src/sbml/SBMLNamespaces.cpp

/**
 * @file    SBMLNamespaces.cpp
 * @brief   SBMLNamespaces class to store level/version and namespace
 * @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
 * ---------------------------------------------------------------------- -->
 */

#include <sbml/SBMLNamespaces.h>
#include <sbml/extension/SBMLExtensionRegistry.h>
#include <sbml/extension/SBMLExtensionException.h>
#include <sstream>
#include <sbml/common/common.h>
#include <iostream>

/** @cond doxygenIgnored */
using namespace std;
/** @endcond */


LIBSBML_CPP_NAMESPACE_BEGIN
#ifdef __cplusplus

/** @cond doxygenLibsbmlInternal */
void
SBMLNamespaces::initSBMLNamespace()
{
  mNamespaces = new XMLNamespaces();

  switch (mLevel)
  {
  case 1:
    switch (mVersion)
    {
    case 1:
    case 2:
      mNamespaces->add(SBML_XMLNS_L1);
      break;
    }
    break;
  case 2:
    switch (mVersion)
    {
    case 1:
      mNamespaces->add(SBML_XMLNS_L2V1);
      break;
    case 2:
      mNamespaces->add(SBML_XMLNS_L2V2);
      break;
    case 3:
      mNamespaces->add(SBML_XMLNS_L2V3);
      break;
    case 4:
      mNamespaces->add(SBML_XMLNS_L2V4);
      break;
    case 5:
      mNamespaces->add(SBML_XMLNS_L2V5);
      break;
    }
    break;
  case 3:
    switch (mVersion)
    {
    case 1:
      mNamespaces->add(SBML_XMLNS_L3V1);
      break;
    case 2:
      mNamespaces->add(SBML_XMLNS_L3V2);
      break;
    }
    break;
  }

  if (mNamespaces->getLength() == 0)
  {
    mLevel = SBML_INT_MAX;
    mVersion = SBML_INT_MAX;
    delete mNamespaces;
    mNamespaces = NULL;
  }
}
/** @endcond */


SBMLNamespaces::SBMLNamespaces(unsigned int level, unsigned int version)
 : mLevel(level)
  ,mVersion(version)
{
  initSBMLNamespace();
}


/**
 * (For Extension)
 *
 * Creates a new SBMLNamespaces object corresponding to the combination of
 * (1) the given SBML @p level and @p version, and (2) the given @p package
 * with the @p package @p version.
 *
 */
SBMLNamespaces::SBMLNamespaces(unsigned int level, unsigned int version,
                               const std::string &pkgName, unsigned int pkgVersion,
                               const std::string pkgPrefix)
 : mLevel(level)
  ,mVersion(version)
{
  initSBMLNamespace();

  //
  // checks the URI of the given package
  //
  const SBMLExtension* sbmlext = SBMLExtensionRegistry::getInstance().getExtensionInternal(pkgName);
  if (sbmlext)
  {
    const std::string uri    = sbmlext->getURI(level, version, pkgVersion);
    const std::string prefix = (pkgPrefix.empty()) ? pkgName : pkgPrefix;

    if (!uri.empty() && mNamespaces != NULL)
    {
      mNamespaces->add(uri,prefix);
    }
    else
    {
      std::ostringstream errMsg;

      errMsg << "Package \"" << pkgName << "\" SBML level " << level << " SBML version "
             << version << " package version " << pkgVersion << " is not supported.";

      throw SBMLExtensionException(errMsg.str());
    }
  }
  else
  {
    std::ostringstream errMsg;

    errMsg << pkgName << " : No such package registered.";

    throw SBMLExtensionException(errMsg.str());
  }
}

SBMLNamespaces::~SBMLNamespaces()
{
  if (mNamespaces != NULL)
    delete mNamespaces;
}


