check for empty hints/reqs

Author: mr-c

cwltool/process.py

@@ -578,7 +578,15 @@ def __init__(
         self.names = make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY], Loader({}))
         self.tool = toolpath_object
         self.requirements = copy.deepcopy(getdefault(loadingContext.requirements, []))
-        self.requirements.extend(self.tool.get("requirements", []))
+        tool_requirements = self.tool.get("requirements", [])
+        if tool_requirements is None:
+            raise ValidationException(
+                SourceLine(self.tool, "requirements").makeError(
+                    "If 'requirements' is present then it must be a list "
+                    "or map/dictionary, not empty."
+                )
+            )
+        self.requirements.extend(tool_requirements)
         if "id" not in self.tool:
             self.tool["id"] = "_:" + str(uuid.uuid4())
         self.requirements.extend(
@@ -590,7 +598,15 @@ def __init__(
             )
         )
         self.hints = copy.deepcopy(getdefault(loadingContext.hints, []))
-        self.hints.extend(self.tool.get("hints", []))
+        tool_hints = self.tool.get("hints", [])
+        if tool_hints is None:
+            raise ValidationException(
+                SourceLine(self.tool, "hints").makeError(
+                    "If 'hints' is present then it must be a list "
+                    "or map/dictionary, not empty."
+                )
+            )
+        self.hints.extend(tool_hints)
         # Versions of requirements and hints which aren't mutated.
         self.original_requirements = copy.deepcopy(self.requirements)
         self.original_hints = copy.deepcopy(self.hints)

tests/test_examples.py

@@ -1398,3 +1398,23 @@ def test_scatter_output_filenames(tmp_path: Path) -> None:
             and locations[1].endswith("output.txt_2")
             and locations[2].endswith("output.txt_3")
         ), f"Locations {locations} do not end with {output_names}"
+
+
+def test_malformed_hints() -> None:
+    """Confirm that empty hints section is caught."""
+    factory = cwltool.factory.Factory()
+    with pytest.raises(
+        ValidationException,
+        match=r".*wc-tool-bad-hints\.cwl:6:1: If 'hints' is\s*present\s*then\s*it\s*must\s*be\s*a\s*list.*",
+    ):
+        factory.make(get_data("tests/wc-tool-bad-hints.cwl"))
+
+
+def test_malformed_reqs() -> None:
+    """Confirm that empty reqs section is caught."""
+    factory = cwltool.factory.Factory()
+    with pytest.raises(
+        ValidationException,
+        match=r".*wc-tool-bad-reqs\.cwl:6:1: If 'requirements' is\s*present\s*then\s*it\s*must\s*be\s*a\s*list.*",
+    ):
+        factory.make(get_data("tests/wc-tool-bad-reqs.cwl"))

tests/wc-tool-bad-hints.cwl

@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.1
+
+hints:
+
+inputs:
+  file1: File
+
+outputs:
+  output:
+    type: File
+    outputBinding: { glob: output }
+
+baseCommand: [wc, -l]
+
+stdin: $(inputs.file1.path)
+stdout: output

tests/wc-tool-bad-reqs.cwl

@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.1
+
+requirements:
+
+inputs:
+  file1: File
+
+outputs:
+  output:
+    type: File
+    outputBinding: { glob: output }
+
+baseCommand: [wc, -l]
+
+stdin: $(inputs.file1.path)
+stdout: output