CellMLToSharedLibraryConverter Class Reference

#include <CellMLToSharedLibraryConverter.hpp>

Collaboration diagram for CellMLToSharedLibraryConverter:

[legend]

List of all members.

Public Member Functions
	CellMLToSharedLibraryConverter (bool preserveGeneratedSources=false, std::string component="heart")
DynamicCellModelLoaderPtr	Convert (const FileFinder &rFilePath, bool isCollective=true)
Static Public Member Functions
static void	CreateOptionsFile (const OutputFileHandler &rHandler, const std::string &rModelName, const std::vector< std::string > &rArgs, const std::string &rExtraXml="")
Private Member Functions
void	ConvertCellmlToSo (const std::string &rCellmlFullPath, const std::string &rCellmlFolder)
Private Attributes
bool	mPreserveGeneratedSources
std::string	mComponentName
Static Private Attributes
static const std::string	msSoSuffix = "so"
Friends
class	TestDynamicallyLoadedCellModels

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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.

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Constructor & Destructor Documentation

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 70 of file CellMLToSharedLibraryConverter.cpp.

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Member Function Documentation

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 77 of file CellMLToSharedLibraryConverter.cpp.

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

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 141 of file CellMLToSharedLibraryConverter.cpp.

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

Referenced by Convert().

void CellMLToSharedLibraryConverter::CreateOptionsFile	(	const OutputFileHandler &	rHandler,
		const std::string &	rModelName,
		const std::vector< std::string > &	rArgs,
		const std::string &	rExtraXml = ""
	)			[static]

Create a PyCml options file for the given model.

Parameters:

	rHandler	where to create the file
	rModelName	base name of the model file (which will be "rModelName.cellml")
	rArgs	extra command-line arguments for the model conversion
	rExtraXml	any extra XML to go in the config file (e.g. LT settings)

Definition at line 243 of file CellMLToSharedLibraryConverter.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), and OutputFileHandler::OpenOutputFile().

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Friends And Related Function Documentation

friend class TestDynamicallyLoadedCellModels [friend]

Test gets access to the msSoSuffix variable

Definition at line 54 of file CellMLToSharedLibraryConverter.hpp.

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Member Data Documentation

std::string CellMLToSharedLibraryConverter::mComponentName [private]

Which component to build the loadable module in.

Definition at line 112 of file CellMLToSharedLibraryConverter.hpp.

Referenced by ConvertCellmlToSo().

bool CellMLToSharedLibraryConverter::mPreserveGeneratedSources [private]

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

Definition at line 109 of file CellMLToSharedLibraryConverter.hpp.

Referenced by ConvertCellmlToSo().

const std::string CellMLToSharedLibraryConverter::msSoSuffix = "so" [static, private]

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 115 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