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-rw-r--r--ravanan/command-line-tool.scm40
1 files changed, 27 insertions, 13 deletions
diff --git a/ravanan/command-line-tool.scm b/ravanan/command-line-tool.scm
index 03faf1a..73b9313 100644
--- a/ravanan/command-line-tool.scm
+++ b/ravanan/command-line-tool.scm
@@ -231,13 +231,19 @@ G-expressions are inserted."
(assoc-ref* argument "valueFrom")))
%nothing))
- (define (collect-bindings inputs+types+bindings)
- (append-map input+type-tree+binding->command-line-binding
- inputs+types+bindings))
+ (define (collect-bindings ids+inputs+types+bindings)
+ (append-map id+input+type-tree+binding->command-line-binding
+ ids+inputs+types+bindings))
- (define input+type-tree+binding->command-line-binding
+ (define id+input+type-tree+binding->command-line-binding
(match-lambda
- ((input type-tree binding)
+ ;; We stretch the idea of an input id, by making it an address that
+ ;; identifies the exact location of a value in a tree that possibly
+ ;; contains array types. For example, '("foo") identifies the input "foo";
+ ;; '("foo" 1) identifies the 1th element of the array input "foo"; '("foo"
+ ;; 37 1) identifies the 1th element of the 37th element of the array input
+ ;; "foo"; etc.
+ ((id input type-tree binding)
;; Check type.
(let* ((type (formal-parameter-type type-tree))
(matched-type (match-type input type)))
@@ -258,17 +264,25 @@ G-expressions are inserted."
position
prefix
matched-type
- (append-map (lambda (input)
- (input+type-tree+binding->command-line-binding
- (list input
+ (append-map (lambda (i input)
+ (id+input+type-tree+binding->command-line-binding
+ (list (append id (list i))
+ input
(assoc-ref type-tree "items")
(maybe-assoc-ref (just type-tree)
"inputBinding"))))
+ (iota (vector-length input))
(vector->list input))
(maybe-assoc-ref binding "itemSeparator"))))
(else
- (list (command-line-binding
- position prefix matched-type input %nothing)))))))))
+ (list (command-line-binding position
+ prefix
+ matched-type
+ ;; We defer access of input values to
+ ;; runtime when inputs have been fully
+ ;; resolved, staging is complete, etc.
+ #~(apply json-ref inputs '#$id)
+ %nothing)))))))))
;; For details of this algorithm, see ยง4.1 Input binding of the CWL
;; 1.2 CommandLineTool specification:
@@ -291,7 +305,8 @@ G-expressions are inserted."
;; Exclude formal inputs without an inputBinding.
(and (assoc "inputBinding" formal-input)
(let ((id (assoc-ref formal-input "id")))
- (list (or (assoc-ref inputs id)
+ (list (list id)
+ (or (assoc-ref inputs id)
(assoc-ref formal-input "default")
'null)
(or (assoc-ref formal-input "type")
@@ -453,8 +468,7 @@ in which the G-expressions are inserted."
((int)
(number->string value))
((File)
- #~(expand-file-name #$(basename (assoc-ref value "location"))
- inputs-directory))
+ #~(assoc-ref* #$value "path"))
(else
(user-error "Invalid formal input type ~a"
type)))))))))