OutputFileHandler Class Reference

#include <OutputFileHandler.hpp>

Collaboration diagram for OutputFileHandler:

Public Member Functions
	OutputFileHandler (const std::string &rDirectory, bool cleanOutputDirectory=true)
	OutputFileHandler (const FileFinder &rDirectory, bool cleanOutputDirectory=true)
std::string	GetOutputDirectoryFullPath () const
std::string	GetRelativePath () const
void	SetArchiveDirectory () const
out_stream	OpenOutputFile (const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
out_stream	OpenOutputFile (const std::string &rFileName, unsigned number, const std::string &rFileFormat, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
FileFinder	CopyFileTo (const FileFinder &rSourceFile) const
FileFinder	FindFile (std::string leafName) const

Static Public Member Functions
static std::string	GetChasteTestOutputDirectory ()

Static Public Attributes
static const std::string	SIG_FILE_NAME

Private Member Functions
void	CommonConstructor (const std::string &rDirectory, bool cleanOutputDirectory)
std::string	MakeFoldersAndReturnFullPath (const std::string &rDirectory) const

Static Private Member Functions
static void	AddTrailingSlash (std::string &rDirectory)

Private Attributes
std::string	mDirectory
	The directory to store output files in (always ends in "/")

Detailed Description

This file abstracts stuff that needs to be done when creating output files for tests. It defines some helpful functions, so that things that are otherwise repeated in lots of places are just done here.

Definition at line 54 of file OutputFileHandler.hpp.

Constructor & Destructor Documentation

OutputFileHandler() [1/2]

OutputFileHandler::OutputFileHandler	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory = true
	)

Create an OutputFileHandler that will create output files in the given directory. The directory name should be relative to the place where Chaste test output is stored. If the user needs to know where this is, use the GetChasteTestOutputDirectory method.

Will check that the directory exists and create it if needed.

Note

This MUST be called collectively, since the directory creation routine contains a barrier call.

Parameters

rDirectory	the directory to put output files in.
cleanOutputDirectory	whether to remove any existing files in the output directory

Definition at line 89 of file OutputFileHandler.cpp.

References CommonConstructor().

OutputFileHandler() [2/2]

OutputFileHandler::OutputFileHandler	(	const FileFinder &	rDirectory,
		bool	cleanOutputDirectory = true
	)

Create an OutputFileHandler that will create output files in the given directory. This must be located inside the folder where Chaste test output is stored, and will typically be obtained with the FindFile method of this class from a parent handler.

Will check that the directory exists and create it if needed.

Note

This MUST be called collectively, since it contains a barrier call.

Parameters

rDirectory	the directory to put output files in
cleanOutputDirectory	whether to remove any existing files in the output directory

Definition at line 96 of file OutputFileHandler.cpp.

References RelativeTo::ChasteTestOutput, CommonConstructor(), EXCEPTION, FileFinder::GetAbsolutePath(), and FileFinder::GetRelativePath().

Member Function Documentation

AddTrailingSlash()

void OutputFileHandler::AddTrailingSlash ( std::string &  rDirectory )

staticprivate

Takes a reference to a string and adds a trailing slash if one is not already present

Parameters

rDirectory

The directory name to add a trailing slash to.

Definition at line 292 of file OutputFileHandler.cpp.

Referenced by GetChasteTestOutputDirectory(), and MakeFoldersAndReturnFullPath().

CommonConstructor()

void OutputFileHandler::CommonConstructor ( const std::string &  rDirectory, bool  cleanOutputDirectory  )

private

Functionality common to both constructors.

Parameters

rDirectory	relative path to the directory to put output files in
cleanOutputDirectory	whether to remove any existing files in the output directory

Definition at line 120 of file OutputFileHandler.cpp.

References RelativeTo::Absolute, PetscTools::AmMaster(), PetscTools::Barrier(), EXCEPTION, FileFinder::Exists(), MakeFoldersAndReturnFullPath(), mDirectory, and SIG_FILE_NAME.

Referenced by OutputFileHandler(), and OutputFileHandler().

