Fix all_non_null single source element (#2220)

Author: LanderOtto

cwltool/checker.py

@@ -395,6 +395,9 @@ def _check_all_types(
 
                 if pickValue in ["first_non_null", "the_only_non_null"]:
                     linkMerge = None
+                elif pickValue == "all_non_null" and linkMerge is None:
+                    sink["linkMerge"] = "merge_nested"
+                    linkMerge = cast(Optional[str], sink["linkMerge"])
 
                 srcs_of_sink: list[CWLObjectType] = []
                 for parm_id in cast(MutableSequence[str], sink[sourceField]):

cwltool/workflow_job.py

@@ -403,7 +403,7 @@ def object_from_state(
                         a_state,
                         iid,
                         inputobj,
-                        cast(
+                        linkMerge=cast(
                             Optional[str],
                             inp.get(
                                 "linkMerge",

tests/single_all_non_null.cwl

@@ -0,0 +1,38 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+
+inputs:
+  inp:
+    type: string?
+    default: null
+
+outputs:
+  out:
+    type: int[]
+    outputSource:
+    - root/out
+    pickValue: all_non_null
+
+steps:
+  root:
+    run:
+      class: ExpressionTool
+      inputs:
+        strs: string[]
+      outputs:
+        out:
+          type: int
+      expression: |
+        ${
+          return {"out": inputs.strs.length}
+        }
+    in:
+      strs:
+        source:
+        - inp
+        pickValue: all_non_null
+    out: [out]

tests/single_all_non_null_err.cwl

@@ -0,0 +1,38 @@
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+
+inputs:
+  inp:
+    type: string?
+    default: null
+
+outputs:
+  out:
+    type: int[]
+    outputSource:
+    - root/out
+    pickValue: all_non_null
+
+steps:
+  root:
+    run:
+      class: ExpressionTool
+      inputs:
+        strs: string
+      outputs:
+        out:
+          type: int
+      expression: |
+        ${
+          return {"out": inputs.strs.length}
+        }
+    in:
+      strs:
+        source:
+        - inp
+        pickValue: all_non_null
+    out: [out]

tests/test_examples.py

@@ -1997,3 +1997,29 @@ def test_anonymous_record_mismatch_error() -> None:
     assert exit_code == 1, stderr
     assert "tests/2205.cwl:11:9: Record comparison failure between this record and " in stdout
     assert "tests/2205.cwl:24:14: Did not match fields for 'missing': None and string." in stdout
+
+
+def test_all_non_null() -> None:
+    """Test pickValue: all_non_null with a single element source"""
+    exit_code, stdout, stderr = get_main_output(
+        [
+            get_data("tests/single_all_non_null.cwl"),
+            get_data("tests/echo-job.yaml"),
+        ]
+    )
+    assert exit_code == 0
+    assert json.loads(stdout)["out"] == [1]
+    exit_code, stdout, stderr = get_main_output(
+        [
+            get_data("tests/single_all_non_null.cwl"),
+        ]
+    )
+    assert exit_code == 0
+    assert json.loads(stdout)["out"] == [0]
+    exit_code, stdout, stderr = get_main_output(
+        [
+            get_data("tests/single_all_non_null_err.cwl"),
+            get_data("tests/echo-job.yaml"),
+        ]
+    )
+    assert exit_code == 1