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;;; ccwl --- Concise Common Workflow Language
;;; Copyright © 2021, 2023–2024 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 (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (ice-9 match)
#:use-module (ccwl ccwl)
#:use-module (ccwl utils)
#:use-module (ccwl yaml)
#:export (workflow->cwl
command->cwl
function->cwl))
(define %cwl-version "v1.2")
(define function->cwl
(match-lambda*
(((? workflow? workflow) port)
(workflow->cwl workflow port))
(((? command? command) port)
(command->cwl command port))
(((? js-expression? expression) port)
(js-expression->cwl expression port))))
(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)
,@(if (every (compose null? step-scattered-inputs)
(workflow-steps workflow))
'()
'((ScatterFeatureRequirement)))))
,@(workflow-other workflow)
(inputs . ,(map input->cwl-scm
(workflow-inputs workflow)))
(outputs . ,(map (cut output->cwl-scm <> #:workflow? #t)
(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))
((? js-expression? expression)
(js-expression->cwl-scm expression))
((? cwl-workflow? cwl-workflow)
(cwl-workflow-file cwl-workflow))
((? workflow? workflow)
(workflow->cwl-scm workflow))
(tree tree)))
,@(match (step-scattered-inputs step)
(() '())
(scattered-inputs
`((scatter . ,(list->vector scattered-inputs))
(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
`((type . ,(type->cwl (output-type output)))
;; outputBinding is relevant only to commands, and
;; outputSource is relevant only to workflows.
,@(if workflow?
`((outputSource . ,(match (output-source output)
((? string? source) source)
((? input? input) (input-id input)))))
`((outputBinding . ,(output-binding output))))))
'())
,@(output-other output)))
(define (command->cwl command port)
"Render @var{command}, a @code{<command>} object, to @var{port} as a
CWL YAML specification."
(scm->yaml (command->cwl-scm command)
port))
(define (input->cwl-scm input)
"Render @var{input}, a @code{<input>} object, into a CWL tree."
`(,(input-id input)
(type . ,(type->cwl (input-type input)))
,@(or (filter-alist
`((label . ,(input-label input))
(default . ,(and (not (unspecified-default? (input-default input)))
(input-default input)))
;; inputBinding is only relevant to commands, not
;; workflows. But, the input position and prefix are not set
;; for worklow inputs and therefore this sub-expression has
;; no effect. So, leave this be.
(inputBinding . ,(filter-alist
`((position . ,(input-position input))
(prefix . ,(input-prefix input))
(itemSeparator . ,(input-separator input)))))))
'())
,@(input-other input)))
(define (staging-requirements inputs)
"Return @samp{InitialWorkDirRequirement} to stage any @var{inputs} that
must be staged."
(if (any input-stage? inputs)
;; Stage any inputs that need to be.
`((InitialWorkDirRequirement
(listing . ,(list->vector
(filter-map (lambda (input)
(and (input-stage? input)
(string-append "$(inputs."
(symbol->string (input-id input))
")")))
inputs)))))
'()))
(define (command->cwl-scm command)
"Render COMMAND, a <command> object, into a CWL tree."
`((cwlVersion . ,%cwl-version)
(class . CommandLineTool)
(requirements
,@(staging-requirements (command-inputs command))
,@(command-requirements command))
,@(command-other command)
(arguments . ,(list->vector
;; Put string arguments into the arguments array.
(filter-mapi (lambda (arg index)
(and (string? arg)
`((position . ,index)
(valueFrom . ,arg))))
(command-args command))))
(inputs . ,(map input->cwl-scm
(command-inputs command)))
(outputs . ,(map output->cwl-scm (command-outputs command)))
,@(if (command-stdin command)
`((stdin . ,(string-append "$(inputs."
(symbol->string
(command-stdin command))
".path)")))
'())
,@(if (command-stderr command)
`((stderr . ,(command-stderr command)))
'())
,@(if (command-stdout command)
`((stdout . ,(command-stdout command)))
'())))
(define (js-expression->cwl expression port)
"Render @var{expression}, a @code{<js-expression>} object, to
@var{port} as a CWL YAML specification."
(scm->yaml (js-expression->cwl-scm expression)
port))
(define (js-expression->cwl-scm expression)
"Render @var{expression}, a @code{<js-expression>} object, into
a CWL tree."
`((cwlVersion . ,%cwl-version)
(class . ExpressionTool)
(requirements
(InlineJavascriptRequirement)
,@(staging-requirements (js-expression-inputs expression))
,@(js-expression-requirements expression))
,@(js-expression-other expression)
(inputs . ,(map input->cwl-scm
(js-expression-inputs expression)))
(outputs . ,(map output->cwl-scm
(js-expression-outputs expression)))
(expression . ,(js-expression-expression expression))))
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