/*
 * Copy constructor; creates a copy of a SBMLNamespaces.
 */
SBMLNamespaces::SBMLNamespaces(const SBMLNamespaces& orig)
 : mLevel(orig.mLevel)
 , mVersion(orig.mVersion)
 , mNamespaces(NULL)
{
  if(orig.mNamespaces != NULL)
    this->mNamespaces =
          new XMLNamespaces(*const_cast<SBMLNamespaces&>(orig).mNamespaces);
}


const List *
SBMLNamespaces::getSupportedNamespaces()
{
  List *result = new List();
  result->add(new SBMLNamespaces(1,1));
  result->add(new SBMLNamespaces(1,2));
  result->add(new SBMLNamespaces(2,1));
  result->add(new SBMLNamespaces(2,2));
  result->add(new SBMLNamespaces(2,3));
  result->add(new SBMLNamespaces(2,4));
  result->add(new SBMLNamespaces(2,5));
  result->add(new SBMLNamespaces(3,1));
  result->add(new SBMLNamespaces(3,2));
  return result;
}


void
SBMLNamespaces::freeSBMLNamespaces(List * supportedNS)
{
  if (supportedNS == NULL) return;
  for (unsigned int i = 0; i < supportedNS->getSize(); i++)
  {
    delete (SBMLNamespaces*)supportedNS->get(i);
  }
  delete supportedNS;
}

/*
 * Assignment operator for SBMLNamespaces.
 */
SBMLNamespaces&
SBMLNamespaces::operator=(const SBMLNamespaces& rhs)
{
  if (&rhs != this)
  {
    mLevel   = rhs.mLevel;
    mVersion = rhs.mVersion;
    delete this->mNamespaces;
    if(rhs.mNamespaces != NULL)
      this->mNamespaces =
            new XMLNamespaces(*const_cast<SBMLNamespaces&>(rhs).mNamespaces);
    else
      this->mNamespaces = NULL;
  }

  return *this;
}


/*
 * Creates and returns a deep copy of this SBMLNamespaces.
 */
SBMLNamespaces *
SBMLNamespaces::clone () const
{
  return new SBMLNamespaces(*this);
}


std::string
SBMLNamespaces::getSBMLNamespaceURI(unsigned int level,
                                 unsigned int version)
{
  std::string uri = "";
  switch (level)
  {
  case 1:
    uri = SBML_XMLNS_L1;
    break;
  case 3:
    switch(version)
    {
    case 1:
      uri = SBML_XMLNS_L3V1;
      break;
    case 2:
    default:
      uri = SBML_XMLNS_L3V2;
      break;
    }
    break;
  case 2:
  default:
    switch (version)
    {
    case 1:
      uri = SBML_XMLNS_L2V1;
      break;
    case 2:
      uri = SBML_XMLNS_L2V2;
      break;
    case 3:
      uri = SBML_XMLNS_L2V3;
      break;
    case 4:
      uri = SBML_XMLNS_L2V4;
      break;
    case 5:
    default:
      uri = SBML_XMLNS_L2V5;
      break;
    }
    break;
  }
  return uri;
}


std::string
SBMLNamespaces::getURI() const
{
  return getSBMLNamespaceURI(mLevel,mVersion);
}


unsigned int
SBMLNamespaces::getLevel()
{
  return mLevel;
}


unsigned int
SBMLNamespaces::getLevel() const
{
  return mLevel;
}


unsigned int
SBMLNamespaces::getVersion()
{
  return mVersion;
}


unsigned int
SBMLNamespaces::getVersion() const
{
  return mVersion;
}


XMLNamespaces *
SBMLNamespaces::getNamespaces()
{
  return mNamespaces;
}


const XMLNamespaces *
SBMLNamespaces::getNamespaces() const
{
  return mNamespaces;
}


int
SBMLNamespaces::addNamespaces(const XMLNamespaces * xmlns)
{
  int success = LIBSBML_OPERATION_SUCCESS;

  if (xmlns == NULL)
    return LIBSBML_INVALID_OBJECT;