CopyFileTo()

FileFinder OutputFileHandler::CopyFileTo

(

const FileFinder &

rSourceFile

)

const

Copy the given file to this output directory.

Note

This MUST be called collectively, since it contains a barrier call.

Parameters

rSourceFile

the file to copy

Returns

the copied file

Definition at line 301 of file OutputFileHandler.cpp.

References RelativeTo::Absolute, PetscTools::AmMaster(), PetscTools::Barrier(), EXCEPTION, FileFinder::GetAbsolutePath(), GetOutputDirectoryFullPath(), FileFinder::IsFile(), and TERMINATE.

Referenced by CellMLLoader::LoadCellMLFile().

FindFile()

FileFinder OutputFileHandler::FindFile

(

std::string

leafName

)

const

Returns

a FileFinder for a file in this output directory.

Parameters

leafName

the name of the file to find

Definition at line 327 of file OutputFileHandler.cpp.

References RelativeTo::Absolute, and GetOutputDirectoryFullPath().

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator::HoneycombMeshGenerator(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacSimulation::CreateAndRun(), GetRelativePath(), ImmersedBoundaryCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), and CellMLLoader::LoadCellMLFile().

GetChasteTestOutputDirectory()

std::string OutputFileHandler::GetChasteTestOutputDirectory ( )

static

Static method for getting the test output directory (the directory where chaste stores test output). This is set from the environment variable CHASTE_TEST_OUTPUT, and defaults to "/tmp/$USER/testoutput" if it is not set.

Attempts to return an absolute path, but may get confused by odd setups.

Static so an output file handler does not have to be created if the test output directory is wanted for, say, reading a file.

Returns

the test output directory name (CHASTE_TEST_OUTPUT)

Definition at line 161 of file OutputFileHandler.cpp.

References RelativeTo::AbsoluteOrCwd, AddTrailingSlash(), FileFinder::GetAbsolutePath(), and FileFinder::SetPath().

Referenced by ArchiveLocationInfo::GetArchiveRelativePath(), ExecutableSupport::GetBuildInfo(), ArchiveLocationInfo::GetIsDirRelativeToChasteTestOutput(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), MakeFoldersAndReturnFullPath(), FileFinder::PrivateRemove(), and FileFinder::SetPath().

GetOutputDirectoryFullPath()

std::string OutputFileHandler::GetOutputDirectoryFullPath

(

)

const

Returns

the full pathname to the directory this object will create files in.

Definition at line 249 of file OutputFileHandler.cpp.

References mDirectory.

Referenced by ColumnDataReader::ColumnDataReader(), CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator::HoneycombMeshGenerator(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), CopyFileTo(), CardiacSimulation::CreateResumeXmlFile(), FindFile(), ColumnDataWriter::GetOutputDirectory(), ImmersedBoundaryCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationSetup(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), SetArchiveDirectory(), and HeartConfig::Write().

GetRelativePath()

std::string OutputFileHandler::GetRelativePath

(

)

const

Returns

the path to this output directory, relative to the Chaste root output folder.

Definition at line 254 of file OutputFileHandler.cpp.

References RelativeTo::ChasteTestOutput, FindFile(), and FileFinder::GetRelativePath().

MakeFoldersAndReturnFullPath()

std::string OutputFileHandler::MakeFoldersAndReturnFullPath ( const std::string &  rDirectory ) const

private

Check that the desired output directory exists and is writable by us. Create it if needed. Return the full pathname of the output directory.

The environment variable CHASTE_TEST_OUTPUT will be examined. If it is set and non-empty it is taken to be a directory where test output should be stored. Otherwise the current directory is used.

Note

Contains a barrier, so must be called collectively.

Parameters

rDirectory

pathname of the output directory, relative to where Chaste output will be stored (user shouldn't care about this).

Returns

full pathname to the output directory

Definition at line 193 of file OutputFileHandler.cpp.

References AddTrailingSlash(), PetscTools::AmMaster(), PetscTools::Barrier(), GetChasteTestOutputDirectory(), SIG_FILE_NAME, and TERMINATE.

Referenced by CommonConstructor().

