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-rw-r--r--genenetwork/services/genenetwork.scm123
1 files changed, 99 insertions, 24 deletions
diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index 34d70df..b93654f 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -30,7 +30,9 @@
#:use-module (gnu system file-systems)
#:use-module (gnu system shadow)
#:use-module (guix build python-build-system)
+ #:use-module (guix diagnostics)
#:use-module (guix gexp)
+ #:use-module (guix i18n)
#:use-module (guix packages)
#:use-module (guix profiles)
#:use-module (guix records)
@@ -83,10 +85,14 @@
(default 8083))
(gn-auth-port genenetwork-configuration-gn-auth-port
(default 8084))
+ (gn3-alias-server-port genenetwork-gn3-alias-server-port
+ (default 8000))
(sql-uri genenetwork-configuration-sql-uri
(default "mysql://username:password@localhost/database"))
(auth-db genenetwork-configuration-auth-db
(default "/var/genenetwork/auth.db"))
+ (llm-db-path genenetwork-configuration-llm-db-path
+ (default "/var/genenetwork/llm.db"))
(xapian-db genenetwork-configuration-xapian-db
(default "/var/genenetwork/xapian"))
(genotype-files genenetwork-configuration-genotype-files
@@ -94,7 +100,7 @@
(sparql-endpoint genenetwork-configuration-sparql-endpoint
(default "http://localhost:8081/sparql"))
(gn-sourcecode-directory genenetwork-configuration-gn-sourcecode-directory
- (default "/var/empty"))
+ (default "/var/empty"))
(gn3-data-directory genenetwork-configuration-gn3-data-directory
(default "/var/genenetwork"))
(gn2-secrets genenetwork-configuration-gn2-secrets
@@ -102,7 +108,10 @@
(gn3-secrets genenetwork-configuration-gn3-secrets
(default "/etc/genenetwork/gn3-secrets.py"))
(gn-auth-secrets genenetwork-configuration-gn-auth-secrets
- (default "/etc/genenetwork")))
+ (default "/etc/genenetwork"))
+ (log-level genenetwork-configuration-log-level
+ (default 'warning)
+ (sanitize sanitize-log-level)))
(define-record-type* <gn-uploader-configuration>
gn-uploader-configuration make-gn-uploader-configuration
@@ -119,11 +128,20 @@
(default "/var/genenetwork"))
(secrets gn-uploader-configuration-secrets
(default "/etc/genenetwork/gn-uploader-secrets.py"))
- (auth-server-url gn-uploader-auth-server-url
+ (auth-server-url gn-uploader-configuration-auth-server-url
(default "https://auth.genenetwork.org"))
- (gn2-server-url gn-uploader-gn2-server-url
+ (gn2-server-url gn-uploader-configuration-gn2-server-url
(default "https://genenetwork.org"))
- (log-level gn-uploader-log-level (default "WARNING")))
+ (log-level gn-uploader-configuration-log-level
+ (default 'warning)
+ (sanitize sanitize-log-level)))
+
+(define (sanitize-log-level log-level)
+ (case log-level
+ ((fatal error warning info debug trace) log-level)
+ (else
+ (leave (G_ "Log level ~a is invalid. It must be one of the following symbols---fatal, error, warn, info, debug or trace.~%")
+ log-level))))
(define %genenetwork-accounts
(list (user-group
@@ -146,8 +164,8 @@
(herd (file-append shepherd "/bin/herd"))
(index-genenetwork (file-append genenetwork3 "/bin/index-genenetwork"))
(gn3-profile (profile
- (content (package->development-manifest genenetwork3))
- (allow-collisions? #t)))
+ (content (package->development-manifest genenetwork3))
+ (allow-collisions? #t)))
(python3-version (python-version (package-version python))))
(with-imported-modules '((guix build utils))
#~(begin
@@ -277,7 +295,7 @@ G-expressions or numbers."
described by @var{config}, a @code{<genenetwork-configuration>}
object."
(match-record config <genenetwork-configuration>
- (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets)
+ (genenetwork2 genenetwork3 gn-auth server-name gn-auth-server-name gn2-port gn3-port gn-auth-port sql-uri auth-db xapian-db genotype-files sparql-endpoint gn-sourcecode-directory gn3-data-directory gn2-secrets gn3-secrets gn-auth-secrets llm-db-path log-level)
;; If we mapped only the mysqld.sock socket file, it would break
;; when the external mysqld server is restarted.
