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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 (cwl-conformance)
#:use-module ((cwltest-package) #:select (cwltest))
#:use-module ((ravanan-package) #:select (ravanan))
#:use-module ((gnu packages bioinformatics) #:select (ccwl))
#:use-module ((gnu packages nss) #:select (nss-certs))
#:use-module ((gnu packages python) #:select (python))
#:use-module ((gnu packages python-web) #:select (python-pybadges))
#:use-module (guix build utils)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix profiles)
#:use-module (guix utils)
#:use-module (ice-9 match))
(define* (cwltest-suite-gexp cwltest-suite manifest-file #:key (skip-tests '()))
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils)
(ice-9 match))
;; cwltest writes out output directories to TMPDIR, but does not clean
;; up after. So, we set TMPDIR to our own temporary directory that we
;; can manage easily. See pending issue on cleaning up temporary output
;; directories:
;; https://github.com/common-workflow-language/cwltest/issues/249
(mkdir "tmpdir")
(setenv "TMPDIR" "tmpdir")
(apply invoke
#$(file-append cwltest "/bin/cwltest")
"--test" #$cwltest-suite
"--tool" #$(file-append ravanan "/bin/ravanan")
"--badgedir" "badges"
(append '#$(match skip-tests
(() '())
(_ (list "-S" (string-join skip-tests ","))))
(list "--"
"--store=store"
(string-append "--guix-manifest=" #$manifest-file)))))))
(define cwl-v1.2-conformance-suite
(let ((version "1.2.1"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/common-workflow-language/cwl-v1.2")
(commit (string-append "v" version))))
(file-name (git-file-name "cwl-v1.2" version))
(sha256
(base32
"03q8pd0niaaff52n6sn07l3rjnvwi4da649lnc8mn928sh0vywf3")))))
(define-public cwl-v1.2-conformance
(program-file "cwl-v1.2-conformance"
(cwltest-suite-gexp
(file-append cwl-v1.2-conformance-suite
"/conformance_tests.yaml")
(local-file "../cwl-conformance/manifest.scm")
;; With these tests, evil things happen and too much memory is
;; consumed. So, disable for now.
#:skip-tests (list "env_home_tmpdir"
"env_home_tmpdir_docker"
"env_home_tmpdir_docker_no_return_code"))))
(define (ccwl-compile source-file)
#~(begin
(use-modules (rnrs io ports)
(srfi srfi-26)
(ice-9 match)
(ice-9 popen))
(define (call-with-input-pipe command proc)
(match command
((prog args ...)
(let ((port #f))
(dynamic-wind
(lambda ()
(set! port (apply open-pipe* OPEN_READ prog args)))
(cut proc port)
(lambda ()
(unless (zero? (close-pipe port))
(error "Command invocation failed" command))))))))
(call-with-output-file #$output
(cut display
(call-with-input-pipe '(#$(file-append ccwl "/bin/ccwl")
"compile"
#$source-file)
get-string-all)
<>))))
(define e2e-tools-ccwl-sources
`(("hello-world.scm" . ,(local-file "../e2e-tests/tools/hello-world.scm"))))
(define e2e-tools
(file-union "e2e-tools"
(map (match-lambda
((ccwl-source-filename . ccwl-source-file)
(let ((cwl-filename (string-append (basename ccwl-source-filename ".scm")
".cwl")))
(list cwl-filename
(computed-file cwl-filename
(ccwl-compile ccwl-source-file))))))
e2e-tools-ccwl-sources)))
(define e2e-test-suite
(file-union "e2e-test-suite"
`(("tests.yaml" ,(local-file "../e2e-tests/tests.yaml"))
("tools" ,e2e-tools)
("jobs" ,(local-file "../e2e-tests/jobs"
#:recursive? #t)))))
(define-public e2e-tests
(program-file "e2e-tests"
(cwltest-suite-gexp (file-append e2e-test-suite "/tests.yaml")
(local-file "../e2e-tests/manifest.scm"))))
(define generate-badges-gexp
(with-imported-modules '((guix build utils))
#~(begin
(use-modules (guix build utils)
(ice-9 match))
(match (command-line)
((_ cwltest-badgedir output-directory)
(set-path-environment-variable
"GUIX_PYTHONPATH"
'(#$(string-append "lib/python"
(version-major+minor (package-version python))
"/site-packages"))
(list #$(profile
(content (packages->manifest
(list python python-pybadges))))))
(invoke #$(file-append python "/bin/python3")
#$(local-file "../cwl-conformance/badgegen.py")
cwltest-badgedir
#$(local-file "../cwl-conformance/commonwl.svg")
output-directory))
((program _ ...)
(format (current-error-port)
"Usage: ~a CWLTEST_BADGEDIR OUTPUT-DIRECTORY~%"
program)
(exit #f))))))
(define-public generate-badges
(program-file "generate-badges"
generate-badges-gexp))
cwl-v1.2-conformance
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