Basic file handling operations. More...

#include <OpenMS/SYSTEM/File.h>

Collaboration diagram for File:

Classes
class	TempDir
	Class representing a temporary directory. More...

class	TemporaryFiles_
	Internal helper class, which holds temporary filenames and deletes these files at program exit. More...

Public Types
enum class	CopyOptions { OVERWRITE , SKIP , CANCEL }
	Copy directory recursively. More...

enum class	MatchingFileListsStatus { MATCH = 0 , ORDER_MISMATCH = 1 , SET_MISMATCH = 2 }

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

static bool	exists (const std::string &file)
	Method used to test if a `file` exists.

static bool	empty (const std::string &file)
	Return true if the file does not exist or the file is empty.

static bool	executable (const std::string &file)
	Method used to test if a `file` is executable.

static UInt64	fileSize (const std::string &file)
	The filesize in bytes (or -1 on error, e.g. if the file does not exist)

static bool	rename (const std::string &from, const std::string &to, bool overwrite_existing=true, bool verbose=true)
	Rename a file.

static bool	copyDirRecursively (const std::string &from_dir, const std::string &to_dir, File::CopyOptions option=CopyOptions::OVERWRITE)

static bool	copy (const std::string &from, const std::string &to)
	Copy a file (if it exists). Returns true if successful.

static bool	remove (const std::string &file)
	Removes a file (if it exists).

static bool	removeDirRecursively (const std::string &dir_name)
	Removes a directory and all its contents recursively (absolute path). Returns true if successful.

static bool	removeDir (const std::string &dir_name)
	Removes a directory and all its contents (absolute path). Returns true if successful.

static bool	makeDir (const std::string &dir_name)

static std::string	absolutePath (const std::string &file)
	Replaces the relative path in the argument with the absolute path.

static std::string	basename (const std::string &file)

static std::string	stemName (const std::string &file)

static std::string	extension (const std::string &file)

static StringList	listDirectories (const std::string &dir)

static std::string	path (const std::string &file)

static bool	readable (const std::string &file)
	Return true if the file exists and is readable.

static bool	writable (const std::string &file)
	Return true if the file is writable.

static bool	isDirectory (const std::string &path)
	Return true if the given path specifies a directory.

static std::string	find (const std::string &filename, StringList directories=StringList())
	Looks up the location of the file `filename`.

static bool	fileList (const std::string &dir, const std::string &file_pattern, StringList &output, bool full_path=false)
	Retrieves a list of files matching `file_pattern` in directory `dir` (returns filenames without paths unless `full_path` is true)

static std::string	findDoc (const std::string &filename)
	Resolves a partial file name to a documentation file in the doc-folder.

static std::string	getUniqueName (bool include_hostname=true)
	Returns a string, consisting of date, time, hostname, process id, and a incrementing number. This can be used for temporary files.

static std::string	getOpenMSDataPath ()
	Returns the OpenMS data path (environment variable overwrites the default installation path)

static std::string	getOpenMSHomePath ()
	Returns the OpenMS home path (environment variable overwrites the default home path)

static std::string	getOpenMSConfigDir ()
	Returns the per-user OpenMS configuration directory (the directory that holds OpenMS.ini)

static std::string	getTempDirectory ()

static std::string	getUserDirectory ()

static Param	getSystemParameters ()

static std::string	findDatabase (const std::string &db_name)

static StringList	getPathLocations ()
	Extract list of directories from a concatenated string (usually $PATH).

static StringList	getPathLocations (const std::string &path)
	Extract list of directories from an explicit concatenated path string.

static bool	findExecutable (std::string &exe_filename)
	Searches for an executable with the given name (similar to where (Windows) or which (Linux/MacOS)

static std::string	findSiblingTOPPExecutable (const std::string &toolName)
	Searches for an executable with the given name.

static std::string	getTemporaryFile (const std::string &alternative_file="")
	Obtain a temporary filename, ensuring automatic deletion upon exit.

static MatchingFileListsStatus	validateMatchingFileNames (const StringList &sl1, const StringList &sl2, bool basename=true, bool ignore_extension=true)
	Helper function to test if filenames provided in two StringLists match.

