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sedmlfile.cpp
1240 lines (939 loc) · 55.8 KB
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sedmlfile.cpp
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/*******************************************************************************
Copyright (C) The University of Auckland
OpenCOR is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenCOR is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*******************************************************************************/
//==============================================================================
// SED-ML file
//==============================================================================
#include "cellmlfile.h"
#include "corecliutils.h"
#include "coreguiutils.h"
#include "filemanager.h"
#include "interfaces.h"
#include "sedmlfile.h"
#include "sedmlsupport.h"
#include "solverinterface.h"
//==============================================================================
#include <QDir>
#include <QRegularExpression>
#include <QTemporaryFile>
//==============================================================================
#include "sedmlapibegin.h"
#include "sedml/SedAlgorithm.h"
#include "sedml/SedDocument.h"
#include "sedml/SedOneStep.h"
#include "sedml/SedPlot2D.h"
#include "sedml/SedReader.h"
#include "sedml/SedRepeatedTask.h"
#include "sedml/SedWriter.h"
#include "sedml/SedUniformTimeCourse.h"
#include "sedml/SedVectorRange.h"
#include "sedmlapiend.h"
//==============================================================================
namespace OpenCOR {
namespace SEDMLSupport {
//==============================================================================
SedmlFile::SedmlFile(const QString &pFileName, const QString &pOwnerFileName,
const bool &pNew) :
StandardSupport::StandardFile(pFileName),
mOwnerFileName(pOwnerFileName),
mSedmlDocument(0),
mNew(pNew),
mCellmlFile(0)
{
// Reset ourselves
reset();
}
//==============================================================================
SedmlFile::SedmlFile(const QString &pFileName, const bool &pNew) :
SedmlFile(pFileName, QString(), pNew)
{
}
//==============================================================================
SedmlFile::~SedmlFile()
{
// Reset ourselves
reset();
}
//==============================================================================
void SedmlFile::reset()
{
// Ask our file manager to unmanage our corresponding CellML file, if we
// have previously retrieved it, and if it is a remote one (indeed, it will
// have been managed by cellmlFile() below, so that CellML 1.1 files can be
// properly instantiated)
if (mCellmlFile) {
Core::FileManager *fileManagerInstance = Core::FileManager::instance();
QString cellmlFileName = mCellmlFile->fileName();
if (fileManagerInstance->isRemote(cellmlFileName))
fileManagerInstance->unmanage(cellmlFileName);
}
// Reset all of our properties
delete mSedmlDocument;
mSedmlDocument = 0;
mLoadingNeeded = true;
delete mCellmlFile;
mCellmlFile = 0;
mIssues = SedmlFileIssues();
}
//==============================================================================
libsedml::SedDocument * SedmlFile::sedmlDocument()
{
// Return the SED-ML document associated with our SED-ML file, after loading
// ourselves if necessary
load();
return mSedmlDocument;
}
//==============================================================================
bool SedmlFile::load()
{
// Check whether the file is already loaded and without any (fatal) errors
if (!mLoadingNeeded) {
return !mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_ERROR)
&& !mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_FATAL);
}
mLoadingNeeded = false;
// Create a new SED-ML document, if needed, or try to load our file
if (mNew)
mSedmlDocument = new libsedml::SedDocument();
else
mSedmlDocument = libsedml::readSedML(mFileName.toUtf8().constData());
return !mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_ERROR)
&& !mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_FATAL);
}
//==============================================================================
bool SedmlFile::save(const QString &pFileName)
{
// Make sure that we are properly loaded and have no (fatal) errors
if ( mLoadingNeeded
|| mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_ERROR)
|| mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_FATAL)) {
return false;
}
// Save ourselves, after having reformatted ourselves, and stop considering
// ourselves as new anymore (in case we were), if the saving went fine
QDomDocument domDocument;
domDocument.setContent(QString(libsedml::writeSedMLToString(mSedmlDocument)));
bool res = Core::writeFileContentsToFile(pFileName, Core::serialiseDomDocument(domDocument));
if (res)
mNew = false;
return res;
}
//==============================================================================
bool SedmlFile::isValid(const QString &pFileContents, SedmlFileIssues &pIssues)
{
// Make sure that we are loaded, if the given file contents is empty (i.e.
