Fix bug on spaced files name

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

@@ -71,9 +71,9 @@ 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 + "'"
     }
   }
 

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

@@ -18,7 +18,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/dir/nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s 'target.txt' '/dir/nested/link.txt'")
   }
 
   @Test(description = "Target is one level above link, relative set to true")
@@ -27,7 +27,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/dir/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s ../target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s '../target.txt' '/dir/nested/link.txt'")
   }
 
   @Test(description = "Target is two levels above link, relative set to true")
@@ -36,7 +36,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s ../../target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "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")
@@ -45,7 +45,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/dir/another_nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s ../another_nested/target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s '../another_nested/target.txt' '/dir/nested/link.txt'")
   }
 
   @Test(description = "Target is one level below link, relative set to true")
@@ -54,7 +54,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/dir/nested/deeper/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s deeper/target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s 'deeper/target.txt' '/dir/nested/link.txt'")
   }
 
   @Test(description = "Target is two levels below link, relative set to true")
@@ -63,7 +63,7 @@ class LnUnitTest {
     ln.relative = true
     ln.in = new File("/dir/nested/even/deeper/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s even/deeper/target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s 'even/deeper/target.txt' '/dir/nested/link.txt'")
   }
 
   @Test(description = "Relative set to false")
@@ -72,7 +72,7 @@ class LnUnitTest {
     ln.relative = false
     ln.in = new File("/dir/nested/target.txt")
     ln.out = new File("/dir/nested/link.txt")
-    Assert.assertEquals(ln.cmd, "ln -s /dir/nested/target.txt /dir/nested/link.txt")
+    Assert.assertEquals(ln.cmd, "ln -s '/dir/nested/target.txt' '/dir/nested/link.txt'")
   }
 
   // TODO: test for case where abosolute is true and input paths are relative?