Better error message when parsing hints

Removed unnecessary checks for reqs/steps; the schema loader catches
those

Author: mr-c

cwltool/update.py

@@ -55,28 +55,26 @@ def v1_0to1_1(
     def rewrite_requirements(t: CWLObjectType) -> None:
         if "requirements" in t:
             for r in cast(MutableSequence[CWLObjectType], t["requirements"]):
-                if isinstance(r, MutableMapping):
-                    cls = cast(str, r["class"])
-                    if cls in rewrite:
-                        r["class"] = rewrite[cls]
-                else:
-                    raise ValidationException(
-                        "requirements entries must be dictionaries: {} {}.".format(type(r), r)
-                    )
+                cls = cast(str, r["class"])
+                if cls in rewrite:
+                    r["class"] = rewrite[cls]
         if "hints" in t:
-            for r in cast(MutableSequence[CWLObjectType], t["hints"]):
+            for index, r in enumerate(cast(MutableSequence[CWLObjectType], t["hints"])):
                 if isinstance(r, MutableMapping):
+                    if "class" not in r:
+                        raise SourceLine(r, None, ValidationException).makeError(
+                            "'hints' entry missing required key 'class'."
+                        )
                     cls = cast(str, r["class"])
                     if cls in rewrite:
                         r["class"] = rewrite[cls]
                 else:
-                    raise ValidationException(f"hints entries must be dictionaries: {type(r)} {r}.")
+                    raise SourceLine(t["hints"], index, ValidationException).makeError(
+                        f"'hints' entries must be dictionaries: {type(r)} {r}."
+                    )
         if "steps" in t:
             for s in cast(MutableSequence[CWLObjectType], t["steps"]):
-                if isinstance(s, MutableMapping):
-                    rewrite_requirements(s)
-                else:
-                    raise ValidationException(f"steps entries must be dictionaries: {type(s)} {s}.")
+                rewrite_requirements(s)
 
     def update_secondaryFiles(
         t: CWLOutputType, top: bool = False

tests/test_load_tool.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 import pytest
+from schema_salad.exceptions import ValidationException
 
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.errors import WorkflowException
@@ -143,3 +144,25 @@ def test_import_tracked() -> None:
 
     assert tool.doc_loader is not None
     assert path in tool.doc_loader.idx
+
+
+def test_load_badhints() -> None:
+    """Check for expected error while update a bads hints list."""
+    loadingContext = LoadingContext()
+    uri = Path(get_data("tests/wf/hello-workflow-badhints.cwl")).as_uri()
+    with pytest.raises(
+        ValidationException,
+        match=r".*tests\/wf\/hello-workflow-badhints\.cwl\:18:4:\s*'hints'\s*entry\s*missing\s*required\s*key\s*'class'\.",
+    ):
+        load_tool(uri, loadingContext)
+
+
+def test_load_badhints_nodict() -> None:
+    """Check for expected error while update a hints list with a numerical entry."""
+    loadingContext = LoadingContext()
+    uri = Path(get_data("tests/wf/hello-workflow-badhints2.cwl")).as_uri()
+    with pytest.raises(
+        ValidationException,
+        match=r".*tests\/wf\/hello-workflow-badhints2\.cwl:41:5:\s*'hints'\s*entries\s*must\s*be\s*dictionaries:\s*<class\s*'int'>\s*42\.",
+    ):
+        load_tool(uri, loadingContext)

tests/wf/hello-workflow-badhints.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs:
+  usermessage: string
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+hints:
+ - {}
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          doc: "The message to print"
+          default: "Hello World"
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      arguments:
+         - "-n"
+         - "-e"
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]

tests/wf/hello-workflow-badhints2.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs:
+  usermessage: string
+
+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
+      arguments:
+         - "-n"
+         - "-e"
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]
+
+hints:
+  - 42