Merge pull request #491 from common-workflow-language/version_fix

load_tool: when no version or incorrect cwlVersion is found, create fatal error

Author: mr-c

cwltool/load_tool.py

@@ -22,6 +22,7 @@
 from . import process, update
 from .errors import WorkflowException
 from .process import Process, shortname
+from .update import ALLUPDATES
 
 _logger = logging.getLogger("cwltool")
 
@@ -161,12 +162,17 @@ def validate_document(document_loader,  # type: Loader
     if "cwlVersion" in workflowobj:
         if not isinstance(workflowobj["cwlVersion"], (str, Text)):
             raise Exception("'cwlVersion' must be a string, got %s" % type(workflowobj["cwlVersion"]))
+        if workflowobj["cwlVersion"] not in list(ALLUPDATES):
+            # print out all the Supported Versions of cwlVersion
+            versions = list(ALLUPDATES) # ALLUPDATES is a dict
+            versions.sort()
+            raise ValidationException("'cwlVersion' not valid. Supported CWL versions are: \n{}".format("\n".join(versions)))
         workflowobj["cwlVersion"] = re.sub(
             r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
             workflowobj["cwlVersion"])
     else:
-        _logger.warning("No cwlVersion found, treating this file as draft-2.")
-        workflowobj["cwlVersion"] = "draft-2"
+        raise ValidationException("No cwlVersion found."
+            "Use the following syntax in your CWL workflow to declare version: cwlVersion: <version>")
 
     if workflowobj["cwlVersion"] == "draft-2":
         workflowobj = cast(CommentedMap, cmap(update._draft2toDraft3dev1(

tests/test_cwl_version.py

@@ -0,0 +1,14 @@
+from __future__ import absolute_import
+import unittest
+
+from cwltool.main import main
+
+from .util import get_data
+
+class CWL_Version_Checks(unittest.TestCase):
+    # no cwlVersion in the workflow
+    def test_missing_cwl_version(self):
+        self.assertEqual(main([get_data('tests/wf/missing_cwlVersion.cwl')]), 1)
+    # using cwlVersion: v0.1 in the workflow
+    def test_incorrect_cwl_version(self):
+        self.assertEqual(main([get_data('tests/wf/wrong_cwlVersion.cwl')]), 1)

tests/wf/missing_cwlVersion.cwl

@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs: []
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          doc: "The message to print"
+          default: "Hello World"
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in: []
+    out: [response]

tests/wf/wrong_cwlVersion.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v0.1
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs: []
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          doc: "The message to print"
+          default: "Hello World"
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in: []
+    out: [response]