diff options
| -rw-r--r-- | genenetwork-development.scm | 82 |
1 files changed, 41 insertions, 41 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index a015154..5fafc12 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -252,7 +252,7 @@ genenetwork3 source from the latest commit of @var{project}." (setenv "PYTHONPATH" (getcwd)) (invoke "./scripts/index-genenetwork" "create-xapian-index" xapian-build-directory - "mysql://webqtlout:webqtlout@localhost/db_webqtl" + "mysql://webqtlout:webqtlout@localhost/db_webqtl" "http://localhost:9082/sparql") ;; Stop genenetwork3, replace old xapian index and ;; start genenetwork3. @@ -351,9 +351,9 @@ genenetwork3 source from the latest commit of @var{project}." (module '(genenetwork3-package)) (name 'genenetwork3))) #:guix-daemon-uri %guix-daemon-uri)) - ;; If tests run successfully, redeploy - ;; genenetwork3 and trigger genenetwork2 tests. - (after (with-imported-modules '((guix build utils)) + ;; If tests run successfully, redeploy + ;; genenetwork3 and trigger genenetwork2 tests. + (after (with-imported-modules '((guix build utils)) #~(begin (use-modules (guix build utils)) @@ -379,7 +379,7 @@ genenetwork3 source from the latest commit of @var{project}." (run (build-xapian-index-gexp this-forge-project)) (trigger? #f)))) (ci-jobs-trigger 'webhook)) - (forge-project + (forge-project (name "gn-auth") (repository gn-auth-repository) (ci-jobs (list (forge-laminar-job @@ -394,7 +394,7 @@ genenetwork3 source from the latest commit of @var{project}." (name 'gn-auth))) #:guix-daemon-uri %guix-daemon-uri)) ;; If unit tests pass, restart the auth server. - (after (with-imported-modules '((guix build utils)) + (after (with-imported-modules '((guix build utils)) #~(begin (use-modules (guix build utils)) @@ -402,7 +402,7 @@ genenetwork3 source from the latest commit of @var{project}." (invoke #$sudo #$(file-append shepherd "/bin/herd") "restart" "gn-auth") - (invoke #$(file-append laminar "/bin/laminarc") + (invoke #$(file-append laminar "/bin/laminarc") "queue" "genenetwork2")))))) (forge-laminar-job (name "gn-auth-all-tests") @@ -457,27 +457,27 @@ server described by CONFIG, a <genenetwork-configuration> object." (setenv "GN2_PROFILE" #$(profile (content (package->development-manifest genenetwork2)) (allow-collisions? #t))) - (setenv "GN_SERVER_URL" "https://cd.genenetwork.org/api3/") - (setenv "GN3_LOCAL_URL" - #$(string-append "http://localhost:" - (number->string gn3-port))) + (setenv "GN_SERVER_URL" "https://cd.genenetwork.org/api3/") + (setenv "GN3_LOCAL_URL" + #$(string-append "http://localhost:" + (number->string gn3-port))) (setenv "GENENETWORK_FILES" #$genotype-files) - (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl") + (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl") (setenv "HOME" "/tmp") (setenv "NO_REDIS" "no-redis") - (setenv "RUST_BACKTRACE" "1") - - (setenv - "GN2_SETTINGS" - #$(mixed-text-file "gn2.conf" - "GN2_SECRETS=\"" gn2-secrets "/gn2-secrets.py\"\n" - "GN3_LOCAL_URL=\"" - (string-append "http://localhost:" - (number->string gn3-port)) - "\"\n" - "GN_SERVER_URL=\"https://cd.genenetwork.org/api3/\"\n" - "AUTH_SERVER_URL=\"https://auth-cd.genenetwork.org/\"\n" - "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl\"\n" + (setenv "RUST_BACKTRACE" "1") + + (setenv + "GN2_SETTINGS" + #$(mixed-text-file "gn2.conf" + "GN2_SECRETS=\"" gn2-secrets "/gn2-secrets.py\"\n" + "GN3_LOCAL_URL=\"" + (string-append "http://localhost:" + (number->string gn3-port)) + "\"\n" + "GN_SERVER_URL=\"https://cd.genenetwork.org/api3/\"\n" + "AUTH_SERVER_URL=\"https://auth-cd.genenetwork.org/\"\n" + "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl\"\n" "SSL_PRIVATE_KEY=\"" gn2-secrets "/gn2-ssl-private-key.pem\"\n" "AUTH_SERVER_SSL_PUBLIC_KEY=\"" gn2-secrets "/gn-auth-ssl-public-key.pem\"\n")) @@ -520,7 +520,7 @@ server described by CONFIG, a <genenetwork-configuration> object." "AUTH_DB=\"" auth-db-path "\"\n" "LLM_DB_PATH=\"" llm-db-path "\"\n")) (setenv "HOME" "/tmp") - (setenv "GN3_SECRETS" #$gn3-secrets) + (setenv "GN3_SECRETS" #$gn3-secrets) ;; Run genenetwork3. (with-directory-excursion "genenetwork3" (show-head-commit) @@ -561,12 +561,12 @@ server described by CONFIG, a <genenetwork-configuration> object." ;; Configure gn-auth. (setenv "GN_AUTH_CONF" #$(mixed-text-file "gn-auth.conf" - "AUTH_DB=\"" auth-db-path "\"\n" + "AUTH_DB=\"" auth-db-path "\"\n" "GN_AUTH_SECRETS=\"" gn-auth-secrets "/gn-auth-secrets.py\"\n" "CLIENTS_SSL_PUBLIC_KEYS_DIR=\"" gn-auth-secrets "/clients-public-keys\"\n" "SSL_PRIVATE_KEY=\"" gn-auth-secrets "/gn-auth-ssl-private-key.pem\"\n")) (setenv "HOME" "/tmp") - (setenv "AUTHLIB_INSECURE_TRANSPORT" "true") + (setenv "AUTHLIB_INSECURE_TRANSPORT" "true") ;; Run gn-auth. (with-directory-excursion "gn-auth" (show-head-commit) @@ -600,7 +600,7 @@ described by CONFIG, a <genenetwork-configuration> object." (source "/run/mysqld") (target source) (writable? #t)) - (file-system-mapping + (file-system-mapping (source gn2-secrets) (target source) (writable? #t))) @@ -632,7 +632,7 @@ described by CONFIG, a <genenetwork-configuration> object." (file-system-mapping (source xapian-db-path) (target source)) - (file-system-mapping + (file-system-mapping (source "/etc/genenetwork/conf/gn3") (target source) (writable? #t)) @@ -650,7 +650,7 @@ described by CONFIG, a <genenetwork-configuration> object." #:group "genenetwork" #:log-file "/var/log/cd/genenetwork3.log")) (stop #~(make-kill-destructor))) - (shepherd-service + (shepherd-service (documentation "Run gn-auth development server.") (provision '(gn-auth)) (requirement '(networking)) @@ -673,7 +673,7 @@ described by CONFIG, a <genenetwork-configuration> object." (source auth-db-path) (target source) (writable? #t)) - (file-system-mapping + (file-system-mapping (source gn-auth-secrets) (target source) (writable? #t))) @@ -1060,7 +1060,7 @@ GeneNetwork2 and GeneNetwork3 are listening on." (body (list (string-append "proxy_pass http://localhost:" (number->string gn2-port) ";") "proxy_set_header Host $host;" - "proxy_set_header X-Forwarded-Proto $scheme;"))) + "proxy_set_header X-Forwarded-Proto $scheme;"))) (nginx-location-configuration ;; Reverse proxy genenetwork3. (uri "/api3") @@ -1131,10 +1131,10 @@ gn-auth." (server-name '("auth-cd.genenetwork.org")) (locations (list (nginx-location-configuration - (uri "/") + (uri "/") (body (list (string-append "proxy_pass http://localhost:" - (number->string %gn-auth-port) - ";") + (number->string %gn-auth-port) + ";") "proxy_set_header Host $host;"))))))) ;; Port on which webhook is listening @@ -1209,16 +1209,16 @@ gn-auth." (service redis-service-type) (service virtuoso-service-type (virtuoso-configuration - (number-of-buffers 4000000) - (maximum-dirty-buffers 3000000) + (number-of-buffers 4000000) + (maximum-dirty-buffers 3000000) (server-port 9081) - (dirs-allowed "/var/lib/data") + (dirs-allowed "/var/lib/data") (http-server-port %virtuoso-sparql-port))) (service genenetwork-service-type (genenetwork-configuration (gn2-port %genenetwork2-port) (gn3-port %genenetwork3-port) - (gn-auth-port %gn-auth-port) + (gn-auth-port %gn-auth-port) (gn2-secrets "/etc/genenetwork/conf/gn2") (gn3-secrets "/etc/genenetwork/conf/gn3/secrets.py") (gn-auth-secrets "/etc/genenetwork/conf/gn-auth") @@ -1267,7 +1267,7 @@ gn-auth." "localhost:9089" %webhook-port (list 'gn-bioinformatics)) (tissue-reverse-proxy-server-block) - (gn-auth-reverse-proxy-server-block))))) + (gn-auth-reverse-proxy-server-block))))) (service acme-service-type (acme-configuration (email "arunisaac@systemreboot.net"))) |