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sedmlfile.cpp
1443 lines (1076 loc) · 63.8 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 <https://gnu.org/licenses>.
*******************************************************************************/
//==============================================================================
// SED-ML file
//==============================================================================
#include "cellmlfile.h"
#include "centralwidget.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 "libsedmlbegin.h"
#include "sedml/SedAlgorithm.h"
#include "sedml/SedCurve.h"
#include "sedml/SedDocument.h"
#include "sedml/SedOneStep.h"
#include "sedml/SedPlot2D.h"
#include "sedml/SedReader.h"
#include "sedml/SedRepeatedTask.h"
#include "sedml/SedTask.h"
#include "sedml/SedWriter.h"
#include "sedml/SedUniformTimeCourse.h"
#include "sedml/SedVectorRange.h"
#include "libsedmlend.h"
//==============================================================================
namespace OpenCOR {
namespace SEDMLSupport {
//==============================================================================
SedmlFile::SedmlFile(const QString &pFileName, const QString &pOwnerFileName,
bool pNew) :
StandardSupport::StandardFile(pFileName),
mOwnerFileName(pOwnerFileName)
{
// Override our inherited value of mNew with our given one
mNew = pNew;
// Reset ourselves
reset();
}
//==============================================================================
SedmlFile::SedmlFile(const QString &pFileName, bool pNew) :
SedmlFile(pFileName, QString(), pNew)
{
}
//==============================================================================
SedmlFile::~SedmlFile()
{
// Reset ourselves
reset();
}
//==============================================================================
void SedmlFile::reset()
{
// Don't reset ourselves if we were updated
if (mUpdated) {
mUpdated = false;
return;
}
// 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 != nullptr) {
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 = nullptr;
mLoadingNeeded = true;
delete mCellmlFile;
mCellmlFile = nullptr;
mIssues.clear();
}
//==============================================================================
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::isSedmlFile() const
{
// Return whether our current SED-ML document is indeed a SED-ML file
// Note: a non-SED-ML file results in our SED-ML document having at least
// one error, the first of which being of id
// libsedml::SedNotSchemaConformant (e.g. a CellML file, i.e. an XML
// file, but not a SED-ML one) or XMLContentEmpty (e.g. a COMBINE
// archive, i.e. not an XML file). So, we use this fact to determine
// whether our current SED-ML document is indeed a SED-ML file...
return (mSedmlDocument->getNumErrors() == 0)
|| ( (mSedmlDocument->getError(0)->getErrorId() != libsedml::SedNotSchemaConformant)
&& (mSedmlDocument->getError(0)->getErrorId() != XMLContentEmpty));
}
//==============================================================================
bool SedmlFile::hasErrors() const
{
// Return whether our current SED-ML document has errors, be they normal
// errors or fatal errors
return (mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_ERROR) != 0)
|| (mSedmlDocument->getNumErrors(libsedml::LIBSEDML_SEV_FATAL) != 0);
}
//==============================================================================
bool SedmlFile::load()
{
// Check whether the file is already loaded and without any (fatal) errors
if (!mLoadingNeeded) {
return isSedmlFile();
}
mLoadingNeeded = false;
// Create a new L1V3 SED-ML document, if needed, or try to load our file
mSedmlDocument = mNew?
