Stopped Loop requirement propagation

Author: GlassOfWhiskey

cwltool/workflow.py

@@ -218,7 +218,7 @@ def __init__(
                 if parent_req["class"] == step_req["class"]:
                     found_in_step = True
                     break
-            if not found_in_step:
+            if not found_in_step and parent_req.get('class') != 'http://commonwl.org/cwltool#Loop':
                 loadingContext.requirements.append(parent_req)
         loadingContext.requirements.extend(
             cast(

tests/loop/multi-source-loop.cwl

@@ -0,0 +1,68 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+requirements:
+  InlineJavascriptRequirement: {}
+  ScatterFeatureRequirement: {}
+  SubworkflowFeatureRequirement: {}
+inputs:
+  i1: int
+outputs:
+  o1:
+    type: int[]
+    outputSource: [loop/osmall, loop/obig]
+    linkMerge: merge_flattened
+    pickValue: all_non_null
+steps:
+  loop:
+    run:
+      class: Workflow
+      inputs:
+        i1: int
+      outputs:
+        osmall:
+          type: int?
+          outputSource: small_values/o1
+        obig:
+          type: int?
+          outputSource: big_values/o1
+      steps:
+        small_values:
+          when: $(inputs.i1 < 5)
+          run:
+            class: ExpressionTool
+            inputs:
+              i1: int
+            outputs:
+              o1: int
+            expression: >
+              ${return {'o1': inputs.i1 + 1};}
+          in:
+            i1: i1
+          out: [o1]
+        big_values:
+          when: $(inputs.i1 >= 5)
+          run:
+            class: ExpressionTool
+            inputs:
+              i1: int
+            outputs:
+              o1: int
+            expression: >
+              ${return {'o1': inputs.i1 + 3};}
+          in:
+            i1: i1
+          out: [ o1 ]
+    in:
+      i1: i1
+    out: [osmall, obig]
+    requirements:
+      cwltool:Loop:
+        loop_when: $(inputs.i1 < 20)
+        loop:
+          i1:
+            loop_source: [osmall, obig]
+            pickValue: the_only_non_null
+        outputMethod: all

tests/test_loop.py

@@ -154,4 +154,18 @@ def test_nested_loops_all() -> None:
     ]
     main(params, stdout=stream)
     expected = {'o1': [[2], [2, 3], [2, 3, 4]]}
-    assert json.loads(stream.getvalue()) == expected
+    assert json.loads(stream.getvalue()) == expected
+
+
+def test_multi_source_loop_input() -> None:
+    """Test a loop with two sources, which are selected through a pickValue directive."""
+    stream = StringIO()
+    params = [
+        "--enable-ext",
+        "--validate",
+        get_data("tests/loop/multi-source-loop.cwl"),
+        get_data("tests/loop/single-var-loop-job.yml")
+    ]
+    main(params, stdout=stream)
+    expected = {'o1': [2, 3, 4, 5, 8, 11, 14, 17, 20]}
+    assert json.loads(stream.getvalue()) == expected