Merge branch 'feature-ln-fix' into 'develop'

Feature ln fix

@w.arindrarto , could you check this first?

the ' single-quotes are giving me trouble in executing as a InProgressFunction.

See merge request !26

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

 package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
-import scala.sys.process.Process
+import scala.sys.process.{ Process, ProcessLogger }
 import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -71,15 +71,21 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
 
     if (relative) {
       // workaround until we have `ln` that works with relative path (i.e. `ln -r`)
-      "ln -s '" + inRelative + "' '" + outCanonical + "'"
+      "ln -s " + inRelative + " " + outCanonical
     } else {
-      "ln -s '" + inCanonical + "' '" + outCanonical + "'"
+      "ln -s " + inCanonical + " " + outCanonical
     }
   }
 
   override def run {
-    val process = Process(cmd).run
-    logger.info("cmd: '" + cmd + "', exitcode: " + process.exitValue)
+    val stdout = new StringBuffer()
+    val stderr = new StringBuffer()
+    val process = Process(cmd).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
+    val exitcode = process.exitValue
+    if (exitcode != 0) {
+      throw new Exception("Error creating symbolic link, this was the original message: \n" + stderr)
+    }
+    logger.info("cmd: '" + cmd + "', exitcode: " + exitcode)
   }
 }
 

biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala

@@ -19,7 +19,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/dir/nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s 'target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Target is one level above link, relative set to true")
@@ -28,7 +28,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/dir/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s '../target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s ../target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Target is two levels above link, relative set to true")
@@ -37,7 +37,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s '../../target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s ../../target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Target is a child of a directory one level above link, relative set to true")
@@ -46,7 +46,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/dir/another_nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s '../another_nested/target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s ../another_nested/target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Target is one level below link, relative set to true")
@@ -55,7 +55,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/dir/nested/deeper/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s 'deeper/target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s deeper/target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Target is two levels below link, relative set to true")
@@ -64,7 +64,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = true
     ln.in = new File("/dir/nested/even/deeper/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s 'even/deeper/target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s even/deeper/target.txt /dir/nested/link.txt")
   }
 
   @Test(description = "Relative set to false")
@@ -73,7 +73,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
     ln.relative = false
     ln.in = new File("/dir/nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    ln.cmd should ===("ln -s '/dir/nested/target.txt' '/dir/nested/link.txt'")
+    ln.cmd should ===("ln -s /dir/nested/target.txt /dir/nested/link.txt")
   }
 
   // TODO: test for case where abosolute is true and input paths are relative?