new libsedml::SedDocument(1, 3):
libsedml::readSedML(mFileName.toUtf8().constData());
return isSedmlFile();
}
//==============================================================================
bool SedmlFile::save(const QString &pFileName)
{
// Make sure that we are properly loaded and have no (fatal) errors
if (mLoadingNeeded || hasErrors()) {
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)));
if (Core::writeFile(pFileName.isEmpty()?mFileName:pFileName,
Core::serialiseDomDocument(domDocument))) {
mNew = false;
return StandardFile::save(pFileName);
}
return false;
}
//==============================================================================
bool SedmlFile::update(const QString &pFileName)
{
// Our SED-ML file has been updated (e.g. through the Simulation Experiment
// view) and we want to update ourselves accordingly, so save ourselves and
// keep track of the fact that we were 'simply' updated
mUpdated = save(pFileName);
return mUpdated;
}
//==============================================================================
void SedmlFile::forceNew()
{
// Force our SED-ML file to act as if it was 'new'
mNew = true;
delete mSedmlDocument;
mSedmlDocument = nullptr;
mLoadingNeeded = true;
}
//==============================================================================
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();
}
for (uint i = 0, iMax = sedmlDocument->getNumErrors(); i < iMax; ++i) {
const libsedml::SedError *error = sedmlDocument->getError(i);
SedmlFileIssue::Type issueType = SedmlFileIssue::Type::Fatal;
switch (error->getSeverity()) {
case LIBSBML_SEV_INFO:
issueType = SedmlFileIssue::Type::Information;
break;
case LIBSBML_SEV_ERROR:
issueType = SedmlFileIssue::Type::Error;
break;
case LIBSBML_SEV_WARNING:
issueType = SedmlFileIssue::Type::Warning;
break;
case LIBSBML_SEV_FATAL:
issueType = SedmlFileIssue::Type::Fatal;
break;
}
// Add the issue to our list, but only if it's not already in there
// Note: indeed, for some reasons, libSEDML may generate several copies
// of the same error...
static const QRegularExpression TrailingEmptyLinesRegEx = QRegularExpression("[\\n]*$");
SedmlFileIssue issue = SedmlFileIssue(issueType,
int(error->getLine()),
int(error->getColumn()),
QString::fromStdString(error->getMessage()).remove(TrailingEmptyLinesRegEx));
if (!pIssues.contains(issue)) {
pIssues << issue;
}
}
// Only consider our SED-ML document valid if it has no (fatal) errors
bool res = !hasErrors();
if (!pFileContents.isEmpty()) {
delete sedmlDocument;
}
return res;
}
//==============================================================================
bool SedmlFile::isValid()
{
// Return whether we are valid
return isValid(QString(), mIssues);
}
//==============================================================================
SolverInterface * SedmlFile::solverInterface(const QString &pKisaoId)
{
// Retrieve and return the solver interface for the given KiSAO id and make
// sure that it's of the type we want
for (auto solverInterface : Core::solverInterfaces()) {
if (solverInterface->id(pKisaoId) == solverInterface->solverName()) {
if (solverInterface->solverType() != Solver::Type::Ode) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("%1 (%2) is an NLA solver while an ODE solver is expected").arg(solverInterface->solverName(),
pKisaoId));
return nullptr;
}
return solverInterface;
}
}
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("unsupported algorithm (%1)").arg(pKisaoId));
return nullptr;
}
//==============================================================================
bool SedmlFile::validAlgorithmParameters(const libsedml::SedListOfAlgorithmParameters *pSedmlAlgorithmParameters,
SolverInterface *pSolverInterface)
{
// Make sure that we have a solver interface
if (pSolverInterface == nullptr) {
return false;
}
// Recursively check whether the parameters of the given algorithm are valid
for (uint i = 0, iMax = pSedmlAlgorithmParameters->getNumAlgorithmParameters(); i < iMax; ++i) {
QString parameterKisaoId = QString::fromStdString(pSedmlAlgorithmParameters->get(i)->getKisaoID());
QString id = pSolverInterface->id(parameterKisaoId);
if (id.isEmpty() || (id == pSolverInterface->solverName())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("unsupported algorithm parameter (%1)").arg(parameterKisaoId));
return false;
}
}
return true;
}
