Added tests

Author: GlassOfWhiskey

cwltool/command_line_tool.py

@@ -1258,17 +1258,20 @@ def collect_output_ports(
                 if compute_checksum:
                     adjustFileObjs(ret, partial(compute_checksums, fs_access))
             expected_schema = cast(RecordSchema, self.names.get_name("outputs_record_schema", None))
-            for k in list(ret.keys()):  # so we don't edit the loops iterable later
-                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)
+            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)
             validate_ex(
                 expected_schema,
                 ret,

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

@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: v1.0
+requirements:
+  - class: ShellCommandRequirement
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs: {}

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

@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: v1.1
+requirements:
+  - class: ShellCommandRequirement
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs: {}

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

@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: v1.2
+requirements:
+  - class: ShellCommandRequirement
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test_cwl_output_json.py

@@ -0,0 +1,24 @@
+import json
+
+from .util import get_data, get_main_output
+
+
+def test_cwl_outpu_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_outpu_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_outpu_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)