// we want to validate ourselves rather than some given file contents)
if (pFileContents.isEmpty())
load();
// Check whether our SED-ML document or the given file contents is SED-ML
// valid and, if not, populate pIssues with the problems found (after having
// emptied its contents)
// Note: in case we have to validate the given file contents, we would
// normally create a temporary SED-ML document using
// libsedml::readSedMLFromString(), but if the given file contents
// doesn't start with:
// <?xml version='1.0' encoding='UTF-8'?>
// then libsedml::readSedMLFromString() will prepend it to our given
// file contents, which is not what we want. So, instead, we create a
// temporary file which contents is that of our given file contents,
// and simply call libsedml::readSedML()...
pIssues.clear();
libsedml::SedDocument *sedmlDocument = mSedmlDocument;
if (!pFileContents.isEmpty()) {
QTemporaryFile file;
QByteArray fileContentsByteArray = pFileContents.toUtf8();
file.open();
file.write(fileContentsByteArray);
file.flush();
sedmlDocument = libsedml::readSedML(file.fileName().toUtf8().constData());
file.close();
}
libsedml::SedErrorLog *errorLog = sedmlDocument->getErrorLog();
for (uint i = 0, iMax = errorLog->getNumErrors(); i < iMax; ++i) {
const libsedml::SedError *error = errorLog->getError(i);
SedmlFileIssue::Type issueType;
switch (error->getSeverity()) {
case LIBSBML_SEV_INFO:
issueType = SedmlFileIssue::Information;
break;
case LIBSBML_SEV_ERROR:
issueType = SedmlFileIssue::Error;
break;
case LIBSBML_SEV_WARNING:
issueType = SedmlFileIssue::Warning;
break;
case LIBSBML_SEV_FATAL:
issueType = SedmlFileIssue::Fatal;
break;
}
static const QRegularExpression TrailingEmptyLinesRegEx = QRegularExpression("[\\n]*$");
QString errorMessage = QString::fromStdString(error->getMessage()).remove(TrailingEmptyLinesRegEx);
pIssues << SedmlFileIssue(issueType, error->getLine(), error->getColumn(), errorMessage);
}
// Only consider our SED-ML document valid if it has no (fatal) errors
bool res = !sedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_ERROR)
&& !sedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_FATAL);
if (!pFileContents.isEmpty())
delete sedmlDocument;
return res;
}
//==============================================================================
bool SedmlFile::isValid()
{
// Return whether we are valid
return isValid(QString(), mIssues);
}
//==============================================================================
bool SedmlFile::validListPropertyValue(const libsbml::XMLNode &pPropertyNode,
const QString &pPropertyNodeValue,
const QString &pPropertyName,
const QStringList &pValuesList)
{
// Check whether the given list property is valid
if (!pValuesList.contains(pPropertyNodeValue)) {
QString values = QString();
int i = -1;
int lastValueIndex = pValuesList.count()-1;
foreach (const QString &lineStyle, pValuesList) {
if (++i)
values += (i == lastValueIndex)?" "+tr("or")+" ":", ";
values += "'"+lineStyle+"'";
}
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
pPropertyNode.getLine(),
pPropertyNode.getColumn(),
tr("the '%1' property must have a value of %2").arg(pPropertyName, values));
return false;
} else {
return true;
}
}
//==============================================================================
bool SedmlFile::validColorPropertyValue(const libsbml::XMLNode &pPropertyNode,
const QString &pPropertyNodeValue,
const QString &pPropertyName)
{
// Check whether the given color property is valid
static const QRegularExpression ColorRegEx = QRegularExpression("^#([[:xdigit:]]{6}|[[:xdigit:]]{8})$");
if (!ColorRegEx.match(pPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
pPropertyNode.getLine(),
pPropertyNode.getColumn(),
tr("the '%1' property must have a value of '#RRGGBB' or '#AARRGGBB'").arg(pPropertyName));
return false;
} else {
return true;
}
}
//==============================================================================
