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;;; ccwl --- Concise Common Workflow Language
;;; Copyright © 2021 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/>.
;;; Commentary:
;; This file implements conversion from ccwl objects (<workflow>,
;; <command>, <input>, <output>, <step>) to CWL YAML.
;;; Code:
(define-module (ccwl cwl)
#:use-module (ice-9 match)
#:use-module (ccwl ccwl)
#:use-module (ccwl utils)
#:use-module (ccwl yaml)
#:export (workflow->cwl))
(define %cwl-version "v1.2")
(define (workflow->cwl workflow port)
"Render WORKFLOW, a <workflow> object, to PORT as a CWL YAML
specification."
(scm->yaml (workflow->cwl-scm workflow)
port))
(define (filter-alist alist)
"Filter ALIST removing entries with #f as the value. If the
resulting association list is empty, return #f. Else, return that
association list."
(match (filter (match-lambda
((_ . #f) #f)
(_ #t))
alist)
(() #f)
(result result)))
(define* (workflow->cwl-scm workflow)
"Render WORKFLOW, a <workflow> object, into a CWL tree."
`((cwlVersion . ,%cwl-version)
(class . Workflow)
(requirements (SubworkflowFeatureRequirement))
,@(workflow-other workflow)
(inputs . ,(map (lambda (input)
`(,(input-id input)
,@(filter-alist
`((type . ,(input-type input))
(label . ,(input-label input))
(default . ,(and (not (unspecified-default? (input-default input)))
(input-default input)))))
,@(input-other input)))
(workflow-inputs workflow)))
(outputs . ,(map (lambda (output)
`(,(output-id output)
(type . ,(match (output-type output)
('stdout 'File)
(some-other-type some-other-type)))
(outputSource . ,(match (output-source output)
((? string? source) source)
((? input? input) (input-id input))))))
(workflow-outputs workflow)))
(steps . ,(map (lambda (step)
`(,(step-id step)
(in . ,(map (lambda (in)
(match in
((id . (? string? source))
in)
((id . (? input? input))
(cons id (input-id input)))))
(step-in step)))
(out . ,(list->vector (map output-id (step-out step))))
(run . ,(match (step-run step)
((? command? command)
(command->cwl-scm command))
((? cwl-workflow? cwl-workflow)
(cwl-workflow-file cwl-workflow))
(tree tree)))))
(workflow-steps workflow)))))
(define (output->cwl-scm output)
"Render OUTPUT, a <output> object, into a CWL tree."
`(,(output-id output)
,@(filter identity
(list (and (output-type output)
(cons 'type (output-type output)))
(and (output-binding output)
(cons 'outputBinding (output-binding output)))))
,@(output-other output)))
(define (command->cwl-scm command)
"Render COMMAND, a <command> object, into a CWL tree."
`((cwlVersion . ,%cwl-version)
(class . CommandLineTool)
,@(command-other command)
(arguments . ,(list->vector
;; Put string arguments into the arguments array.
(filter-mapi (lambda (arg index)
(and (string? arg)
`((position . ,index)
(valueFrom . ,arg))))
(command-args command))))
(inputs . ,(map (lambda (input)
`(,(input-id input)
,@(filter-alist
`((type . ,(input-type input))
(label . ,(input-label input))
(default . ,(and (not (unspecified-default? (input-default input)))
(input-default input)))
(inputBinding . ,(filter-alist
`((position . ,(input-position input))
(prefix . ,(input-prefix input)))))))
,@(input-other input)))
(command-inputs command)))
(outputs . ,(map output->cwl-scm (command-outputs command)))
,@(if (command-stdin command)
`((stdin . ,(string-append "$(inputs."
(symbol->string
(command-stdin command))
".path)")))
'())))
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