propnet: Support optional inputs.

* ravanan/propnet.scm (<propagator>)[optional-inputs]: New field.
* ravanan/propnet.scm (activate-propagator): Activate propagator even
when optional inputs are absent.
* ravanan/workflow.scm: Import (ravanan work utils).
(command-line-tool->propagator, workflow-class->propagators): Specify
optional inputs of propagators.
(workflow->command-line-tool-steps): Inherit defaults down to the steps from the
containing workflow.
[inherit-defaults]: New function.

2 files changed, 36 insertions, 4 deletions

diff --git a/ravanan/propnet.scm b/ravanan/propnet.scm
index 396f6d5..4eef452 100644
--- a/ravanan/propnet.scm
+++ b/ravanan/propnet.scm
@@ -34,6 +34,7 @@
             propagator-name
             propagator-proc
             propagator-inputs
+            propagator-optional-inputs
             propagator-outputs
             scheduler
             scheduler-schedule
@@ -51,11 +52,12 @@
   (scheduler propnet-scheduler))
 
 (define-immutable-record-type <propagator>
-  (propagator name proc inputs outputs)
+  (propagator name proc inputs optional-inputs outputs)
   propagator?
   (name propagator-name)
   (proc propagator-proc)
   (inputs propagator-inputs)
+  (optional-inputs propagator-optional-inputs)
   (outputs propagator-outputs))
 
 (define-immutable-record-type <scheduler>
@@ -76,7 +78,8 @@ required inputs are absent, do nothing. Schedule the propagator using
                                (propagator-inputs propagator))
                           (map (match-lambda
                                  ((input-name . _) input-name))
-                               inputs-alist))
+                               inputs-alist)
+                          (propagator-optional-inputs propagator))
     (() (just (schedule (propagator-proc propagator) inputs-alist)))
     (_ %nothing)))
 
diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm
index 6764269..b30c386 100644
--- a/ravanan/workflow.scm
+++ b/ravanan/workflow.scm
@@ -28,6 +28,7 @@
   #:use-module (ravanan utils)
   #:use-module (ravanan vectors)
   #:use-module (ravanan work command-line-tool)
+  #:use-module (ravanan work utils)
   #:export (run-workflow))
 
 (define %supported-requirements
@@ -130,6 +131,15 @@ propagator."
                                   (cons (assoc-ref input "id")
                                         (assoc-ref input "id")))
                                 (assoc-ref cwl "inputs"))
+              ;; Inputs that either have a default or accept null values are
+              ;; optional.
+              (vector-filter-map->list (lambda (input)
+                                         (and (or (assoc-ref input "default")
+                                                  (match-type 'null
+                                                              (formal-parameter-type
+                                                               (assoc-ref* input "type"))))
+                                              (assoc-ref input "id")))
+                                       (assoc-ref cwl "inputs"))
               (vector-map->list (lambda (output)
                                   (cons (assoc-ref output "id")
                                         (assoc-ref output "id")))
@@ -138,11 +148,29 @@ propagator."
 (define (workflow->command-line-tool-steps cwl)
   "Recursively traverse @var{cwl} tree and return a list of
 @code{CommandLineTool} class steps."
+  (define (inherit-defaults step-run step-in)
+    "Augment the @var{step-run} CWL tree with defaults from the containing
+workflow. @var{step-in} is the inputs mapping association list of the step."
+    (assoc-set step-run
+      (cons "inputs"
+            (vector-map (lambda (input)
+                          (let* ((input-id (assoc-ref input "id"))
+                                 (input-source (assoc-ref step-in input-id)))
+                            (maybe-assoc-set input
+                              (cons "default"
+                                    (maybe-assoc-ref (just cwl)
+                                                     "inputs"
+                                                     input-source
+                                                     "default")))))
+                        (assoc-ref* step-run "inputs")))))
+
   (vector-append-map->list (lambda (step)
-                             (let ((run (assoc-ref step "run")))
+                             (let ((run (inherit-defaults (assoc-ref step "run")
+                                                          (assoc-ref step "in"))))
                                (if (string=? (assoc-ref run "class")
                                              "CommandLineTool")
-                                   (list step)
+                                   (list (assoc-set step
+                                           (cons "run" run)))
                                    (workflow->command-line-tool-steps
                                     (inherit-requirements-and-hints
                                      run
@@ -173,6 +201,7 @@ their own namespaces."
                                     (propagator-name step-propagator))
                        (propagator-proc step-propagator)
                        (assoc-ref step "in")
+                       (propagator-optional-inputs step-propagator)
                        (vector-map->list (lambda (output-name)
                                            (cons output-name
                                                  (prefix-name step-id output-name)))