diff options
| -rwxr-xr-x | bin/ravanan | 26 | ||||
| -rw-r--r-- | ravanan/command-line-tool.scm | 40 | ||||
| -rw-r--r-- | ravanan/workflow.scm | 10 |
3 files changed, 40 insertions, 36 deletions
diff --git a/bin/ravanan b/bin/ravanan index 19bb8b5..cc9005d 100755 --- a/bin/ravanan +++ b/bin/ravanan @@ -97,27 +97,6 @@ files that have the token in the @verbatim{SLURM_JWT=token} format." string-trim-both get-string-all))) -(define (load-manifest manifest-file) - "Load manifest from @var{manifest-file} and return it." - ;; We load the manifest file into a dummy module of its own so that any - ;; definitions from there don't leak out. We also ensure that this dummy - ;; module is different for different manifest files so that definitions from - ;; one manifest file don't leak into other manifest files. - (let ((manifest-file-path (canonicalize-file-name manifest-file)) - (manifest-module (resolve-module (match (file-name-split manifest-file-path) - (("" parts ...) - (map string->symbol parts)))))) - ;; Import modules required for loading manifests. - (for-each (lambda (module-name) - (module-use! manifest-module (resolve-interface module-name))) - '((guile) - (gnu packages) - (guix profiles))) - (save-module-excursion - (lambda () - (set-current-module manifest-module) - (load manifest-file-path))))) - (define main (match-lambda ((program args ...) @@ -151,9 +130,8 @@ files that have the token in the @verbatim{SLURM_JWT=token} format." ;; We must not try to compile guix manifest files. (set! %load-should-auto-compile #f) (scm->json (run-workflow (file-name-stem workflow-file) - (load-manifest - (canonicalize-path - (assq-ref args 'guix-manifest-file))) + (canonicalize-path + (assq-ref args 'guix-manifest-file)) (read-workflow workflow-file) (read-inputs inputs-file) (case (assq-ref args 'batch-system) diff --git a/ravanan/command-line-tool.scm b/ravanan/command-line-tool.scm index 54a92cf..19f3703 100644 --- a/ravanan/command-line-tool.scm +++ b/ravanan/command-line-tool.scm @@ -367,19 +367,19 @@ path." (string-append (basename script) ".stderr")) store)) -(define* (run-command-line-tool name manifest cwl inputs +(define* (run-command-line-tool name manifest-file cwl inputs scratch store batch-system #:key guix-daemon-socket slurm-api-endpoint slurm-jwt) "Run @code{CommandLineTool} class workflow @var{cwl} named @var{name} with -@var{inputs} using tools from Guix @var{manifest}. +@var{inputs} using tools from Guix manifest in @var{manifest-file}. @var{scratch}, @var{store}, @var{batch-system}, @var{guix-daemon-socket}, @var{slurm-api-endpoint} and @var{slurm-jwt} are the same as in @code{run-workflow} from @code{(ravanan workflow)}." ;; TODO: Write to the store atomically. (let* ((script - (build-command-line-tool-script name manifest cwl inputs + (build-command-line-tool-script name manifest-file cwl inputs scratch store batch-system guix-daemon-socket)) (requirements (inherit-requirements (or (assoc-ref cwl "requirements") @@ -547,12 +547,37 @@ maybe-monadic value." class)) requirements)) -(define (build-command-line-tool-script name manifest cwl inputs +(define (load-manifest manifest-file) + "Load Guix manifest from @var{manifest-file} and return it." + ;; We load the manifest file into a dummy module of its own so that any + ;; definitions from there don't leak into this module. We also ensure that + ;; this dummy module is different for different manifest files so that + ;; definitions from one manifest file don't leak into other manifest files. + (let ((manifest-module + (resolve-module (match (file-name-split (canonicalize-file-name manifest-file)) + (("" parts ...) + (map string->symbol parts)))))) + ;; Import modules required for loading manifests. + (for-each (lambda (module-name) + (module-use! manifest-module (resolve-interface module-name))) + '((guile) + (gnu packages) + (guix profiles))) + (save-module-excursion + (lambda () + (set-current-module manifest-module) + ;; Our use of load triggers a "Add #:declarative? #f to your + ;; define-module invocation" warning during compilation. But, it is + ;; probably safe to ignore this warning since we use load only within a + ;; dummy module. + (load (canonicalize-path manifest-file)))))) + +(define (build-command-line-tool-script name manifest-file cwl inputs 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} and on @var{batch-system}. +named @var{name} with @var{inputs} using tools from Guix manifest in +@var{manifest-file} 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)}." @@ -706,7 +731,8 @@ named @var{name} with @var{inputs} using tools from Guix manifest (or (assoc-ref cwl "hints") #()))) (initial-work-dir-requirement (find-requirement requirements - "InitialWorkDirRequirement"))) + "InitialWorkDirRequirement")) + (manifest (load-manifest manifest-file))) (with-imported-modules (source-module-closure '((ravanan work command-line-tool) (ravanan work monads) (ravanan work ui) diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm index 42fa349..95dfb73 100644 --- a/ravanan/workflow.scm +++ b/ravanan/workflow.scm @@ -245,7 +245,7 @@ propagator." merge-values scheduler)) -(define* (workflow-scheduler manifest scratch store batch-system +(define* (workflow-scheduler manifest-file scratch store batch-system #:key guix-daemon-socket slurm-api-endpoint slurm-jwt) (define (schedule proc inputs scheduler) @@ -290,7 +290,7 @@ job state object. @var{proc} may either be a @code{<propnet>} object or a ((string=? class "CommandLineTool") (command-line-tool-state (run-command-line-tool name - manifest + manifest-file cwl inputs scratch @@ -570,12 +570,12 @@ error out." formal-inputs)) formal-inputs)) -(define* (run-workflow name manifest cwl inputs +(define* (run-workflow name manifest-file cwl inputs scratch store batch-system #:key guix-daemon-socket slurm-api-endpoint slurm-jwt) "Run a workflow @var{cwl} named @var{name} with @var{inputs} using -tools from Guix @var{manifest}. +tools from Guix manifest in @var{manifest-file}. @var{scratch} is the path to the scratch area on all worker nodes. The scratch area need not be shared. @var{store} is the path to the shared @@ -591,7 +591,7 @@ authenticate to the slurm API with. @var{slurm-api-endpoint} and @var{slurm-jwt} are only used when @var{batch-system} is @code{'slurm-api}." (let ((scheduler (workflow-scheduler - manifest scratch store batch-system + manifest-file scratch store batch-system #:guix-daemon-socket guix-daemon-socket #:slurm-api-endpoint slurm-api-endpoint #:slurm-jwt slurm-jwt))) |