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...

Static Public Member Functions
static String	getExecutablePath ()

static bool	exists (const String &file)
	Method used to test if a `file` exists. More...

static bool	empty (const String &file)
	Return true if the file does not exist or the file is empty. More...

static bool	executable (const String &file)
	Method used to test if a `file` is executable. More...

static bool	rename (const String &from, const String &to, bool overwrite_existing=true, bool verbose=true)
	Rename a file. More...

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

static bool	remove (const String &file)
	Removes a file (if it exists). More...

static bool	removeDirRecursively (const String &dir_name)
	Removes the subdirectories of the specified directory (absolute path). Returns true if successful. More...

static bool	removeDir (const QString &dir_name)
	Removes the directory and all subdirectories (absolute path). More...

static String	absolutePath (const String &file)
	Replaces the relative path in the argument with the absolute path. More...

static String	basename (const String &file)

static String	path (const String &file)

static bool	readable (const String &file)
	Return true if the file exists and is readable. More...

static bool	writable (const String &file)
	Return true if the file is writable. More...

static bool	isDirectory (const String &path)
	Return true if the given path specifies a directory. More...

static String	find (const String &filename, StringList directories=StringList())
	Looks up the location of the file `filename`. More...

static bool	fileList (const String &dir, const 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) More...

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

static 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. More...

static String	getOpenMSDataPath ()
	Returns the OpenMS data path (environment variable overwrites the default installation path) More...

static String	getOpenMSHomePath ()
	Returns the OpenMS home path (environment variable overwrites the default home path) More...

static String	getTempDirectory ()

static String	getUserDirectory ()

static Param	getSystemParameters ()

static String	findDatabase (const String &db_name)

static StringList	getPathLocations (const String &path=std::getenv("PATH"))
	Extract list of directories from a concatenated string (usually $PATH). More...

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

static String	findSiblingTOPPExecutable (const String &toolName)
	Searches for an executable with the given name. More...

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

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

static void	download (const std::string &url, const std::string &download_folder)
	Download file from given URL into a download folder. Returns when done. Throws FileNotFound exception if download failed. If a file with same filename already exists, continues download and appends '.#number' to basename. More...

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

static bool	isOpenMSDataPath_ (const String &path)
	Check if the given path is a valid OPENMS_DATA_PATH. More...

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

Friends
class	TOPPBase

Detailed Description

Basic file handling operations.

Member Enumeration Documentation

◆ CopyOptions

enum 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

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

Returns: True on success

Enumerator
OVERWRITE
SKIP
CANCEL

Member Function Documentation

◆ absolutePath()

static String absolutePath ( const String & file )

static

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

Referenced by TOPPViewBase::addDataFile().

◆ basename()

static String basename ( const 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(), DTAFile::load(), NucleicAcidSearchEngine::main_(), TOPPASBase::refreshParameters(), AccurateMassSearchEngine::resolveAutoMode_(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineAs(), and INIFileEditorWindow::updateWindowTitle().

◆ copyDirRecursively()

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

static

◆ download()

static void download	(	const std::string &	url,
		const std::string &	download_folder
	)

static

Download file from given URL into a download folder. Returns when done. Throws FileNotFound exception if download failed. If a file with same filename already exists, continues download and appends '.#number' to basename.

◆ empty()

static bool empty ( const String & file )

static

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

◆ executable()

static bool executable ( const String & file )

static

Method used to test if a file is executable.

◆ exists()

static bool exists ( const String & file )

static

Method used to test if a file exists.

Referenced by TOPPViewBase::addDataFile(), MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), TOPPASBase::loadPreferences(), and TOPPViewBase::loadPreferences().

◆ fileList()

static bool fileList	(	const String &	dir,
		const 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

◆ find()

static String find	(	const 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(), and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::readEnzymesFromFile_().

◆ findDatabase()

static String findDatabase ( const 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 String findDoc ( const 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

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 ( OpenMS::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 String findSiblingTOPPExecutable ( const String & toolName )

static

Searches for an executable with the given name.

Parameters

toolName The executable to search for.

Exceptions

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

Referenced by TOPPViewBase::runTOPPTool_().

