diff options
| -rw-r--r-- | ravanan/command-line-tool.scm | 55 | ||||
| -rw-r--r-- | ravanan/workflow.scm | 29 |
2 files changed, 64 insertions, 20 deletions
diff --git a/ravanan/command-line-tool.scm b/ravanan/command-line-tool.scm index 1e32767..6a48a20 100644 --- a/ravanan/command-line-tool.scm +++ b/ravanan/command-line-tool.scm @@ -48,6 +48,7 @@ check-requirements inherit-requirements %command-line-tool-supported-requirements + command-line-tool-supported-requirements script->store-stdout-file script->store-stderr-file capture-command-line-tool-output @@ -70,6 +71,9 @@ "InlineJavascriptRequirement" "InitialWorkDirRequirement")) +(define (command-line-tool-supported-requirements batch-system) + %command-line-tool-supported-requirements) + ;; node executable for evaluating javascript on worker nodes (define %worker-node (file-append node "/bin/node")) @@ -99,18 +103,34 @@ (load-listing? output-binding-load-listing?) (output-eval output-binding-output-eval)) -(define* (check-requirements requirements supported-requirements +(define* (check-requirements requirements + batch-system + supported-requirements-for-batch-system + supported-requirements #:optional hint?) - "Error out if any of @var{requirements} are not in -@var{supported-requirements}. If @var{hint?} is @code{#t}, only print a warning." + "Error out if any of @var{requirements} are not supported by @var{batch-system}. +If @var{hint?} is @code{#t}, only print a warning. +@var{supported-requirements-for-batch-system} is a function that when passed a +batch system returns the requirements supported by it. +@var{supported-requirements} is the list of requirements supported by at least +one batch system." (vector-for-each (lambda (requirement) (let ((class (assoc-ref requirement "class"))) - (unless (member class supported-requirements) + (unless (member class + (supported-requirements-for-batch-system batch-system)) (if hint? - (warning "Ignoring ~a hint; it is not supported" - class) - (user-error "Requirement ~a not supported" - class))))) + (if (member class supported-requirements) + (warning "Ignoring ~a hint; it is not supported for batch system ~a" + class + batch-system) + (warning "Ignoring ~a hint; it is not supported" + class)) + (if (member class supported-requirements) + (user-error "Requirement ~a not supported for batch system ~a" + class + batch-system) + (user-error "Requirement ~a not supported" + class)))))) requirements)) (define (inherit-requirements requirements supplementary-requirements) @@ -384,7 +404,8 @@ path." ;; TODO: Write to the store atomically. (let* ((script (build-command-line-tool-script name manifest cwl inputs - scratch store guix-daemon-socket)) + scratch store batch-system + guix-daemon-socket)) (store-files-directory (script->store-files-directory script store)) (store-data-file (script->store-data-file script store)) (stdout-file (script->store-stdout-file script store)) @@ -548,10 +569,11 @@ order of keys." (else tree))) (define (build-command-line-tool-script name manifest cwl inputs - scratch store guix-daemon-socket) + scratch store batch-system + guix-daemon-socket) "Build and return script to run @code{CommandLineTool} class workflow @var{cwl} named @var{name} with @var{inputs} using tools from Guix manifest -@var{manifest}. +@var{manifest} and on @var{batch-system}. @var{scratch}, @var{store} and @var{guix-daemon-socket} are the same as in @code{run-workflow} from @code{(ravanan workflow)}." @@ -685,9 +707,16 @@ named @var{name} with @var{inputs} using tools from Guix manifest (newline out))))) (maybe-let* ((requirements (maybe-assoc-ref (just cwl) "requirements"))) - (check-requirements requirements %command-line-tool-supported-requirements)) + (check-requirements requirements + batch-system + command-line-tool-supported-requirements + %command-line-tool-supported-requirements)) (maybe-let* ((hints (maybe-assoc-ref (just cwl) "hints"))) - (check-requirements hints %command-line-tool-supported-requirements #t)) + (check-requirements hints + batch-system + command-line-tool-supported-requirements + %command-line-tool-supported-requirements + #t)) ;; Copy input files and update corresponding input objects. (build-gexp-script name (let* ((requirements (inherit-requirements (or (assoc-ref cwl "requirements") diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm index 92aec96..af720a8 100644 --- a/ravanan/workflow.scm +++ b/ravanan/workflow.scm @@ -38,10 +38,17 @@ #:use-module (ravanan work vectors) #:export (run-workflow)) +(define %workflow-only-requirements + (list "ScatterFeatureRequirement" + "SubworkflowFeatureRequirement")) + (define %supported-requirements - (cons* "ScatterFeatureRequirement" - "SubworkflowFeatureRequirement" - %command-line-tool-supported-requirements)) + (append %workflow-only-requirements + %command-line-tool-supported-requirements)) + +(define (supported-requirements batch-system) + (append %workflow-only-requirements + (command-line-tool-supported-requirements batch-system))) ;; In batch systems that require it, poll job completion status every ;; 5 seconds. @@ -188,9 +195,10 @@ propagator." (assoc-ref output "id"))) (assoc-ref cwl "outputs")))) -(define* (workflow-class->propnet name cwl scheduler) - "Return a propagator network scheduled using @var{scheduler} for @var{cwl}, a -@code{Workflow} class workflow with @var{name}." +(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 +@var{name}." (define (normalize-scatter-method scatter-method) (assoc-ref* '(("dotproduct" . dot-product) ("nested_crossproduct" . nested-cross-product) @@ -233,9 +241,13 @@ propagator." (maybe-let* ((requirements (maybe-assoc-ref (just cwl) "requirements"))) (check-requirements requirements + batch-system + supported-requirements %supported-requirements)) (maybe-let* ((hints (maybe-assoc-ref (just cwl) "hints"))) (check-requirements hints + batch-system + supported-requirements %supported-requirements #t)) (propnet (vector-map->list step->propagator @@ -296,7 +308,10 @@ job state object. @var{proc} may either be a @code{<propnet>} object or a ((string=? class "ExpressionTool") (error "Workflow class not implemented yet" class)) ((string=? class "Workflow") - (workflow-state (schedule-propnet (workflow-class->propnet name cwl scheduler) + (workflow-state (schedule-propnet (workflow-class->propnet name + cwl + scheduler + batch-system) inputs) (assoc-ref* cwl "outputs")))))) |