diff options
| -rw-r--r-- | ravanan/workflow.scm | 83 |
1 files changed, 33 insertions, 50 deletions
diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm index ee01942..25a42c1 100644 --- a/ravanan/workflow.scm +++ b/ravanan/workflow.scm @@ -168,24 +168,6 @@ requirements and hints of the step." (assoc-ref* input "type")))) (assoc-ref input "id"))) -(define* (command-line-tool->propagator name cwl) - "Convert @code{CommandLineTool} workflow @var{cwl} of @var{name} to a -propagator." - (propagator name - (scheduler-proc name cwl %nothing %nothing) - (vector-map->list (lambda (input) - (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 optional-input? - (assoc-ref cwl "inputs")) - (vector-map->list (lambda (output) - (cons (assoc-ref output "id") - (assoc-ref output "id"))) - (assoc-ref cwl "outputs")))) - (define* (workflow-class->propnet name cwl scheduler batch-system) "Return a propagator network scheduled using @var{scheduler} on @var{batch-system} for @var{cwl}, a @code{Workflow} class workflow with @@ -197,38 +179,39 @@ propagator." scatter-method)) (define (step->propagator step) - (let* ((step-id (assoc-ref* step "id")) - (step-propagator - (command-line-tool->propagator step-id (assoc-ref* step "run")))) - (propagator (propagator-name step-propagator) - (let ((proc (propagator-proc step-propagator))) - (scheduler-proc (scheduler-proc-name proc) - (inherit-requirements-and-hints - (scheduler-proc-cwl proc) - (or (assoc-ref cwl "requirements") - #()) - (or (assoc-ref cwl "hints") - #()) - (or (assoc-ref step "requirements") - #()) - (or (assoc-ref step "hints") - #())) - (maybe-assoc-ref (just step) "scatter") - (maybe-bind (maybe-assoc-ref (just step) "scatterMethod") - (compose just normalize-scatter-method)))) - (map (match-lambda - ((input-id . _) - (cons input-id - (json-ref step "in" input-id)))) - (propagator-inputs step-propagator)) - (propagator-optional-inputs step-propagator) - (filter-map (match-lambda - ((output . cell) - (and (vector-member output - (assoc-ref* step "out")) - (cons output - (string-append step-id "/" cell))))) - (propagator-outputs step-propagator))))) + (let ((step-id (assoc-ref* step "id")) + (run (assoc-ref* step "run"))) + (propagator step-id + (scheduler-proc step-id + (inherit-requirements-and-hints + run + (or (assoc-ref cwl "requirements") + #()) + (or (assoc-ref cwl "hints") + #()) + (or (assoc-ref step "requirements") + #()) + (or (assoc-ref step "hints") + #())) + (maybe-assoc-ref (just step) "scatter") + (maybe-bind (maybe-assoc-ref (just step) "scatterMethod") + (compose just normalize-scatter-method))) + (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")) + ;; Inputs that either have a default or accept null values are + ;; optional. + (vector-filter-map->list optional-input? + (assoc-ref run "inputs")) + (vector-map->list (lambda (output) + (let ((output-id (assoc-ref output "id"))) + (and (vector-member output-id + (assoc-ref* step "out")) + (cons output-id + (string-append step-id "/" output-id))))) + (assoc-ref run "outputs"))))) (maybe-let* ((requirements (maybe-assoc-ref (just cwl) "requirements"))) (check-requirements requirements |