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-rw-r--r--genenetwork-development.scm379
1 files changed, 266 insertions, 113 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index 5fafc12..f841255 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -21,8 +21,9 @@
;;; <https://www.gnu.org/licenses/>.
(use-modules (gnu)
- ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth))
+ ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-libs))
(gn services databases)
+ ((gn packages guile) #:select (gn-guile))
(gnu build linux-container)
((gnu packages admin) #:select (shepherd shadow))
((gnu packages base) #:select (gnu-make tar))
@@ -64,6 +65,7 @@
(guix packages)
(guix profiles)
(guix records)
+ (guix search-paths)
(guix store)
(guix utils)
(forge acme)
@@ -120,7 +122,9 @@ be imported into G-expressions."
(gn3-repository genenetwork-configuration-gn3-repository
(default "https://github.com/genenetwork/genenetwork3"))
(gn-auth-repository genenetwork-configuration-gn-auth-repository
- (default "https://git.genenetwork.org/gn-auth"))
+ (default "/home/git/public/gn-auth"))
+ (gn-libs-repository genenetwork-configuration-gn-libs-repository
+ (default "/home/git/public/gn-libs"))
(gn2-port genenetwork-configuration-gn2-port
(default 8082))
(gn3-port genenetwork-configuration-gn3-port
@@ -144,7 +148,11 @@ be imported into G-expressions."
(auth-db-path genenetwork-auth-db-path
(default "/export/data/genenetwork-sqlite/auth.db"))
(llm-db-path genenetwork-llm-db-path
- (default "/export/data/genenetwork-sqlite/llm.db")))
+ (default "/export/data/genenetwork-sqlite/llm.db"))
+ (gn-guile-port genenetwork-configuration-gn-guile-port
+ (default 8091))
+ (gn-doc-git-checkout genenetwork-configuration-gn-doc-git-checkout
+ (default "/export/data/gn-docs")))
;;;
@@ -182,11 +190,12 @@ described by CONFIG, a <genenetwork-configuration>
object. TEST-COMMAND is a list of strings specifying the command to be
executed."
(match-record config <genenetwork-configuration>
- (gn2-repository gn3-repository gn3-port genotype-files)
+ (gn2-repository gn3-repository gn-libs-repository gn3-port genotype-files)
(with-imported-modules '((guix build utils))
(with-packages (list bash coreutils git-minimal nss-certs)
#~(begin
- (use-modules (guix build utils))
+ (use-modules (guix build utils)
+ (srfi srfi-26))
(define (hline)
"Print a horizontal line 50 '=' characters long."
@@ -199,9 +208,19 @@ executed."
(invoke "git" "log" "--max-count" "1")
(hline))
+ (define (call-with-temporary-directory proc)
+ (let ((tmp-dir (mkdtemp "/tmp/gn.XXXXXX")))
+ (dynamic-wind
+ (const #t)
+ (cut proc tmp-dir)
+ (cut delete-file-recursively tmp-dir))))
+
(invoke "git" "clone" "--depth" "1" #$gn3-repository)
(with-directory-excursion "genenetwork3"
(show-head-commit))
+ (invoke "git" "clone" "--depth" "1" #$gn-libs-repository)
+ (with-directory-excursion "gn-libs"
+ (show-head-commit))
(invoke "git" "clone" "--depth" "1" #$gn2-repository)
(with-directory-excursion "genenetwork2"
(show-head-commit))
@@ -222,9 +241,15 @@ executed."
(setenv "GN3_LOCAL_URL" (string-append "http://localhost:" (number->string #$gn3-port)))
(setenv "GENENETWORK_FILES" #$genotype-files)
(setenv "HOME" "/tmp")
- (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+ (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock")
(chdir "genenetwork2")
- (apply invoke '#$test-command))))))
+ ;; XXXX: FIXME: R/Qtl tests fail because files are generated in
+ ;; the "/tmp" directory. Currently, "/tmp" is mapped by gn2/gn3
+ ;; so tests will fail because of permission issues.
+ (call-with-temporary-directory
+ (lambda (tmp-dir)
+ (setenv "TMPDIR" tmp-dir)
+ (apply invoke '#$test-command))))))))
(define %xapian-directory
"/export/data/genenetwork-xapian")
@@ -252,7 +277,7 @@ genenetwork3 source from the latest commit of @var{project}."
(setenv "PYTHONPATH" (getcwd))
(invoke "./scripts/index-genenetwork" "create-xapian-index"
xapian-build-directory
- "mysql://webqtlout:webqtlout@localhost/db_webqtl"
+ "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock"
"http://localhost:9082/sparql")
;; Stop genenetwork3, replace old xapian index and
;; start genenetwork3.
@@ -297,7 +322,7 @@ genenetwork3 source from the latest commit of @var{project}."
(system* (string-append gn3-dir "/scripts/index-genenetwork")
"is-data-modified"
#$%xapian-directory
- "mysql://webqtlout:webqtlout@localhost/db_webqtl"
+ "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock"
"http://localhost:9082/sparql"))))
(setenv "LAMINAR_REASON" "Nightly xapian index rebuild")
(invoke #$(file-append laminar "/bin/laminarc")
@@ -307,7 +332,7 @@ genenetwork3 source from the latest commit of @var{project}."
