Discard undeclared fields from cwl.output.json (#2177)

Discards all fields that are present in a `cwl.output.json` file but have not been declared in the `output` object of the related `CommandLineTool`, implementing common-workflow-language/cwl-v1.3#80.

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: GlassOfWhiskey

cwltool/command_line_tool.py

@@ -26,7 +26,7 @@
 
 from mypy_extensions import mypyc_attr
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from schema_salad.avro.schema import Schema
+from schema_salad.avro.schema import RecordSchema
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine
@@ -1216,6 +1216,7 @@ def collect_output_ports(
         if cwl_version != "v1.0":
             builder.resources["exitCode"] = rcode
         try:
+            expected_schema = cast(RecordSchema, self.names.get_name("outputs_record_schema", None))
             fs_access = builder.make_fs_access(outdir)
             custom_output = fs_access.join(outdir, "cwl.output.json")
             if fs_access.exists(custom_output):
@@ -1227,6 +1228,20 @@ def collect_output_ports(
                         custom_output,
                         json_dumps(ret, indent=4),
                     )
+                if ORDERED_VERSIONS.index(cast(str, cwl_version)) >= ORDERED_VERSIONS.index(
+                    "v1.3.0-dev1"
+                ):
+                    for k in list(ret):
+                        found = False
+                        for field in expected_schema.fields:
+                            if k == field.name:
+                                found = True
+                                break
+                        if not found:
+                            _logger.warning(
+                                f"Discarded undeclared output named {k!r} from {custom_output}."
+                            )
+                            ret.pop(k)
             else:
                 for i, port in enumerate(ports):
                     with SourceLine(
@@ -1257,7 +1272,6 @@ def collect_output_ports(
 
                 if compute_checksum:
                     adjustFileObjs(ret, partial(compute_checksums, fs_access))
-            expected_schema = cast(Schema, self.names.get_name("outputs_record_schema", None))
             validate_ex(
                 expected_schema,
                 ret,

tests/test-cwl-out-v1.0.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.0
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.1.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.1
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.2.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.2
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.3.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test_cwl_output_json.py

@@ -0,0 +1,34 @@
+import json
+
+from .util import get_data, get_main_output
+
+
+def test_cwl_output_json_missing_field_v1_0() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.0."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.0.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_1() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.1."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.1.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_2() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.2."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.2.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_3() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.3."""
+    err_code, stdout, stderr = get_main_output(
+        ["--enable-dev", get_data("tests/test-cwl-out-v1.3.cwl")]
+    )
+    assert err_code == 0
+    assert "foo" not in json.loads(stdout)
+    assert "Discarded undeclared output named 'foo' from" in stderr