Fix for argument with empty prefix and separate False (#1166)

Fix for argument with empty prefix and separate False

Author: bogdang989

cwltool/builder.py

@@ -426,7 +426,7 @@ def generate_arg(self, binding):  # type: (Dict[Text, Any]) -> List[Text]
             if sep:
                 args.extend([prefix, self.tostr(j)])
             else:
-                args.append("" if not prefix else prefix + self.tostr(j))
+                args.append(self.tostr(j) if prefix is None else prefix + self.tostr(j))
 
         return [a for a in args if a is not None]
 

tests/arg-empty-prefix-separate-false.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: []
+inputs:
+  echo: boolean
+outputs: []
+arguments:
+- position: 1
+  shellQuote: false
+  prefix: ''
+  valueFrom: "non_existing_app"
+- position: 0
+  prefix: ''
+  separate: false
+  shellQuote: false
+  valueFrom: "echo"
+requirements:
+- class: ShellCommandRequirement

tests/test_examples.py

@@ -1018,3 +1018,11 @@ def test_env_filtering(factor):
     else:
         target = 4
     assert json.loads(stdout)['env_count'] == target, (error_code, stdout, stderr)
+
+@windows_needs_docker
+def test_v1_0_arg_empty_prefix_separate_false():
+    test_file = "tests/arg-empty-prefix-separate-false.cwl"
+    error_code, stdout, stderr = get_main_output(
+        ['--debug', get_data(test_file), "--echo"])
+    assert "completed success" in stderr
+    assert error_code == 0