OpenMS
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Basic file handling operations. More...
#include <OpenMS/SYSTEM/File.h>
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 UInt64 | fileSize (const String &file) |
The filesize in bytes (or -1 on error, e.g. if the file does not exist) 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 | copy (const String &from, const String &to) |
Copy a file (if it exists). Returns true if successful. More... | |
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 bool | makeDir (const String &dir_name) |
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. 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 |
Basic file handling operations.
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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.
from_dir | Source directory |
to_dir | Target directory |
option | Specify the copy option (OVERWRITE, SKIP, CANCEL) |
Enumerator | |
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OVERWRITE | |
SKIP | |
CANCEL |
Replaces the relative path in the argument with the absolute path.
Referenced by TOPPViewBase::addDataFile().
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().
Copy a file (if it exists). Returns true if successful.
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Download file from given URL into a download folder. Returns when done.
If a file with same filename already exists, continues download and appends '.#number' to basename.
FileNotFound | exception if download failed. |
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Return true if the file does not exist or the file is empty.
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Method used to test if a file
is executable.
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Method used to test if a file
exists.
Referenced by TOPPViewBase::addDataFile(), MascotGenericFile::load(), MascotInfile::load(), MS2File::load(), TOPPASBase::loadPreferences(), and TOPPViewBase::loadPreferences().
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Retrieves a list of files matching file_pattern
in directory dir
(returns filenames without paths unless full_path
is true)
The filesize in bytes (or -1 on error, e.g. if the file does not exist)
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Looks up the location of the file filename
.
The following locations are checked in this order:
directories
FileNotFound | is thrown, if the file is not found |
Referenced by QApplicationTOPP::QApplicationTOPP(), and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::readEnzymesFromFile_().
uses File::find() to search for a file names db_name
in the 'id_db_dir' param of the OpenMS system parameters
FileNotFound | is thrown, if the file is not found |
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.
filename | The doc file name to find. |
FileNotFound | is thrown, if the file is not found |
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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.
[in,out] | exe_filename | The executable to search for. |
exe_filename
could be resolved to a full path and it exists Searches for an executable with the given name.
toolName | The executable to search for. |
FileNotFound | is thrown, if the tool executable was not found. |
Referenced by TOPPViewBase::runTOPPTool_().
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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"
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Returns the OpenMS data path (environment variable overwrites the default installation path)
Referenced by TOPPASBase::openExampleDialog().
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Returns the OpenMS home path (environment variable overwrites the default home path)
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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).
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get defaults for the system's Temp-path, user home directory etc.
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get the system's default OpenMS.ini file in the users home directory (<home>/OpenMS/OpenMS.ini) or create/repair it if required order:
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The current OpenMS temporary data path (for temporary files). Looks up the following locations, taking the first one which is non-null:
Referenced by TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::showTOPPDialog_(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().
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.
alternative_file | If this string is not empty, no action is taken and it is used as return value |
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Returns a string, consisting of date, time, hostname, process id, and a incrementing number. This can be used for temporary files.
include_hostname | add hostname into result - potentially a long string |
Referenced by TOPPViewBase::showTOPPDialog_(), and TOPPASBase::TOPPASBase().
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The current OpenMS user data path (for result files) Tries to set the user directory in following order:
Referenced by TOPPViewBase::initializeDefaultParameters_(), and TOPPViewBase::loadPreferences().
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Return true if the given path specifies a directory.
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Check if the given path is a valid OPENMS_DATA_PATH.
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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.
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().
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Return true if the file exists and is readable.
Referenced by TOPPViewBase::finishTOPPToolExecution(), MS2File::load(), and INIFileEditorWindow::openFile().
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Removes a file (if it exists).
Referenced by TOPPViewBase::finishTOPPToolExecution(), and TOPPViewBase::runTOPPTool_().
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Removes the directory and all subdirectories (absolute path).
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Removes the subdirectories of the specified directory (absolute path). Returns true if successful.
Referenced by TOPPASBase::~TOPPASBase().
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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.
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. |
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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:
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.
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. |
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Return true if the file is writable.
Referenced by TOPPViewBase::runTOPPTool_(), and TOPPViewBase::showTOPPDialog_().
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private list of temporary filenames, which are deleted upon program exit