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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)
(ravanan work vectors))
(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 inputs with only location"
(canonicalize-json
(let ((path (canonicalize-path "test-data/foo")))
`(("class" . "File")
("location" . ,(uri->string (build-uri 'file
#:host ""
#:path path
#:validate? #f)))
("path" . ,path)
("basename" . "foo")
("nameroot" . "foo")
("nameext" . "")
("size" . 0)
("checksum" . "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"))))
(call-with-values
(cut read-workflow+inputs
"test-data/workflow-with-a-file-input.cwl"
"test-data/input-file-with-location-only.yaml")
(lambda (workflow inputs)
(canonicalize-json (assoc-ref inputs "foo")))))
(test-equal "Normalize inputs with only path"
(canonicalize-json
(let ((path (canonicalize-path "test-data/foo")))
`(("class" . "File")
("location" . ,(uri->string (build-uri 'file
#:host ""
#:path path
#:validate? #f)))
("path" . ,path)
("basename" . "foo")
("nameroot" . "foo")
("nameext" . "")
("size" . 0)
("checksum" . "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709"))))
(call-with-values
(cut read-workflow+inputs
"test-data/workflow-with-a-file-input.cwl"
"test-data/input-file-with-path-only.yaml")
(lambda (workflow inputs)
(canonicalize-json (assoc-ref inputs "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-equal "Resolve type ambiguities in workflow default inputs"
'(("number" . 13)
("flag" . #t)
("reverseflag" . #f)
("foo" . "bar")
("arr" . #(1 2 3)))
(call-with-values
(cut read-workflow+inputs
"test-data/workflow-with-default-inputs.cwl"
"test-data/empty.yaml")
(lambda (workflow inputs)
(vector-map->list (lambda (input)
(cons (assoc-ref input "id")
(assoc-ref input "default")))
(assoc-ref workflow "inputs")))))
(test-equal "Normalize File type formals"
(list (vector-map canonicalize-json
#((("id" . "infoo")
("type" . "File")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t)))))
(("id" . "inbar")
("type"
("type" . "array")
("items" . "File"))
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t)))))
(("id" . "infoobar")
("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #t)))))))
(vector-map canonicalize-json
#((("id" . "outfoo")
("type" . "File")
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f)))))
(("id" . "outbar")
("type"
("type" . "array")
("items" . "File"))
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f)))))
(("id" . "outfoobar")
("type"
("type" . "array")
("items" . (("type" . "array")
("items" . "File"))))
("secondaryFiles" . #((("pattern" . ".bai")
("required" . #f))))))))
(call-with-values
(cut read-workflow+inputs
"test-data/workflow-with-various-file-type-formals.cwl"
"test-data/empty.yaml")
(lambda (workflow inputs)
(list (vector-map canonicalize-json
(assoc-ref workflow "inputs"))
(vector-map canonicalize-json
(assoc-ref workflow "outputs"))))))
(test-end "reader")
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