Test for getting cwlVersion from root document in load_tool.

Author: Peter Amstutz

cwltool/load_tool.py

@@ -221,7 +221,7 @@ def resolve_and_validate_document(loadingContext,
         cwlVersion = workflowobj.get("cwlVersion")
     if not cwlVersion and fileuri != uri:
         # The tool we're loading is a fragment of a bigger file.  Get
-        # the document root element and look for cwlVersion there
+        # the document root element and look for cwlVersion there.
         metadata = fetch_document(fileuri, loadingContext)[1]
         cwlVersion = metadata.get("cwlVersion")
     if not cwlVersion:
@@ -304,6 +304,8 @@ def resolve_and_validate_document(loadingContext,
 
     # None means default behavior (do update)
     if loadingContext.do_update in (True, None):
+        if "cwlVersion" not in metadata:
+            metadata["cwlVersion"] = cwlVersion
         processobj = cast(CommentedMap, cmap(update.update(
             processobj, document_loader, fileuri, loadingContext.enable_dev, metadata)))
         if isinstance(processobj, MutableMapping):

tests/test_load_tool.py

@@ -1,6 +1,7 @@
 from cwltool.load_tool import load_tool
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.errors import WorkflowException
+from cwltool.update import INTERNAL_VERSION
 import pytest
 from .util import (get_data, get_main_output,
                    get_windows_safe_factory,
@@ -60,3 +61,21 @@ def test_checklink_outputSource():
     loadingContext = LoadingContext({"do_validate": False})
     tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext)
     assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc
+
+def test_load_graph_fragment():
+    """Test that outputSource is resolved correctly independent of value
+    of do_validate.
+
+    """
+
+    loadingContext = LoadingContext()
+    uri = Path(get_data("tests/wf/scatter-wf4.cwl")).as_uri()+"#main"
+    tool = load_tool(uri, loadingContext)
+
+    rs, metadata = tool.doc_loader.resolve_ref(uri)
+    # Reload from a dict (in 'rs'), not a URI.  The dict is a fragment
+    # of original document and doesn't have cwlVersion set, so test
+    # that it correctly looks up the root document to get the
+    # cwlVersion.
+    tool = load_tool(tool.tool, loadingContext)
+    assert tool.metadata["cwlVersion"] == INTERNAL_VERSION