bool SedmlFile::isSupported()
{
// Make sure that we are valid
if (!isValid())
return false;
// Make sure that there is only one model
if (mSedmlDocument->getNumModels() != 1) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with one model are supported"));
return false;
}
// Make sure that the model is of CellML type
libsedml::SedModel *model = mSedmlDocument->getModel(0);
QString language = QString::fromStdString(model->getLanguage());
if ( language.compare(Language::Cellml)
&& language.compare(Language::Cellml_1_0)
&& language.compare(Language::Cellml_1_1)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with a CellML file are supported"));
return false;
}
// Make sure that there is either one or two simulations
int nbOfSimulations = mSedmlDocument->getNumSimulations();
if ((nbOfSimulations != 1) && (nbOfSimulations != 2)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with one or two simulations are supported"));
return false;
}
// Make sure that the first simulation is a uniform time course simulation
libsedml::SedSimulation *firstSimulation = mSedmlDocument->getSimulation(0);
if (firstSimulation->getTypeCode() != libsedml::SEDML_SIMULATION_UNIFORMTIMECOURSE) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with a uniform time course as a (first) simulation are supported"));
return false;
}
// Make sure that the initial time and output start time are the same, that
// the output start time and output end time are different, and that the
// number of points is greater than zero
libsedml::SedUniformTimeCourse *uniformTimeCourse = static_cast<libsedml::SedUniformTimeCourse *>(firstSimulation);
double initialTime = uniformTimeCourse->getInitialTime();
double outputStartTime = uniformTimeCourse->getOutputStartTime();
double outputEndTime = uniformTimeCourse->getOutputEndTime();
int nbOfPoints = uniformTimeCourse->getNumberOfPoints();
if (initialTime != outputStartTime) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with the same values for 'initialTime' and 'outputStartTime' are supported"));
return false;
}
if (outputStartTime == outputEndTime) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
tr("the values for 'outputStartTime' and 'outputEndTime' must be different"));
return false;
}
if (nbOfPoints <= 0) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
tr("the value for 'numberOfPoints' must be greater than zero"));
return false;
}
// Make sure that we have an algorithm for the first simulation
const libsedml::SedAlgorithm *firstSimulationAlgorithm = firstSimulation->getAlgorithm();
libsbml::XMLNode *annotation;
if (firstSimulationAlgorithm) {
// Make sure that the algorithm relies on an algorithm that we support
SolverInterface *usedSolverInterface = 0;
QString kisaoId = QString::fromStdString(firstSimulationAlgorithm->getKisaoID());
foreach (SolverInterface *solverInterface, Core::solverInterfaces()) {
if (!solverInterface->id(kisaoId).compare(solverInterface->solverName())) {
usedSolverInterface = solverInterface;
break;
}
}
if (!usedSolverInterface) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("unsupported algorithm (%1)").arg(kisaoId));
return false;
}
// Make sure that the algorithm parameters are also supported
for (int i = 0, iMax = firstSimulationAlgorithm->getNumAlgorithmParameters(); i < iMax; ++i) {
QString kisaoId = QString::fromStdString(firstSimulationAlgorithm->getAlgorithmParameter(i)->getKisaoID());
QString id = usedSolverInterface->id(kisaoId);
if (id.isEmpty() || !id.compare(usedSolverInterface->solverName())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("unsupported algorithm parameter (%1)").arg(kisaoId));
return false;
}
}
// Make sure that the first simulation algorithm annotation, if any,
// contains at least the kind of information we would expect
annotation = firstSimulationAlgorithm->getAnnotation();
if (annotation) {
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
