diff options
| -rw-r--r-- | e2e-tests/jobs/unseparated-prefix-arguments.yaml | 1 | ||||
| -rw-r--r-- | e2e-tests/tests.yaml | 9 | ||||
| -rw-r--r-- | e2e-tests/tools/unseparated-prefix-arguments.scm | 3 | ||||
| -rw-r--r-- | ravanan/reader.scm | 18 | ||||
| -rw-r--r-- | ravanan/work/command-line-tool.scm | 44 |
5 files changed, 56 insertions, 19 deletions
diff --git a/e2e-tests/jobs/unseparated-prefix-arguments.yaml b/e2e-tests/jobs/unseparated-prefix-arguments.yaml new file mode 100644 index 0000000..e179c1b --- /dev/null +++ b/e2e-tests/jobs/unseparated-prefix-arguments.yaml @@ -0,0 +1 @@ +message: foo diff --git a/e2e-tests/tests.yaml b/e2e-tests/tests.yaml index 6604e39..70f90f1 100644 --- a/e2e-tests/tests.yaml +++ b/e2e-tests/tests.yaml @@ -250,3 +250,12 @@ class: File size: 8 checksum: sha1$d53a205a336e07cf9eac45471b3870f9489288ec +- id: unseparated-prefix-arguments + doc: Prefix arguments with separate as false + tool: tools/unseparated-prefix-arguments.cwl + job: jobs/unseparated-prefix-arguments.yaml + output: + output_message: + class: File + size: 12 + checksum: sha1$598114d347c67f3f6142f60a4b5afcb3482f27a8 diff --git a/e2e-tests/tools/unseparated-prefix-arguments.scm b/e2e-tests/tools/unseparated-prefix-arguments.scm new file mode 100644 index 0000000..03f68e2 --- /dev/null +++ b/e2e-tests/tools/unseparated-prefix-arguments.scm @@ -0,0 +1,3 @@ +(command #:inputs (message #:type string) + #:run "echo" ("-a" message #:separate? #f) ("-b" "bar" #:separate? #f) + #:outputs (output_message #:type stdout)) diff --git a/ravanan/reader.scm b/ravanan/reader.scm index bb825ed..35545dd 100644 --- a/ravanan/reader.scm +++ b/ravanan/reader.scm @@ -156,6 +156,17 @@ the @code{required} field when it is not specified." (vector `(("pattern" . ,secondary-files) ("required" . ,default-required)))))) +(define (normalize-command-line-binding binding) + "Normalize @code{CommandLineBinding} @var{binding}." + (assoc-set binding + (cons "separate" + (cond + ((assoc "separate" binding) + => (match-lambda + ((_ . separate) + (coerce-type separate 'boolean)))) + (else #t))))) + (define (normalize-formal-input input) "Normalize formal @var{input}." (maybe-assoc-set input @@ -167,7 +178,10 @@ the @code{required} field when it is not specified." (cons "secondaryFiles" (maybe-bind (maybe-assoc-ref (just input) "secondaryFiles") (compose just - (cut normalize-secondary-files <> #t)))))) + (cut normalize-secondary-files <> #t)))) + (cons "inputBinding" + (maybe-bind (maybe-assoc-ref (just input) "inputBinding") + (compose just normalize-command-line-binding))))) (define (normalize-formal-output output) "Normalize formal @var{output}." @@ -192,7 +206,7 @@ the @code{required} field when it is not specified." ((string? argument) `(("valueFrom" . ,argument))) ((list? argument) - argument) + (normalize-command-line-binding argument)) (else (error "Invalid argument" argument)))) arguments)))) diff --git a/ravanan/work/command-line-tool.scm b/ravanan/work/command-line-tool.scm index 95d69f5..cb945f9 100644 --- a/ravanan/work/command-line-tool.scm +++ b/ravanan/work/command-line-tool.scm @@ -296,12 +296,13 @@ condition on unsupported URI schemes." json->scm))) (define-immutable-record-type <command-line-binding> - (command-line-binding position prefix type value item-separator) + (command-line-binding position prefix type value separate? item-separator) command-line-binding? (position command-line-binding-position) (prefix command-line-binding-prefix) (type command-line-binding-type) (value command-line-binding-value) + (separate? command-line-binding-separate?) (item-separator command-line-binding-item-separator)) (define (command-line-binding->args binding) @@ -332,17 +333,20 @@ the G-expressions are inserted." (just (list (string-join args item-separator)))) args)))))) (else - (append (maybe->list prefix) - (list (case type - ((string) - value) - ((int float) - (number->string value)) - ((File) - (assoc-ref* value "path")) - (else - (user-error "Invalid formal input type ~a" - type))))))))) + (let ((args (append (maybe->list prefix) + (list (case type + ((string) + value) + ((int float) + (number->string value)) + ((File) + (assoc-ref* value "path")) + (else + (user-error "Invalid formal input type ~a" + type))))))) + (if (command-line-binding-separate? binding) + args + (list (string-join args "")))))))) (define (build-command base-command arguments formal-inputs inputs) "Return a list of @code{<command-line-binding>} objects for a @@ -351,7 +355,7 @@ the G-expressions are inserted." @code{<command-line-binding>} objects may be strings or G-expressions. The G-expressions may reference @var{inputs} and @var{runtime} variables that must be defined in the context in which the G-expressions are inserted." - (define (value->command-line-binding position prefix value) + (define (value->command-line-binding position prefix value separate?) (let ((type (object-type value))) (cond ((cwl-array-type? type) @@ -361,11 +365,13 @@ be defined in the context in which the G-expressions are inserted." (vector-map (cut value->command-line-binding %nothing %nothing - <>) + <> + #f) value) + separate? %nothing)) (else - (command-line-binding position prefix type value %nothing))))) + (command-line-binding position prefix type value separate? %nothing))))) (define (argument->command-line-binding i argument) (value->command-line-binding (cond @@ -373,7 +379,8 @@ be defined in the context in which the G-expressions are inserted." => string->number) (else i)) (maybe-assoc-ref (just argument) "prefix") - (assoc-ref* argument "valueFrom"))) + (assoc-ref* argument "valueFrom") + (assoc-ref* argument "separate"))) (define (collect-bindings ids+inputs+types+bindings) (map id+input+type-tree+binding->command-line-binding @@ -399,7 +406,8 @@ be defined in the context in which the G-expressions are inserted." (just (string->number position))) ;; FIXME: Why a default value of 0? 0)) - (prefix (maybe-assoc-ref binding "prefix"))) + (prefix (maybe-assoc-ref binding "prefix")) + (separate? (maybe-bind binding (cut assoc-ref* <> "separate")))) (cond ;; Recurse over array types. ;; TODO: Implement record and enum types. @@ -416,12 +424,14 @@ be defined in the context in which the G-expressions are inserted." (maybe-assoc-ref (just type-tree) "inputBinding")))) input) + separate? (maybe-assoc-ref binding "itemSeparator"))) (else (command-line-binding position prefix matched-type (apply json-ref inputs id) + separate? %nothing)))))))) ;; For details of this algorithm, see ยง4.1 Input binding of the CWL |