From c4307f5706b84f9d56dc0432b070b5fc81e239c3 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Tue, 14 Nov 2023 16:22:32 +0000
Subject: ccwl: Convert stdout type outputs to File type in ccwl.scm.

This conversation should be in ccwl.scm, not in cwl.scm. cwl.scm
should only deal with CWL serialization concerns.

* ccwl/cwl.scm (output->cwl-scm): Move conversion to ...
* ccwl/ccwl.scm (key->output): ... here.
(<output>)[type]: Add setter.
---
 ccwl/ccwl.scm | 17 +++++++++++------
 ccwl/cwl.scm  | 15 ++++-----------
 2 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm
index e174159..47b4e5f 100644
--- a/ccwl/ccwl.scm
+++ b/ccwl/ccwl.scm
@@ -197,7 +197,7 @@ compared using @code{equal?}."
   (make-output id type binding source other)
   output?
   (id output-id set-output-id)
-  (type output-type)
+  (type output-type set-output-type)
   (binding output-binding)
   (source output-source set-output-source)
   (other output-other))
@@ -697,11 +697,16 @@ a <key> object, in STEPS, a list of <step> objects. If no such
                    (function-object
                     (step-run step-with-output)))))
            (output
-            ;; Set output id and source fields from key.
-            (set-output-id
-             (set-output-source output-for-key
-                                (cwl-key-address key))
-             (key-name key))))
+            (set-output-type
+             ;; Set output id and source fields from key.
+             (set-output-id
+              (set-output-source output-for-key
+                                 (cwl-key-address key))
+              (key-name key))
+             ;; Convert stdout type outputs to File type outputs.
+             (if (eq? (output-type output-for-key) 'stdout)
+                 'File
+                 (output-type output-for-key)))))
       ;; Construct syntax to recreate output object.
       #`(make-output
          #,(with-syntax ((id (datum->syntax #f (output-id output))))
diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm
index e57cc79..c61d8a8 100644
--- a/ccwl/cwl.scm
+++ b/ccwl/cwl.scm
@@ -93,17 +93,10 @@ association list."
 @var{workflow?} is @code{#t}, this is a workflow output."
   `(,(output-id output)
     ,@(or (filter-alist
-           `(,@(cond
-                ((array-type? (output-type output))
-                 `((type . ((type . array)
-                            (items . ,(array-type-member-type (output-type output)))))))
-                ;; In workflows, convert stdout outputs to File
-                ;; outputs.
-                ((and workflow?
-                      (eq? (output-type output) 'stdout))
-                 `((type . File)))
-                (else
-                 `((type . ,(output-type output)))))
+           `(,@(if (array-type? (output-type output))
+                   `((type . ((type . array)
+                              (items . ,(array-type-member-type (output-type output))))))
+                   `((type . ,(output-type output))))
              ;; outputBinding is relevant only to commands, and
              ;; outputSource is relevant only to workflows.
              ,@(if workflow?
-- 
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