ccwl: Support nested arrays.

* ccwl/ccwl.scm (construct-type-syntax): Construct types recursively
to support nested arrays.
(key->output): Recursively convert stdout types to File types.
* ccwl/cwl.scm (type->cwl): New function.
(input->cwl-scm, output->cwl-scm): Use type->cwl.
* tests/ccwl.scm (make-array-type): New function.
(construct-type-syntax-wrapper): New syntax.
("construct-type-syntax on primitive types", "construct-type-syntax on
array types", "construct-type-syntax on nested array types"): New
tests.
* tests/cwl.scm, doc/array-types.scm, doc/nested-array-types.scm: New
files.
* doc/ccwl.skb (Cookbook)[Array types]: New section.

2 files changed, 19 insertions, 22 deletions

diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm
index 66a8ab7..5ae0761 100644
--- a/ccwl/ccwl.scm
+++ b/ccwl/ccwl.scm
@@ -132,11 +132,9 @@ compared using @code{equal?}."
 
 (define (construct-type-syntax type-spec)
   "Return syntax to build a type from @var{type-spec}."
-  ;; TODO: Does CWL support arrays of arrays? If so, support such
-  ;; recursive type definitions.
   (syntax-case type-spec (array)
     ((array member-type)
-     #'(make-array-type 'member-type))
+     #`(make-array-type #,(construct-type-syntax #'member-type)))
     (primitive-type
      #''primitive-type)))
 
@@ -714,6 +712,14 @@ a <key> object, in STEPS, a list of <step> objects. If no such
 <output> object is found, return #f. Note that the returned syntax is
 only applicable to construct <output> objects for workflows, not in
 commands."
+  (define (stdout->file-type type)
+    "Recursively convert stdout types in @var{type} to File types."
+    (cond
+     ((array-type? type)
+      (make-array-type (stdout->file-type (array-type-member-type type))))
+     ((eq? type 'stdout) 'File)
+     (else type)))
+
   (and-let* ((step-with-output (find (lambda (step)
                                        (eq? (step-id step)
                                             (key-step key)))
@@ -734,17 +740,7 @@ commands."
                                  (cwl-key-address key))
               (key-name key))
              ;; Convert stdout type outputs to File type outputs.
-             (let ((type
-                    (cond
-                     ((eq? (output-type output-for-key)
-                           'stdout)
-                      'File)
-                     ((and (array-type? (output-type output-for-key))
-                           (eq? (array-type-member-type (output-type output-for-key))
-                                'stdout))
-                      (make-array-type 'File))
-                     (else
-                      (output-type output-for-key)))))
+             (let ((type (stdout->file-type (output-type output-for-key))))
                ;; If step scatters, convert to an array type.
                (if (null? (step-scattered-inputs step-with-output))
                    type
diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm
index cdb4503..cdd65ca 100644
--- a/ccwl/cwl.scm
+++ b/ccwl/cwl.scm
@@ -97,15 +97,19 @@ association list."
                               (scatterMethod . ,(step-scatter-method step)))))))
                    (workflow-steps workflow)))))
 
+(define (type->cwl type)
+  "Render @var{type} into a CWL tree."
+  (if (array-type? type)
+      `((type . array)
+        (items . ,(type->cwl (array-type-member-type type))))
+      type))
+
 (define* (output->cwl-scm output #:key workflow?)
   "Render @var{output}, a @code{<output>} object, into a CWL tree. If
 @var{workflow?} is @code{#t}, this is a workflow output."
   `(,(output-id output)
     ,@(or (filter-alist
-           `(,@(if (array-type? (output-type output))
-                   `((type . ((type . array)
-                              (items . ,(array-type-member-type (output-type output))))))
-                   `((type . ,(output-type output))))
+           `((type . ,(type->cwl (output-type output)))
              ;; outputBinding is relevant only to commands, and
              ;; outputSource is relevant only to workflows.
              ,@(if workflow?
@@ -125,10 +129,7 @@ CWL YAML specification."
 (define (input->cwl-scm input)
   "Render @var{input}, a @code{<input>} object, into a CWL tree."
   `(,(input-id input)
-    ,@(if (array-type? (input-type input))
-          `((type . ((type . array)
-                     (items . ,(array-type-member-type (input-type input))))))
-          `((type . ,(input-type input))))
+    (type . ,(type->cwl (input-type input)))
     ,@(or (filter-alist
            `((label . ,(input-label input))
              (default . ,(and (not (unspecified-default? (input-default input)))