == NULL)
{
param = m.getParameter(child->getName());
}
if (param == NULL && m.getLevel() > 2)
{
// could be a species reference
sr = m.getSpeciesReference(child->getName());
}
}
if (param != NULL)
{
/* We found a parameter with this identifier. */
if (UnitDefinition::areEquivalent(&dim, unitsArgPower) || undeclaredUnitsPower)
{
value = param->getValue();
if (value != 0)
{
if (ceil(value) == value)
{
isInteger = 1;
}
}
}
else
{
/* No parameter definition found for child->getName() */
logUnitConflict(node, sb);
}
}
else if (sr != NULL)
{
// technically here there is an issue
// stoichiometry is dimensionless
SBMLTransforms::mapComponentValues(&m);
double value = SBMLTransforms::evaluateASTNode(child, &m);
SBMLTransforms::clearComponentValues();
// but it may not be an integer
#if defined(__linux)
if (!std::isnan(value))
#else
if (!isnan(value))
#endif
// we cant check
{
isExpression = 1;
}
else
{
if (ceil(value) == value)
{
isInteger = 1;
}
}
}
}
if (isRational == 1)
{
//FIX-ME will need sorting for double exponents
//* (2) if the second argument b is a rational number n/m,
//* it must be possible to derive the m-th root of (a{unit})n,
//* where {unit} signifies the units associated with a;
unsigned int impossible = 0;
for (unsigned int n = 0; impossible == 0 && n < unitsArg1->getNumUnits(); n++)
{
if ((int)(unitsArg1->getUnit(n)->getExponent()) * child->getInteger() %
child->getDenominator() != 0)
impossible = 1;
}
if (impossible)
logRationalPowerConflict(node, sb);
}
else if (isExpression == 1)
{
logExpressionPowerConflict(node, sb);
}
else if (isInteger == 0)
{
logNonIntegerPowerConflict(node, sb);
}
}
// if (!areEquivalent(dim, unitsPower))
// {
// /* 'v' does not have units of dimensionless. */
// /* If the power 'n' is a parameter, check if its units are either
// * undeclared or declared as dimensionless. If either is the case,
// * the value of 'n' must be an integer.
// */
// const Parameter *param = NULL;
// if (child->isName())
// {
// /* Parameters may be declared in two places (the model and the
// * kinetic law's local parameter list), so we have to check both.
// */
// if (sb.getTypeCode() == SBML_KINETIC_LAW)
// {
// const KineticLaw* kl = dynamic_cast<const KineticLaw*>(&sb);
// /* First try local parameters and if null is returned, try
// * the global parameters */
// if (kl != NULL)
// {
// param = kl->getParameter(child->getName());
// }
// }
// if (param == NULL)
// {
// param = m.getParameter(child->getName());
// }
//
// }
// if (param != NULL)
// {
// /* We found a parameter with this identifier. */
// if (areEquivalent(dim, unitsArgPower) || unitFormat->hasUndeclaredUnits(child))
// {
// value = param->getValue();
// if (value != 0)
// {
// if (ceil(value) != value)
// {
// logUnitConflict(node, sb);
// }
// }
// }
// else
// {
///* No parameter definition found for child->getName() */
// logUnitConflict(node, sb);
// }
// }
// else if (child->isFunction() || child->isOperator())
// {
// /* cannot test whether the value will be appropriate */
// if (!areEquivalent(dim, unitsArgPower))
// {
// logUnitConflict(node, sb);
// }
// }
// /* power must be an integer
// * but need to check that it is not a real
// * number that is integral
// * i.e. mathml <cn> 2 </cn> will record a "real"
// */
// else if (!child->isInteger())
// {
// if (!child->isReal())
// {
// logUnitConflict(node, sb);
// }
// else if (ceil(child->getReal()) != child->getReal())
// {
// logUnitConflict(node, sb);
// }
// }
// }
// else if (!areEquivalent(dim, unitsArgPower))
// {
// /* power (3, k) */
// logUnitConflict(node, sb);
// }
checkUnits(m, *node.getLeftChild(), sb, inKL, reactNo);
delete unitFormat;
delete unitsArg1;
delete unitsArgPower;
}