CellMLToSharedLibraryConverter Class Reference

#include <CellMLToSharedLibraryConverter.hpp>

Collaboration diagram for CellMLToSharedLibraryConverter:

Public Member Functions
	CellMLToSharedLibraryConverter (bool preserveGeneratedSources=false, std::string component="heart")
DynamicCellModelLoaderPtr	Convert (const FileFinder &rFilePath, bool isCollective=true)
void	SetOptions (const std::vector< std::string > &rArgs)

Private Member Functions
void	ConvertCellmlToSo (const std::string &rCellmlFullPath, const std::string &rCellmlFolder)

Private Attributes
bool	mPreserveGeneratedSources
std::string	mComponentName
std::string	codegen_args

Static Private Attributes
static const std::string	msSoSuffix = "so"

Friends
class	TestDynamicallyLoadedCellModels

Detailed Description

This class encapsulates all the complexity needed to generate a loadable module from a CellML file.

Definition at line 50 of file CellMLToSharedLibraryConverter.hpp.

Constructor & Destructor Documentation

CellMLToSharedLibraryConverter()

CellMLToSharedLibraryConverter::CellMLToSharedLibraryConverter	(	bool	preserveGeneratedSources = false,
		std::string	component = "heart"
	)

Create a converter.

Parameters

preserveGeneratedSources	whether to save copies of generated C++ source files in the directory containing the .cellml file.
component	the name of the Chaste component (or project) in which to build the loadable module (if required). Allows projects to have specialised base classes for dynamically loaded cell models.

Definition at line 68 of file CellMLToSharedLibraryConverter.cpp.

Member Function Documentation

Convert()

DynamicCellModelLoaderPtr CellMLToSharedLibraryConverter::Convert	(	const FileFinder &	rFilePath,
		bool	isCollective = true
	)

Returns

a loadable module from the given file, and return a loader for it. The file can be a .so, in which case there isn't much to do, just create the loader. The interesting case comes when it is a .cellml file. If the file has any other extension, an exception is thrown.

Parameters

rFilePath	the model to load
isCollective	whether this method is being called collectively. If it is not, then we require the .so to already exist, rather than trying to avoid race conditions.

Note

If you do not pass isCollective=false, must be called collectively.

Definition at line 75 of file CellMLToSharedLibraryConverter.cpp.

References RelativeTo::Absolute, ConvertCellmlToSo(), EXCEPTION, FileFinder::Exists(), FileFinder::GetAbsolutePath(), DynamicModelLoaderRegistry::GetLoader(), DynamicModelLoaderRegistry::Instance(), FileFinder::IsNewerThan(), msSoSuffix, and FileFinder::SetPath().

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::LoadDynamicModel().

ConvertCellmlToSo()

void CellMLToSharedLibraryConverter::ConvertCellmlToSo ( const std::string &  rCellmlFullPath, const std::string &  rCellmlFolder  )

private

Helper method performing the actual conversion of a .cellml file to a .so.

Note

Must be called collectively.

Parameters

rCellmlFullPath	full path to the .cellml file
rCellmlFolder	folder containing the CellML file, with trailing slash

Definition at line 140 of file CellMLToSharedLibraryConverter.cpp.

References RelativeTo::Absolute, PetscTools::AmMaster(), ChasteBuildDirName(), RelativeTo::ChasteBuildRoot, ChasteBuildType(), RelativeTo::ChasteSourceRoot, codegen_args, FileFinder::CopyTo(), FileFinder::DangerousRemove(), EXCEPT_IF_NOT, EXCEPTION, FileFinder::Exists(), EXPECT0, FileFinder::FindMatches(), FileFinder::GetAbsolutePath(), FileFinder::GetLeafNameNoExtension(), FileFinder::GetParent(), IGNORE_RET, FileFinder::IsDir(), FileFinder::IsPathSet(), mComponentName, mPreserveGeneratedSources, msSoSuffix, PetscTools::ReplicateException(), and FileFinder::SetPath().

Referenced by Convert().

SetOptions()

void CellMLToSharedLibraryConverter::SetOptions

(

const std::vector< std::string > &

rArgs

)

Set the options to be passed to chaste_codegen for the given model.

Parameters

rArgs

extra command-line arguments for the model conversion

Definition at line 266 of file CellMLToSharedLibraryConverter.cpp.

References codegen_args.

Friends And Related Symbol Documentation

TestDynamicallyLoadedCellModels

friend class TestDynamicallyLoadedCellModels

friend

Test gets access to the msSoSuffix variable

Definition at line 54 of file CellMLToSharedLibraryConverter.hpp.

Member Data Documentation

codegen_args

std::string CellMLToSharedLibraryConverter::codegen_args

private

The options to pass to codegen

Definition at line 112 of file CellMLToSharedLibraryConverter.hpp.

Referenced by ConvertCellmlToSo(), and SetOptions().

mComponentName

std::string CellMLToSharedLibraryConverter::mComponentName

private

Which component to build the loadable module in.

Definition at line 106 of file CellMLToSharedLibraryConverter.hpp.

Referenced by ConvertCellmlToSo().

mPreserveGeneratedSources

bool CellMLToSharedLibraryConverter::mPreserveGeneratedSources

private

Whether to save copies of generated C++ source files.

Definition at line 103 of file CellMLToSharedLibraryConverter.hpp.

Referenced by ConvertCellmlToSo().

msSoSuffix

const std::string CellMLToSharedLibraryConverter::msSoSuffix = "so"

staticprivate

The .so suffix is nearly always "so" (as you might expect). On Mac OSX this is redefined to "dylib"

Set the .so suffix

Definition at line 109 of file CellMLToSharedLibraryConverter.hpp.

Referenced by Convert(), and ConvertCellmlToSo().

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The documentation for this class was generated from the following files:

• heart/src/odes/CellMLToSharedLibraryConverter.hpp
• heart/src/odes/CellMLToSharedLibraryConverter.cpp