(let* ((database-mapping (file-system-mapping
@@ -287,6 +305,7 @@ object."
(gn2-profile (profile
(content (package->development-manifest genenetwork2))
(allow-collisions? #t)))
+ (gn2-ca-bundle (file-append gn2-profile "/etc/ssl/certs/ca-certificates.crt"))
(gn2-conf (computed-file "gn2.conf"
(configuration-file-gexp
`(("GN2_SECRETS" ,(string-append gn2-secrets "/gn2-secrets.py"))
@@ -300,16 +319,27 @@ object."
("JS_GUIX_PATH" ,(file-append gn2-profile "/share/genenetwork2/javascript"))
("PLINK_COMMAND" ,(file-append gn2-profile "/bin/plink2"))
("SQL_URI" ,sql-uri)
- ("SSL_PRIVATE_KEY" ,(string-append gn2-secrets "/gn2-ssl-private-key.pem"))
- ("AUTH_SERVER_SSL_PUBLIC_KEY" ,(string-append gn2-secrets "/gn-auth-ssl-public-key.pem"))))))
+ ("AI_SEARCH_ENABLED" "True")))))
+ (gn3-profile (profile
+ (content (package->development-manifest genenetwork3))
+ (allow-collisions? #t)))
+ (gn3-ca-bundle (file-append gn3-profile "/etc/ssl/certs/ca-certificates.crt"))
(gn3-conf (computed-file "gn3.conf"
(configuration-file-gexp
`(("AUTH_DB" ,auth-db)
+ ("AUTH_SERVER_URL" ,(string-append "https://" gn-auth-server-name "/"))
("DATA_DIR" ,gn3-data-directory)
("SOURCE_DIR" ,gn-sourcecode-directory)
("SPARQL_ENDPOINT" ,sparql-endpoint)
("SQL_URI" ,sql-uri)
- ("XAPIAN_DB_PATH" ,xapian-db)))))
+ ("XAPIAN_DB_PATH" ,xapian-db)
+ ("GENOTYPE_FILES" ,genotype-files)
+ ("REAPER_COMMAND" ,(file-append gn2-profile "/bin/qtlreaper"))
+ ("LLM_DB_PATH" ,llm-db-path)))))
+ (gn-auth-profile (profile
+ (content (package->development-manifest gn-auth))
+ (allow-collisions? #t)))
+ (gn-auth-ca-bundle (file-append gn-auth-profile "/etc/ssl/certs/ca-certificates.crt"))
(gn-auth-conf (computed-file "gn-auth.conf"
(configuration-file-gexp
`(("GN_AUTH_SECRETS" ,(string-append gn-auth-secrets "/gn-auth-secrets.py"))
@@ -337,7 +367,10 @@ object."
(value gn2-conf))
(environment-variable
(name "HOME")
- (value "/tmp"))))
+ (value "/tmp"))
+ (environment-variable
+ (name "REQUESTS_CA_BUNDLE")
+ (value gn2-ca-bundle))))
(mappings (list database-mapping
(file-system-mapping
(source genotype-files)
@@ -358,7 +391,13 @@ object."
(file-system-mapping
(source gn2-secrets)
(target source)
- (writable? #t)))))
+ (writable? #t))
+ (file-system-mapping
+ (source gn2-ca-bundle)
+ (target source))))
+ (extra-cli-arguments
+ (list "--log-level"
+ (string-upcase (symbol->string log-level)))))
(gunicorn-app
(name "genenetwork3")
(package genenetwork3)
@@ -382,7 +421,10 @@ object."
(value gn3-secrets))
(environment-variable
(name "HOME")
- (value "/tmp"))))
+ (value "/tmp"))
+ (environment-variable
+ (name "REQUESTS_CA_BUNDLE")
+ (value gn3-ca-bundle))))
(mappings (list database-mapping
(file-system-mapping
(source gn3-conf)
@@ -407,9 +449,15 @@ object."
