Add CWL generator for CommandLineTool workflows

1 files changed, 130 insertions, 0 deletions

diff --git a/scripts/generate-cwl.scm b/scripts/generate-cwl.scm
new file mode 100644
index 0000000..a28cdb0
--- /dev/null
+++ b/scripts/generate-cwl.scm
@@ -0,0 +1,130 @@
+;;
+;; CWL generator
+;;
+;; This file implements a generator to generate CWL files.
+
+(define-module (generate-cwl)
+  #:use-module (rnrs records syntactic)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-71)
+  #:use-module (ice-9 match)
+  #:export (clitool
+            workflow
+            input
+            output
+            step
+            workflow-output))
+
+(define-record-type (<input> make-input input?)
+  (fields (immutable id input-id)
+          (immutable type input-type)
+          (immutable default input-default)
+          (immutable label input-label)
+          (immutable other input-other)))
+
+(define-record-type unspecified-default)
+
+(define* (input id #:key type label (default (make-unspecified-default)) (other '()))
+  "Build and return an <input> object."
+  (make-input id type default label other))
+
+(define-record-type (<output> make-output output?)
+  (fields (immutable id output-id)
+          (immutable type output-type)
+          (immutable binding output-binding)
+          (immutable other output-other)))
+
+(define* (output id #:key type binding (other '()))
+  "Build and return an <output> object."
+  (make-output id type binding other))
+
+(define* (parse-arguments args #:optional (position 1))
+  "Parse ARGS, a list of command line arguments and return a parse
+tree of labelled arguments. POSITION is an internal recursion
+variable."
+  (match args
+    (((? string? head) tail ...)
+     (if (string-prefix? "-" head)
+         (match tail
+           ((tail-head tail ...)
+            (cons (list 'keyword head tail-head)
+                  (parse-arguments tail position))))
+         (error "Unrecognized argument" head)))
+    ((head tail ...)
+     (cons (list 'positional position head)
+           (parse-arguments tail (1+ position))))
+    (() '())))
+
+(define (parse-command args)
+  "Parse ARGS, a list of command line arguments and return two
+lists---the base command and the actual arguments."
+  (let ((base-command arguments
+                      (break (match-lambda
+                               ((arg next)
+                                (and (string? arg)
+                                     (string-prefix? "-" arg)
+                                     (input? next))))
+                             (map list args (drop args 1)))))
+    (values (append (map (match-lambda
+                           ((arg next) arg))
+                         base-command)
+                    (if (input? (last args))
+                        (list)
+                        (take-right args 1)))
+            (parse-arguments
+             (append (map (match-lambda
+                            ((arg next) arg))
+                          arguments)
+                     (if (input? (last args))
+                         (take-right args 1)
+                         (list)))))))
+
+(define (input->tree input)
+  "Convert INPUT, an <input> object, to a tree."
+  `(,(input-id input)
+    ,@(filter identity
+              (list (and (input-type input)
+                         (cons 'type (input-type input)))
+                    (and (input-label input)
+                         (cons 'label (input-label input)))
+                    (and (not (unspecified-default? (input-default input)))
+                         (cons 'default (input-default input)))))
+    ,@(input-other input)))
+
+(define* (clitool args #:key (additional-inputs '()) (outputs '()) stdout stderr (other '()))
+  "Build a CommandLineTool class CWL workflow."
+  (let ((base-command arguments (parse-command args)))
+    `((cwl-version . "v1.1")
+      (class . Command-line-tool)
+      ,@other
+      (base-command . ,(list->vector base-command))
+      ,@(let ((inputs (append arguments additional-inputs)))
+          (if (not (null? inputs))
+              `((inputs . ,(map (match-lambda
+                                  (('keyword prefix input)
+                                   (append (input->tree input)
+                                           `((input-binding (prefix . ,prefix)))))
+                                  (('positional position input)
+                                   (append (input->tree input)
+                                           `((input-binding (position . ,position)))))
+                                  (input
+                                   (input->tree input)))
+                                inputs)))
+              (list)))
+      ,@(if (or (not (null? outputs)) stdout stderr)
+            `((outputs . ,(map (lambda (output)
+                                 `(,(output-id output)
+                                   ,@(filter identity
+                                             (list (and (output-type output)
+                                                        (cons 'type (output-type output)))
+                                                   (and (output-binding output)
+                                                        (cons 'output-binding (output-binding output)))))
+                                   ,@(output-other output)))
+                               outputs)))
+            (list))
+      ,@(if stdout
+            `((stdout . ,stdout))
+            '())
+      ,@(if stderr
+            `((stderr . ,stderr))
+            '()))))