Merge remote-tracking branch 'origin/master' into draft-4-pa

Author: mr-c

cwltool/main.py

@@ -288,8 +288,13 @@ def generate_parser(toolparser, tool, namemap):
             _logger.debug(u"Can't make command line argument from %s", inptype)
             return None
 
+        if inptype != "boolean":
+            typekw = { 'type': atype }
+        else:
+            typekw = {}
+
         toolparser.add_argument(flag + name, required=required,
-                help=ahelp, action=action, type=atype, default=default)
+                help=ahelp, action=action, default=default, **typekw)
 
     return toolparser
 

cwltool/workflow.py

@@ -93,6 +93,8 @@ def are_same_type(src, sink):  # type: (Any, Any) -> bool
     """
     if isinstance(src, dict) and isinstance(sink, dict):
         if src["type"] == "array" and sink["type"] == "array":
+            if 'null' in sink["items"]:
+                return are_same_type([src["items"]], [it for it in sink["items"] if it != 'null'])
             return are_same_type(src["items"], sink["items"])
         elif src["type"] == sink["type"]:
             return True

tests/test_toolargparse.py

@@ -24,10 +24,38 @@ class ToolArgparse(unittest.TestCase):
       glob: test.txt
 stdout: test.txt
 baseCommand: [cat]
+'''
+
+    script2='''
+#!/usr/bin/env cwl-runner
+cwlVersion: 'cwl:draft-3'
+class: CommandLineTool
+inputs:
+  - id: bdg
+    type: "boolean"
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: foo
+baseCommand:
+  - echo
+  - "ff"
+stdout: foo
 '''
 
     def test_help(self):
         with NamedTemporaryFile() as f:
             f.write(self.script)
             f.flush()
             self.assertEquals(main(["--debug", f.name, '--input', 'README.rst']), 0)
+            self.assertEquals(main(["--debug", f.name, '--input', 'README.rst']), 0)
+
+    def test_bool(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script2)
+            f.flush()
+            try:
+                self.assertEquals(main([f.name, '--help']), 0)
+            except SystemExit as e:
+                self.assertEquals(e.code, 0)