Static Private Member Functions
static Param	getSystemParameterDefaults_ ()
	get defaults for the system's Temp-path, user home directory etc.

static bool	isOpenMSDataPath_ (const std::string &path)
	Check if the given path is a valid OPENMS_DATA_PATH.

Static Private Attributes
static TemporaryFiles_	temporary_files_
	private list of temporary filenames, which are deleted upon program exit

Detailed Description

Basic file handling operations.

Member Enumeration Documentation

◆ CopyOptions

enum class CopyOptions

strong

Copy directory recursively.

Copies a source directory to a new target directory (recursive). If the target directory already exists, files will be added. If files from the source already exist in the target, option allows for the following behaviour:

OVERWRITE: Overwrite the file in the target directory if it already exists. SKIP: Skip the file in the target directory if it already exists. CANCEL: Cancel the copy process if file already exists in target directory - return false.

Parameters

[in]	from_dir	Source directory
[in]	to_dir	Target directory
[in]	option	Specify the copy option (OVERWRITE, SKIP, CANCEL)

Returns: True on success

Enumerator
OVERWRITE
SKIP
CANCEL

◆ MatchingFileListsStatus

enum class MatchingFileListsStatus

strong

Enumerator
MATCH
ORDER_MISMATCH
SET_MISMATCH

Member Function Documentation

◆ absolutePath()

static std::string absolutePath ( const std::string & file )

static

Replaces the relative path in the argument with the absolute path.

Referenced by TOPPViewBase::addDataFile().

◆ basename()

static std::string basename ( const std::string & file )

static

Returns the basename of the file (without the path). No checking is done on the filesystem, i.e. '/path/some_entity' will return 'some_entity', irrespective of 'some_entity' is a file or a directory. However, '/path/some_entity/' will return ''.

Referenced by TOPPViewBase::addDataFile(), TOPPASBase::addTOPPASFile(), NucleicAcidSearchEngine::main_(), TOPPASBase::refreshParameters(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineAs(), and INIFileEditorWindow::updateWindowTitle().

◆ copy()

static bool copy	(	const std::string &	from,
		const std::string &	to
	)

static

Copy a file (if it exists). Returns true if successful.

◆ copyDirRecursively()

static bool copyDirRecursively	(	const std::string &	from_dir,
		const std::string &	to_dir,
		File::CopyOptions	option = `CopyOptions::OVERWRITE`
	)

static

◆ empty()

static bool empty ( const std::string & file )

static

Return true if the file does not exist or the file is empty.

◆ executable()

static bool executable ( const std::string & file )

static

Method used to test if a file is executable.

◆ exists()

static bool exists ( const std::string & file )

static

Method used to test if a file exists.

Referenced by TOPPViewBase::addDataFile(), TOPPASBase::loadPreferences(), and TOPPViewBase::loadPreferences().

◆ extension()

static std::string extension ( const std::string & file )

static

Returns the file extension including the leading dot. Recognizes compound OpenMS extensions like ".mzML.gz". E.g., "/path/sample.mzML.gz" returns ".mzML.gz", "/path/file.txt" returns ".txt". Returns empty string if there is no extension: "/path/file" returns "".

◆ fileList()

static bool fileList	(	const std::string &	dir,
		const std::string &	file_pattern,
		StringList &	output,
		bool	full_path = `false`
	)

static

Retrieves a list of files matching file_pattern in directory dir (returns filenames without paths unless full_path is true)

Returns: true => there are matching files

◆ fileSize()

static UInt64 fileSize ( const std::string & file )

static

The filesize in bytes (or -1 on error, e.g. if the file does not exist)

◆ find()

static std::string find	(	const std::string &	filename,
		StringList	directories = `StringList()`
	)

static

Looks up the location of the file filename.

The following locations are checked in this order:

the directories in directories
the directory contained in the environment variable $OPENMS_DATA_PATH
the 'share/OpenMS/' directory of the OpenMS install directory

Exceptions

FileNotFound is thrown, if the file is not found

Referenced by QApplicationTOPP::QApplicationTOPP().

