diff options
Diffstat (limited to 'genenetwork-development.scm')
| -rw-r--r-- | genenetwork-development.scm | 36 |
1 files changed, 27 insertions, 9 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 8e4e1e8..bfd2fc1 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -21,6 +21,7 @@ ;;; <https://www.gnu.org/licenses/>. (use-modules (gnu) + (gn-machines services monitoring) ((gn-machines genenetwork) #:select (genenetwork2 genenetwork3 gn-auth)) (gn services databases) ((gn packages guile) #:select (gn-guile)) @@ -529,8 +530,11 @@ server described by CONFIG, a <genenetwork-configuration> object." (getenv "GN2_PROFILE") "/etc/ssl/certs/ca-certificates.crt")) (setenv "PYTHONPATH" (string-append - (getenv "GN2_PROFILE") - "/lib/python3.11/site-packages")) + (getenv "GN3_PYTHONPATH") + ":" + (string-append + (getenv "GN2_PROFILE") + "/lib/python3.11/site-packages"))) (setenv "PATH" (string-append (getenv "GN2_PROFILE") "/bin:$PATH")) (setenv "R_LIBS_SITE" (string-append (getenv "GN2_PROFILE") "/site-library")) (setenv "JS_GUIX_PATH" (string-append (getenv "GN2_PROFILE") "/share/genenetwork2/javascript")) @@ -732,6 +736,7 @@ server described by CONFIG, a <genenetwork-configuration> object." (setenv "GIT_SSL_CAINFO" (getenv "SSL_CERT_FILE")) (setenv "CURL_CA_BUNDLE" (getenv "SSL_CERT_FILE")) (setenv "REQUESTS_CA_BUNDLE" (getenv "SSL_CERT_FILE")) + (setenv "SPARQL-ENDPOINT" "http://localhost:9082/sparql/") (setenv "GIT_PAGER" #$(file-append coreutils-minimal "/bin/cat")) (let ((current-repo-path "/home/genenetwork/gn-docs")) (setenv "CURRENT_REPO_PATH" current-repo-path) @@ -1131,12 +1136,6 @@ described by CONFIG, a <genenetwork-configuration> object." (copy-recursively build-directory #$virtuoso-data-dir) ;; Load RDF into virtuoso. (invoke "./pre-inst-env" "./load-rdf.scm" #$connection-settings) - ;; Visualize schema and archive results. - (invoke "./pre-inst-env" "./visualize-schema.scm" #$connection-settings) - (invoke #$(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")) (delete-file-recursively build-directory))))))) (define transform-genenetwork-database-project @@ -1429,6 +1428,19 @@ gn-auth." ";") "proxy_set_header Host $host;"))))))) +(define (gn-guile-reverse-proxy-server-block) + "Return an <nginx-server-configuration> object to reverse proxy +gn-guile to display RDF pages." + (nginx-server-configuration + (server-name '("rdf.genenetwork.org")) + (locations + (list (nginx-location-configuration + (uri "/") + (body (list (string-append "proxy_pass http://localhost:" + (number->string %gn-guile-port) + ";") + "proxy_set_header Host $host;"))))))) + (define set-build-directory-permissions-gexp (with-imported-modules '((guix build utils)) #~(begin @@ -1453,6 +1465,8 @@ gn-auth." (define %gn-auth-port 9094) ;; Port on which virtuoso's SPARQL endpoint is listening (define %virtuoso-sparql-port 9082) +;; Port on which gn-guile is listening +(define %gn-guile-port 8091) (operating-system (host-name "genenetwork-development") @@ -1577,7 +1591,11 @@ gn-auth." (list 'gn-bioinformatics 'guix-bioinformatics)) (tissue-reverse-proxy-server-block) - (gn-auth-reverse-proxy-server-block))))) + (gn-auth-reverse-proxy-server-block) + (gn-guile-reverse-proxy-server-block))))) + (service guile-sheepdog-service-type + (guile-sheepdog-configuration + (settings-file "/etc/genenetwork/conf/sheepdog.scm"))) (service acme-service-type (acme-configuration (email "arunisaac@systemreboot.net"))) |