Fixed bug in Ln

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

@@ -49,52 +49,32 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
 
   /** return commandline to execute */
   lazy val cmd: String = {
-    lazy val inCanonical: String = {
+    val inCanonical: String = {
       // need to remove "/~" to correctly expand path with tilde
       input.getAbsolutePath.replace("/~", "")
     }
 
-    lazy val outCanonical: String = output.getAbsolutePath.replace("/~", "")
+    val outCanonical: String = output.getAbsolutePath.replace("/~", "")
 
-    lazy val inToks: Array[String] = inCanonical.split(File.separator)
+    if (relative) {
+      val inToks: Array[String] = inCanonical.split(File.separator)
 
-    lazy val outToks: Array[String] = outCanonical.split(File.separator)
+      val outToks: Array[String] = outCanonical.split(File.separator)
 
-    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
-    }
+      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
+      }
 
-    lazy val inUnique: String = {
-      inToks.slice(commonPrefixLength, inToks.length).mkString(File.separator)
-    }
+      val inUnique = inToks.slice(commonPrefixLength, inToks.length)
 
-    lazy val outUnique: String = {
-      outToks.slice(commonPrefixLength, outToks.length).mkString(File.separator)
-    }
+      val outUnique = outToks.slice(commonPrefixLength, outToks.length)
 
-    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 dist =
-        // relative path differs depending on which of the input or target is in the 'higher' directory
-        if (inToks.length > outToks.length)
-          scala.math.max(0, inUnique.split(File.separator).length - 1)
-        else
-          scala.math.max(0, outUnique.split(File.separator).length - 1)
-
-      val result =
-        if (dist == 0 || inToks.length > outToks.length)
-          inUnique
-        else
-          ((".." + File.separator) * dist) + inUnique
-
-      result
-    }
+      val inRelative: String =
+        ((".." + File.separator) * (outUnique.length - 1)) + inUnique.mkString(File.separator)
 
-    if (relative) {
       // workaround until we have `ln` that works with relative path (i.e. `ln -r`)
       "ln -s " + inRelative + " " + outCanonical
     } else {

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala

@@ -59,6 +59,42 @@ class LnTest extends TestNGSuite with Matchers {
     ln.cmd should ===("ln -s ../another_nested/target.txt /dir/nested/link.txt")
   }
 
+  @Test(description = "Target is a child of a directory multi level above link, relative set to true")
+  def testTargetMultiLevelAboveChildRelative1() {
+    val ln = new Ln(null)
+    ln.relative = true
+    ln.input = new File("/dir/another_nested/1/2/3/4/target.txt")
+    ln.output = new File("/dir/nested/link.txt")
+    ln.cmd should ===("ln -s ../another_nested/1/2/3/4/target.txt /dir/nested/link.txt")
+  }
+
+  @Test(description = "Target is a child of a directory multi level above link, relative set to true")
+  def testTargetMultiLevelAboveChildRelative2() {
+    val ln = new Ln(null)
+    ln.relative = true
+    ln.input = new File("/dir/another_nested/1/2/3/4/target.txt")
+    ln.output = new File("/dir/nested/2/link.txt")
+    ln.cmd should ===("ln -s ../../another_nested/1/2/3/4/target.txt /dir/nested/2/link.txt")
+  }
+
+  @Test(description = "Source is a child of a directory multi level above link, relative set to true")
+  def testSourceMultiLevelAboveChildRelative() {
+    val ln = new Ln(null)
+    ln.relative = true
+    ln.output = new File("/dir/another_nested/1/2/3/4/link.txt")
+    ln.input = new File("/dir/nested/2/output.txt")
+    ln.cmd should ===("ln -s ../../../../../nested/2/output.txt /dir/another_nested/1/2/3/4/link.txt")
+  }
+
+  @Test(description = "Target is a child of a directory multi level above link, relative set to false")
+  def testTargetMultiLevelAboveChild() {
+    val ln = new Ln(null)
+    ln.relative = false
+    ln.input = new File("/dir/another_nested/1/2/3/4/target.txt")
+    ln.output = new File("/dir/nested/link.txt")
+    ln.cmd should ===("ln -s /dir/another_nested/1/2/3/4/target.txt /dir/nested/link.txt")
+  }
+
   @Test(description = "Target is one level below link, relative set to true")
   def testTargetOneLevelBelowRelative() {
     val ln = new Ln(null)