◆ findDatabase()

static std::string findDatabase ( const std::string & db_name )

static

uses File::find() to search for a file names db_name in the 'id_db_dir' param of the OpenMS system parameters

Exceptions

FileNotFound is thrown, if the file is not found

◆ findDoc()

static std::string findDoc ( const std::string & filename )

static

Resolves a partial file name to a documentation file in the doc-folder.

Using find() to locate the documentation file under OPENMS_DATA_PATH, OPENMS_SOURCE_PATH, OPENMS_BINARY_PATH + "/../../doc" (or a variation for MacOS packages)

Will return the filename with the full path to the local documentation. If this call fails, try the web documentation (http://www.openms.de/current_doxygen/) instead.

Parameters

[in] filename The doc file name to find.

Returns: The full path to the requested file.

Exceptions

FileNotFound is thrown, if the file is not found

◆ findExecutable()

static bool findExecutable ( std::string & exe_filename )

static

Searches for an executable with the given name (similar to where (Windows) or which (Linux/MacOS)

This function can be used to find the full path+filename to an executable in the PATH environment. Only the first hit (by order in PATH) is returned. If the exe_filename has a relative or full path which points to an existing file, PATH information will not be used. The function returns true if the filename was found (exists) and false otherwise. Note: this does not require the file to have executable permission set (this is not tested) The returned content of exe_filename is only valid if true is returned.

Parameters

[in,out] exe_filename The executable to search for.

Returns: true if exe_filename could be resolved to a full path and it exists

◆ findSiblingTOPPExecutable()

static std::string findSiblingTOPPExecutable ( const std::string & toolName )

static

Searches for an executable with the given name.

Parameters

[in] toolName The executable to search for.

Exceptions

FileNotFound is thrown, if the tool executable was not found.

Referenced by TOPPViewBase::runTOPPTool_().

◆ getExecutablePath()

static std::string getExecutablePath ( )

static

Retrieve path of current executable (useful to find other TOPP tools) The returned path is either just an EMPTY string if the call to system subroutines failed or the complete path including a trailing "/", to enable usage of this function as File::getExecutablePath() + "mytool"

◆ getOpenMSConfigDir()

static std::string getOpenMSConfigDir ( )

static

Returns the per-user OpenMS configuration directory (the directory that holds OpenMS.ini)

Follows the XDG base directory specification on unix-like systems (<XDG_CONFIG_HOME>/OpenMS or <home>/.config/OpenMS) and uses <home>/.OpenMS otherwise. The returned path has no trailing separator and the directory is not guaranteed to exist.

Returns: String containing the per-user OpenMS configuration directory path

◆ getOpenMSDataPath()

static std::string getOpenMSDataPath ( )

static

Returns the OpenMS data path (environment variable overwrites the default installation path)

Referenced by TOPPASBase::openExampleDialog().

◆ getOpenMSHomePath()

static std::string getOpenMSHomePath ( )

static

Returns the OpenMS home path (environment variable overwrites the default home path)

◆ getPathLocations() [1/2]

static StringList getPathLocations ( )

static

Extract list of directories from a concatenated string (usually $PATH).

Depending on platform, the components are split based on ":" (Linux/Mac) or ";" (Windows). All paths use the '/' as separator and end in '/'. E.g. for 'PATH=/usr/bin:/home/unicorn' the result is {"/usr/bin/", "/home/unicorn/"} or 'PATH=c:\temp;c:\Windows' the result is {"c:/temp/", "c:/Windows/"}

Uses the value of the $PATH environment variable (or an empty string if $PATH is unset).

◆ getPathLocations() [2/2]

static StringList getPathLocations ( const std::string & path )

static

Extract list of directories from an explicit concatenated path string.

Depending on platform, the components are split based on ":" (Linux/Mac) or ";" (Windows). All paths use the '/' as separator and end in '/'. Note: the path string is passed as input to enable proper testing (env vars are usually read-only).

