/*
* Writes the given Sed document to the output stream.
*
* @return true on success and false if one of the underlying parser
* components fail (rare).
*/
bool
SedWriter::writeSedML (const SedDocument* d, std::ostream& stream)
{
bool result = false;
try
{
stream.exceptions(ios_base::badbit | ios_base::failbit | ios_base::eofbit);
XMLOutputStream xos(stream, "UTF-8", true, mProgramName,
mProgramVersion);
d->write(xos);
stream << endl;
result = true;
}
catch (ios_base::failure&)
{
SedErrorLog *log = (const_cast<SedDocument *>(d))->getErrorLog();
log->logError(XMLFileOperationError);
}
return result;
}
/*
* Reads the expected attributes into the member data variables
*/
void
SedRepeatedTask::readAttributes(
const LIBSBML_CPP_NAMESPACE_QUALIFIER
XMLAttributes& attributes,
const LIBSBML_CPP_NAMESPACE_QUALIFIER
ExpectedAttributes& expectedAttributes)
{
unsigned int level = getLevel();
unsigned int version = getVersion();
unsigned int numErrs;
bool assigned = false;
SedErrorLog* log = getErrorLog();
SedTask::readAttributes(attributes, expectedAttributes);
numErrs = log->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (log->getError(n)->getErrorId() == SedUnknownCoreAttribute)
{
const std::string details = log->getError(n)->getMessage();
log->remove(SedUnknownCoreAttribute);
log->logError(SedmlSedRepeatedTaskAllowedAttributes, level, version,
details);
}
}
//
// range SIdRef (use = "optional" )
//
assigned = attributes.readInto("range", mRangeId);
if (assigned == true)
{
if (mRangeId.empty() == true)
{
logEmptyString(mRangeId, level, version, "<SedRepeatedTask>");
}
else if (SyntaxChecker::isValidSBMLSId(mRangeId) == false)
{
logError(SedmlRepeatedTaskRangeIdMustBeRange, level, version, "The "
"attribute range='" + mRangeId + "' does not conform to the syntax.");
}
}
//
// resetModel bool (use = "optional" )
//
mIsSetResetModel = attributes.readInto("resetModel", mResetModel);
}
/*
* Writes the given Sed document to filename.
*
* If the filename ends with @em .gz, the file will be compressed by @em gzip.
* Similary, if the filename ends with @em .zip or @em .bz2, the file will be
* compressed by @em zip or @em bzip2, respectively. Otherwise, the fill will be
* uncompressed.
* If the filename ends with @em .zip, a filename that will be added to the
* zip archive file will end with @em .xml or @em .sbml. For example, the filename
* in the zip archive will be @em test.xml if the given filename is @em test.xml.zip
* or @em test.zip. Also, the filename in the archive will be @em test.sbml if the
* given filename is @em test.sbml.zip.
*
* @note To create a gzip/zip file, underlying libSed needs to be linked with zlib at
* compile time. Also, underlying libSed needs to be linked with bzip2 to create a
* bzip2 file.
* File unwritable error will be logged and @c false will be returned if a compressed
* file name is given and underlying libSed is not linked with the corresponding
* required library.
* SedWriter::hasZlib() and SedWriter::hasBzip2() can be used to check whether
* underlying libSed is linked with the library.
*
* @return true on success and false if the filename could not be opened
* for writing.
*/
bool
SedWriter::writeSedML (const SedDocument* d, const std::string& filename)
{
std::ostream* stream = NULL;
try
{
// open an uncompressed XML file.
if ( string::npos != filename.find(".xml", filename.length() - 4) )
{
stream = new(std::nothrow) std::ofstream(filename.c_str());
}
// open a gzip file
else if ( string::npos != filename.find(".gz", filename.length() - 3) )
{
stream = OutputCompressor::openGzipOStream(filename);
}
// open a bz2 file
else if ( string::npos != filename.find(".bz2", filename.length() - 4) )
{
stream = OutputCompressor::openBzip2OStream(filename);
}
// open a zip file
else if ( string::npos != filename.find(".zip", filename.length() - 4) )
{
std::string filenameinzip = filename.substr(0, filename.length() - 4);
if ( ( string::npos == filenameinzip.find(".xml", filenameinzip.length() - 4) ) &&
( string::npos == filenameinzip.find(".sbml", filenameinzip.length() - 5) )
)
{
filenameinzip += ".xml";
}
#if defined(WIN32) && !defined(CYGWIN)
char sepr = '\\';
#else
char sepr = '/';
#endif
size_t spos = filenameinzip.rfind(sepr, filenameinzip.length() - 1);
if( spos != string::npos )
{
filenameinzip = filenameinzip.substr(spos + 1, filenameinzip.length() - 1);
}
stream = OutputCompressor::openZipOStream(filename, filenameinzip);
}
else
{
stream = new(std::nothrow) std::ofstream(filename.c_str());
}
}
catch ( ZlibNotLinked& )
{
// libSed is not linked with zlib.
XMLErrorLog *log = (const_cast<SedDocument *>(d))->getErrorLog();
std::ostringstream oss;
oss << "Tried to write " << filename << ". Writing a gzip/zip file is not enabled because "
<< "underlying libSed is not linked with zlib.";
log->add(XMLError( XMLFileUnwritable, oss.str(), 0, 0) );
return false;
}
catch ( Bzip2NotLinked& )
{
// libSed is not linked with bzip2.
