Workflow checker: ignore 'null' when comparing arrays of types

Author: mr-c

cwltool/checker.py

@@ -81,7 +81,8 @@ def can_assign_src_to_sink(
     src: admissible source types
     sink: admissible sink types
 
-    In non-strict comparison, at least one source type must match one sink type.
+    In non-strict comparison, at least one source type must match one sink type,
+       except for 'null'.
     In strict comparison, all source types must match at least one sink type.
     """
     if src == "Any" or sink == "Any":
@@ -119,7 +120,9 @@ def can_assign_src_to_sink(
                     return False
             return True
         for this_src in src:
-            if can_assign_src_to_sink(cast(SinkType, this_src), sink):
+            if this_src != "null" and can_assign_src_to_sink(
+                cast(SinkType, this_src), sink
+            ):
                 return True
         return False
     if isinstance(sink, MutableSequence):

tests/checker_wf/optional_array_mismatch.cwl

@@ -0,0 +1,21 @@
+cwlVersion: v1.0
+class: Workflow
+inputs:
+  first_wf_input: string[]?
+
+steps:
+  first_step:
+    run:
+      class: CommandLineTool
+      inputs:
+        first_clt_input:
+          type: File[]?
+          inputBinding:
+            position: 1
+      baseCommand: [ ls, -l ]
+      outputs: []
+    in:
+      first_clt_input: first_wf_input
+    out: []
+
+outputs: []

tests/test_examples.py

@@ -1788,3 +1788,22 @@ def tests_outputsource_valid_identifier_invalid_source() -> None:
     stderr = re.sub(r"\s\s+", " ", stderr)
     assert "tests/checker_wf/broken-wf4.cwl:12:5: outputSource not found" in stderr
     assert "tests/checker_wf/broken-wf4.cwl#echo_w" in stderr
+
+
+def test_mismatched_optional_arrays() -> None:
+    """Ignore 'null' when comparing array types."""
+    factory = cwltool.factory.Factory()
+
+    with pytest.raises(ValidationException):
+        factory.make(get_data("tests/checker_wf/optional_array_mismatch.cwl"))
+
+
+def test_validate_optional_src_with_mandatory_sink() -> None:
+    """Confirm expected warning with an optional File connected to a mandatory File."""
+    exit_code, stdout, stderr = get_main_output(
+        ["--validate", get_data("tests/wf/optional_src_mandatory_sink.cwl")]
+    )
+    assert exit_code == 0
+    stderr = re.sub(r"\s\s+", " ", stderr)
+    assert 'Source \'opt_file\' of type ["null", "File"] may be incompatible' in stderr
+    assert "with sink 'r' of type \"File\"" in stderr

tests/wf/optional_src_mandatory_sink.cwl

@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+ opt_file: File?
+
+steps:
+ my_only_step:
+   run: ./cat.cwl
+   in:
+     r: opt_file
+   out: []
+
+outputs: []