  if (!mNamespaces)
  {
    initSBMLNamespace();
  }

  /* check whether the namespace already exists
   * add if it does not
   */
  for (int i = 0; i < xmlns->getLength(); i++)
  {
    if (mNamespaces != NULL && !(mNamespaces->hasNS(xmlns->getURI(i), xmlns->getPrefix(i))))
    {
      success = mNamespaces->add(xmlns->getURI(i), xmlns->getPrefix(i));
    }
  }

  return success;
}

/*
 * (For Extension)
 *
 * Add an XML namespace (a pair of URI and prefix) of a package extension
 * to the set of namespaces within this SBMLNamespaces object.
 *
 */
int
SBMLNamespaces::addPackageNamespace(const std::string &pkgName, unsigned int pkgVersion,
                                const std::string &pkgPrefix)
{
  if (!mNamespaces)
  {
    initSBMLNamespace();
  }

  //
  // checks the URI of the given package
  //
  const SBMLExtension* sbmlext = SBMLExtensionRegistry::getInstance().getExtensionInternal(pkgName);
  if (sbmlext)
  {
    const std::string uri    = sbmlext->getURI(mLevel, mVersion, pkgVersion);
    const std::string prefix = (pkgPrefix.empty()) ? pkgName : pkgPrefix;
    if (!uri.empty() && mNamespaces != NULL)
    {
      return mNamespaces->add(uri,prefix);
    }
    else
    {
      return LIBSBML_INVALID_ATTRIBUTE_VALUE;
    }
  }
  else
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }

//  return LIBSBML_OPERATION_SUCCESS;
}


/** @cond doxygenLibsbmlInternal */
/*
 * (For Extension)
 *
 * Add an XML namespace (a pair of URI and prefix) of a package extension
 * to the set of namespaces within this SBMLNamespaces object.
 *
 */
int
SBMLNamespaces::addPkgNamespace(const std::string &pkgName, unsigned int pkgVersion,
                                const std::string &pkgPrefix)
{

  return addPackageNamespace(pkgName, pkgVersion, pkgPrefix);
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
/*
 * Add the XML namespaces of package extensions in the given
 * XMLNamespace object to the set of namespaces within this
 * SBMLNamespaces object (Non-package XML namespaces are not added
 * by this function).
 */
int
SBMLNamespaces::addPackageNamespaces (const XMLNamespaces *xmlns)
{
  if (!mNamespaces)
  {
    initSBMLNamespace();
  }

  if (!xmlns)
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }

  for (int i=0; i < xmlns->getLength(); i++)
  {
    const std::string uri = xmlns->getURI(i);

    if (mNamespaces != NULL && SBMLExtensionRegistry::getInstance().isRegistered(uri))
    {
      mNamespaces->add(uri, xmlns->getPrefix(i));
    }
  }

  return LIBSBML_OPERATION_SUCCESS;
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
int
SBMLNamespaces::addPkgNamespaces (const XMLNamespaces *xmlns)
{
  return addPackageNamespaces(xmlns);
}
/** @endcond */

int
SBMLNamespaces::addNamespace(const std::string &uri, const std::string &prefix)
{
  if (!mNamespaces)
  {
    initSBMLNamespace();
  }

  return mNamespaces != NULL ? mNamespaces->add(uri, prefix) : LIBSBML_INVALID_OBJECT;
}


int
SBMLNamespaces::removeNamespace(const std::string &uri)
{
  if (!mNamespaces)
  {
    initSBMLNamespace();
  }

  return mNamespaces != NULL ? mNamespaces->remove(mNamespaces->getIndex(uri)) : LIBSBML_INVALID_OBJECT;
}


