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-rw-r--r--ccwl/ccwl.scm24
-rw-r--r--ccwl/cwl.scm17
-rw-r--r--doc/array-types.scm2
-rw-r--r--doc/ccwl.skb5
-rw-r--r--doc/nested-array-types.scm2
-rw-r--r--tests/ccwl.scm22
-rw-r--r--tests/cwl.scm44
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")