validator/constraints/ModelingPracticeConstraints.cpp

/**
 * @cond doxygenLibsbmlInternal
 *
 * @file    ModelingPracticeConstraints.cpp
 * @brief   ModelingPractice check constraints.
 * @author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2020 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. University of Heidelberg, Heidelberg, Germany
 *     3. University College London, London, UK
 *
 * Copyright (C) 2019 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2013-2018 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *     3. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2009-2013 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA
 *
 * Copyright (C) 2002-2005 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * ---------------------------------------------------------------------- -->*/

#ifndef AddingConstraintsToValidator
#include <sbml/validator/VConstraint.h>
#endif

#include <sbml/validator/ConstraintMacros.h>

#include "LocalParameterShadowsIdInModel.h"
/** @cond doxygenIgnored */
using namespace std;
/** @endcond */

// Compartment validation

START_CONSTRAINT (80501, Compartment, c)
{
  pre( c.getLevel() > 1);
  pre( c.getSpatialDimensions() != 0 );

  //msg =
  //  "It is recommended that the size of a compartment is set.";

  bool fail = true;

  // is size set on the element
  if (c.isSetSize() == true)
  {
    fail = false;
  }
  else if (c.isSetSpatialDimensions() && c.getSpatialDimensions()==0) {
    //Compartments with spatialDimensions of 0 should
    //(and, for some levels/versions, *must*) not have a 'size'.
    fail = false;
  }
  else
  {
    pre (c.isSetId() == true);
    // is there an initial assignment/assignment rule that would set the value
    if (m.getInitialAssignmentBySymbol(c.getId()) != NULL)
    {
      fail = false;
    }
    else if (m.getAssignmentRuleByVariable(c.getId()) != NULL)
    {
      fail = false;
    }
    // Need something like the following to check if the initial value is
    // set by an algebraic rule.  However, there is no 'hasVariable'
    // function for an ASTNode yet.
    /*
    else if (!c.getConstant())
    {
      for (unsigned int alg=0; alg<m.getNumRules(); alg++)
      {
        const Rule* rule = m.getRule(alg);
        if (rule->isAlgebraic() && rule->getMath()->hasVariable(c.getId()))
        {
          fail = false;
        }
      }
    }
    */
    else
    {
      msg = "The <compartment> with the id '" + c.getId();
      msg += "' does not have a 'size' attribute, nor is its initial value ";
      msg += "set by an <initialAssignment> or <assignmentRule>.";
    }
  }

  inv( fail == false);
}
END_CONSTRAINT


START_CONSTRAINT (80601, Species, s)
{
  bool fail = true;

  if (s.isSetInitialAmount() == true || s.isSetInitialConcentration() == true)
  {
    fail = false;
  }
  else
  {
    pre (s.isSetId() == true);
    // is there an initial assignment/assignment rule that would set the value
    if (m.getInitialAssignmentBySymbol(s.getId()) != NULL)
    {
      fail = false;
    }
    else if (m.getAssignmentRuleByVariable(s.getId()) != NULL)
    {
      fail = false;
    }
    // Need something like the following to check if the initial value is
    // set by an algebraic rule.  However, there is no 'hasVariable' function
    // for an ASTNode yet.
    /*
    else if (!s.getConstant())
    {
      for (unsigned int alg=0; alg<m.getNumRules(); alg++)
      {
        const Rule* rule = m.getRule(alg);
        if (rule->isAlgebraic() && rule->getMath()->hasVariable(s.getId()))
        {
          fail = false;
        }
      }
    }
    */
    else
    {
      msg = "The <species> with the id '" + s.getId();
      msg += "' does not have an 'initialConcentration' or 'initialAmount' ";
      msg += "attribute, nor is its initial value set by an <initialAssignment> ";
      msg += "or <assignmentRule>.";
    }
  }

  inv (fail == false);
}
END_CONSTRAINT


// Parameters
EXTERN_CONSTRAINT( 81121, LocalParameterShadowsIdInModel             )


START_CONSTRAINT (80701, Parameter, p)
{
  if(p.isSetId())
  {
    msg = "The <parameter> with the id '" + p.getId() + "' does not have a 'units' attribute.";
  }
  inv(p.isSetUnits() == true);
}
END_CONSTRAINT


START_CONSTRAINT (80701, LocalParameter, p)
{
  if(p.isSetId())
  {
    msg = "The <localParameter> with the id '" + p.getId() + "' does not have a 'units' attribute.";
  }
  inv(p.isSetUnits() == true);
}
END_CONSTRAINT


START_CONSTRAINT (80702, Parameter, p)
{
  bool fail = true;

  if (p.isSetValue() == true)
  {
    fail = false;
  }
  else
  {
    pre (p.isSetId() == true);
    // is there an initial assignment/assignment rule that would set the value
    if (m.getInitialAssignmentBySymbol(p.getId()) != NULL)
    {
      fail = false;
    }
    else if (m.getAssignmentRuleByVariable(p.getId()) != NULL)
    {
      fail = false;
    }
    // Need something like the following to check if the initial value is
    // set by an algebraic rule.  However, there is no 'hasVariable' function
    // for an ASTNode yet.
    /*
    else if (!p.getConstant())
    {
      for (unsigned int alg=0; alg<m.getNumRules(); alg++)
      {
        const Rule* rule = m.getRule(alg);
        if (rule->isAlgebraic() && rule->getMath()->hasVariable(p.getId()))
        {
          fail = false;
        }
      }
    }
    */
    else
    {
      msg = "The <parameter> with the id '" + p.getId();
      msg += "' does not have 'value' ";
      msg += "attribute, nor is its initial value set by an <initialAssignment> ";
      msg += "or <assignmentRule>.";
    }
  }

  inv (fail == false);
}
END_CONSTRAINT


START_CONSTRAINT (80702, LocalParameter, p)
{
  if(p.isSetId())
  {
    msg = "The <localParameter> with the id '" + p.getId() + "' does not have a 'value' attribute.";
  }
  inv(p.isSetValue() == true);
}
END_CONSTRAINT

  /** @endcond */