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;;; ravanan --- High-reproducibility CWL runner powered by Guix
;;; Copyright © 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/>.
(define-module (cwltest-package)
#:use-module ((gnu packages bioinformatics)
#:select (cwltool python-schema-salad))
#:use-module ((gnu packages check)
#:select (python-pytest python-pytest-xdist))
#:use-module ((gnu packages node) #:select (node))
#:use-module ((gnu packages python-build)
#:select (python-setuptools python-setuptools-scm python-wheel))
#:use-module ((gnu packages python-check) #:select (python-junit-xml))
#:use-module ((gnu packages xml) #:select (python-defusedxml))
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages))
;; cwltest uses cwltool as a library. so, create a library version of cwltool
;; where inputs become propagated inputs.
(define python-cwltool
(package
(inherit cwltool)
(name "python-cwltool")
(inputs
(list node))
(propagated-inputs
(modify-inputs (package-inputs cwltool)
(delete "node")))))
;; cwltest requires cwl-runner, the implementation-agnostic entry point to
;; cwltool, for its tests.
(define cwl-runner
(file-union "cwl-runner"
`(("bin/cwl-runner" ,(file-append cwltool "/bin/cwltool")))))
(define-public cwltest
(package
(name "cwltest")
(version "2.6.20250314152537")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cwltest" version))
(sha256
(base32 "0h2w9bllb6cz8d5pja5lbbd1kj08yga40jdi3300anwllczcnfq6"))))
(build-system pyproject-build-system)
(arguments
(list #:modules `((rnrs io ports)
(srfi srfi-1)
(srfi srfi-26)
(srfi srfi-171)
(guix build pyproject-build-system)
(guix build utils))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'disable-docker-in-tests
(lambda _
;; Remove DockerRequirement (lines 7–10).
(let* ((file "tests/test-data/v1.0/cat1-testcli.cwl")
(lines (call-with-input-file file
(cut port-transduce
identity
rcons
get-line
<>))))
(call-with-output-file file
(lambda (port)
(for-each (lambda (line)
(display line port)
(newline port))
(append (take lines 6)
(drop lines 10))))))))
(add-after 'install 'fix-permissions
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make test scripts executable.
(for-each (lambda (file)
(chmod (string-append (site-packages inputs outputs)
"/cwltest/tests/test-data/"
file)
#o755))
(list "dummy-executor.sh"
"mock_cwl_runner.py")))))))
(inputs (list python-defusedxml
python-junit-xml
python-pytest
python-schema-salad))
(native-inputs (list cwl-runner
python-cwltool
python-pytest
python-pytest-xdist
python-setuptools
python-setuptools-scm
python-wheel))
(home-page "https://github.com/common-workflow-language/cwltest")
(synopsis "Common Workflow Language testing framework")
(description "Common Workflow Language testing framework.")
(license license:asl2.0)))
cwltest
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