diff options
| -rw-r--r-- | genenetwork-development.scm | 28 |
1 files changed, 21 insertions, 7 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index b18cee8..055d701 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -29,10 +29,11 @@ ((gnu packages certs) #:select (nss-certs)) ((gnu packages check) #:select (python-pylint)) ((gnu packages ci) #:select (laminar)) + ((gnu packages databases) #:select (virtuoso-ose)) ((gnu packages gnupg) #:select (guile-gcrypt)) ((gnu packages graphviz) #:select (graphviz)) ((gnu packages guile) #:select (guile-3.0 guile-zlib)) - ((gnu packages guile-xyz) #:select (guile-dbd-mysql guile-dbi guile-libyaml)) + ((gnu packages guile-xyz) #:select (guile-dbd-mysql guile-dbi guile-hashing guile-libyaml)) ((gnu packages guile-xyz) #:select (guile-sparql) #:prefix guix:) ((gnu packages haskell-apps) #:select (shellcheck)) ((gnu packages python-check) #:select (python-mypy)) @@ -552,8 +553,9 @@ command to be executed." (define (dump-genenetwork-database project) (with-imported-modules '((guix build utils)) - (with-packages (list git-minimal guile-3.0 guile-dbd-mysql - guile-dbi nss-certs) + (with-packages (list ccwl git-minimal guile-3.0 guile-dbd-mysql + guile-dbi guile-hashing guile-libyaml guile-sparql + nss-certs virtuoso-ose) #~(begin (use-modules (guix build utils)) @@ -561,15 +563,16 @@ command to be executed." "--depth" "1" #$(forge-project-repository project) ".") - (let ((dump-directory #$(string-append %dump-genenetwork-database-export-directory + (let ((connection-settings-file #$(string-append %dump-genenetwork-database-export-directory + "/conn.scm")) + (dump-directory #$(string-append %dump-genenetwork-database-export-directory "/dump"))) (when (file-exists? dump-directory) (delete-file-recursively dump-directory)) (mkdir-p dump-directory) ;; Dump data to RDF. (invoke "./pre-inst-env" "./dump.scm" - #$(string-append %dump-genenetwork-database-export-directory - "/conn.scm") + connection-settings-file dump-directory) ;; Validate dumped RDF. (invoke #$(file-append raptor2 "/bin/rapper") @@ -578,7 +581,18 @@ command to be executed." ;; We use --ignore-errors because we don't want to ;; print out potentially sensitive data. "--ignore-errors" - (string-append dump-directory "/dump.ttl"))))))) + (string-append dump-directory "/dump.ttl")) + ;; Load RDF into virtuoso. + (invoke "./pre-inst-env" "./load-rdf.scm" + connection-settings-file + (string-append dump-directory "/dump.ttl")) + ;; Visualize schema and archive results. + (invoke "./pre-inst-env" "./visualize-schema.scm" + connection-settings-file) + (invoke #$(file-append graphviz "/bin/dot") + "-Tsvg" "sql.dot" (string-append "-o" (getenv "ARCHIVE") "/sql.svg")) + (invoke #$(file-append graphviz "/bin/dot") + "-Tsvg" "rdf.dot" (string-append "-o" (getenv "ARCHIVE") "/rdf.svg"))))))) (define dump-genenetwork-database-project (forge-project |