const libsbml::XMLNode &solverPropertiesNode = annotation->getChild(i);
if ( QString::fromStdString(solverPropertiesNode.getURI()).compare(OpencorNamespace)
|| QString::fromStdString(solverPropertiesNode.getName()).compare(SolverProperties)) {
continue;
}
bool validSolverProperties = true;
for (uint j = 0, jMax = solverPropertiesNode.getNumChildren(); j < jMax; ++j) {
const libsbml::XMLNode &solverPropertyNode = solverPropertiesNode.getChild(j);
if ( QString::fromStdString(solverPropertyNode.getURI()).compare(OpencorNamespace)
|| QString::fromStdString(solverPropertyNode.getName()).compare(SolverProperty)) {
continue;
}
int idIndex = solverPropertyNode.getAttrIndex(Id.toStdString());
int valueIndex = solverPropertyNode.getAttrIndex(Value.toStdString());
if ( (idIndex == -1) || (valueIndex == -1)
|| solverPropertyNode.getAttrValue(idIndex).empty()
|| solverPropertyNode.getAttrValue(valueIndex).empty()) {
validSolverProperties = false;
break;
}
}
if (!validSolverProperties) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
solverPropertiesNode.getLine(),
solverPropertiesNode.getColumn(),
tr("incomplete algorithm annotation (missing algorithm property information)"));
return false;
}
}
}
// Make sure that the first simulation annotation, if any, contains at
// least the kind of information we would expect
annotation = firstSimulation->getAnnotation();
if (annotation) {
bool hasNlaSolver = false;
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
const libsbml::XMLNode &nlaSolverNode = annotation->getChild(i);
if ( QString::fromStdString(nlaSolverNode.getURI()).compare(OpencorNamespace)
|| QString::fromStdString(nlaSolverNode.getName()).compare(NlaSolver)) {
continue;
}
int nameIndex = nlaSolverNode.getAttrIndex(Name.toStdString());
if ((nameIndex != -1) && !nlaSolverNode.getAttrValue(nameIndex).empty()) {
if (hasNlaSolver) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
tr("only one NLA solver is allowed"));
return false;
} else {
hasNlaSolver = true;
}
} else {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
nlaSolverNode.getLine(),
nlaSolverNode.getColumn(),
tr("incomplete simulation annotation (missing NLA solver name)"));
return false;
}
}
}
} else {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with one or two simulations with an algorithm are supported"));
return false;
}
// Check whether there is a second simulation
libsedml::SedSimulation *secondSimulation = mSedmlDocument->getSimulation(1);
if (secondSimulation) {
// Make sure that the second simulation is a one-step simulation
if (secondSimulation->getTypeCode() != libsedml::SEDML_SIMULATION_ONESTEP) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with a one-step as a second simulation are supported"));
return false;
}
// Make sure that its step is greater than zero
if (static_cast<libsedml::SedOneStep *>(secondSimulation)->getStep() <= 0) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
tr("the value for step must be greater than zero"));
return false;
}
// Make sure that its algorithm and annotation(s), if any, are the same
// as for the first simulation
std::stringstream firstStream;
std::stringstream secondStream;
libsbml::XMLOutputStream firstXmlStream(firstStream);
libsbml::XMLOutputStream secondXmlStream(secondStream);
const libsedml::SedAlgorithm *secondSimulationAlgorithm = secondSimulation->getAlgorithm();
firstSimulationAlgorithm->write(firstXmlStream);
if (secondSimulationAlgorithm)
secondSimulationAlgorithm->write(secondXmlStream);
libsbml::XMLNode *firstAnnotation = firstSimulationAlgorithm->getAnnotation();
libsbml::XMLNode *secondAnnotation = secondSimulationAlgorithm->getAnnotation();
if (firstAnnotation)
firstAnnotation->write(firstXmlStream);
if (secondAnnotation)
secondAnnotation->write(secondXmlStream);
firstAnnotation = firstSimulation->getAnnotation();
secondAnnotation = secondSimulation->getAnnotation();
if (firstAnnotation)
firstAnnotation->write(firstXmlStream);
if (secondAnnotation)
