Fix #811 (SchemaDefRequirements not working in workflows)

Author: ThomasHickman

cwltool/workflow.py

@@ -243,6 +243,14 @@ def __init__(
         validation_errors = []
         self.tool = toolpath_object = copy.deepcopy(toolpath_object)
         bound = set()
+
+        if self.embedded_tool.get_requirement("SchemaDefRequirement")[0]:
+            if "requirements" not in toolpath_object:
+                toolpath_object["requirements"] = []
+            toolpath_object["requirements"].append(
+                self.embedded_tool.get_requirement("SchemaDefRequirement")[0]
+            )
+
         for stepfield, toolfield in (("in", "inputs"), ("out", "outputs")):
             toolpath_object[toolfield] = []
             for index, step_entry in enumerate(toolpath_object[stepfield]):

tests/test_examples.py

@@ -1576,3 +1576,14 @@ def test_staging_files_in_any() -> None:
         [get_data("tests/wf/816_wf.cwl"), "--file", get_data("tests/echo-job.yaml")]
     )
     assert err_code == 0
+
+
+def test_custom_type_in_step_process() -> None:
+    """Test that any needed custom types are available when processing a WorkflowStep."""
+    err_code, _, stderr = get_main_output(
+        [
+            get_data("tests/wf/811.cwl"),
+            get_data("tests/wf/811_inputs.yml"),
+        ]
+    )
+    assert err_code == 0

tests/wf/811.cwl

@@ -0,0 +1,15 @@
+cwlVersion: v1.0
+class: Workflow
+
+inputs:
+  - id: hello
+    type: Any
+outputs: []
+
+steps:
+  step:
+    id: step
+    run: schemadef-tool.cwl
+    in:
+      hello: hello
+    out: []

tests/wf/811_inputs.yml

@@ -0,0 +1,4 @@
+hello:
+  a: one
+  b: two
+

tests/wf/schemadef-tool.cwl

@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.0
+hints:
+  ResourceRequirement:
+    ramMin: 8
+
+requirements:
+  - $import: schemadef-type.yml
+
+inputs:
+    - id: hello
+      type: "schemadef-type.yml#HelloType"
+      inputBinding:
+        valueFrom: $(self.a)/$(self.b)
+
+outputs:
+    - id: output
+      type: File
+      outputBinding:
+        glob: output.txt
+
+stdout: output.txt
+baseCommand: echo

tests/wf/schemadef-type.yml

@@ -0,0 +1,9 @@
+class: SchemaDefRequirement
+types:
+  - name: HelloType
+    type: record
+    fields:
+      - name: a
+        type: string
+      - name: b
+        type: string