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Some minor cleaning up.
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@agarny
agarny committed Feb 5, 2020
1 parent 1d552c2 commit 776b7f9
Showing 1 changed file with 36 additions and 96 deletions.
132 changes: 36 additions & 96 deletions src/plugins/support/CellMLSupport/src/cellmlfilecellml10exporter.cpp
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Expand Up @@ -57,9 +57,7 @@ CellmlFileCellml10Exporter::CellmlFileCellml10Exporter(iface::cellml_api::Model
{
// Create an empty CellML 1.0 model

ObjRef<iface::cellml_api::CellMLBootstrap> cellmlBootstrap = CreateCellMLBootstrap();

mExportedModel = cellmlBootstrap->createModel(L"1.0");
mExportedModel = CreateCellMLBootstrap()->createModel(L"1.0");

// Set the model's name and cmeta:id, if any

Expand All @@ -73,15 +71,12 @@ CellmlFileCellml10Exporter::CellmlFileCellml10Exporter(iface::cellml_api::Model

// Create an annotation set to manage annotations

ObjRef<iface::cellml_services::AnnotationToolService> annotationToolService = CreateAnnotationToolService();

mAnnotationSet = annotationToolService->createAnnotationSet();
mAnnotationSet = CreateAnnotationToolService()->createAnnotationSet();

// Create a CellML Variable Association Service object so that we can find
// relevant components

ObjRef<iface::cellml_services::CeVASBootstrap> cevasBootstrap = CreateCeVASBootstrap();
ObjRef<iface::cellml_services::CeVAS> cevas = cevasBootstrap->createCeVASForModel(pModel);
ObjRef<iface::cellml_services::CeVAS> cevas = CreateCeVASBootstrap()->createCeVASForModel(pModel);

std::wstring cevasError = cevas->modelError();

Expand All @@ -94,9 +89,7 @@ CellmlFileCellml10Exporter::CellmlFileCellml10Exporter(iface::cellml_api::Model
// Copy all (i.e. both local and imported) model-level units to our exported
// model

ObjRef<iface::cellml_api::UnitsSet> unitsSet = pModel->allUnits();

copyUnitsSet(unitsSet, mExportedModel);
copyUnitsSet(pModel->allUnits(), mExportedModel);

// Annotate imported components since they may have been renamed

Expand Down Expand Up @@ -174,8 +167,7 @@ void CellmlFileCellml10Exporter::copyUnitsSet(iface::cellml_api::UnitsSet *pUnit

// Copy the units' unit references to the new units

ObjRef<iface::cellml_api::UnitSet> unitSet = units->unitCollection();
ObjRef<iface::cellml_api::UnitIterator> unitIter = unitSet->iterateUnits();
ObjRef<iface::cellml_api::UnitIterator> unitIter = units->unitCollection()->iterateUnits();

for (ObjRef<iface::cellml_api::Unit> unit = unitIter->nextUnit();
unit != nullptr; unit = unitIter->nextUnit()) {
Expand Down Expand Up @@ -218,12 +210,9 @@ iface::cellml_api::CellMLComponent * CellmlFileCellml10Exporter::findRealCompone

for (ObjRef<iface::cellml_api::ImportComponent> importComponent = QueryInterface(component);
importComponent != nullptr; importComponent = QueryInterface(component)) {
ObjRef<iface::cellml_api::CellMLElement> importComponentParentElement = importComponent->parentElement();
ObjRef<iface::cellml_api::CellMLImport> import = QueryInterface(importComponentParentElement);
ObjRef<iface::cellml_api::Model> model = import->importedModel();
ObjRef<iface::cellml_api::CellMLComponentSet> components = model->modelComponents();
ObjRef<iface::cellml_api::CellMLImport> import = QueryInterface(importComponent->parentElement());

component = components->getComponent(importComponent->componentRef());
component = import->importedModel()->modelComponents()->getComponent(importComponent->componentRef());

if (component == nullptr) {
// No 'real' component exists
Expand All @@ -246,33 +235,24 @@ void CellmlFileCellml10Exporter::annotateImportedComponents(iface::cellml_api::M
// Recursively annotate all imported components with the name they are given
// by the importing model

ObjRef<iface::cellml_api::CellMLImportSet> imports = pModel->imports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = imports->iterateImports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = pModel->imports()->iterateImports();

for (ObjRef<iface::cellml_api::CellMLImport> import = importsIter->nextImport();
import != nullptr; import = importsIter->nextImport()) {
// Recursively annotate the components imported by the given model
// Note: depth first processing means that imported components renamed
// twice end up with the right name...