OpenOutputFile() [1/2]

out_stream OutputFileHandler::OpenOutputFile	(	const std::string &	rFileName,
		std::ios_base::openmode	mode = std::ios::out | std::ios::trunc
	)		const

Open an output file in our directory, and check it was opened successfully. Throws an Exception if not.

Parameters

rFileName	the name of the file to open, relative to the output directory.
mode	optionally, flags to use when opening the file (defaults are as for std::ofstream).

Returns

a managed pointer to the opened file stream.

Definition at line 265 of file OutputFileHandler.cpp.

References EXCEPTION, and mDirectory.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), Hdf5ToTxtConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToTxtConverter(), HoneycombMeshGenerator::HoneycombMeshGenerator(), ProgressReporter::ProgressReporter(), SimpleDataWriter::SimpleDataWriter(), ToroidalHoneycombMeshGenerator::ToroidalHoneycombMeshGenerator(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), ColumnDataWriter::CreateFixedDimensionFile(), ColumnDataWriter::CreateInfoFile(), CardiacSimulation::CreateResumeXmlFile(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::DetermineWatchedNodes(), ColumnDataWriter::EndDefineMode(), ActivationOutputModifier::FinaliseAtEnd(), ImmersedBoundaryCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), SingleTraceOutputModifier::InitialiseAtStart(), OpenOutputFile(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFile(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationSetup(), StreeterFibreGenerator< SPACE_DIM >::PreWriteCalculations(), ExecutableSupport::PrintError(), LogFile::Set(), AbstractPdeModifier< DIM >::SetupSolve(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SolveAndWriteResultsToFile(), ImmersedBoundarySvgWriter< DIM >::UpdateAtEndOfTimeStep(), AbstractPerElementWriter< ELEMENT_DIM, SPACE_DIM, DATA_SIZE >::WriteData(), PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteGenericFileToMeshalyzer(), HeartGeometryInformation< SPACE_DIM >::WriteLayerForEachNode(), ExecutableSupport::WriteMachineInfoFile(), ExecutableSupport::WriteProvenanceInfoFile(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg(), and DiscreteSystemForceCalculator::WriteResultsToFile().

OpenOutputFile() [2/2]

out_stream OutputFileHandler::OpenOutputFile	(	const std::string &	rFileName,
		unsigned	number,
		const std::string &	rFileFormat,
		std::ios_base::openmode	mode = std::ios::out | std::ios::trunc
	)		const

This just calls the other OpenOutputFile after concatenating the first three arguments together to make the full filename. For example OpenOutputFile("results_", 3, ".dat") creates results_3.dat. See documentation for OpenOutputFile(std::string, std::ios_base::openmode).

Parameters

rFileName	the root name of the file to open
number	the number to append to the root name of the file
rFileFormat	the file format (extension)
mode	optionally, flags to use when opening the file (defaults are as for std::ofstream).

Returns

a managed pointer to the opened file stream.

Definition at line 276 of file OutputFileHandler.cpp.

References OpenOutputFile().

SetArchiveDirectory()

void OutputFileHandler::SetArchiveDirectory

(

)

const

Helper method to set up ArchiveLocationInfo.

Definition at line 286 of file OutputFileHandler.cpp.

References RelativeTo::Absolute, GetOutputDirectoryFullPath(), and ArchiveLocationInfo::SetArchiveDirectory().

Member Data Documentation

mDirectory

std::string OutputFileHandler::mDirectory

private

The directory to store output files in (always ends in "/")

Definition at line 168 of file OutputFileHandler.hpp.

Referenced by CommonConstructor(), GetOutputDirectoryFullPath(), and OpenOutputFile().

SIG_FILE_NAME

const std::string OutputFileHandler::SIG_FILE_NAME

static

The name of the Chaste signature file added to folders we create.

Definition at line 165 of file OutputFileHandler.hpp.

Referenced by CommonConstructor(), MakeFoldersAndReturnFullPath(), and FileFinder::PrivateRemove().

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

• global/src/OutputFileHandler.hpp
• global/src/OutputFileHandler.cpp