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;;; ccwl --- Concise Common Workflow Language
;;; Copyright © 2021, 2022, 2023 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/>.
(use-modules (rnrs exceptions)
(srfi srfi-64)
(ccwl ccwl)
(ccwl conditions))
(define input
(@@ (ccwl ccwl) input))
(define output
(@@ (ccwl ccwl) output))
(test-begin "ccwl")
(test-assert "stdin input should not have inputBinding"
(not (assoc-ref
(assoc-ref
(assoc-ref
((@@ (ccwl cwl) command->cwl-scm)
(command #:inputs (file #:type File)
#:run "wc" "-c"
#:stdin file))
'inputs)
'file)
'inputBinding)))
(test-equal "read all forms of inputs and outputs from a CWL workflow"
'(((spam string))
((ham stdout)
(eggs stdout)))
(let ((cwl-workflow (cwl-workflow "tests/input-output-parameters.cwl")))
(list (map (lambda (input)
(list (input-id input)
(input-type input)))
(cwl-workflow-inputs cwl-workflow))
(map (lambda (output)
(list (output-id output)
(output-type output)))
(cwl-workflow-outputs cwl-workflow)))))
(test-assert "input, when passed more than one positional argument, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (input #'(message string))
#f)))
(test-assert "input, when passed an unrecognized keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (input #'(message #:foo string))
#f)))
(test-assert "input, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (input #'(message #:type int string))
#f)))
(test-assert "output, when passed more than one positional argument, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (output #'(message string))
#f)))
(test-assert "output, when passed an unrecognized keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (output #'(message #:foo string))
#f)))
(test-assert "output, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (output #'(message #:type int string))
#f)))
(test-assert "command, when passed positional arguments, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (macroexpand
'(command foo
#:inputs (message #:type string)
#:run "echo" message
#:outputs (stdout #:type stdout)))
#f)))
(test-assert "command, when passed an unrecognized keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (macroexpand
'(command #:foo (message #:type string)
#:run "echo" message
#:outputs (stdout #:type stdout)))
#f)))
(test-assert "command, when passed multiple arguments to a unary keyword, must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (macroexpand
'(command #:inputs (message #:type string)
#:run "echo" message
#:outputs (stdout #:type stdout)
#:stdin "foo" "bar"))
#f)))
;; TODO: Define this in the lexical scope of the test that requires
;; it.
(define print
(command #:inputs (message #:type string)
#:run "echo" message
#:outputs (printed-message #:type stdout)))
(test-equal "rename should work even on the final output of a workflow"
(map output-id
(workflow-outputs
(workflow ((message1 #:type string)
(message2 #:type string))
(tee (pipe (print (print1) #:message message1)
(rename #:out1 printed-message))
(print (print2) #:message message2)))))
(list 'out1 'printed-message))
;; TODO: Define this in the lexical scope of the test that requires
;; it.
(define print-with-default
(command #:inputs (message #:type string #:default "Hello")
#:run "echo" message
#:outputs (printed-message #:type stdout)))
(test-assert "allow steps with unspecified default arguments"
(workflow ()
(print-with-default)))
(test-assert "allow steps with expressions that evaluate to commands"
(workflow ((message #:type string))
((and #t print)
(print)
#:message message)))
(test-assert "step with expression that evaluates to a command but without a step identifier must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (macroexpand
'(workflow ((message #:type string))
((and #t print)
#:message message)))
#f)))
(test-assert "allow literal strings as arguments"
(workflow ()
(print #:message "Hello")))
;; TODO: Define this in the lexical scope of the test that requires
;; it.
(define print-int
(command #:inputs (number #:type int)
#:run "echo" number
#:outputs (printed-number #:type stdout)))
(test-assert "allow literal ints as arguments"
(workflow ()
(print-int #:number 42)))
(test-assert "step supplied with an unknown key must raise a &ccwl-violation condition"
(guard (exception
(else (ccwl-violation? exception)))
(begin (macroexpand
'(workflow ((message #:type string))
(print #:message mess)))
#f)))
(test-assert "unrecognized workflow syntaxes must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Unrecognized workflow syntax [expected (workflow (input ...) tree)]"))))
(begin (macroexpand
'(workflow foo ((message #:type string))
(print #:message message)))
#f)))
(test-assert "multiple expressions in workflow body must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"More than one expression ~a in workflow body. Perhaps you need to combine them with a pipe or a tee?"))))
(begin (macroexpand
'(workflow ((message1 #:type string)
(message2 #:type string))
(print (print1) #:message message1)
(print (print2) #:message message2)))
#f)))
(test-assert "commands with non-string #:stderr parameters must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Invalid #:stderr parameter ~a. #:stderr parameter must be a string"))))
(begin (macroexpand
'(command #:inputs (message #:type string)
#:run "echo" message
#:outputs (printed #:type stderr)
#:stderr captured-stderr))
#f)))
(test-assert "commands with non-string #:stdout parameters must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Invalid #:stdout parameter ~a. #:stdout parameter must be a string"))))
(begin (macroexpand
'(command #:inputs (message #:type string)
#:run "echo" message
#:outputs (printed #:type stdout)
#:stdout captured-stdout))
#f)))
(test-assert "command definitions with undefined inputs in their #:run arguments must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Undefined input ~a"))))
(begin (macroexpand
'(command #:inputs (number #:type int)
#:run "echo" n))
#f)))
(test-assert "command definitions with undefined prefix inputs in their #:run arguments must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Undefined input ~a"))))
(begin (macroexpand
'(command #:inputs (number #:type int)
#:run "echo" ("-x" n)))
#f)))
(test-assert "command definitions with invalid #:run arguments must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Invalid command element ~a. Command elements must either be input identifiers or literal strings."))))
(begin (macroexpand
'(command #:run "echo" 42))
#f)))
(test-assert "tolerate prefixed string arguments in command definitions"
(command #:run "echo" ("-x" "foo")))
(test-assert "command definitions with non-string prefixes in prefixed inputs must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Invalid prefix ~a. Prefixes must be strings."))))
(begin (macroexpand
'(command #:inputs (number #:type int)
#:run "echo" (-x number)))
#f)))
(test-assert "inputs with an invalid #:stage? parameter must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"Invalid #:stage? parameter ~a. #:stage? must either be #t or #f."))))
(begin (macroexpand
'(command #:inputs (file #:type File
#:stage? 42)
#:run "cat" file))
#f)))
(test-assert "inputs with #:other parameters that fail to evaluate must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"#:other parameter not serializable to YAML"))))
(begin (macroexpand
'(command #:inputs (file #:type File
#:other '((secondaryFiles . ".fai")))
#:run "cat" file))
#f)))
(test-assert "outputs with #:other parameters that fail to evaluate must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"#:other parameter not serializable to YAML"))))
(begin (macroexpand
'(command #:outputs (file #:type File
#:other '((secondaryFiles . ".fai")))
#:run "cat" file))
#f)))
(test-assert "commands with #:other parameters that fail to evaluate must raise a &ccwl-violation condition"
(guard (exception
(else (and (ccwl-violation? exception)
(string=? (formatted-message-format exception)
"#:other parameter not serializable to YAML"))))
(begin (macroexpand
'(command #:run "cat" file
#:other '((secondaryFiles . ".fai"))))
#f)))
(test-end "ccwl")
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