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| author | Arun Isaac | 2023-11-18 22:35:31 +0000 |
|---|---|---|
| committer | Arun Isaac | 2023-11-18 22:35:31 +0000 |
| commit | 7622601e5f99ca98933ffc52908c5749d333dec2 (patch) | |
| tree | a62e686f9f532f28efc17c5e07dc0c95b2fda189 /ccwl | |
| parent | 299a60b666e64df20f1c7065b58aa43e163caae9 (diff) | |
| download | ccwl-7622601e5f99ca98933ffc52908c5749d333dec2.tar.gz ccwl-7622601e5f99ca98933ffc52908c5749d333dec2.tar.lz ccwl-7622601e5f99ca98933ffc52908c5749d333dec2.zip | |
ccwl: Report non-existent external CWL workflow files.
cwl-workflow needs to be a macro so we have access to syntax objects
necessary to raise a &cwl-violation condition.
* ccwl/ccwl.scm (cwl-workflow): Rewrite as macro. Report error if CWL
file does not exist.
Diffstat (limited to 'ccwl')
| -rw-r--r-- | ccwl/ccwl.scm | 75 |
1 files changed, 43 insertions, 32 deletions
diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm index 0b8f701..429bbed 100644 --- a/ccwl/ccwl.scm +++ b/ccwl/ccwl.scm @@ -463,38 +463,49 @@ identifiers defined in the commands." '#,other)) #'(args ...))))))) -(define (cwl-workflow file) - (define (parameters->id+type parameters) - (if (vector? parameters) - ;; Vector of dictionaries - (map (lambda (alist) - (cons (string->symbol (assoc-ref alist "id")) - (string->symbol (assoc-ref alist "type")))) - (vector->list parameters)) - ;; One dictionary - (map (match-lambda - ((id . (? string? type)) - (cons (string->symbol id) - (string->symbol type))) - ((id . alist) - (cons (string->symbol id) - (string->symbol (assoc-ref alist "type"))))) - parameters))) - - (unless (file-exists? file) - (error "CWL workflow file does not exist" file)) - ;; Read inputs/outputs from CWL workflow YAML file and build a - ;; <cwl-workflow> object. - (let ((yaml (read-yaml-file file))) - (make-cwl-workflow file - (map (match-lambda - ((id . type) - (make-input id type #f #f #f #f #f #f))) - (parameters->id+type (assoc-ref yaml "inputs"))) - (map (match-lambda - ((id . type) - (make-output id type #f #f #f))) - (parameters->id+type (assoc-ref yaml "outputs")))))) +(define-syntax cwl-workflow + (lambda (x) + (syntax-case x () + ((_ file-syntax) + (let ((file (syntax->datum #'file-syntax)) + (parameters->id+type + (lambda (parameters) + (if (vector? parameters) + ;; Vector of dictionaries + (map (lambda (alist) + (cons (string->symbol (assoc-ref alist "id")) + (string->symbol (assoc-ref alist "type")))) + (vector->list parameters)) + ;; One dictionary + (map (match-lambda + ((id . (? string? type)) + (cons (string->symbol id) + (string->symbol type))) + ((id . alist) + (cons (string->symbol id) + (string->symbol (assoc-ref alist "type"))))) + parameters))))) + (unless (file-exists? file) + (raise-exception + (condition (ccwl-violation #'file-syntax) + (formatted-message "CWL workflow file ~a does not exist" file)))) + ;; Read inputs/outputs from CWL workflow YAML file and build + ;; a <cwl-workflow> object. + (let ((yaml (read-yaml-file file))) + #`(make-cwl-workflow + file-syntax + (list #,@(map (match-lambda + ((id . type) + (with-syntax ((id (datum->syntax #f id)) + (type (datum->syntax #f type))) + #`(make-input 'id 'type #f #f #f #f #f #f)))) + (parameters->id+type (assoc-ref yaml "inputs")))) + (list #,@(map (match-lambda + ((id . type) + (with-syntax ((id (datum->syntax #f id)) + (type (datum->syntax #f type))) + #`(make-output 'id 'type #f #f #f)))) + (parameters->id+type (assoc-ref yaml "outputs"))))))))))) (define (function-inputs function) "Return the list of inputs accepted by @var{function}---a |