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;;; ravanan --- High-reproducibility CWL runner powered by Guix
;;; Copyright © 2024, 2025 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of ravanan.
;;;
;;; ravanan 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.
;;;
;;; ravanan 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 ravanan. If not, see <https://www.gnu.org/licenses/>.
(use-modules (srfi srfi-26)
(srfi srfi-64)
(ice-9 filesystem)
(ice-9 match)
(web uri)
(ravanan reader)
(ravanan work command-line-tool)
(ravanan work types)
(ravanan work utils))
(define normalize-formal-input
(@@ (ravanan reader) normalize-formal-input))
(define normalize-formal-output
(@@ (ravanan reader) normalize-formal-output))
(define normalize-input
(@@ (ravanan reader) normalize-input))
(test-begin "reader")
(test-equal "Coerce to boolean (true)"
#t
(coerce-type "true" 'boolean))
(test-equal "Coerce to boolean (false)"
#f
(coerce-type "false" 'boolean))
(test-equal "Coerce to int"
37
(coerce-type "37" 'int))
(test-equal "Coerce to float"
37.1
(coerce-type "37.1" 'float))
(test-equal "Coerce to double"
37.1
(coerce-type "37.1" 'double))
(test-equal "Coerce to string"
"37"
(coerce-type "37" 'string))
(test-equal "Coerce to File"
'(("class" . "File")
("location" . "foo"))
(coerce-type '(("class" . "File")
("location" . "foo"))
'File))
(test-equal "Coerce to array"
#(1 2 3)
(coerce-type #("1" "2" "3")
(cwl-array-type 'int)))
(test-equal "Coerce to union type (int first)"
37
(coerce-type "37"
(cwl-union-type 'int 'string)))
(test-equal "Coerce to union type (string first)"
"37"
(coerce-type "37"
(cwl-union-type 'string 'int)))
(test-equal "Coerce int to int"
37
(coerce-type 37 'int))
(test-equal "Normalize File type formal input"
(canonicalize-json '(("type" . "File")
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t))))))
(canonicalize-json (normalize-formal-input
'(("type" . "File")
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(test-equal "Normalize File array type formal input"
(canonicalize-json '(("type"
("type" . "array")
("items" . "File"))
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t))))))
(canonicalize-json (normalize-formal-input
'(("type"
("type" . "array")
("items" . "File"))
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(test-equal "Normalize array of File arrays type formal input"
(canonicalize-json '(("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t))))))
(canonicalize-json (normalize-formal-input
'(("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(test-equal "Normalize File type formal output"
(canonicalize-json '(("type" . "File")
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f))))))
(canonicalize-json (normalize-formal-output
'(("type" . "File")
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(test-equal "Normalize File array type formal output"
(canonicalize-json '(("type"
("type" . "array")
("items" . "File"))
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f))))))
(canonicalize-json (normalize-formal-output
'(("type"
("type" . "array")
("items" . "File"))
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(test-equal "Normalize array of File arrays type formal output"
(canonicalize-json '(("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("id" . "foo")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f))))))
(canonicalize-json (normalize-formal-output
'(("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("id" . "foo")
("secondaryFiles" . #(".bai"))))))
(call-with-temporary-directory
(lambda (dir)
(test-equal "Normalize inputs with only location"
(canonicalize-json
(let ((path (expand-file-name "foo" dir)))
`(("class" . "File")
("location" . ,(uri->string (build-uri 'file
#:host ""
#:path path
#:validate? #f)))
("path" . ,path)
("basename" . "foo")
("nameroot" . "foo")
("nameext" . "")
("size" . 0)
("checksum" . "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"))))
(canonicalize-json
(call-with-current-directory dir
(lambda ()
;; Create an actual file called "foo" so that canonicalize-path works.
(call-with-output-file "foo"
(const #t))
(normalize-input '(("class" . "File")
("location" . "foo")))))))))
(call-with-temporary-directory
(lambda (dir)
(test-equal "Normalize inputs with only path"
(canonicalize-json
(let ((path (expand-file-name "foo" dir)))
`(("class" . "File")
("location" . ,(uri->string (build-uri 'file
#:host ""
#:path path
#:validate? #f)))
("path" . ,path)
("basename" . "foo")
("nameroot" . "foo")
("nameext" . "")
("size" . 0)
("checksum" . "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"))))
(canonicalize-json
(call-with-current-directory dir
(lambda ()
;; Create an actual file called "foo" so that canonicalize-path
;; works.
(call-with-output-file "foo"
(const #t))
(normalize-input '(("class" . "File")
("path" . "foo")))))))))
(test-equal "Read YAML inputs file with type ambiguities"
'(("number" . 13)
("flag" . #t)
("reverseflag" . #f)
("foo" . "bar")
("arr" . #(1 2 3)))
(call-with-values
(cut read-workflow+inputs
"test-data/workflow-for-inputs-with-type-ambiguities.cwl"
"test-data/inputs-with-type-ambiguities.yaml")
(lambda (workflow inputs)
inputs)))
(test-end "reader")
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