Fix scandeps with File object inside a seperately declared Directory object (#732)

* When scandeps merges a real directory with a synthetic directory
literal, real directory takes precedence.

* Add test for scandeps.

Author: tetron

cwltool/process.py

@@ -804,8 +804,11 @@ def mergedirs(listing):
     for e in listing:
         if e["basename"] not in ents:
             ents[e["basename"]] = e
-        elif e["class"] == "Directory" and e.get("listing"):
-            ents[e["basename"]].setdefault("listing", []).extend(e["listing"])
+        elif e["class"] == "Directory":
+            if e.get("listing"):
+                ents[e["basename"]].setdefault("listing", []).extend(e["listing"])
+            if ents[e["basename"]]["location"].startswith("_:"):
+                ents[e["basename"]]["location"] = e["location"]
     for e in six.itervalues(ents):
         if e["class"] == "Directory" and "listing" in e:
             e["listing"] = mergedirs(e["listing"])

tests/test_examples.py

@@ -4,9 +4,10 @@
 import subprocess
 from os import path
 import sys
+import json
 import logging
 
-from io import StringIO
+from io import StringIO, BytesIO
 
 from cwltool.errors import WorkflowException
 
@@ -296,6 +297,14 @@ def loadref(base, p):
             "location": "file:///example/bar.cwl"
         }], sc)
 
+    def test_trick_scandeps(self):
+        if sys.version_info[0] < 3:
+            stream = BytesIO()
+        else:
+            stream = StringIO()
+        main(["--print-deps", "--debug", get_data("tests/wf/trick_defaults.cwl")], stdout=stream)
+        self.assertNotEquals(json.loads(stream.getvalue())["secondaryFiles"][0]["location"][:2], "_:")
+
 
 class TestDedup(unittest.TestCase):
     def test_dedup(self):

tests/wf/trick_defaults.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+  inp1:
+    type: File
+    default:
+      class: File
+      location: indir1/hello.txt
+  inp2:
+    type: Directory
+    default:
+      class: Directory
+      location: indir1
+outputs: []
+baseCommand: true