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-rw-r--r--genenetwork-development.scm82
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")))