(source xapian-db)
(target source))
(file-system-mapping
- (source auth-db)
+ (source llm-db-path)
(target source)
- (writable? #t)))))
+ (writable? #t))
+ (file-system-mapping
+ (source gn3-ca-bundle)
+ (target source))))
+ (extra-cli-arguments
+ (list "--log-level"
+ (string-upcase (symbol->string log-level)))))
(gunicorn-app
(name "gn-auth")
(package gn-auth)
@@ -426,7 +474,10 @@ object."
(value "/tmp"))
(environment-variable
(name "AUTHLIB_INSECURE_TRANSPORT")
- (value "true"))))
+ (value "true"))
+ (environment-variable
+ (name "REQUESTS_CA_BUNDLE")
+ (value gn-auth-ca-bundle))))
(mappings (list database-mapping
(file-system-mapping
(source gn-auth-conf)
@@ -438,14 +489,20 @@ object."
(file-system-mapping
(source gn-auth-secrets)
(target source)
- (writable? #t)))))))))
+ (writable? #t))
+ (file-system-mapping
+ (source gn-auth-ca-bundle)
+ (target source))))
+ (extra-cli-arguments
+ (list "--log-level"
+ (string-upcase (symbol->string log-level)))))))))
(define (genenetwork-nginx-server-blocks config)
"Return a list of @code{<nginx-server-configuration>} records specifying
reverse proxies for the genenetwork service described by @var{config},
a @code{<genenetwork-configuration>} record."
(match-record config <genenetwork-configuration>
- (server-name gn-auth-server-name gn2-port gn3-port gn-auth-port)
+ (server-name gn-auth-server-name gn2-port gn3-port gn-auth-port gn3-alias-server-port)
(list (nginx-server-configuration
(server-name (list server-name))
(locations
@@ -461,7 +518,16 @@ a @code{<genenetwork-configuration>} record."
(body (list "rewrite /api3/(.*) /api/$1 break;"
(string-append "proxy_pass http://localhost:"
(number->string gn3-port) ";")
- "proxy_set_header Host $host;"))))))
+ "proxy_set_header Host $host;")))
+ (nginx-location-configuration
+ (uri "/gn3/")
+ (body
+ (list "rewrite /gn3/(.*) /$1 break;"
+ (string-append "proxy_pass http://localhost:"
+ (number->string gn3-alias-server-port)
+ ";")
+ "proxy_redirect off;"
+ "proxy_set_header Host $host;"))))))
(nginx-server-configuration
(server-name (list gn-auth-server-name))
(locations
@@ -535,7 +601,8 @@ a @code{<genenetwork-configuration>} record."
("GN2_SERVER_URL" ,gn2-server-url)))))
(gn-uploader-profile (profile
(content (package->development-manifest gn-uploader))
- (allow-collisions? #t))))
+ (allow-collisions? #t)))
+ (gn-uploader-ca-bundle (file-append gn-uploader-profile "/etc/ssl/certs/ca-certificates.crt")))
(list (gunicorn-app
(name "gn-uploader")
(package gn-uploader)
@@ -552,7 +619,10 @@ a @code{<genenetwork-configuration>} record."
(value "/tmp"))
(environment-variable
(name "GN_UPLOADER_ENVIRONMENT")
- (value gn-uploader-profile))))
+ (value gn-uploader-profile))
+ (environment-variable
+ (name "REQUESTS_CA_BUNDLE")
+ (value gn-uploader-ca-bundle))))
(mappings (list database-mapping
(file-system-mapping
(source gn-uploader-conf)
@@ -566,8 +636,13 @@ a @code{<genenetwork-configuration>} record."
(writable? #t))
(file-system-mapping
(source gn-uploader-profile)
+ (target source))
+ (file-system-mapping
+ (source gn-uploader-ca-bundle)
(target source))))
- (extra-cli-arguments (list "--log-level" log-level)))))))
+ (extra-cli-arguments
+ (list "--log-level"
+ (string-upcase (symbol->string log-level)))))))))
(define (gn-uploader-nginx-server-block config)
(match-record config <gn-uploader-configuration>
@@ -582,7 +657,7 @@ a @code{<genenetwork-configuration>} record."
#$(file-append gn-uploader
"/lib/python"
(python-version (package-version python))
- "/site-packages/qc_app;")))))
+ "/site-packages/uploader;")))))
(nginx-location-configuration
(uri "/")
(body (list (string-append "proxy_pass http://localhost:"
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-12 22:44:25 +0000