diff options
| -rw-r--r-- | ravanan/reader.scm | 29 | ||||
| -rw-r--r-- | ravanan/store.scm | 3 | ||||
| -rw-r--r-- | ravanan/utils.scm | 4 | ||||
| -rw-r--r-- | ravanan/workflow.scm | 3 | ||||
| -rw-r--r-- | tests/store.scm | 80 |
5 files changed, 107 insertions, 12 deletions
diff --git a/ravanan/reader.scm b/ravanan/reader.scm index a4e57c7..fd959de 100644 --- a/ravanan/reader.scm +++ b/ravanan/reader.scm @@ -101,18 +101,31 @@ each association list of the returned vector of association lists. If (define (normalize-env-var-requirement env-var-requirement) (assoc-set env-var-requirement - (cons "envDef" - (coerce-alist->vector - (assoc-ref env-var-requirement "envDef") - "envName" "envValue")))) + (cons "envDef" + (coerce-alist->vector + (assoc-ref env-var-requirement "envDef") + "envName" "envValue")))) + +(define (normalize-software-requirement software-requirement) + (maybe-assoc-set software-requirement + ;; Canonicalize manifest file path so that we look it up with respect to the + ;; path of the workflow file. + (cons "manifest" + (maybe-bind (maybe-assoc-ref (just software-requirement) + "manifest") + (compose just canonicalize-path))))) (define (normalize-requirements maybe-requirements) (maybe-let* ((requirements maybe-requirements)) (just (vector-map (lambda (requirement) - (if (string=? (assoc-ref requirement "class") - "EnvVarRequirement") - (normalize-env-var-requirement requirement) - requirement)) + (let ((class (assoc-ref requirement "class"))) + (cond + ((string=? class "EnvVarRequirement") + (normalize-env-var-requirement requirement)) + ((string=? class "SoftwareRequirement") + (normalize-software-requirement requirement)) + (else + requirement)))) (coerce-alist->vector requirements "class"))))) (define (normalize-secondary-files secondary-files default-required) diff --git a/ravanan/store.scm b/ravanan/store.scm index 9bd5bcc..ba66076 100644 --- a/ravanan/store.scm +++ b/ravanan/store.scm @@ -26,6 +26,7 @@ #:use-module (guix build utils) #:use-module (ravanan work command-line-tool) #:use-module (ravanan work monads) + #:use-module (ravanan work utils) #:use-module (ravanan work vectors) #:export (%store-files-directory %store-data-directory @@ -75,7 +76,7 @@ already exists, do nothing." (define (step-store-basename script inputs) "Return the basename in the store for files of CWL step with @var{script} and @var{inputs}." - (string-append (sha1-hash-sexp (cons script inputs)) + (string-append (sha1-hash-sexp (cons script (canonicalize-json inputs))) "-" (strip-store-file-name script))) diff --git a/ravanan/utils.scm b/ravanan/utils.scm index a76a14c..e4fad9c 100644 --- a/ravanan/utils.scm +++ b/ravanan/utils.scm @@ -1,5 +1,5 @@ ;;; ravanan --- High-reproducibility CWL runner powered by Guix -;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2024, 2025 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of ravanan. ;;; @@ -54,4 +54,4 @@ before loading script." ;; 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 script-file)))))) + (load script-file))))) diff --git a/ravanan/workflow.scm b/ravanan/workflow.scm index 402dea7..2de254b 100644 --- a/ravanan/workflow.scm +++ b/ravanan/workflow.scm @@ -333,7 +333,8 @@ object." (schedule (scheduler-proc name script-or-propnet (scheduler-proc-formal-inputs proc) - (scheduler-proc-formal-outputs proc)) + (scheduler-proc-formal-outputs proc) + (scheduler-proc-resource-requirement proc)) ;; Replace scattered inputs with single ;; elements. (apply assoc-set diff --git a/tests/store.scm b/tests/store.scm new file mode 100644 index 0000000..f209583 --- /dev/null +++ b/tests/store.scm @@ -0,0 +1,80 @@ +;;; ravanan --- High-reproducibility CWL runner powered by Guix +;;; Copyright © 2025 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of ravanan. +;;; +;;; ravanan is free software: you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation, either version 3 of the License, or +;;; (at your option) any later version. +;;; +;;; ravanan is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +;;; General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with ravanan. If not, see <https://www.gnu.org/licenses/>. + +(use-modules (srfi srfi-64) + (ravanan store)) + +(test-begin "store") + +(test-equal "step-store-files-directory must be insensitive to order of inputs" + (step-store-files-directory "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("foobar" . 3) + ("bar" . (("aal" . 1) + ("vel" . 2)))) + "store") + (step-store-files-directory "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("bar" . (("vel" . 2) + ("aal" . 1))) + ("foobar" . 3)) + "store")) + +(test-equal "step-store-data-file must be insensitive to order of inputs" + (step-store-data-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("foobar" . 3) + ("bar" . (("aal" . 1) + ("vel" . 2)))) + "store") + (step-store-data-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("bar" . (("vel" . 2) + ("aal" . 1))) + ("foobar" . 3)) + "store")) + +(test-equal "step-store-stdout-file must be insensitive to order of inputs" + (step-store-stdout-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("foobar" . 3) + ("bar" . (("aal" . 1) + ("vel" . 2)))) + "store") + (step-store-stdout-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("bar" . (("vel" . 2) + ("aal" . 1))) + ("foobar" . 3)) + "store")) + +(test-equal "step-store-stderr-file must be insensitive to order of inputs" + (step-store-stderr-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("foobar" . 3) + ("bar" . (("aal" . 1) + ("vel" . 2)))) + "store") + (step-store-stderr-file "/gnu/store/hl96c0xd19ngvl8rf4cyw452rpgqsi1b-foo" + '(("foo" . 1) + ("bar" . (("vel" . 2) + ("aal" . 1))) + ("foobar" . 3)) + "store")) + +(test-end "store") |