XMLErrorLog *log = (const_cast<SedDocument *>(d))->getErrorLog();
std::ostringstream oss;
oss << "Tried to write " << filename << ". Writing a bzip2 file is not enabled because "
<< "underlying libSed is not linked with bzip2.";
log->add(XMLError( XMLFileUnwritable, oss.str(), 0, 0) );
return false;
}
if ( stream == NULL || stream->fail() || stream->bad())
{
SedErrorLog *log = (const_cast<SedDocument *>(d))->getErrorLog();
log->logError(XMLFileUnwritable);
return false;
}
bool result = writeSedML(d, *stream);
delete stream;
return result;
}
/*
* Reads the expected attributes into the member data variables
*/
void
SedSimulation::readAttributes(
const LIBSBML_CPP_NAMESPACE_QUALIFIER
XMLAttributes& attributes,
const LIBSBML_CPP_NAMESPACE_QUALIFIER
ExpectedAttributes& expectedAttributes)
{
unsigned int level = getLevel();
unsigned int version = getVersion();
unsigned int numErrs;
bool assigned = false;
SedErrorLog* log = getErrorLog();
if (static_cast<SedListOfSimulations*>(getParentSedObject())->size() < 2)
{
numErrs = log->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (log->getError(n)->getErrorId() == SedUnknownCoreAttribute)
{
const std::string details = log->getError(n)->getMessage();
log->remove(SedUnknownCoreAttribute);
log->logError(SedmlLOSimulationsAllowedCoreAttributes, level, version,
details);
}
}
}
SedBase::readAttributes(attributes, expectedAttributes);
numErrs = log->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (log->getError(n)->getErrorId() == SedUnknownCoreAttribute)
{
const std::string details = log->getError(n)->getMessage();
log->remove(SedUnknownCoreAttribute);
log->logError(SedmlSedSimulationAllowedAttributes, level, version,
details);
}
}
//
// id SId (use = "required" )
//
assigned = attributes.readInto("id", mId);
if (assigned == true)
{
if (mId.empty() == true)
{
logEmptyString(mId, level, version, "<SedSimulation>");
}
else if (SyntaxChecker::isValidSBMLSId(mId) == false)
{
logError(SedmlIdSyntaxRule, level, version, "The id '" + mId + "' does "
"not conform to the syntax.");
}
}
else
{
std::string message = "Sedml attribute 'id' is missing from the "
"<SedSimulation> element.";
log->logError(SedmlSimulationAllowedAttributes, level, version, message);
}
//
// name string (use = "optional" )
//
assigned = attributes.readInto("name", mName);
if (assigned == true)
{
if (mName.empty() == true)
{
logEmptyString(mName, level, version, "<SedSimulation>");
}
}
}
/*
* Reads the expected attributes into the member data variables
*/
void
SedSetValue::readAttributes(
const LIBSBML_CPP_NAMESPACE_QUALIFIER
XMLAttributes& attributes,
const LIBSBML_CPP_NAMESPACE_QUALIFIER
ExpectedAttributes& expectedAttributes)
{
unsigned int level = getLevel();
unsigned int version = getVersion();
unsigned int numErrs;
bool assigned = false;
SedErrorLog* log = getErrorLog();
if (static_cast<SedListOfSetValues*>(getParentSedObject())->size() < 2)
{
numErrs = log->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (log->getError(n)->getErrorId() == SedUnknownCoreAttribute)
{
const std::string details = log->getError(n)->getMessage();
log->remove(SedUnknownCoreAttribute);
log->logError(SedmlLOSetValuesAllowedCoreAttributes, level, version,
details);
}
}
}
SedBase::readAttributes(attributes, expectedAttributes);
numErrs = log->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (log->getError(n)->getErrorId() == SedUnknownCoreAttribute)
{
const std::string details = log->getError(n)->getMessage();
log->remove(SedUnknownCoreAttribute);
log->logError(SedmlSedSetValueAllowedAttributes, level, version,
details);
}
}
//
// modelReference SIdRef (use = "required" )
//
assigned = attributes.readInto("modelReference", mModelReference);
if (assigned == true)
{
if (mModelReference.empty() == true)
{
logEmptyString(mModelReference, level, version, "<SedSetValue>");
}
else if (SyntaxChecker::isValidSBMLSId(mModelReference) == false)
{
logError(SedmlSetValueModelReferenceMustBeModel, level, version, "The "
"attribute modelReference='" + mModelReference + "' does not conform to "
"the syntax.");
}
}
else
{
std::string message = "Sedml attribute 'modelReference' is missing from the "
"<SedSetValue> element.";
log->logError(SedmlSetValueAllowedAttributes, level, version, message);
}
//
// symbol string (use = "optional" )
//
assigned = attributes.readInto("symbol", mSymbol);
if (assigned == true)
{
if (mSymbol.empty() == true)
{
logEmptyString(mSymbol, level, version, "<SedSetValue>");
}
}
//
// target string (use = "optional" )
//
assigned = attributes.readInto("target", mTarget);
if (assigned == true)
{
if (mTarget.empty() == true)
{
logEmptyString(mTarget, level, version, "<SedSetValue>");
}
}
//
// range SIdRef (use = "optional" )
//
assigned = attributes.readInto("range", mRange);
if (assigned == true)
{
if (mRange.empty() == true)
{
logEmptyString(mRange, level, version, "<SedSetValue>");
}
else if (SyntaxChecker::isValidSBMLSId(mRange) == false)
{
logError(SedmlSetValueRangeMustBeRange, level, version, "The attribute "
"range='" + mRange + "' does not conform to the syntax.");
}
}
}