/*
 * Removes an XML namespace of a package extension from the set of namespaces
 * within this SBMLNamespaces object.
 */
int
SBMLNamespaces::removePackageNamespace(unsigned int level, unsigned version, const std::string &pkgName,
                                   unsigned int pkgVersion)
{
  //
  // checks the URI of the given package
  //
  const SBMLExtension* sbmlext = SBMLExtensionRegistry::getInstance().getExtensionInternal(pkgName);
  if (sbmlext)
  {
    if (!mNamespaces)
    {
      return LIBSBML_OPERATION_SUCCESS;
    }

    const std::string uri = sbmlext->getURI(level, version, pkgVersion);
    if (!uri.empty())
    {
      return mNamespaces->remove(mNamespaces->getIndex(uri));
    }
    else
    {
      return LIBSBML_INVALID_ATTRIBUTE_VALUE;
    }
  }
  else
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
}

/** @cond doxygenLibsbmlInternal */
int
SBMLNamespaces::removePkgNamespace(unsigned int level, unsigned version, const std::string &pkgName,
                                   unsigned int pkgVersion)
{
  return removePackageNamespace(level, version, pkgName, pkgVersion);
}
/** @endcond */

/*
 * Predicate returning @c true if the given
 * URL is one of SBML XML namespaces.
 */
bool
SBMLNamespaces::isSBMLNamespace(const std::string& uri)
{
  if (uri == SBML_XMLNS_L1)   return true;
  if (uri == SBML_XMLNS_L2V1) return true;
  if (uri == SBML_XMLNS_L2V2) return true;
  if (uri == SBML_XMLNS_L2V3) return true;
  if (uri == SBML_XMLNS_L2V4) return true;
  if (uri == SBML_XMLNS_L2V5) return true;
  if (uri == SBML_XMLNS_L3V1) return true;
  if (uri == SBML_XMLNS_L3V2) return true;

  return false;
}

bool
SBMLNamespaces::isValidCombination()
{
  bool valid = true;
  bool sbmlDeclared = false;
  std::string declaredURI("");
  unsigned int version = getVersion();
  XMLNamespaces *xmlns = getNamespaces();

  if (xmlns != NULL)
  {
    //
    // checks defined SBML XMLNamespace
    // returns false if different SBML XMLNamespaces
    // (e.g. SBML_XMLNS_L2V1 and SBML_XMLNS_L2V3) are defined.
    //
    int numNS = 0;

    if (xmlns->hasURI(SBML_XMLNS_L3V2))
    {
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L3V2);
    }

    if (xmlns->hasURI(SBML_XMLNS_L3V1))
    {
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L3V1);
    }

    if (xmlns->hasURI(SBML_XMLNS_L2V5))
    {
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L2V5);
    }

    if (xmlns->hasURI(SBML_XMLNS_L2V4))
    {
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L2V4);
    }

    if (xmlns->hasURI(SBML_XMLNS_L2V3))
    {
      // checks different SBML XMLNamespaces
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L2V3);
    }

    if (xmlns->hasURI(SBML_XMLNS_L2V2))
    {
      // checks different SBML XMLNamespaces
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L2V2);
    }

    if (xmlns->hasURI(SBML_XMLNS_L2V1))
    {
      // checks different SBML XMLNamespaces
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L2V1);
    }

    if (xmlns->hasURI(SBML_XMLNS_L1))
    {
      // checks different SBML XMLNamespaces
      if (numNS > 0) return false;
      ++numNS;
      declaredURI.assign(SBML_XMLNS_L1);
    }

    // checks if the SBML Namespace is explicitly defined.
    for (int i=0; i < xmlns->getLength(); i++)
    {
      if (!declaredURI.empty() &&
                      xmlns->getURI(i) == declaredURI)
      {
        sbmlDeclared = true;
        break;
      }
    }
  }