secondAnnotation->write(secondXmlStream);
if (firstStream.str().compare(secondStream.str())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with two simulations with the same algorithm are supported"));
return false;
}
}
// Make sure that we have only one repeated task, which aim is to execute
// each simulation (using a sub-task) once
uint totalNbOfTasks = secondSimulation?3:2;
if (mSedmlDocument->getNumTasks() != totalNbOfTasks) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files that execute one or two simulations once are supported"));
return false;
}
libsedml::SedRepeatedTask *repeatedTask = 0;
bool repeatedTaskOk = false;
std::string repeatedTaskFirstSubTaskId = std::string();
std::string repeatedTaskSecondSubTaskId = std::string();
bool firstSubTaskOk = false;
std::string firstSubTaskId = std::string();
bool secondSubTaskOk = false;
std::string secondSubTaskId = std::string();
for (uint i = 0; i < totalNbOfTasks; ++i) {
libsedml::SedTask *task = mSedmlDocument->getTask(i);
if (task->getTypeCode() == libsedml::SEDML_TASK_REPEATEDTASK) {
// Make sure that the repeated task asks for the model to be reset,
// that it has one range, no task change and one/two sub-task/s
repeatedTask = static_cast<libsedml::SedRepeatedTask *>(task);
if ( repeatedTask->getResetModel()
&& (repeatedTask->getNumRanges() == 1)
&& !repeatedTask->getNumTaskChanges()
&& (repeatedTask->getNumSubTasks() == totalNbOfTasks-1)) {
// Make sure that the range is a vector range and that it's the
// one referenced in the repeated task
libsedml::SedRange *range = repeatedTask->getRange(0);
if ( (range->getTypeCode() == libsedml::SEDML_RANGE_VECTORRANGE)
&& !repeatedTask->getRangeId().compare(range->getId())) {
// Make sure that the vector range has one value that is
// equal to 1
libsedml::SedVectorRange *vectorRange = static_cast<libsedml::SedVectorRange *>(range);
if ( (vectorRange->getNumValues() == 1)
&& (vectorRange->getValues().front() == 1)) {
// Make sure that the one/two sub-tasks have the correct
// order and retrieve their id
for (uint i = 0, iMax = totalNbOfTasks-1; i < iMax; ++i) {
libsedml::SedSubTask *subTask = repeatedTask->getSubTask(i);
if (subTask->getOrder() == 1)
repeatedTaskFirstSubTaskId = subTask->getTask();
else if (subTask->getOrder() == 2)
repeatedTaskSecondSubTaskId = subTask->getTask();
}
repeatedTaskOk = true;
}
}
}
} else if (task->getTypeCode() == libsedml::SEDML_TASK) {
// Make sure the sub-task references the correct model and
// simulation
if ( !task->getModelReference().compare(model->getId())
&& !task->getSimulationReference().compare(firstSimulation->getId())) {
firstSubTaskOk = true;
firstSubTaskId = task->getId();
} else if ( secondSimulation
&& !task->getModelReference().compare(model->getId())
&& !task->getSimulationReference().compare(secondSimulation->getId())) {
secondSubTaskOk = true;
secondSubTaskId = task->getId();
}
}
}
if ( !repeatedTaskOk
|| !firstSubTaskOk || repeatedTaskFirstSubTaskId.compare(firstSubTaskId)
|| ( secondSimulation
&& (!secondSubTaskOk || repeatedTaskSecondSubTaskId.compare(secondSubTaskId)))) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files that execute one or two simulations once are supported"));
return false;
}
// Make sure that all the data generators have one variable that references
// the repeated task, that follows the correct CellML format for their
// target (and OpenCOR format for their degree, if any), and that is not
// modified
for (uint i = 0, iMax = mSedmlDocument->getNumDataGenerators(); i < iMax; ++i) {
libsedml::SedDataGenerator *dataGenerator = mSedmlDocument->getDataGenerator(i);
if ((dataGenerator->getNumVariables() != 1) || dataGenerator->getNumParameters()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with data generators for one variable are supported"));
return false;
}
libsedml::SedVariable *variable = dataGenerator->getVariable(0);