//==============================================================================
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;
for (const auto &lineStyle : pValuesList) {
if (++i != 0) {
values += (i == lastValueIndex)?" "+tr("or")+" ":", ";
}
values += "'"+lineStyle+"'";
}
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
int(pPropertyNode.getLine()),
int(pPropertyNode.getColumn()),
tr("the '%1' property must have a value of %2").arg(pPropertyName,
values));
return false;
}
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::Type::Error,
int(pPropertyNode.getLine()),
int(pPropertyNode.getColumn()),
tr("the '%1' property must have a value of '#RRGGBB' or '#AARRGGBB'").arg(pPropertyName));
return false;
}
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::Type::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 != Language::Cellml)
&& (language != Language::Cellml_1_0)
&& (language != Language::Cellml_1_1)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("only SED-ML files with a CellML file are supported"));
return false;
}
// Make sure that there is either one or two simulations
uint nbOfSimulations = mSedmlDocument->getNumSimulations();
if ((nbOfSimulations != 1) && (nbOfSimulations != 2)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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::Type::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
auto uniformTimeCourse = static_cast<libsedml::SedUniformTimeCourse *>(firstSimulation);
double initialTime = uniformTimeCourse->getInitialTime();
double outputStartTime = uniformTimeCourse->getOutputStartTime();
double outputEndTime = uniformTimeCourse->getOutputEndTime();
int nbOfPoints = uniformTimeCourse->getNumberOfPoints();
if (!qFuzzyCompare(initialTime, outputStartTime)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("only SED-ML files with the same values for 'initialTime' and 'outputStartTime' are supported"));
return false;
}
if (qFuzzyCompare(outputStartTime, outputEndTime)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
tr("the values for 'outputStartTime' and 'outputEndTime' must be different"));
return false;
}
if (nbOfPoints <= 0) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
tr("the value for 'numberOfPoints' must be greater than zero"));
return false;
}
// Make sure that we have an algorithm for the first simulation
libsedml::SedAlgorithm *firstSimulationAlgorithm = firstSimulation->getAlgorithm();
libsbml::XMLNode *annotation = nullptr;
if (firstSimulationAlgorithm != nullptr) {
// Make sure that the algorithm relies on an algorithm that we support
// and that its parameters are also supported
if (!validAlgorithmParameters(firstSimulationAlgorithm->getListOfAlgorithmParameters(),
solverInterface(QString::fromStdString(firstSimulationAlgorithm->getKisaoID())))) {
return false;
}
// Make sure that the first simulation algorithm annotation, if any,
// contains at least the kind of information we would expect, i.e.
// solver properties that somehow don't have KiSAO ids
annotation = firstSimulationAlgorithm->getAnnotation();
if (annotation != nullptr) {
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
libsbml::XMLNode &solverPropertiesNode = annotation->getChild(i);
if ( (QString::fromStdString(solverPropertiesNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(solverPropertiesNode.getName()) == SolverProperties)) {
bool validSolverProperties = true;
for (uint j = 0, jMax = solverPropertiesNode.getNumChildren(); j < jMax; ++j) {
libsbml::XMLNode &solverPropertyNode = solverPropertiesNode.getChild(j);
if ( (QString::fromStdString(solverPropertyNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(solverPropertyNode.getName()) == SolverProperty)) {
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::Type::Information,
int(solverPropertiesNode.getLine()),
int(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 != nullptr) {
bool hasNlaSolver = false;
for (uint i = 0, iMax = annotation->getNumChildren(); i < iMax; ++i) {
libsbml::XMLNode &nlaSolverNode = annotation->getChild(i);
if ( (QString::fromStdString(nlaSolverNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(nlaSolverNode.getName()) == NlaSolver)) {
int nameIndex = nlaSolverNode.getAttrIndex(Name.toStdString());
if ((nameIndex != -1) && !nlaSolverNode.getAttrValue(nameIndex).empty()) {
