diff options
| -rw-r--r-- | ccwl/ccwl.scm | 41 | ||||
| -rw-r--r-- | ccwl/cwl.scm | 8 |
2 files changed, 46 insertions, 3 deletions
diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm index 03e1264..2ece5d9 100644 --- a/ccwl/ccwl.scm +++ b/ccwl/ccwl.scm @@ -73,6 +73,8 @@ output-binding output-source output-other + array-type? + array-type-member-type step? step-id step-run @@ -92,6 +94,27 @@ (stage? input-stage?) (other input-other)) +(define (memoize proc) + "Return a memoized version of @var{proc}. Arguments to @var{proc} are +compared using @code{equal?}." + (let ((memoized-results (list))) + (lambda args + (unless (assoc args memoized-results) + (set! memoized-results + (acons args (apply proc args) + memoized-results))) + (assoc-ref memoized-results args)))) + +(define-immutable-record-type <array-type> + (-make-array-type member-type) + array-type? + (member-type array-type-member-type)) + +;; We memoize the <array-type> constructor to enable easy comparison +;; using eq?. +(define make-array-type + (memoize -make-array-type)) + (define-immutable-record-type <unspecified-default> (make-unspecified-default) unspecified-default?) @@ -105,6 +128,16 @@ (condition (ccwl-violation tree) (formatted-message "#:other parameter not serializable to YAML"))))) +(define (construct-type-syntax type-spec) + "Return syntax to build a type from @var{type-spec}." + ;; TODO: Does CWL support arrays of arrays? If so, support such + ;; recursive type definitions. + (syntax-case type-spec (array) + ((array member-type) + #'(make-array-type 'member-type)) + (primitive-type + #''primitive-type))) + (define (input input-spec) "Return syntax to build an <input> object from INPUT-SPEC." (syntax-case input-spec () @@ -149,7 +182,9 @@ (ensure-yaml-serializable other) (let ((position #f) (prefix #f)) - #`(make-input '#,id '#,type #,label + #`(make-input '#,id + #,(construct-type-syntax type) + #,label #,(if (unspecified-default? default) #'(make-unspecified-default) default) @@ -203,7 +238,9 @@ (formatted-message "Output has no identifier"))))))) (apply (syntax-lambda** (id #:key (type #'File) binding source (other #'())) (ensure-yaml-serializable other) - #`(make-output '#,id '#,type #,binding #,source '#,other)) + #`(make-output '#,id + #,(construct-type-syntax type) + #,binding #,source '#,other)) #'(id args ...)))) (id (identifier? #'id) (output #'(id))) (_ (error "Invalid output:" (syntax->datum output-spec))))) diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm index f032211..e57cc79 100644 --- a/ccwl/cwl.scm +++ b/ccwl/cwl.scm @@ -94,6 +94,9 @@ association list." `(,(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? @@ -120,7 +123,10 @@ CWL YAML specification." (define (input->cwl-scm input) "Render @var{input}, a @code{<input>} object, into a CWL tree." `(,(input-id input) - (type . ,(input-type input)) + ,@(if (array-type? (input-type input)) + `((type . ((type . array) + (items . ,(array-type-member-type (input-type input)))))) + `((type . ,(input-type input)))) ,@(or (filter-alist `((label . ,(input-label input)) (default . ,(and (not (unspecified-default? (input-default input))) |