Better errors for expressions in input format fields

Author: mr-c

Diff for: cwltool/builder.py

@@ -555,18 +555,32 @@ def addsf(
                     if isinstance(eval_format, str):
                         evaluated_format: Union[str, List[str]] = eval_format
                     elif isinstance(eval_format, MutableSequence):
-                        for entry in eval_format:
+                        for index, entry in enumerate(eval_format):
+                            message = None
                             if not isinstance(entry, str):
-                                raise SourceLine(
-                                    schema, "format", WorkflowException, debug
-                                ).makeError(
+                                message = (
                                     "An expression in the 'format' field must "
                                     "evaluate to a string, or list of strings. "
                                     "However a non-string item was received: "
                                     f"'{entry}' of type '{type(entry)}'. "
                                     f"The expression was '{schema['format']}' and "
                                     f"its fully evaluated result is '{eval_format}'."
                                 )
+                            if expression.needs_parsing(entry):
+                                message = (
+                                    "For inputs, 'format' field can either "
+                                    "contain a single CWL Expression or CWL Parameter "
+                                    "Reference, a single format string, or a list of "
+                                    "format strings. But the list cannot contain CWL "
+                                    "Expressions or CWL Parameter References. List "
+                                    f"entry number {index+1} contains the following "
+                                    "unallowed CWL Parameter Reference or Expression: "
+                                    f"'{entry}'."
+                                )
+                            if message:
+                                raise SourceLine(
+                                    schema["format"], index, WorkflowException, debug
+                                ).makeError(message)
                         evaluated_format = cast(List[str], eval_format)
                     else:
                         raise SourceLine(

Diff for: tests/test_examples.py

@@ -827,6 +827,26 @@ def test_format_expr_error() -> None:
     )
 
 
+def test_format_expr_error2() -> None:
+    """Better format expression error, for a list of formats."""
+    error_code, _, stderr = get_main_output(
+        [
+            get_data("tests/wf/bad_formattest2.cwl"),
+            get_data("tests/wf/formattest-job.json"),
+        ]
+    )
+    assert error_code != 0
+    stderr = re.sub(r"\s\s+", " ", stderr)
+    assert (
+        "bad_formattest2.cwl:14:9: For inputs, 'format' field can either contain "
+        "a single CWL Expression or CWL Parameter Reference, a single format string, "
+        "or a list of format strings. But the list cannot contain CWL Expressions "
+        "or CWL Parameter References. List entry number 1 contains the following "
+        "unallowed CWL Parameter Reference or Expression: '${ return "
+        '["http://edamontology.org/format_2330", 42];}' in stderr
+    )
+
+
 def test_static_checker() -> None:
     # check that the static checker raises exception when a source type
     # mismatches its sink type.

Diff for: tests/wf/bad_formattest2.cwl

@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+$namespaces:
+  edam: "http://edamontology.org/"
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+doc: "Reverse each line using the `rev` command"
+inputs:
+  input:
+    type: File
+    inputBinding: {}
+    format:
+      - |
+        ${ return ["http://edamontology.org/format_2330", 42];}
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: output.txt
+    format: |
+      ${return "http://edamontology.org/format_2330";}
+
+baseCommand: rev
+stdout: output.txt