Package ubic.basecode.util

Class FileTools

java.lang.Object

ubic.basecode.util.FileTools

public class FileTools
extends Object

Author:

keshav, Pavlidis, Will Braynen

Field Summary

Fields

Modifier and Type	Field	Description
protected static String[]	DATA_EXTENSIONS
static String	DEFAULT_DATA_EXTENSION
static String	DEFAULT_IMAGE_EXTENSION
static String	DEFAULT_XML_EXTENSION
protected static String	GIF_EXTENSION
protected static String[]	IMAGE_EXTENSIONS
protected static String[]	XML_EXTENSIONS

Constructor Summary

Constructors

Constructor	Description
FileTools()

Method Summary

Modifier and Type	Method	Description
static String	addDataExtension(String filename)
static String	addImageExtension(String filename)
static String	changeExtension(String filename, String newExtension)
static void	checkPathIsReadableFile(String file)
static String	chompExtension(String filename)
static String	cleanForFileName(String name)	Avoid getting file names with spaces, slashes, quotes, # etc; replace them with "_".
static void	copy(InputStream input, OutputStream output)	On completion streams are closed.
static File	copyPlainOrCompressedFile(String sourcePath, String outputFilePath)
static File	createDir(String directory)	Creates the directory if it does not exist.
static int	deleteDir(File directory)	Deletes the directory and subdirectories if empty.
static int	deleteFiles(Collection<File> files)	Deletes the specified Collection of files.
static String	getExtension(String filename)	Returns the extension of a file.
static InputStream	getInputStreamFromPlainOrCompressedFile(String fileName)	Open a non-compresed, zipped, or gzipped file.
static List<String>	getLines(File file)	opens a file and returns its contents as a list of lines.
static List<String>	getLines(String filename)	opens a file and returns its contents as a list of lines.
static List<String>	getStringListFromFile(File f)	Used for reading output generated by Collection.toString().
static boolean	hasImageExtension(String filename)
static boolean	hasXMLExtension(String filename)
static boolean	isGZipped(String fileName)
static boolean	isZipped(String filename)
static Collection<File>	listDirectoryFiles(File directory)	Given a File object representing a directory, return a collection of File objects representing the files contained in that directory.
static Collection<File>	listSubDirectories(File directory)	Given a File object representing a directory, return a collection of File objects representing the directories contained in that directory.
static String	resourceToPath(String resourcePath)
static void	stringsToFile(Collection<String> lines, File f)	Outputs a many strings to a file, one line at a time.
static void	stringsToFile(Collection<String> lines, File f, boolean append)	Outputs many strings to a file, one line at a time.
static void	stringsToFile(Collection<String> lines, String f)	Outputs a many strings to a file, one line at a time.
static void	stringToFile(String s, File f)	Outputs a string to a file.
static void	stringToFile(String s, File f, boolean append)	Outputs a string to a file, one line at a time.
static boolean	testDir(String dirname)
static boolean	testFile(File file)	Test whether a File is writeable.
static boolean	testFile(String filename)
static void	touch(File f)	Create or update the modification date of the given file.
static String	unGzipFile(String seekFile)	Given the path to a gzipped-file, unzips it into the same directory.
static Collection<File>	unZipFiles(String seekFile)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_DATA_EXTENSION

public static final String DEFAULT_DATA_EXTENSION

See Also:

Constant Field Values

DEFAULT_IMAGE_EXTENSION

public static final String DEFAULT_IMAGE_EXTENSION

See Also:

Constant Field Values

DEFAULT_XML_EXTENSION

public static final String DEFAULT_XML_EXTENSION

See Also:

Constant Field Values

DATA_EXTENSIONS

protected static final String[] DATA_EXTENSIONS

GIF_EXTENSION

protected static final String GIF_EXTENSION

See Also:

Constant Field Values

IMAGE_EXTENSIONS

protected static final String[] IMAGE_EXTENSIONS

XML_EXTENSIONS

protected static final String[] XML_EXTENSIONS

Constructor Detail

FileTools

public FileTools()

Method Detail

addDataExtension

public static String addDataExtension(String filename)

Parameters:

filename -

Returns:

the new filename with the added extension, but does not modify the filename parameter.

addImageExtension

public static String addImageExtension(String filename)

Parameters:

filename -

Returns:

the new filename with the added extension, but does not modify the filename parameter.

changeExtension

public static String changeExtension(String filename,
                                     String newExtension)

Parameters:

filename -

newExtension -

Returns:

the new filename with the changed extension, but does not modify the filename parameter.

checkPathIsReadableFile

public static void checkPathIsReadableFile(String file)
                                    throws IOException

Parameters:

file -

Throws:

IOException

chompExtension

public static String chompExtension(String filename)

Parameters:

filename -

Returns:

cleanForFileName

public static String cleanForFileName(String name)

Avoid getting file names with spaces, slashes, quotes, # etc; replace them with "_".

Parameters:

ee -

Returns:

Throws:

IllegalArgumentException - if the resulting string is empty, or if the input is empty.

copy

public static void copy(InputStream input,
                        OutputStream output)
                 throws IOException

On completion streams are closed.

