diff options
| -rw-r--r-- | .guix/e2e-tests.scm | 6 | ||||
| -rw-r--r-- | HACKING.md | 2 | ||||
| -rw-r--r-- | e2e-tests/jobs/command-line-tool-with-array-input.yaml | 3 | ||||
| -rw-r--r-- | e2e-tests/jobs/unseparated-prefix-arguments.yaml | 1 | ||||
| -rw-r--r-- | e2e-tests/tests.yaml | 18 | ||||
| -rw-r--r-- | e2e-tests/tools/command-line-tool-with-array-input.scm | 3 | ||||
| -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 | 85 | ||||
| -rw-r--r-- | ravanan/workflow.scm | 15 |
10 files changed, 104 insertions, 50 deletions
diff --git a/.guix/e2e-tests.scm b/.guix/e2e-tests.scm index 4dfc8b0..201d482 100644 --- a/.guix/e2e-tests.scm +++ b/.guix/e2e-tests.scm @@ -26,8 +26,8 @@ #:use-module (ice-9 match)) (define-public ccwl - (let ((commit "5f6e0d93bb08446d2c6f99484523697a2bda7b4d") - (revision "1")) + (let ((commit "4f757fc0a4d4af067e0d22ad4020c1b18cc3fd24") + (revision "2")) (package (inherit guix:ccwl) (name "ccwl") @@ -40,7 +40,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "19hwkgj8gsfw24fs682b4wxs5chnwj6hv0rvs23vmq7309mgf242")))) + "0jch7pr85r2cd9g4b4gq748mbnbi5jg0dqyp8ixhhwac2yqbmyqh")))) (native-inputs (modify-inputs (package-native-inputs guix:ccwl) (prepend guile-run64)))))) diff --git a/HACKING.md b/HACKING.md index 4d8b6fe..7df6d02 100644 --- a/HACKING.md +++ b/HACKING.md @@ -18,8 +18,6 @@ $(guix build -L ../.guix -f ../.guix/e2e-tests.scm) ``` Since ravanan depends on guix, and that guix may be too old, you may need to run this command outside the usual development environment. -## Run specific end-to-end test - When hacking on ravanan, you may be trying to get a specific test to pass, and may want to repeatedly run that specific test alone. You can do this by passing additional cwltest arguments. For example, to only run the `hello-world` test: ``` $(guix build -L ../.guix -f ../.guix/e2e-tests.scm) -s hello-world diff --git a/e2e-tests/jobs/command-line-tool-with-array-input.yaml b/e2e-tests/jobs/command-line-tool-with-array-input.yaml new file mode 100644 index 0000000..a0fc50c --- /dev/null +++ b/e2e-tests/jobs/command-line-tool-with-array-input.yaml @@ -0,0 +1,3 @@ +messages: + - foo + - bar 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 d14b93a..70f90f1 100644 --- a/e2e-tests/tests.yaml +++ b/e2e-tests/tests.yaml @@ -241,3 +241,21 @@ class: File size: 13 checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b +- id: command-line-tool-with-array-input + doc: CommandLineTool with array input + tool: tools/command-line-tool-with-array-input.cwl + job: jobs/command-line-tool-with-array-input.yaml + output: + output_message: + class: File + size: 8 + checksum: sha1$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/command-line-tool-with-array-input.scm b/e2e-tests/tools/command-line-tool-with-array-input.scm new file mode 100644 index 0000000..38a8722 --- /dev/null +++ b/e2e-tests/tools/command-line-tool-with-array-input.scm @@ -0,0 +1,3 @@ +(command #:inputs (messages #:type (array string)) + #:run "echo" messages + #:outputs (output_message #:type stdout)) 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 175a561..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 @@ -373,11 +379,12 @@ 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) - (append-map id+input+type-tree+binding->command-line-binding - ids+inputs+types+bindings)) + (map id+input+type-tree+binding->command-line-binding + ids+inputs+types+bindings)) (define id+input+type-tree+binding->command-line-binding (match-lambda @@ -399,31 +406,33 @@ 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. ((cwl-array-type? matched-type) - (list (command-line-binding - position - prefix - matched-type - (append-map (lambda (i input) - (id+input+type-tree+binding->command-line-binding - (list (append id (list i)) - input - (assoc-ref type-tree "items") - (maybe-assoc-ref (just type-tree) - "inputBinding")))) - (iota (vector-length input)) - (vector->list input)) - (maybe-assoc-ref binding "itemSeparator")))) + (command-line-binding + position + prefix + matched-type + (vector-map-indexed (lambda (i input) + (id+input+type-tree+binding->command-line-binding + (list (append id (list i)) + input + (assoc-ref type-tree "items") + (maybe-assoc-ref (just type-tree) + "inputBinding")))) + input) + separate? + (maybe-assoc-ref binding "itemSeparator"))) (else - (list (command-line-binding position - prefix - matched-type - (apply json-ref inputs id) - %nothing))))))))) + (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 ;; 1.2 CommandLineTool specification: diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm index 2fd00d6..0451f68 100644 --- a/ravanan/workflow.scm +++ b/ravanan/workflow.scm @@ -279,11 +279,16 @@ command-line-tool)}." #()) (or (assoc-ref cwl "hints") #())) - (vector-map->list (lambda (input) - (let ((input-id (assoc-ref input "id"))) - (cons input-id - (json-ref step "in" input-id)))) - (assoc-ref run "inputs")) + (vector-filter-map->list (lambda (input) + (let ((input-id (assoc-ref* input "id"))) + (match (assoc input-id + (assoc-ref* step "in")) + ((_ . source) + (cons input-id source)) + ;; Optional inputs may be + ;; missing a source; drop them. + (#f #f)))) + (assoc-ref* run "inputs")) ;; Inputs that either have a default or accept null values are ;; optional. (vector-filter-map->list (lambda (input) |