if (hasNlaSolver) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
tr("only one NLA solver is allowed"));
return false;
}
hasNlaSolver = true;
} else {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
int(nlaSolverNode.getLine()),
int(nlaSolverNode.getColumn()),
tr("incomplete simulation annotation (missing NLA solver name)"));
return false;
}
}
}
}
} else {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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 != nullptr) {
// Make sure that the second simulation is a one-step simulation
if (secondSimulation->getTypeCode() != libsedml::SEDML_SIMULATION_ONESTEP) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("only SED-ML files with a one-step simulation 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::Type::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);
libsedml::SedAlgorithm *secondSimulationAlgorithm = secondSimulation->getAlgorithm();
firstSimulationAlgorithm->write(firstXmlStream);
if (secondSimulationAlgorithm != nullptr) {
secondSimulationAlgorithm->write(secondXmlStream);
}
libsbml::XMLNode *firstAnnotation = firstSimulationAlgorithm->getAnnotation();
libsbml::XMLNode *secondAnnotation = secondSimulationAlgorithm->getAnnotation();
if (firstAnnotation != nullptr) {
firstAnnotation->write(firstXmlStream);
}
if (secondAnnotation != nullptr) {
secondAnnotation->write(secondXmlStream);
}
firstAnnotation = firstSimulation->getAnnotation();
secondAnnotation = secondSimulation->getAnnotation();
if (firstAnnotation != nullptr) {
firstAnnotation->write(firstXmlStream);
}
if (secondAnnotation != nullptr) {
secondAnnotation->write(secondXmlStream);
}
if (firstStream.str() != secondStream.str()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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 != nullptr)?3:2;
if (mSedmlDocument->getNumTasks() != totalNbOfTasks) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Information,
tr("only SED-ML files that execute one or two simulations once are supported"));
return false;
}
libsedml::SedRepeatedTask *repeatedTask = nullptr;
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) {
auto task = static_cast<libsedml::SedTask *>(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 = reinterpret_cast<libsedml::SedRepeatedTask *>(task);
if ( repeatedTask->getResetModel()
&& (repeatedTask->getNumRanges() == 1)
&& (repeatedTask->getNumTaskChanges() == 0)
&& (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() == range->getId())) {
// Make sure that the vector range has one value that is
// equal to 1
auto vectorRange = static_cast<libsedml::SedVectorRange *>(range);
if ( (vectorRange->getNumValues() == 1)
&& (qFuzzyCompare(vectorRange->getValues().front(), 1.0))) {
// Make sure that the one/two sub-tasks have the correct
// order and retrieve their id
for (uint j = 0, jMax = totalNbOfTasks-1; j < jMax; ++j) {
libsedml::SedSubTask *subTask = repeatedTask->getSubTask(j);
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() == model->getId())
&& (task->getSimulationReference() == firstSimulation->getId())) {
firstSubTaskOk = true;
firstSubTaskId = task->getId();
} else if ( (secondSimulation != nullptr)
&& (task->getModelReference() == model->getId())
&& (task->getSimulationReference() == secondSimulation->getId())) {
secondSubTaskOk = true;
secondSubTaskId = task->getId();
}
}
}
if ( !repeatedTaskOk
|| !firstSubTaskOk || (repeatedTaskFirstSubTaskId != firstSubTaskId)
|| ( (secondSimulation != nullptr)
&& (!secondSubTaskOk || (repeatedTaskSecondSubTaskId != secondSubTaskId)))) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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() != 0)) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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().empty() || !variable->getModelReference().empty()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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() != repeatedTask->getId()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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(R"(^\/cellml:model\/cellml:component\[@name=')");
static const QRegularExpression TargetMiddleRegEx = QRegularExpression(R"(']\/cellml:variable\[@name=')");
static const QRegularExpression TargetEndRegEx = QRegularExpression(R"('\]$)");
bool referencingCellmlVariable = false;
QString target = QString::fromStdString(variable->getTarget());