◆ getExecutablePath()

static 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"

◆ getOpenMSDataPath()

static String getOpenMSDataPath ( )

static

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

Referenced by TOPPASBase::openExampleDialog().

◆ getOpenMSHomePath()

static String getOpenMSHomePath ( )

static

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

◆ getPathLocations()

static StringList getPathLocations ( const String & path = std::getenv("PATH") )

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/"}

Note: the environment variable 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: 1. <OPENMS_HOME_DIR>/OpenMS/OpenMS.ini if environmental variable set 2. user home directory <home>/OpenMS/OpenMS.ini

◆ getTempDirectory()

static 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 String getTemporaryFile ( const 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

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 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

include_hostname add hostname into result - potentially a long string

Returns: a unique name

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

◆ getUserDirectory()

static String getUserDirectory ( )

static

The current OpenMS user data path (for result files) Tries to set the user directory in following order: 1. OPENMS_HOME_DIR if environmental variable set 2. "home_dir" entry in OpenMS.ini 3. user home directory

Referenced by TOPPViewBase::initializeDefaultParameters_(), and TOPPViewBase::loadPreferences().

◆ isDirectory()

static bool isDirectory ( const String & path )

static

Return true if the given path specifies a directory.

◆ isOpenMSDataPath_()

static bool isOpenMSDataPath_ ( const String & path )

staticprivate

Check if the given path is a valid OPENMS_DATA_PATH.

◆ path()

static String path ( const 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 String & file )

static

Return true if the file exists and is readable.

Referenced by TOPPViewBase::finishTOPPToolExecution(), MS2File::load(), and INIFileEditorWindow::openFile().

◆ remove()

static bool remove ( const 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 QString & dir_name )

static

Removes the directory and all subdirectories (absolute path).

◆ removeDirRecursively()

static bool removeDirRecursively ( const String & dir_name )

static

Removes the subdirectories of the specified directory (absolute path). Returns true if successful.

Referenced by TOPPASBase::~TOPPASBase().

◆ rename()

static bool rename	(	const String &	from,
		const 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

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

Returns: True on success

◆ validateMatchingFileNames()

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

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. To check for common mistakes this helper function checks:

if both file lists have the same length (returns false otherwise)
if the content is the same and provided in exactly the same order (returns false otherwise)

Note: Because workflow systems may assign file names randomly a non-strict comparison mode is enabled by default. Instead of the strict comparison (which returns false if there is a single mismatch), the non-strict comparison mode only returns false if the unique set of filenames match but some positions differ, i.e., only the order has been mixed up.

Parameters

sl1	First StringList with filenames
sl2	Second StringList with filenames
basename	If set to true, only basenames are compared
ignore_extension	If set to true, extensions are ignored (e.g., useful to compare spectra filenames to ID filenames)
strict	If set to true, no mismatches (respecting basename and ignore_extension parameter) are allowed. If set to false, only the order is compared if both share the same filenames.

Returns: False, if both StringLists are different (respecting the parameters)

◆ writable()

static bool writable ( const String & file )

static

Return true if the file is writable.

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

Friends And Related Function Documentation

◆ TOPPBase

friend class TOPPBase

friend

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

Friends

Detailed Description

Member Enumeration Documentation

◆ CopyOptions

Member Function Documentation

◆ absolutePath()

◆ basename()

◆ copyDirRecursively()

◆ download()

◆ empty()

◆ executable()

◆ exists()

◆ fileList()

◆ find()

◆ findDatabase()

◆ findDoc()

◆ findExecutable()

◆ findSiblingTOPPExecutable()

◆ getExecutablePath()

◆ getOpenMSDataPath()

◆ getOpenMSHomePath()

◆ getPathLocations()

◆ getSystemParameterDefaults_()

◆ getSystemParameters()

◆ getTempDirectory()

◆ getTemporaryFile()

◆ getUniqueName()

◆ getUserDirectory()

◆ isDirectory()

◆ isOpenMSDataPath_()

◆ path()

◆ readable()

◆ remove()

◆ removeDir()

◆ removeDirRecursively()

◆ rename()

◆ validateMatchingFileNames()

◆ writable()

Friends And Related Function Documentation

◆ TOPPBase

Member Data Documentation

◆ temporary_files_