ObjRef<iface::cellml_api::Model> importedModel = import->importedModel();

annotateImportedComponents(importedModel);

// Annotate the imported components

ObjRef<iface::cellml_api::ImportComponentSet> importComponents = import->components();
annotateImportedComponents(import->importedModel());

// Go through the imported components and annotate them with the name
// they are given by the importing model

ObjRef<iface::cellml_api::ImportComponentIterator> importComponentsIter = importComponents->iterateImportComponents();
ObjRef<iface::cellml_api::ImportComponentIterator> importComponentsIter = import->components()->iterateImportComponents();

for (ObjRef<iface::cellml_api::ImportComponent> importComponent = importComponentsIter->nextImportComponent();
importComponent != nullptr; importComponent = importComponentsIter->nextImportComponent()) {
ObjRef<iface::cellml_api::CellMLComponent> realComponent = findRealComponent(importComponent);

mAnnotationSet->setStringAnnotation(realComponent, L"renamed", importComponent->name());
mAnnotationSet->setStringAnnotation(findRealComponent(importComponent), L"renamed", importComponent->name());
}
}
}
Expand Down Expand Up @@ -350,19 +330,15 @@ iface::dom::Element * CellmlFileCellml10Exporter::copyDomElement(iface::dom::Ele
switch (childNode->nodeType()) {
case iface::dom::Node::ELEMENT_NODE: {
ObjRef<iface::dom::Element> elementNode = QueryInterface(childNode);
ObjRef<iface::dom::Element> newElementNode = copyDomElement(elementNode);

res->appendChild(newElementNode)->release_ref();
res->appendChild(copyDomElement(elementNode))->release_ref();

break;
}
case iface::dom::Node::TEXT_NODE: {
ObjRef<iface::dom::Text> newTextNode = document->createTextNode(childNode->nodeValue());

res->appendChild(newTextNode)->release_ref();
case iface::dom::Node::TEXT_NODE:
res->appendChild(document->createTextNode(childNode->nodeValue()))->release_ref();

break;
}
default:
// Not a relevant type, so do nothing

Expand All @@ -386,14 +362,10 @@ void CellmlFileCellml10Exporter::copyExtensionElements(iface::cellml_api::CellML

ObjRef<iface::cellml_api::ExtensionElementList> elements = pFromElement->extensionElements();
ObjRef<iface::cellml_api::CellMLDOMElement> cellmlDomElement = QueryInterface(pToElement);
ObjRef<iface::dom::Element> domElement = cellmlDomElement->domElement();
ObjRef<iface::dom::Document> document = domElement->ownerDocument();
ObjRef<iface::dom::Document> document = cellmlDomElement->domElement()->ownerDocument();

for (uint i = 0, iMax = elements->length(); i < iMax; ++i) {
ObjRef<iface::dom::Element> element = elements->getAt(i);

ObjRef<iface::dom::Node> node = document->importNode(element, true);
ObjRef<iface::dom::Element> nodeElement = QueryInterface(node);
ObjRef<iface::dom::Element> nodeElement = QueryInterface(document->importNode(elements->getAt(i), true));

pToElement->appendExtensionElement(nodeElement);
}
Expand Down Expand Up @@ -450,14 +422,11 @@ void CellmlFileCellml10Exporter::copyComponent(iface::cellml_api::CellMLComponen

// Copy the units to our new component

ObjRef<iface::cellml_api::UnitsSet> componentUnitsSet = pComponent->units();

copyUnitsSet(componentUnitsSet, newComponent);
copyUnitsSet(pComponent->units(), newComponent);

