diff options
| -rw-r--r-- | ravanan/command-line-tool.scm | 58 |
1 files changed, 33 insertions, 25 deletions
diff --git a/ravanan/command-line-tool.scm b/ravanan/command-line-tool.scm index 50fc48a..03faf1a 100644 --- a/ravanan/command-line-tool.scm +++ b/ravanan/command-line-tool.scm @@ -769,8 +769,9 @@ named @var{name} with @var{inputs} using tools from Guix manifest (list)) ((File) (list (cons output-id - (canonicalize-file-value output-value - workflow-output-directory)))) + (copy-file-value + (canonicalize-file-value output-value) + workflow-output-directory)))) (else (list (cons output-id output-value)))))) '#$(vector->list (assoc-ref cwl "outputs")))) @@ -843,24 +844,29 @@ named @var{name} with @var{inputs} using tools from Guix manifest (guix search-paths) (json)) - (define (canonicalize-file-value value workflow-output-directory) - (let* ((path (or (assoc-ref value "location") - (assoc-ref value "path"))) - (workflow-output-path - (expand-file-name (basename path) - workflow-output-directory))) - ;; Copy file to the workflow output directory in the store. - (copy-file path workflow-output-path) - ;; Populate all fields of the File type value. + (define (copy-file-value value directory) + ;; Copy file represented by value to directory and return the + ;; new File value. + (let* ((path (assoc-ref* value "path")) + (destination-path (expand-file-name (basename path) + directory))) + (copy-file path destination-path) (assoc-set value - (cons "location" (string-append "file://" - workflow-output-path)) - (cons "path" workflow-output-path) - (cons "basename" (basename path)) - (cons "nameroot" (file-name-stem path)) - (cons "nameext" (file-name-extension path)) - (cons "size" (stat:size (stat path))) - (cons "checksum" (checksum path))))) + (cons "location" (string-append "file://" destination-path)) + (cons "path" destination-path)))) + + (define (canonicalize-file-value value) + (let ((path (or (assoc-ref value "location") + (assoc-ref value "path")))) + ;; Populate all fields of the File type value. + `(("class" . "File") + ("location" . ,(string-append "file://" path)) + ("path" . ,path) + ("basename" . ,(basename path)) + ("nameroot" . ,(file-name-stem path)) + ("nameext" . ,(file-name-extension path)) + ("size" . ,(stat:size (stat path))) + ("checksum" . ,(checksum path))))) (define (capture-secondary-file path secondary-file workflow-output-directory) @@ -874,9 +880,10 @@ directory of the workflow." (secondary-file-path (string-append path pattern)) (secondary-file-value (and (file-exists? secondary-file-path) - (canonicalize-file-value `(("class" . "File") - ("path" . ,secondary-file-path)) - workflow-output-directory)))) + (copy-file-value (canonicalize-file-value + `(("class" . "File") + ("path" . ,secondary-file-path))) + workflow-output-directory)))) (if (and (assoc-ref* secondary-file "required") (not secondary-file-value)) (user-error "Secondary file ~a missing for output path ~a" @@ -885,9 +892,10 @@ directory of the workflow." secondary-file-value))) (define (path->value path workflow-output-directory maybe-secondary-files) - (maybe-assoc-set (canonicalize-file-value `(("class" . "File") - ("path" . ,path)) - workflow-output-directory) + (maybe-assoc-set (copy-file-value (canonicalize-file-value + `(("class" . "File") + ("path" . ,path))) + workflow-output-directory) (cons "secondaryFiles" (maybe-let* ((secondary-files maybe-secondary-files)) (just (vector-filter-map (cut capture-secondary-file |