136 lines
4.7 KiB
Scala
136 lines
4.7 KiB
Scala
package org.broadinstitute.sting.queue.util
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import java.io.{IOException, File}
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/**
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* A collection of utilities for modifying java.io.
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*/
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object IOUtils {
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/** The current directory "." */
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val CURRENT_DIR = new File(".")
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/**
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* Returns the sub path rooted at the parent.
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* If the sub path is already absolute, returns the sub path.
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* If the parent is the current directory, returns the sub path.
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* If the sub bath is the current directory, returns the parent.
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* Else returns new File(parent, subPath)
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* @param parent The parent directory
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* @param path The sub path to append to the parent, if the path is not absolute.
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* @return The absolute path to the file in the parent dir if the path was not absolute, otherwise the original path.
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*/
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def subDir(dir: File, path: String): File =
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subDir(dir, new File(path))
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/**
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* Returns the sub path rooted at the parent.
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* If the sub path is already absolute, returns the sub path.
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* If the parent is the current directory, returns the sub path.
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* If the sub path is the current directory, returns the parent.
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* Else returns new File(parent, subPath)
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* @param parent The parent directory
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* @param file The sub path to append to the parent, if the path is not absolute.
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* @return The absolute path to the file in the parent dir if the path was not absolute, otherwise the original path.
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*/
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def subDir(parent: File, file: File): File = {
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val parentAbs = absolute(parent)
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val fileAbs = absolute(file)
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val currentAbs = absolute(CURRENT_DIR)
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if (parentAbs == currentAbs && fileAbs == currentAbs)
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absolute(CURRENT_DIR.getCanonicalFile)
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else if (parentAbs == currentAbs || file.isAbsolute)
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fileAbs
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else if (fileAbs == currentAbs)
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parentAbs
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else
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absolute(new File(parentAbs, file.getPath))
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}
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/**
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* Resets the parent of the file to the directory.
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* @param dir New parent directory.
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* @param file Path to the file to be re-rooted.
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* @return Absolute path to the new file.
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*/
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def resetParent(dir: File, file: File) = absolute(subDir(dir, file.getName))
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/**
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* Creates a scatterGatherTempDir directory with the prefix and optional suffix.
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* @param prefix Prefix for the directory name.
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* @param suffix Optional suffix for the directory name. Defaults to "".
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* @return The created temporary directory.
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* @throws IOException if the directory could not be created.
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*/
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def tempDir(prefix: String, suffix: String = "") = {
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// Keep the temp directory from having pluses in it, which can cause problems with the Google Reflections library.
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// see also: http://benjchristensen.com/2009/09/22/mac-osx-10-6-java-java-io-tmpdir/
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if (System.getProperty("java.io.tmpdir").startsWith("/var/folders/"))
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System.setProperty("java.io.tmpdir", "/tmp/");
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val tempDirParent = new File(System.getProperty("java.io.tmpdir"))
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if (!tempDirParent.exists && !tempDirParent.mkdirs)
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throw new IOException("Could not create temp directory: " + tempDirParent)
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val temp = File.createTempFile(prefix + "-", suffix)
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if (!temp.delete)
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throw new IOException("Could not delete sub file: " + temp.getAbsolutePath())
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if (!temp.mkdir)
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throw new IOException("Could not create sub directory: " + temp.getAbsolutePath())
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absolute(temp)
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}
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/**
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* Returns the directory at the number of levels deep.
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* For example 2 levels of /path/to/dir will return /path/to
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* @param dir Directory path.
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* @param level how many levels deep from the root.
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* @return The path to the parent directory that is level-levels deep.
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*/
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def dirLevel(dir: File, level: Int): File = {
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var directories = List.empty[File]
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var parentDir = absolute(dir)
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while (parentDir != null) {
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directories +:= parentDir
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parentDir = parentDir.getParentFile
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}
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if (directories.size <= level)
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directories.last
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else
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directories(level)
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}
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def absolute(file: File) = {
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var fileAbs = file.getAbsoluteFile
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var names = List.empty[String]
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while (fileAbs != null) {
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val name = fileAbs.getName
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fileAbs = fileAbs.getParentFile
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if (name == ".") {
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/* skip */
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/* TODO: What do we do for ".."?
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} else if (name == "..") {
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CentOS tcsh says use getCanonicalFile:
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~ $ mkdir -p test1/test2
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~ $ ln -s test1/test2 test3
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~ $ cd test3/..
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~/test1 $
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Mac bash says keep going with getAbsoluteFile:
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~ $ mkdir -p test1/test2
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~ $ ln -s test1/test2 test3
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~ $ cd test3/..
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~ $
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For now, leave it and let the shell figure it out.
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*/
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} else {
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names +:= name
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}
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}
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new File(names.mkString("/", "/", ""))
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}
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}
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