// Copy the variables to our new component

ObjRef<iface::cellml_api::CellMLVariableSet> componentVariables = pComponent->variables();
ObjRef<iface::cellml_api::CellMLVariableIterator> componentVariablesIter = componentVariables->iterateVariables();
ObjRef<iface::cellml_api::CellMLVariableIterator> componentVariablesIter = pComponent->variables()->iterateVariables();

for (ObjRef<iface::cellml_api::CellMLVariable> componentVariable = componentVariablesIter->nextVariable();
componentVariable != nullptr; componentVariable = componentVariablesIter->nextVariable()) {
Expand Down Expand Up @@ -486,8 +455,7 @@ void CellmlFileCellml10Exporter::copyComponent(iface::cellml_api::CellMLComponen

// Copy the math nodes to our new component

ObjRef<iface::cellml_api::MathList> componentMath = pComponent->math();
ObjRef<iface::cellml_api::MathMLElementIterator> componentMathIter = componentMath->iterate();
ObjRef<iface::cellml_api::MathMLElementIterator> componentMathIter = pComponent->math()->iterate();

for (ObjRef<iface::mathml_dom::MathMLElement> componentMathNode = componentMathIter->next();
componentMathNode != nullptr; componentMathNode = componentMathIter->next()) {
Expand Down Expand Up @@ -543,13 +511,9 @@ void CellmlFileCellml10Exporter::copyGroup(iface::cellml_api::Model *pModel,
continue;
}

// Find the real component object
// Find the real component object and check whether it has been copied

ObjRef<iface::cellml_api::CellMLComponent> realComponent = findRealComponent(referencedComponent);

// Has the real component been copied?

ObjRef<iface::cellml_api::CellMLComponent> copiedComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(realComponent, L"copy"));
ObjRef<iface::cellml_api::CellMLComponent> copiedComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(findRealComponent(referencedComponent), L"copy"));

if (copiedComponent == nullptr) {
continue;
Expand Down Expand Up @@ -587,9 +551,7 @@ void CellmlFileCellml10Exporter::copyGroup(iface::cellml_api::Model *pModel,

// Copy any children of our component reference

ObjRef<iface::cellml_api::ComponentRefSet> componentReferences = componentReference->componentRefs();

copyGroup(pModel, componentReferences, newComponentReference);
copyGroup(pModel, componentReference->componentRefs(), newComponentReference);
}
}

Expand All @@ -600,27 +562,20 @@ void CellmlFileCellml10Exporter::copyGroups(iface::cellml_api::Model *pModel)
// Iterate only groups defining an encapsulation hierarchy and copy them
// into our exported model

ObjRef<iface::cellml_api::GroupSet> groups = pModel->groups();
ObjRef<iface::cellml_api::GroupSet> encapsulationGroups = groups->subsetInvolvingEncapsulation();
ObjRef<iface::cellml_api::GroupIterator> encapsulationGroupsIter = encapsulationGroups->iterateGroups();
ObjRef<iface::cellml_api::GroupIterator> encapsulationGroupsIter = pModel->groups()->subsetInvolvingEncapsulation()->iterateGroups();

for (ObjRef<iface::cellml_api::Group> encapsulationGroup = encapsulationGroupsIter->nextGroup();
encapsulationGroup != nullptr; encapsulationGroup = encapsulationGroupsIter->nextGroup()) {
ObjRef<iface::cellml_api::ComponentRefSet> encapsulationGroupComponentReferences = encapsulationGroup->componentRefs();

copyGroup(pModel, encapsulationGroupComponentReferences);
copyGroup(pModel, encapsulationGroup->componentRefs());
}

// Recursively process imported models

ObjRef<iface::cellml_api::CellMLImportSet> imports = pModel->imports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = imports->iterateImports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = pModel->imports()->iterateImports();

for (ObjRef<iface::cellml_api::CellMLImport> import = importsIter->nextImport();
import != nullptr; import = importsIter->nextImport()) {
ObjRef<iface::cellml_api::Model> importedModel = import->importedModel();

copyGroups(importedModel);
copyGroups(import->importedModel());
}
}

Expand All @@ -634,18 +589,16 @@ void CellmlFileCellml10Exporter::copyConnection(iface::cellml_api::Connection *p
// been copied across first, and hence have a "copy" annotation...

