From 7b260498229f79ed4fbc82c3de45bc1656b9bbc8 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 29 Jul 2014 14:23:51 +0200
Subject: [PATCH] Add relative symlink option to Ln wrapper
---
.../nl/lumc/sasc/biopet/function/Ln.scala | 62 +++++++++++++++++--
1 file changed, 58 insertions(+), 4 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
index d7e9aad05..b3d148bab 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
@@ -1,10 +1,11 @@
package nl.lumc.sasc.biopet.function
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
import scala.sys.process.Process
+import org.apache.commons.io.FilenameUtils;
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.config.Configurable
class Ln(val root: Configurable) extends InProcessFunction with Configurable {
this.analysisName = getClass.getSimpleName
@@ -15,8 +16,61 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
@Output(doc = "Link destination")
var out: File = _
+ var relative: Boolean = true
+
+ private lazy val inCanonical: String = {
+ // need to remove "/~" to correctly expand path with tilde
+ in.getCanonicalPath().replace("/~", "")
+ }
+
+ private lazy val outCanonical: String = {
+ out.getCanonicalPath().replace("/~", "")
+ }
+
+ private lazy val inToks: Array[String] = {
+ inCanonical.split(File.separator)
+ }
+
+ private lazy val outToks: Array[String] = {
+ outCanonical.split(File.separator)
+ }
+
+ private lazy val commonPrefixLength: Int = {
+ val maxLength = scala.math.min(inToks.length, outToks.length)
+ var i: Int = 0;
+ while (i < maxLength && inToks(i) == outToks(i)) i += 1;
+ i
+ }
+
+ private lazy val inUnique: String = {
+ inToks.slice(commonPrefixLength, inToks.length).mkString(File.separator)
+ }
+
+ private lazy val outUnique: String = {
+ outToks.slice(commonPrefixLength, outToks.length).mkString(File.separator)
+ }
+
+ private lazy val inRelative: String = {
+ // calculate 'distance' from output directory to input
+ // which is the number of directory walks required to get to the inUnique directory from outDir
+ val outDir = FilenameUtils.getFullPathNoEndSeparator(outUnique)
+ val dist: Int = scala.math.max(0, outDir.split(File.separator).length - 1)
+ val result =
+ if (dist > 0)
+ ((".." + File.separator) * dist) + File.separator + inUnique
+ else
+ inUnique
+ result
+ }
+
override def run {
- val cmd = "ln -s " + in + " " + out
+ val cmd =
+ if (relative) {
+ // workaround until we have `ln` that works with relative path (i.e. `ln -r`)
+ "ln -s " + inRelative + " " + outCanonical
+ } else {
+ "ln -s " + inCanonical + " " + outCanonical
+ }
val process = Process(cmd).run
System.out.println("cmd: '" + cmd + "', exitcode: " + process.exitValue)
}
--
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