diff options
| -rw-r--r-- | ccwl/ccwl.scm | 24 | ||||
| -rw-r--r-- | ccwl/cwl.scm | 17 | ||||
| -rw-r--r-- | doc/array-types.scm | 2 | ||||
| -rw-r--r-- | doc/ccwl.skb | 5 | ||||
| -rw-r--r-- | doc/nested-array-types.scm | 2 | ||||
| -rw-r--r-- | tests/ccwl.scm | 22 | ||||
| -rw-r--r-- | tests/cwl.scm | 44 |
7 files changed, 94 insertions, 22 deletions
diff --git a/ccwl/ccwl.scm b/ccwl/ccwl.scm index 66a8ab7..5ae0761 100644 --- a/ccwl/ccwl.scm +++ b/ccwl/ccwl.scm @@ -132,11 +132,9 @@ compared using @code{equal?}." (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)) + #`(make-array-type #,(construct-type-syntax #'member-type))) (primitive-type #''primitive-type))) @@ -714,6 +712,14 @@ a <key> object, in STEPS, a list of <step> objects. If no such <output> object is found, return #f. Note that the returned syntax is only applicable to construct <output> objects for workflows, not in commands." + (define (stdout->file-type type) + "Recursively convert stdout types in @var{type} to File types." + (cond + ((array-type? type) + (make-array-type (stdout->file-type (array-type-member-type type)))) + ((eq? type 'stdout) 'File) + (else type))) + (and-let* ((step-with-output (find (lambda (step) (eq? (step-id step) (key-step key))) @@ -734,17 +740,7 @@ commands." (cwl-key-address key)) (key-name key)) ;; Convert stdout type outputs to File type outputs. - (let ((type - (cond - ((eq? (output-type output-for-key) - 'stdout) - 'File) - ((and (array-type? (output-type output-for-key)) - (eq? (array-type-member-type (output-type output-for-key)) - 'stdout)) - (make-array-type 'File)) - (else - (output-type output-for-key))))) + (let ((type (stdout->file-type (output-type output-for-key)))) ;; If step scatters, convert to an array type. (if (null? (step-scattered-inputs step-with-output)) type diff --git a/ccwl/cwl.scm b/ccwl/cwl.scm index cdb4503..cdd65ca 100644 --- a/ccwl/cwl.scm +++ b/ccwl/cwl.scm @@ -97,15 +97,19 @@ association list." (scatterMethod . ,(step-scatter-method step))))))) (workflow-steps workflow))))) +(define (type->cwl type) + "Render @var{type} into a CWL tree." + (if (array-type? type) + `((type . array) + (items . ,(type->cwl (array-type-member-type type)))) + type)) + (define* (output->cwl-scm output #:key workflow?) "Render @var{output}, a @code{<output>} object, into a CWL tree. If @var{workflow?} is @code{#t}, this is a workflow output." `(,(output-id output) ,@(or (filter-alist - `(,@(if (array-type? (output-type output)) - `((type . ((type . array) - (items . ,(array-type-member-type (output-type output)))))) - `((type . ,(output-type output)))) + `((type . ,(type->cwl (output-type output))) ;; outputBinding is relevant only to commands, and ;; outputSource is relevant only to workflows. ,@(if workflow? @@ -125,10 +129,7 @@ CWL YAML specification." (define (input->cwl-scm input) "Render @var{input}, a @code{<input>} object, into a CWL tree." `(,(input-id input) - ,@(if (array-type? (input-type input)) - `((type . ((type . array) - (items . ,(array-type-member-type (input-type input)))))) - `((type . ,(input-type input)))) + (type . ,(type->cwl (input-type input))) ,@(or (filter-alist `((label . ,(input-label input)) (default . ,(and (not (unspecified-default? (input-default input))) diff --git a/doc/array-types.scm b/doc/array-types.scm new file mode 100644 index 0000000..1722d7c --- /dev/null +++ b/doc/array-types.scm @@ -0,0 +1,2 @@ +(workflow ((foo #:type (array string))) + […]) diff --git a/doc/ccwl.skb b/doc/ccwl.skb index 2e84d58..1ae35f2 100644 --- a/doc/ccwl.skb +++ b/doc/ccwl.skb @@ -332,6 +332,11 @@ to ,(emph "stage") the input file into the output directory. We may express this in ccwl using the ,(code "#:stage?") parameter to the inputs to be staged. Here is a rather concocted example.] (scheme-source "doc/staging-input-files.scm"))) + (section :title [Array types] + (p [ccwl supports array types using the following syntax.] + (scheme-source "doc/array-types.scm")) + (p [Nested array types are also supported.] + (scheme-source "doc/nested-array-types.scm"))) (section :title [Scatter/gather] (p [ccwl supports CWL's dotproduct scatter/gather feature using the following syntax. Here, the ,(code [other-messages]) input to the diff --git a/doc/nested-array-types.scm b/doc/nested-array-types.scm new file mode 100644 index 0000000..7968750 --- /dev/null +++ b/doc/nested-array-types.scm @@ -0,0 +1,2 @@ +(workflow ((foo #:type (array (array string)))) + […]) diff --git a/tests/ccwl.scm b/tests/ccwl.scm index 117f93f..6890017 100644 --- a/tests/ccwl.scm +++ b/tests/ccwl.scm @@ -27,6 +27,16 @@ (define output (@@ (ccwl ccwl) output)) +(define make-array-type + (@@ (ccwl ccwl) make-array-type)) + +(define-syntax construct-type-syntax-wrapper + (lambda (x) + (syntax-case x () + ((_ type-spec) + ((@@ (ccwl ccwl) construct-type-syntax) + #'type-spec))))) + (test-begin "ccwl") (test-assert "stdin input should not have inputBinding" @@ -317,4 +327,16 @@ #:other '((secondaryFiles . ".fai")))) #f))) +(test-eq "construct-type-syntax on primitive types" + 'File + (construct-type-syntax-wrapper File)) + +(test-eq "construct-type-syntax on array types" + (make-array-type 'File) + (construct-type-syntax-wrapper (array File))) + +(test-eq "construct-type-syntax on nested array types" + (make-array-type (make-array-type 'File)) + (construct-type-syntax-wrapper (array (array File)))) + (test-end "ccwl") diff --git a/tests/cwl.scm b/tests/cwl.scm new file mode 100644 index 0000000..ba619ab --- /dev/null +++ b/tests/cwl.scm @@ -0,0 +1,44 @@ +;;; ccwl --- Concise Common Workflow Language +;;; Copyright © 2023 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of ccwl. +;;; +;;; ccwl is free software: you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation, either version 3 of the License, or +;;; (at your option) any later version. +;;; +;;; ccwl is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +;;; General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with ccwl. If not, see <https://www.gnu.org/licenses/>. + +(use-modules (srfi srfi-64)) + +(define type->cwl + (@@ (ccwl cwl) type->cwl)) + +(define make-array-type + (@@ (ccwl ccwl) make-array-type)) + +(test-begin "cwl") + +(test-equal "type->cwl on primitive types" + 'File + (type->cwl 'File)) + +(test-equal "type->cwl on array types" + '((type . array) + (items . File)) + (type->cwl (make-array-type 'File))) + +(test-equal "type->cwl on nested array types" + '((type . array) + (items . ((type . array) + (items . File)))) + (type->cwl (make-array-type (make-array-type 'File)))) + +(test-end "cwl") |