ObjRef<iface::cellml_api::MapComponents> componentMapping = pConnection->componentMapping();
ObjRef<iface::cellml_api::CellMLComponent> firstComponent = componentMapping->firstComponent();
ObjRef<iface::cellml_api::CellMLComponent> secondComponent = componentMapping->secondComponent();

// Check that we have copied the components involved, and get the copies

ObjRef<iface::cellml_api::CellMLComponent> newFirstComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(firstComponent, L"copy"));
ObjRef<iface::cellml_api::CellMLComponent> newFirstComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(componentMapping->firstComponent(), L"copy"));

if (newFirstComponent == nullptr) {
return;
}

ObjRef<iface::cellml_api::CellMLComponent> newSecondComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(secondComponent, L"copy"));
ObjRef<iface::cellml_api::CellMLComponent> newSecondComponent = QueryInterface(mAnnotationSet->getObjectAnnotation(componentMapping->secondComponent(), L"copy"));

if (newSecondComponent == nullptr) {
return;
Expand All @@ -666,8 +619,7 @@ void CellmlFileCellml10Exporter::copyConnection(iface::cellml_api::Connection *p

// Add the variable mappings

ObjRef<iface::cellml_api::MapVariablesSet> variableMappings = pConnection->variableMappings();
ObjRef<iface::cellml_api::MapVariablesIterator> variableMappingsIter = variableMappings->iterateMapVariables();
ObjRef<iface::cellml_api::MapVariablesIterator> variableMappingsIter = pConnection->variableMappings()->iterateMapVariables();

for (ObjRef<iface::cellml_api::MapVariables> variableMapping = variableMappingsIter->nextMapVariables();
variableMapping != nullptr; variableMapping = variableMappingsIter->nextMapVariables()) {
Expand All @@ -686,8 +638,7 @@ void CellmlFileCellml10Exporter::copyConnections(iface::cellml_api::Model *pMode
{
// Copy local connections into our exported model

ObjRef<iface::cellml_api::ConnectionSet> connections = pModel->connections();
ObjRef<iface::cellml_api::ConnectionIterator> connectionsIter = connections->iterateConnections();
ObjRef<iface::cellml_api::ConnectionIterator> connectionsIter = pModel->connections()->iterateConnections();

for (ObjRef<iface::cellml_api::Connection> connection = connectionsIter->nextConnection();
connection != nullptr; connection = connectionsIter->nextConnection()) {
Expand All @@ -696,14 +647,11 @@ void CellmlFileCellml10Exporter::copyConnections(iface::cellml_api::Model *pMode

// Recursively process imported models

ObjRef<iface::cellml_api::CellMLImportSet> imports = pModel->imports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = imports->iterateImports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = pModel->imports()->iterateImports();

for (ObjRef<iface::cellml_api::CellMLImport> import = importsIter->nextImport();
import != nullptr; import = importsIter->nextImport()) {
ObjRef<iface::cellml_api::Model> importedModel = import->importedModel();

copyConnections(importedModel);
copyConnections(import->importedModel());
}
}

Expand All @@ -716,8 +664,7 @@ void CellmlFileCellml10Exporter::propagateInitialValues()
// it has a numeric initial value, the we use that. If not, then it's
// an unavoidable error condition...

ObjRef<iface::cellml_api::CellMLComponentSet> components = mExportedModel->localComponents();
ObjRef<iface::cellml_api::CellMLComponentIterator> componentsIter = components->iterateComponents();
ObjRef<iface::cellml_api::CellMLComponentIterator> componentsIter = mExportedModel->localComponents()->iterateComponents();

for (ObjRef<iface::cellml_api::CellMLComponent> component = componentsIter->nextComponent();
component != nullptr; component = componentsIter->nextComponent()) {
Expand All @@ -744,17 +691,10 @@ void CellmlFileCellml10Exporter::propagateInitialValues()

if (!doubleInitialValueValid) {
// The variable is initialised with the initial value of another
// variable, so retrieve that 'initial' variable

ObjRef<iface::cellml_api::CellMLVariable> initialVariable = componentVariables->getVariable(initialValue);

// Find its source

ObjRef<iface::cellml_api::CellMLVariable> sourceVariable = initialVariable->sourceVariable();

// And copy its initial value
// variable, so retrieve that 'initial' variable, find its
// source and copy its initial value

componentVariable->initialValue(sourceVariable->initialValue());
componentVariable->initialValue(componentVariables->getVariable(initialValue)->sourceVariable()->initialValue());
}
}
}
Expand Down

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