if (variable->getSymbol().size() || variable->getModelReference().size()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with data generators for one variable with a target and a task reference are supported"));
return false;
}
if (variable->getTaskReference().compare(repeatedTask->getId())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with data generators for one variable with a reference to a repeated task are supported"));
return false;
}
static const QRegularExpression TargetStartRegEx = QRegularExpression("^\\/cellml:model\\/cellml:component\\[@name='");
static const QRegularExpression TargetMiddleRegEx = QRegularExpression("']\\/cellml:variable\\[@name='");
static const QRegularExpression TargetEndRegEx = QRegularExpression("'\\]$");
bool referencingCellmlVariable = false;
QString target = QString::fromStdString(variable->getTarget());
if (target.contains(TargetStartRegEx) && target.contains(TargetEndRegEx)) {
static const QString Separator = "|";
target.remove(TargetStartRegEx);
target.replace(TargetMiddleRegEx, Separator);
target.remove(TargetEndRegEx);
QStringList identifiers = target.split(Separator);
if (identifiers.count() == 2) {
static const QRegularExpression IdentifierRegEx = QRegularExpression("^[[:alpha:]_][[:alnum:]_]*$");
QString componentName = identifiers.first();
QString variableName = identifiers.last();
referencingCellmlVariable = IdentifierRegEx.match(componentName).hasMatch()
&& IdentifierRegEx.match(variableName).hasMatch();
}
}
if (!referencingCellmlVariable) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with data generators for one variable with a reference to a CellML variable are supported"));
return false;
}
annotation = variable->getAnnotation();
if (annotation) {
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
const libsbml::XMLNode &variableDegreeNode = annotation->getChild(i);
if ( QString::fromStdString(variableDegreeNode.getURI()).compare(OpencorNamespace)
|| QString::fromStdString(variableDegreeNode.getName()).compare(VariableDegree)) {
continue;
}
bool validVariableDegree = false;
if (variableDegreeNode.getNumChildren() == 1) {
bool conversionOk;
int variableDegree = QString::fromStdString(variableDegreeNode.getChild(0).getCharacters()).toInt(&conversionOk);
validVariableDegree = conversionOk && (variableDegree >= 0);
}
if (!validVariableDegree) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
variableDegreeNode.getLine(),
variableDegreeNode.getColumn(),
tr("only SED-ML files with data generators for one variable that is derived or not are supported"));
return false;
}
}
}
const libsbml::ASTNode *mathNode = dataGenerator->getMath();
if ( (mathNode->getType() != libsbml::AST_NAME)
|| variable->getId().compare(mathNode->getName())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with data generators for one variable that is not modified are supported"));
return false;
}
}
// Make sure that all the outputs are 2D outputs
for (uint i = 0, iMax = mSedmlDocument->getNumOutputs(); i < iMax; ++i) {
libsedml::SedOutput *output = mSedmlDocument->getOutput(i);
if (output->getTypeCode() != libsedml::SEDML_OUTPUT_PLOT2D) {
mIssues << SedmlFileIssue(SedmlFileIssue::Information,
tr("only SED-ML files with 2D outputs are supported"));
return false;
}
static const QRegularExpression IntegerGt0RegEx = QRegularExpression("^[+]?[1-9]\\d*$");
static const QString True = "true";
static const QString False = "false";
annotation = output->getAnnotation();
if (annotation) {
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
const libsbml::XMLNode &plot2dPropertiesNode = annotation->getChild(i);
if ( QString::fromStdString(plot2dPropertiesNode.getURI()).compare(OpencorNamespace)
|| QString::fromStdString(plot2dPropertiesNode.getName()).compare(Properties)) {
continue;
}
for (uint j = 0, jMax = plot2dPropertiesNode.getNumChildren(); j < jMax; ++j) {
// Note: we don't need to check for the title since it is a
// string and that it can therefore have any value...
