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Bug 3130: Applied patch.
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@shoops
shoops committed Nov 25, 2022
1 parent 9e6380b commit 48dad15
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Showing 5 changed files with 108 additions and 38 deletions.
26 changes: 15 additions & 11 deletions copasi/sedml/SEDMLImporter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1005,7 +1005,7 @@ SEDMLImporter::parseSEDML(const std::string & sedmlDocumentText,

case LIBSEDML_SEV_FATAL:

// treat unknown as fatal
// treat unknown as fatal
default:

if (pSEDMLError->getErrorId() == 10804)
Expand Down Expand Up @@ -1064,15 +1064,22 @@ SEDMLImporter::parseSEDML(const std::string & sedmlDocumentText,
// initialize data:
initializeContent();

setSEDMLDocument(pSEDMLDocument);

// merge subtasks if needed
mergeNestedSubtasks();

setSEDMLDocument(pSEDMLDocument);

if (pOptions != NULL && !pOptions->getModelId().empty())
importModel(pOptions->getModelId());
if (pOptions == NULL || pOptions->skipModelImport() == false)
{
if (pOptions != NULL && !pOptions->getModelId().empty())
importModel(pOptions->getModelId());
else
importFirstSBMLModel();
}
else
importFirstSBMLModel();
{
mpCopasiModel = pDataModel->getModel();
}

if (pOptions != NULL && !pOptions->getTaskId().empty())
importTask(mpSEDMLDocument->getTask(pOptions->getTaskId()), false);
Expand All @@ -1083,7 +1090,6 @@ SEDMLImporter::parseSEDML(const std::string & sedmlDocumentText,

assignReportDefinitions();


if (mpProcessReport != NULL)
mpProcessReport->finishItem(mhImportStep);

Expand Down Expand Up @@ -1145,10 +1151,8 @@ void SEDMLImporter::importTasks(CDataVectorN< CCopasiTask > * pTaskList)

importTask(task, pTaskList);
}

}


void SEDMLImporter::assignReportDefinitions(CDataVectorN< CCopasiTask > * pTaskList)
{

Expand Down Expand Up @@ -1292,7 +1296,7 @@ void SEDMLImporter::importTask(
std::stringstream str;
std::vector< double > vals = vrange->getValues();

for (double val : vals)
for (double val : vals)
str << val << " ";

group->setValue< std::string >("Values", str.str());
Expand Down Expand Up @@ -1428,7 +1432,7 @@ SEDMLImporter::convertSimpleFunctionalRange(SedFunctionalRange * frange, SedRepe
knownValues[p->getId()] = p->getValue();
}

for (auto value : oldValues)
for (auto value : oldValues)
{
knownValues[insideVRange->getId()] = value;
newValues.push_back(SBMLTransforms::evaluateASTNode(frange->getMath(), knownValues));
Expand Down
86 changes: 67 additions & 19 deletions copasi/sedml/SEDMLUtils.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -681,6 +681,9 @@ void SEDMLUtils::setLibCombineTempDir()
const CDataObject *
SEDMLUtils::getObjectForSbmlId(const CModel * pModel, const std::string & id, const std::string & SBMLType, bool initial /* = false*/)
{
if (!pModel)
return NULL;

if (SBMLType == "Time")
return static_cast< const CDataObject * >(pModel->getObject(CCommonName("Reference=Time")));

Expand Down Expand Up @@ -959,25 +962,7 @@ SedmlInfo::SedmlInfo(SedDocument * pDocument, bool ownDocument)
if (!pDocument)
return;

std::map< int, int > taskCount;

for (unsigned int i = 0; i < pDocument->getNumTasks(); ++i)
{
auto * current = pDocument->getTask(i);
mTaskMap[current->getId()] = getModelForTask(current);
taskCount[current->getTypeCode()] = taskCount[current->getTypeCode()] + 1;
mReports[current->getId()] = std::vector< std::pair< std::string, std::string > >();
mPlots[current->getId()] = std::vector< std::pair< std::string, std::string > >();
std::stringstream str;

if (current->isSetName())
str << current->getName() << " - ";

str << current->getId();

mTaskNames.push_back(std::make_pair(current->getId(), str.str()));
mComplex |= taskCount[current->getTypeCode()] > 1 || mTaskMap[current->getId()].size() > 1;
}
std::map< std::pair< int, int>, int > taskCount;

for (unsigned int i = 0; i < pDocument->getNumOutputs(); ++i)
{
Expand All @@ -1000,6 +985,57 @@ SedmlInfo::SedmlInfo(SedDocument * pDocument, bool ownDocument)
mPlots[taskId].push_back(std::make_pair(current->getId(), str.str()));
}
}

for (unsigned int i = 0; i < pDocument->getNumTasks(); ++i)
{
auto * current = pDocument->getTask(i);

if (isRecursiveWithoutOutputs(current))
continue;

mTaskMap[current->getId()] = getModelForTask(current);

int simType = SEDML_SIMULATION;

if (current->getTypeCode() == SEDML_TASK)
{
auto * simulation = pDocument->getSimulation(dynamic_cast< SedTask * >(current)->getSimulationReference());

if (simulation != NULL)
simType = simulation->getTypeCode();
}

auto currentKey = std::make_pair(current->getTypeCode(), simType);