◆ getSystemParameterDefaults_()

static Param getSystemParameterDefaults_ ( )

staticprivate

get defaults for the system's Temp-path, user home directory etc.

◆ getSystemParameters()

static Param getSystemParameters ( )

static

get the system's default OpenMS.ini file in the users home directory (<home>/OpenMS/OpenMS.ini) or create/repair it if required order:

<OPENMS_HOME_DIR>/OpenMS/OpenMS.ini if environmental variable set
user home directory <home>/OpenMS/OpenMS.ini

◆ getTempDirectory()

static std::string getTempDirectory ( )

static

The current OpenMS temporary data path (for temporary files). Looks up the following locations, taking the first one which is non-null:

environment variable OPENMS_TMPDIR
'temp_dir' in the ~/OpenMS.ini file
System temp directory (usually defined by environment 'TMP' or 'TEMP'

Referenced by TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::showTOPPDialog_(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().

◆ getTemporaryFile()

static std::string getTemporaryFile ( const std::string & alternative_file = "" )

static

Obtain a temporary filename, ensuring automatic deletion upon exit.

The file is not actually created and only deleted at exit if it exists.

However, if 'alternative_file' is given and not empty, no temporary filename is created and 'alternative_file' is returned (and not destroyed upon exit). This is useful if you have an optional output file, which may, or may not be requested, but you need its content regardless, e.g. for intermediate plotting with R. Thus you can just call this function to get a file which can be used and gets automatically destroyed if needed.

Parameters

[in] alternative_file If this string is not empty, no action is taken and it is used as return value

Returns: Full path to a temporary file

◆ getUniqueName()

static std::string getUniqueName ( bool include_hostname = true )

static

Returns a string, consisting of date, time, hostname, process id, and a incrementing number. This can be used for temporary files.

Parameters

[in] include_hostname add hostname into result - potentially a long string

Returns: a unique name

Referenced by TOPPViewBase::showTOPPDialog_(), and TOPPASBase::TOPPASBase().

◆ getUserDirectory()

static std::string getUserDirectory ( )

static

The current OpenMS user data path (for result files) Tries to set the user directory in following order:

OPENMS_HOME_DIR if environmental variable set
"home_dir" entry in OpenMS.ini
user home directory

◆ isDirectory()

static bool isDirectory ( const std::string & path )

static

Return true if the given path specifies a directory.

◆ isOpenMSDataPath_()

static bool isOpenMSDataPath_ ( const std::string & path )

staticprivate

Check if the given path is a valid OPENMS_DATA_PATH.

◆ listDirectories()

static StringList listDirectories ( const std::string & dir )

static

Returns a sorted list of subdirectory absolute paths (non-recursive) in the given directory. Uses '/' separators. Returns an empty list on any error or if the path is not a directory (no throw).

◆ makeDir()

static bool makeDir ( const std::string & dir_name )

static

Creates a directory (absolute path or relative to the current working dir), even if subdirectories do not exist. Returns true if successful. If the path already exists when this function is called, it will return true.

◆ path()

static std::string path ( const std::string & file )

static

Returns the path of the file (without the file name and without path separator). If just a filename is given without any path, then "." is returned. No checking is done on the filesystem, i.e. '/path/some_entity' will return '/path', irrespective of 'some_entity' is a file or a directory. However, '/path/some_entity/' will return '/path/some_entity'.

Referenced by TOPPViewBase::updateCurrentPath(), and INIFileEditorWindow::updateWindowTitle().

◆ readable()

static bool readable ( const std::string & file )

static

Return true if the file exists and is readable.

Referenced by TOPPViewBase::finishTOPPToolExecution(), and INIFileEditorWindow::openFile().

◆ remove()

static bool remove ( const std::string & file )

static

Removes a file (if it exists).

Returns: Returns true if the file was successfully deleted (or if it did not exist).

Referenced by TOPPViewBase::finishTOPPToolExecution(), and TOPPViewBase::runTOPPTool_().