const libsbml::XMLNode &plot2dPropertyNode = plot2dPropertiesNode.getChild(j);
QString plot2dPropertyNodeName = QString::fromStdString(plot2dPropertyNode.getName());
QString plot2dPropertyNodeValue = QString::fromStdString(plot2dPropertyNode.getChild(0).getCharacters());
if ( !plot2dPropertyNodeName.compare(BackgroundColor)
&& !validColorPropertyValue(plot2dPropertyNode, plot2dPropertyNodeValue, BackgroundColor)) {
return false;
} else if ( !plot2dPropertyNodeName.compare(FontSize)
&& !IntegerGt0RegEx.match(plot2dPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
plot2dPropertyNode.getLine(),
plot2dPropertyNode.getColumn(),
tr("the '%1' property value must be an integer greater than zero").arg(plot2dPropertyNodeName));
return false;
} else if ( !plot2dPropertyNodeName.compare(ForegroundColor)
&& !validColorPropertyValue(plot2dPropertyNode, plot2dPropertyNodeValue, ForegroundColor)) {
return false;
} else if ( !plot2dPropertyNodeName.compare(Height)
&& !IntegerGt0RegEx.match(plot2dPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
plot2dPropertyNode.getLine(),
plot2dPropertyNode.getColumn(),
tr("the '%1' property value must be an integer greater than zero").arg(plot2dPropertyNodeName));
return false;
} else if ( !plot2dPropertyNodeName.compare(Legend)
&& plot2dPropertyNodeValue.compare(True)
&& plot2dPropertyNodeValue.compare(False)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
plot2dPropertyNode.getLine(),
plot2dPropertyNode.getColumn(),
tr("the '%1' property must have a value of 'true' or 'false'").arg(Legend));
return false;
} else if ( !QString::fromStdString(plot2dPropertyNode.getURI()).compare(OpencorNamespace)
&& !QString::fromStdString(plot2dPropertyNode.getName()).compare(GridLines)) {
for (uint k = 0, kMax = plot2dPropertyNode.getNumChildren(); k < kMax; ++k) {
const libsbml::XMLNode &gridLinesPropertyNode = plot2dPropertyNode.getChild(k);
QString gridLinesPropertyNodeName = QString::fromStdString(gridLinesPropertyNode.getName());
QString gridLinesPropertyNodeValue = QString::fromStdString(gridLinesPropertyNode.getChild(0).getCharacters());
if ( !gridLinesPropertyNodeName.compare(Style)
&& !validListPropertyValue(gridLinesPropertyNode, gridLinesPropertyNodeValue, Style, lineStyles())) {
return false;
} else if ( !gridLinesPropertyNodeName.compare(Width)
&& !IntegerGt0RegEx.match(gridLinesPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
gridLinesPropertyNode.getLine(),
gridLinesPropertyNode.getColumn(),
tr("the '%1' property value must be a number greater than zero").arg(gridLinesPropertyNodeName));
return false;
} else if ( !gridLinesPropertyNodeName.compare(Color)
&& !validColorPropertyValue(gridLinesPropertyNode, gridLinesPropertyNodeValue, Color)) {
return false;
}
}
} else if ( !QString::fromStdString(plot2dPropertyNode.getURI()).compare(OpencorNamespace)
&& !QString::fromStdString(plot2dPropertyNode.getName()).compare(PointCoordinates)) {
for (uint k = 0, kMax = plot2dPropertyNode.getNumChildren(); k < kMax; ++k) {
const libsbml::XMLNode &pointCoordinatesPropertyNode = plot2dPropertyNode.getChild(k);
QString pointCoordinatesPropertyNodeName = QString::fromStdString(pointCoordinatesPropertyNode.getName());
QString pointCoordinatesPropertyNodeValue = QString::fromStdString(pointCoordinatesPropertyNode.getChild(0).getCharacters());
if ( !pointCoordinatesPropertyNodeName.compare(Style)
&& !validListPropertyValue(pointCoordinatesPropertyNode, pointCoordinatesPropertyNodeValue, Style, lineStyles())) {
return false;
} else if ( !pointCoordinatesPropertyNodeName.compare(Width)
&& !IntegerGt0RegEx.match(pointCoordinatesPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
pointCoordinatesPropertyNode.getLine(),
pointCoordinatesPropertyNode.getColumn(),
tr("the '%1' property value must be a number greater than zero").arg(pointCoordinatesPropertyNodeName));
return false;
} else if ( !pointCoordinatesPropertyNodeName.compare(Color)
&& !validColorPropertyValue(pointCoordinatesPropertyNode, pointCoordinatesPropertyNodeValue, Color)) {
return false;
} else if ( !pointCoordinatesPropertyNodeName.compare(FontColor)
&& !validColorPropertyValue(pointCoordinatesPropertyNode, pointCoordinatesPropertyNodeValue, FontColor)) {
return false;
}
}
} else if ( !QString::fromStdString(plot2dPropertyNode.getURI()).compare(OpencorNamespace)
&& !QString::fromStdString(plot2dPropertyNode.getName()).compare(XAxis)) {
for (uint k = 0, kMax = plot2dPropertyNode.getNumChildren(); k < kMax; ++k) {
// Note: we don't need to check for the title since
// it is a string and that it can therefore
// have any value...
