diff options
| -rw-r--r-- | ravanan/command-line-tool.scm | 40 |
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))))))))) |