◆ removeDir()

static bool removeDir ( const std::string & dir_name )

static

Removes a directory and all its contents (absolute path). Returns true if successful.

◆ removeDirRecursively()

static bool removeDirRecursively ( const std::string & dir_name )

static

Removes a directory and all its contents recursively (absolute path). Returns true if successful.

Referenced by TOPPASBase::~TOPPASBase().

◆ rename()

static bool rename	(	const std::string &	from,
		const std::string &	to,
		bool	overwrite_existing = `true`,
		bool	verbose = `true`
	)

static

Rename a file.

If from and to point to the same file (symlinks are resolved), no action will be taken and true is returned. If the target already exists (and is not identical to the source), this function will fail unless overwrite_existing is true.

Parameters

[in]	from	Source filename
[in]	to	Target filename
[in]	overwrite_existing	Delete already existing target, before renaming
[in]	verbose	Print message to OPENMS_LOG_ERROR if something goes wrong.

Returns: True on success

◆ stemName()

static std::string stemName ( const std::string & file )

static

Returns the basename of the file without any known file extension. Delegates to FileHandler::stripExtension(File::basename(file)). E.g., "/path/sample.mzML.gz" returns "sample", "/path/data.featureXML" returns "data". Unknown extensions are stripped at the last dot: "/path/file.txt" returns "file". Directories with dots in the path are handled correctly: "/my.dir/file" returns "file".

Referenced by TOPPViewBase::addDataFile().

◆ validateMatchingFileNames()

static MatchingFileListsStatus validateMatchingFileNames	(	const StringList &	sl1,
		const StringList &	sl2,
		bool	basename = `true`,
		bool	ignore_extension = `true`
	)

static

Helper function to test if filenames provided in two StringLists match.

Passing several InputFilesLists is error-prone as users may provide files in a different order. This helper function performs validation and returns one of three states:

MATCH (0): Files match perfectly (considering basename/extension settings)
ORDER_MISMATCH (1): Same set of files but in different order
SET_MISMATCH (2): Different sets of files (including different counts)

Parameters

[in]	sl1	First StringList with filenames
[in]	sl2	Second StringList with filenames
[in]	basename	If set to true, only basenames are compared
[in]	ignore_extension	If set to true, extensions are ignored (e.g., useful to compare spectra filenames to ID filenames)

Returns: MatchingFileListsStatus indicating the validation result

◆ writable()

static bool writable ( const std::string & file )

static

Return true if the file is writable.

Referenced by TOPPViewBase::runTOPPTool_(), and TOPPViewBase::showTOPPDialog_().

Member Data Documentation

◆ temporary_files_

TemporaryFiles_ temporary_files_

staticprivate

private list of temporary filenames, which are deleted upon program exit

Classes

Public Types

Static Public Member Functions

Static Private Member Functions

Static Private Attributes

Detailed Description

Member Enumeration Documentation

◆ CopyOptions

◆ MatchingFileListsStatus

Member Function Documentation

◆ absolutePath()

◆ basename()

◆ copy()

◆ copyDirRecursively()

◆ empty()

◆ executable()

◆ exists()

◆ extension()

◆ fileList()

◆ fileSize()

◆ find()

◆ findDatabase()

◆ findDoc()

◆ findExecutable()

◆ findSiblingTOPPExecutable()

◆ getExecutablePath()

◆ getOpenMSConfigDir()

◆ getOpenMSDataPath()

◆ getOpenMSHomePath()

◆ getPathLocations() [1/2]

◆ getPathLocations() [2/2]

◆ getSystemParameterDefaults_()

◆ getSystemParameters()

◆ getTempDirectory()

◆ getTemporaryFile()

◆ getUniqueName()

◆ getUserDirectory()

◆ isDirectory()

◆ isOpenMSDataPath_()

◆ listDirectories()

◆ makeDir()

◆ path()

◆ readable()

◆ remove()

◆ removeDir()

◆ removeDirRecursively()

◆ rename()

◆ stemName()

◆ validateMatchingFileNames()

◆ writable()

Member Data Documentation

◆ temporary_files_