const libsbml::XMLNode &xAxisPropertyNode = plot2dPropertyNode.getChild(k);
QString xAxisPropertyNodeName = QString::fromStdString(xAxisPropertyNode.getName());
QString xAxisPropertyNodeValue = QString::fromStdString(xAxisPropertyNode.getChild(0).getCharacters());
if ( !xAxisPropertyNodeName.compare(LogarithmicScale)
&& xAxisPropertyNodeValue.compare(True)
&& xAxisPropertyNodeValue.compare(False)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
xAxisPropertyNode.getLine(),
xAxisPropertyNode.getColumn(),
tr("the '%1' property must have a value of 'true' or 'false'").arg(LogarithmicScale));
return false;
}
}
} else if ( !QString::fromStdString(plot2dPropertyNode.getURI()).compare(OpencorNamespace)
&& !QString::fromStdString(plot2dPropertyNode.getName()).compare(YAxis)) {
for (uint k = 0, kMax = plot2dPropertyNode.getNumChildren(); k < kMax; ++k) {
// Note: we don't need to check for the title since
// it is a string and that it can therefore
// have any value...
const libsbml::XMLNode &yAxisPropertyNode = plot2dPropertyNode.getChild(k);
QString yAxisPropertyNodeName = QString::fromStdString(yAxisPropertyNode.getName());
QString yAxisPropertyNodeValue = QString::fromStdString(yAxisPropertyNode.getChild(0).getCharacters());
if ( !yAxisPropertyNodeName.compare(LogarithmicScale)
&& yAxisPropertyNodeValue.compare(True)
&& yAxisPropertyNodeValue.compare(False)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
yAxisPropertyNode.getLine(),
yAxisPropertyNode.getColumn(),
tr("the '%1' property must have a value of 'true' or 'false'").arg(LogarithmicScale));
return false;
}
}
} else if ( !QString::fromStdString(plot2dPropertyNode.getURI()).compare(OpencorNamespace)
&& !QString::fromStdString(plot2dPropertyNode.getName()).compare(ZoomRegion)) {
for (uint k = 0, kMax = plot2dPropertyNode.getNumChildren(); k < kMax; ++k) {
const libsbml::XMLNode &zoomRegionPropertyNode = plot2dPropertyNode.getChild(k);
QString zoomRegionPropertyNodeName = QString::fromStdString(zoomRegionPropertyNode.getName());
QString zoomRegionPropertyNodeValue = QString::fromStdString(zoomRegionPropertyNode.getChild(0).getCharacters());
if ( !zoomRegionPropertyNodeName.compare(Style)
&& !validListPropertyValue(zoomRegionPropertyNode, zoomRegionPropertyNodeValue, Style, lineStyles())) {
return false;
} else if ( !zoomRegionPropertyNodeName.compare(Width)
&& !IntegerGt0RegEx.match(zoomRegionPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
zoomRegionPropertyNode.getLine(),
zoomRegionPropertyNode.getColumn(),
tr("the '%1' property value must be a number greater than zero").arg(zoomRegionPropertyNodeName));
return false;
} else if ( !zoomRegionPropertyNodeName.compare(Color)
&& !validColorPropertyValue(zoomRegionPropertyNode, zoomRegionPropertyNodeValue, Color)) {
return false;
} else if ( !zoomRegionPropertyNodeName.compare(FontColor)
&& !validColorPropertyValue(zoomRegionPropertyNode, zoomRegionPropertyNodeValue, FontColor)) {
return false;
} else if ( !zoomRegionPropertyNodeName.compare(Filled)
&& zoomRegionPropertyNodeValue.compare(True)
&& zoomRegionPropertyNodeValue.compare(False)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Error,
zoomRegionPropertyNode.getLine(),
zoomRegionPropertyNode.getColumn(),
tr("the '%1' property must have a value of 'true' or 'false'").arg(Filled));