Parameters:

input -

output -

Throws:

IOException

copyPlainOrCompressedFile

public static File copyPlainOrCompressedFile(String sourcePath,
                                             String outputFilePath)
                                      throws FileNotFoundException,
                                             IOException

Parameters:

sourcePath -

outputFilePath -

Returns:

Throws:

FileNotFoundException

IOException

createDir

public static File createDir(String directory)

Creates the directory if it does not exist.

Parameters:

directory -

Returns:

deleteDir

public static int deleteDir(File directory)

Deletes the directory and subdirectories if empty.

Parameters:

directory -

Returns:

int The number of directories deleted.

See Also:

File.delete()

deleteFiles

public static int deleteFiles(Collection<File> files)

Deletes the specified Collection of files.

Parameters:

files -

Returns:

int The number of files deleted.

See Also:

File.delete()

getExtension

public static String getExtension(String filename)

Returns the extension of a file.

Parameters:

filename -

Returns:

getInputStreamFromPlainOrCompressedFile

public static InputStream getInputStreamFromPlainOrCompressedFile(String fileName)
                                                           throws IOException,
                                                                  FileNotFoundException

Open a non-compresed, zipped, or gzipped file. Uses the file name pattern to figure this out.

Parameters:

fileName - . If Zipped, only the first file in the archive is used.

Returns:

Throws:

IOException

FileNotFoundException

getLines

public static List<String> getLines(File file)
                             throws IOException

opens a file and returns its contents as a list of lines.

Returns:

- List of strings representing the lines, first line is first in list

Throws:

IOException

getLines

public static List<String> getLines(String filename)
                             throws IOException

opens a file and returns its contents as a list of lines.

Returns:

- List of strings representing the lines, first line is first in list

Throws:

IOException

getStringListFromFile

public static List<String> getStringListFromFile(File f)
                                          throws Exception

Used for reading output generated by Collection.toString(). For example [a,b,c] stored in a file would be converted to a new List containing "a", "b" and "c".

Warning this relies on behaviour of other API's toString.

Parameters:

f - - input file, with only one line for the toString output.

Returns:

- list created from the strings in the file

Throws:

Exception

hasImageExtension

public static boolean hasImageExtension(String filename)

Parameters:

filename -

Returns:

hasXMLExtension

public static boolean hasXMLExtension(String filename)

Parameters:

filename -

Returns:

isGZipped

public static boolean isGZipped(String fileName)

Parameters:

fileName -

Returns:

isZipped

public static boolean isZipped(String filename)

Parameters:

filename -

Returns:

listDirectoryFiles

public static Collection<File> listDirectoryFiles(File directory)

Given a File object representing a directory, return a collection of File objects representing the files contained in that directory.

Parameters:

directory -

Returns:

listSubDirectories

public static Collection<File> listSubDirectories(File directory)

Given a File object representing a directory, return a collection of File objects representing the directories contained in that directory.

Parameters:

directory -

Returns:

resourceToPath

public static String resourceToPath(String resourcePath)
                             throws URISyntaxException

Parameters:

resourcePath -

Returns:

Throws:

URISyntaxException

stringsToFile

public static void stringsToFile(Collection<String> lines,
                                 File f)
                          throws Exception

Outputs a many strings to a file, one line at a time.

Throws:

Exception

stringsToFile

public static void stringsToFile(Collection<String> lines,
                                 File f,
                                 boolean append)
                          throws Exception

Outputs many strings to a file, one line at a time.

Parameters:

lines - - input lines

f - - file that wrote to

append - - add to end of file or overwrite

Throws:

Exception

stringsToFile

public static void stringsToFile(Collection<String> lines,
                                 String f)
                          throws Exception

Outputs a many strings to a file, one line at a time.

Throws:

Exception

stringToFile

public static void stringToFile(String s,
                                File f)
                         throws Exception

Outputs a string to a file.

Throws:

Exception

stringToFile

public static void stringToFile(String s,
                                File f,
                                boolean append)
                         throws Exception

Outputs a string to a file, one line at a time.

Parameters:

s - - input line/string

f - - file that wrote to

append - - add to end of file or overwrite

Throws:

Exception

testDir

public static boolean testDir(String dirname)

Parameters:

dirname - directory name

Returns:

testFile

public static boolean testFile(File file)

Test whether a File is writeable.

Parameters:

file -

Returns:

testFile

public static boolean testFile(String filename)

Parameters:

filename -

Returns:

touch

public static void touch(File f)
                  throws IOException

Create or update the modification date of the given file. If the file does not exist, create it.

Parameters:

f -

Throws:

IOException

unGzipFile

public static String unGzipFile(String seekFile)
                         throws IOException

Given the path to a gzipped-file, unzips it into the same directory. If the file already exists it will be overwritten.

Parameters:

seekFile -

Returns:

path to the unzipped file.

Throws:

IOException

unZipFiles

public static Collection<File> unZipFiles(String seekFile)
                                   throws IOException

Parameters:

seekFile -

Returns:

Collection of File objects

Throws:

IOException