if (target.contains(TargetStartRegEx) && target.contains(TargetEndRegEx)) {
static const QString Separator = "|";
target.remove(TargetStartRegEx);
target.replace(TargetMiddleRegEx, Separator);
target.remove(TargetEndRegEx);
QStringList identifiers = target.split(Separator);
if (identifiers.count() == 2) {
static const QRegularExpression IdentifierRegEx = QRegularExpression("^[[:alpha:]_][[:alnum:]_]*$");
QString componentName = identifiers.first();
QString variableName = identifiers.last();
referencingCellmlVariable = IdentifierRegEx.match(componentName).hasMatch()
&& IdentifierRegEx.match(variableName).hasMatch();
}
}
if (!referencingCellmlVariable) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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 != nullptr) {
for (uint j = 0, jMax = annotation->getNumChildren(); j < jMax; ++j) {
libsbml::XMLNode &variableDegreeNode = annotation->getChild(j);
if ( (QString::fromStdString(variableDegreeNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(variableDegreeNode.getName()) == VariableDegree)) {
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::Type::Information,
int(variableDegreeNode.getLine()),
int(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() != mathNode->getName())) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::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::Type::Information,
tr("only SED-ML files with 2D outputs are supported"));
return false;
}
static const QRegularExpression IntegerGt0RegEx = QRegularExpression("^[+]?[1-9]\\d*$");
static const QString TrueValue = "true";
static const QString FalseValue = "false";
annotation = output->getAnnotation();
if (annotation != nullptr) {
for (uint j = 0, jMax = annotation->getNumChildren(); j < jMax; ++j) {
libsbml::XMLNode &plot2dPropertiesNode = annotation->getChild(j);
if ( (QString::fromStdString(plot2dPropertiesNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(plot2dPropertiesNode.getName()) == Properties)) {
for (uint k = 0, kMax = plot2dPropertiesNode.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...
libsbml::XMLNode &plot2dPropertyNode = plot2dPropertiesNode.getChild(k);
QString plot2dPropertyNodeName = QString::fromStdString(plot2dPropertyNode.getName());
QString plot2dPropertyNodeValue = QString::fromStdString(plot2dPropertyNode.getChild(0).getCharacters());
if ( (plot2dPropertyNodeName == BackgroundColor)
&& !validColorPropertyValue(plot2dPropertyNode, plot2dPropertyNodeValue, BackgroundColor)) {
return false;
}
if ( (plot2dPropertyNodeName == FontSize)
&& !IntegerGt0RegEx.match(plot2dPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
int(plot2dPropertyNode.getLine()),
int(plot2dPropertyNode.getColumn()),
tr("the '%1' property value must be an integer greater than zero").arg(plot2dPropertyNodeName));
return false;
}
if ( (plot2dPropertyNodeName == ForegroundColor)
&& !validColorPropertyValue(plot2dPropertyNode, plot2dPropertyNodeValue, ForegroundColor)) {
return false;
}
if ( (plot2dPropertyNodeName == Height)
&& !IntegerGt0RegEx.match(plot2dPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
int(plot2dPropertyNode.getLine()),
int(plot2dPropertyNode.getColumn()),
tr("the '%1' property value must be an integer greater than zero").arg(plot2dPropertyNodeName));
return false;
}
// Grid lines
if ( (QString::fromStdString(plot2dPropertyNode.getURI()) == OpencorNamespace)
&& (QString::fromStdString(plot2dPropertyNode.getName()) == GridLines)) {
for (uint l = 0, lMax = plot2dPropertyNode.getNumChildren(); l < lMax; ++l) {
libsbml::XMLNode &gridLinesPropertyNode = plot2dPropertyNode.getChild(l);
QString gridLinesPropertyNodeName = QString::fromStdString(gridLinesPropertyNode.getName());
QString gridLinesPropertyNodeValue = QString::fromStdString(gridLinesPropertyNode.getChild(0).getCharacters());
if ( (gridLinesPropertyNodeName == Style)
&& !validListPropertyValue(gridLinesPropertyNode, gridLinesPropertyNodeValue, Style, lineStyles())) {
return false;
}
if ( (gridLinesPropertyNodeName == Width)
&& !IntegerGt0RegEx.match(gridLinesPropertyNodeValue).hasMatch()) {
mIssues << SedmlFileIssue(SedmlFileIssue::Type::Error,
int(gridLinesPropertyNode.getLine()),
int(gridLinesPropertyNode.getColumn()),
tr("the '%1' property value must be a number greater than zero").arg(gridLinesPropertyNodeName));
return false;
}