soften schema; expand arbitrary cycle example

Author: mr-c

cwltool/extensions-v1.2.yml

@@ -127,15 +127,11 @@ $graph:
       type: string?
       jsonldPredicate: "@id"
       doc: "It must reference the `id` of one of the elements in the `in` field of the step."
-    source:
+    loop_source:
       doc: |
         Specifies one or more of the step output parameters that will
         provide input to the loop iterations after the first one (inputs
         of the first iteration are the step input parameters).
-      jsonldPredicate:
-        "_id": "cwl:source"
-        "_type": "@id"
-        refScope: 2
       type:
         - string?
         - string[]?
@@ -231,7 +227,7 @@ $graph:
       jsonldPredicate:
         _id: "cwltool:loop"
         mapSubject: id
-        mapPredicate: source
+        mapPredicate: loop_source
       doc: |
         Defines the input parameters of the loop iterations after the first one
         (inputs of the first iteration are the step input parameters). If no

cwltool/process.py

@@ -121,6 +121,7 @@ def filter(self, record: logging.LogRecord) -> bool:
     "http://commonwl.org/cwltool#LoadListingRequirement",
     "http://commonwl.org/cwltool#InplaceUpdateRequirement",
     "http://commonwl.org/cwltool#CUDARequirement",
+    "http://commonwl.org/cwltool#Loop",
 ]
 
 cwl_files = (

tests/loop.cwl

@@ -1,71 +1,148 @@
 cwlVersion: v1.2
 class: Workflow
 
+doc: |
+  Implementation of http://www.workflowpatterns.com/patterns/control/structural/wcp10.php#fig13
+  the example for the "Arbitrary Cycles" pattern from the Workflow Patterns Initiative
+
 $namespaces:
   cwltool: "http://commonwl.org/cwltool#"
 
+requirements:
+  SubworkflowFeatureRequirement: {}
+
 inputs:
-  i1: Any
+  i1: boolean
 outputs:
   o1:
     type: Any
     outputSource: subworkflow/o1
 steps:
   A:
-    run: A.cwl
     in:
-      in1: in1
+      i1: i1
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+      inputs:
+        i1: boolean
+      expression: |
+        ${
+           if (inputs.in1) {
+              return {"p1": 42, "p2": null};
+           }
+           return {"p1": null, "p2": 23};
+         }
+      outputs:
+        p1: int?
+        p2: int?
     out: [p1, p2]
   B:
-    run: B.cwl
     in:
       p1: A/p1
+    when: $(inputs.p1 !== null)
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+      inputs:
+        p1: int
+      expression: |
+        ${ return {"p3": inputs.p1 * 2}; }
+      outputs:
+        p3: int
     out: [p3]
   C:
-    run: C.cwl
     in:
       p2: A/p2
+    when: $(inputs.p2 !== null)
+    run:
+      class: ExpressionTool
+      requirements:
+        InlineJavascriptRequirement: {}
+      inputs:
+        p2: int
+      expression: |
+        ${ return {"p4": inputs.p2 * 3 }; }
+      outputs:
+        p4: int
     out: [p4]
   subworkflow:
+    in:
+      loop_p3: B/p3
+      p4: C/p4
+    requirements:
+      cwltool:Loop:
+        loop_when: $(outputs.o1 !== null)
+        loop:
+          p3: new_p3
+        outputMethod: last
     run:
       class: Workflow
       inputs:
-        p3: Any
-        p4: Any
+        loop_p3: int?
+        p4: int?
       outputs:
         o1:
-          type: Any
+          type: int
           outputSource: E/o1
-        p3:
-          type: Any
-          outputSource: F/p3
+        new_p3:
+          type: int?
+          outputSource: F/end_p3
       steps:
         D:
-          run: D.cwl
           in:
-            p3: p3
+            start_p3: loop_p3
+          when: $(inputs.p3 !== null)
+          run:
+            class: ExpressionTool
+            requirements:
+              InlineJavascriptRequirement: {}
+            inputs:
+              start_p3: int
+            expression: |
+              ${ return {"p4": inputs.start_p3 * 10 }; }
+            outputs:
+              p4: int
           out: [p4]
         E:
-          run: E.cwl
           in:
             p4:
               source:
               - p4
               - D/p4
               pickValue: the_only_non_null
+          run:
+            class: ExpressionTool
+            requirements:
+              InlineJavascriptRequirement: {}
+            inputs:
+              p4: int
+            expression: |
+              ${ if (inputs.p4 < 100) {
+                   return {"o1": null, "p5": inputs.p4 };
+                 }
+                 return {"o1": inputs.p4, "p5": null };
+               }
+            outputs:
+             o1: int?
+             p5: int?
           out: [o1, p5]
         F:
-          run: F.cwl
           in:
             p5: E/p5
-          out: [p3]
-    in:
-      p3: B/p3
-      p4: C/p4
-    out: [o1, p3]
-    requirements:
-      cwltool:Loop:
-        loop_when: $(outputs.o1 !== null)
-        loop:
-          p3: p3
-        outputMethod: last
+            o1: E/o1
+          when: $(inputs.o1 === null)
+          run:
+            class: ExpressionTool
+            requirements:
+              InlineJavascriptRequirement: {}
+            inputs:
+              p5: int
+            expression: |
+              ${ return {"end_p3": inputs.p5 + 1}; }
+            outputs:
+              end_p3: int
+          out: [end_p3]
+    out: [o1, new_p3]