  switch (getLevel())
  {
    case 1:
     switch (version)
      {
        case 1:
        case 2:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L1))
            {
              valid = false;
            }
          }
          break;
        default:
          valid = false;
          break;
        }
      break;
    case 2:
      switch (version)
      {
        case 1:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L2V1))
            {
              valid = false;
            }
          }
          break;
        case 2:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L2V2))
            {
              valid = false;
            }
          }
          break;
        case 3:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L2V3))
            {
              valid = false;
            }
          }
          break;
        case 4:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L2V4))
            {
              valid = false;
            }
          }
          break;
        case 5:
          // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L2V5))
            {
              valid = false;
            }
          }
          break;
        default:
          valid = false;
          break;
        }
      break;
    case 3:
      switch (version)
      {
        case 1:
         // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L3V1))
            {
              valid = false;
            }
          }
          break;
        case 2:
         // the namespaces contains the sbml namespaces
          // check it is the correct ns for the level/version
          if (sbmlDeclared)
          {
            if (declaredURI != string(SBML_XMLNS_L3V2))
            {
              valid = false;
            }
          }
          break;
        default:
          valid = false;
          break;
      }
      break;
    default:
      valid = false;
      break;
  }

  return valid;
}


/** @cond doxygenLibsbmlInternal */
void
SBMLNamespaces::setLevel(unsigned int level)
{
  mLevel = level;
}


void
SBMLNamespaces::setVersion(unsigned int version)
{
  mVersion = version;
}

const std::string&
SBMLNamespaces::getPackageName () const
{
	static const std::string pkgName = "core";
    return pkgName;
}

void
SBMLNamespaces::setNamespaces(XMLNamespaces * xmlns)
{
  delete mNamespaces;
  if (xmlns != NULL)
    mNamespaces = xmlns->clone();
  else
    mNamespaces = NULL;
}
/** @endcond */

#endif /* __cplusplus */
/** @cond doxygenIgnored */
LIBSBML_EXTERN
SBMLNamespaces_t *
SBMLNamespaces_create(unsigned int level, unsigned int version)
{
  return new SBMLNamespaces(level, version);
}


LIBSBML_EXTERN
void
SBMLNamespaces_free(SBMLNamespaces_t* ns)
{
  if (ns == NULL) return;
  delete static_cast<SBMLNamespaces*>(ns);
}


LIBSBML_EXTERN
unsigned int
SBMLNamespaces_getLevel(SBMLNamespaces_t *sbmlns)
{
  return (sbmlns != NULL) ? sbmlns->getLevel() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
SBMLNamespaces_getVersion(SBMLNamespaces_t *sbmlns)
{
  return (sbmlns != NULL) ? sbmlns->getVersion() : SBML_INT_MAX;
}


LIBSBML_EXTERN
XMLNamespaces_t *
SBMLNamespaces_getNamespaces(SBMLNamespaces_t *sbmlns)
{
  return (sbmlns != NULL) ? sbmlns->getNamespaces() : NULL;
}


LIBSBML_EXTERN
char *
SBMLNamespaces_getSBMLNamespaceURI(unsigned int level, unsigned int version)
{
  return safe_strdup(SBMLNamespaces::getSBMLNamespaceURI(level, version).c_str());
}


LIBSBML_EXTERN
int
SBMLNamespaces_addNamespaces(SBMLNamespaces_t *sbmlns,
                             const XMLNamespaces_t * xmlns)
{
  if (sbmlns != NULL)
    return sbmlns->addNamespaces(xmlns);
  else
    return LIBSBML_INVALID_OBJECT;
}

LIBSBML_EXTERN
SBMLNamespaces_t **
SBMLNamespaces_getSupportedNamespaces(int *length)
{
  if (length == NULL) return NULL;
   const List* supported = SBMLNamespaces::getSupportedNamespaces();

   *length = (int) supported->getSize();
  SBMLNamespaces_t ** result = (SBMLNamespaces_t**)safe_malloc(sizeof(SBMLNamespaces_t*)*((unsigned long)(*length)));
  for (int i = 0; i < *length; i++)
  {
    result[i] = ((SBMLNamespaces*)supported->get((unsigned int)i))->clone();
  }
  SBMLNamespaces::freeSBMLNamespaces(const_cast<List*>(supported));
  return result;
}
/** @endcond */

LIBSBML_CPP_NAMESPACE_END