taskCount[currentKey] = taskCount[currentKey] + 1;
std::stringstream str;

if (current->isSetName())
str << current->getName() << " - ";

str << current->getId();

mTaskNames.push_back(std::make_pair(current->getId(), str.str()));
mComplex |= taskCount[currentKey] > 1 || mTaskMap[current->getId()].size() > 1;
}
}

bool SedmlInfo::hasOutputs(const std::string & taskId)
{
return !(mReports[taskId].empty() && mPlots[taskId].empty());
}

bool SedmlInfo::isRecursiveWithoutOutputs(SedAbstractTask * task)
{
auto * repeat = dynamic_cast< SedRepeatedTask * >(task);

if (repeat == NULL)
return false;

if (hasOutputs(task->getId()))
return false;

return true;
}

SedmlInfo::~SedmlInfo()
Expand Down Expand Up @@ -1283,6 +1319,7 @@ SedmlImportOptions::SedmlImportOptions(
, mPlots(plots)
, mReportId(reportId)
, mReportFile(reportFilename)
, mSkipModelImport(false)
{
}

Expand All @@ -1295,11 +1332,22 @@ SedmlImportOptions & SedmlImportOptions::operator=(const SedmlImportOptions & rh
mPlots = rhs.mPlots;
mReportId = rhs.mReportId;
mReportFile = rhs.mReportFile;
mSkipModelImport = rhs.mSkipModelImport;
}

return *this;
}

void SedmlImportOptions::setSkipModelImport(bool skipModelLoading)
{
mSkipModelImport = skipModelLoading;
}

bool SedmlImportOptions::skipModelImport() const
{
return mSkipModelImport;
}

const std::string & SedmlImportOptions::getTaskId() const
{
return mTaskId;
Expand Down
7 changes: 4 additions & 3 deletions copasi/sedml/SEDMLUtils.h
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ class SedmlInfo
bool isSupported();

/**
* @return true, if the document is complex ( > 1 model, multiple
* @return true, if the document is complex (> 1 model, multiple
tasks of the same type ) requiring the user to choose
which one to import.
*/
Expand All @@ -136,6 +136,9 @@ class SedmlInfo
std::vector< std::pair< std::string, std::string > > getReportsForTask(const std::string & taskId);
std::vector< std::pair< std::string, std::string > > getPlotsForTask(const std::string & taskId);

bool hasOutputs(const std::string & taskId);
bool isRecursiveWithoutOutputs(SedAbstractTask * task);

std::string getReportFileName(const std::string & reportId);
void setReportFileName(const std::string & reportId, const std::string & fileName);

Expand All @@ -146,7 +149,6 @@ class SedmlInfo
static SedmlInfo forFile(const std::string & fileName);
};


/**
* Utility methods for SED-ML Import / Export
*/
Expand Down Expand Up @@ -236,7 +238,6 @@ class SEDMLUtils
static int getAlphaFromArgb(const std::string & argb);
static int getAlphaFromRgba(const std::string & rgba);


/**
* updates the libcombine temp directory to the COPASI temp path
*/
Expand Down
8 changes: 4 additions & 4 deletions copasi/sedml/SedmlImportOptions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ class SedmlImportOptions
std::vector< std::string > mPlots;
std::string mReportId;
std::string mReportFile;
bool mSkipModelImport;

public:
SedmlImportOptions(
Expand All @@ -27,6 +28,9 @@ class SedmlImportOptions

SedmlImportOptions & operator=(const SedmlImportOptions & rhs);

void setSkipModelImport(bool skipModelLoading);
bool skipModelImport() const;

const std::string & getTaskId() const;
const std::string & getModelId() const;
const std::string & getReportId() const;
Expand All @@ -36,8 +40,4 @@ class SedmlImportOptions
bool isValid() const;
};


#endif // SEDML_IMPORT_OPTIONS_H



19 changes: 18 additions & 1 deletion tests/test_sedml.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ TEST_CASE("importing variables with terms", "[copasi,sedml]")
CRootContainer::removeDatamodel(dm);
}

TEST_CASE("export nested scan", "[copasi,sedml]")
TEST_CASE("export / import nested scan", "[copasi,sedml]")
{
auto * dm = CRootContainer::addDatamodel();
REQUIRE(dm != nullptr);
Expand All @@ -156,8 +156,25 @@ TEST_CASE("export nested scan", "[copasi,sedml]")
REQUIRE(doc->getDataGenerator("Rtot_1_task3") == NULL);
REQUIRE(doc->getDataGenerator("Rtot_1_task5") != NULL);

// the model has a timecourse, and a steady state scan with 3 variables, as such it should not be complex
REQUIRE(SedmlInfo(doc).isComplex() == false);

// if we had another time course then it should be complex
{
auto * task = doc->getTask(0)->clone();
task->setId("anotherTaks");
doc->getListOfTasks()->appendAndOwn(task);
REQUIRE(SedmlInfo(doc).isComplex() == true);
}

delete doc;

// now import
SedmlImportOptions opts;
opts.setSkipModelImport(true);
dm->importSEDMLFromString(sedml, "", NULL, true, &opts);
REQUIRE(dynamic_cast< CScanProblem * >(dm->getTaskList()->operator[]("Scan").getProblem())->getNumberOfScanItems() == 3);

CRootContainer::removeDatamodel(dm);
}

Expand Down

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