"Return forge projects for genenetwork described by CONFIG, a
<genenetwork-configuration> object."
(match-record config <genenetwork-configuration>
- (gn2-repository gn3-repository gn-auth-repository gn2-port)
+ (gn2-repository gn3-repository gn-auth-repository gn-libs-repository gn2-port)
(list (forge-project
(name "genenetwork2")
(repository gn2-repository)
@@ -380,6 +405,20 @@ genenetwork3 source from the latest commit of @var{project}."
(trigger? #f))))
(ci-jobs-trigger 'webhook))
(forge-project
+ (name "gn-libs")
+ (repository gn-libs-repository)
+ (ci-jobs (list (forge-laminar-job
+ (name "gn-libs")
+ (run (guix-channel-job-gexp
+ (list (channel
+ (name 'gn-libs)
+ (url (forge-project-repository this-forge-project))
+ (branch "main")))
+ #:variables (list (variable-specification
+ (module '(gn-libs))
+ (name 'gn-libs)))
+ #:guix-daemon-uri %guix-daemon-uri))))))
+ (forge-project
(name "gn-auth")
(repository gn-auth-repository)
(ci-jobs (list (forge-laminar-job
@@ -414,8 +453,7 @@ genenetwork3 source from the latest commit of @var{project}."
#:variables (list (variable-specification
(module '(gn-auth))
(name 'gn-auth-all-tests)))
- #:guix-daemon-uri %guix-daemon-uri)))))
- (ci-jobs-trigger 'webhook)))))
+ #:guix-daemon-uri %guix-daemon-uri)))))))))
(define (genenetwork2-cd-gexp config)
"Return a G-expression that runs the latest genenetwork2 development
@@ -453,31 +491,21 @@ server described by CONFIG, a <genenetwork-configuration> object."
(string-append (getcwd) "/genenetwork3"))
;; Set other environment variables required by
;; genenetwork2.
- (setenv "SERVER_PORT" #$(number->string gn2-port))
(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 "GENENETWORK_FILES" #$genotype-files)
- (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
- (setenv "HOME" "/tmp")
- (setenv "NO_REDIS" "no-redis")
- (setenv "RUST_BACKTRACE" "1")
-
(setenv
"GN2_SETTINGS"
#$(mixed-text-file "gn2.conf"
"GN2_SECRETS=\"" gn2-secrets "/gn2-secrets.py\"\n"
+ "AI_SEARCH_ENABLED=True\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"
+ "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock\"\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"))
@@ -516,11 +544,17 @@ server described by CONFIG, a <genenetwork-configuration> object."
#$(mixed-text-file "gn3.conf"
"SPARQL_ENDPOINT=\"" sparql-endpoint "\"\n"
"DATA_DIR=\"" data-directory "\"\n"
+ "AUTH_SERVER_URL=\"https://auth-cd.genenetwork.org/\"\n"
"XAPIAN_DB_PATH=\"" xapian-db-path "\"\n"
"AUTH_DB=\"" auth-db-path "\"\n"
"LLM_DB_PATH=\"" llm-db-path "\"\n"))
(setenv "HOME" "/tmp")
(setenv "GN3_SECRETS" #$gn3-secrets)
+ (setenv "RSCRIPT" #$(file-append
+ (profile
+ (content (package->development-manifest genenetwork3))
+ (allow-collisions? #t))
+ "/bin/Rscript"))
;; Run genenetwork3.
(with-directory-excursion "genenetwork3"
(show-head-commit)
@@ -575,40 +609,135 @@ server described by CONFIG, a <genenetwork-configuration> object."
"--workers" "8"
"gn_auth.wsgi:app"))))))))
+(define (gn-guile-gexp gn-guile-port)
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+ (let ((current-repo-path (string-append (getcwd) "/gn-docs")))
+ (when (file-exists? current-repo-path)
+ (delete-file-recursively current-repo-path))
+ (setenv "CURRENT_REPO_PATH" current-repo-path)
+ (invoke #$(file-append git-minimal "/bin/git")
+ "clone" "--depth" "1" (getenv "CGIT_REPO_PATH")))
+ (invoke #$(file-append gn-guile "/bin/gn-guile")
+ (number->string #$gn-guile-port)))))
+
(define (genenetwork-shepherd-services config)
"Return shepherd services to run the genenetwork development server
described by CONFIG, a <genenetwork-configuration> object."
(match-record config <genenetwork-configuration>
- (gn2-port gn3-port gn-auth-port genotype-files data-directory xapian-db-path gn2-secrets auth-db-path gn-auth-secrets llm-db-path)
+ (gn2-port gn3-port gn-auth-port genotype-files data-directory xapian-db-path gn2-secrets auth-db-path gn-auth-secrets llm-db-path gn-doc-git-checkout gn-guile-port)
(list (shepherd-service
+ (documentation "Run gn-guile server.")
+ (provision '(gn-guile))
+ (requirement '(networking))
+ (modules '((ice-9 match)
+ (srfi srfi-1)))
+ (start
+ (let* ((gn-guile-settings
+ `(("CGIT_REPO_PATH" ,gn-doc-git-checkout)
+ ("LC_ALL" "en_US.UTF-8")
+ ("GIT_COMMITTER_NAME" "genenetwork")
+ ("GIT_COMMITTER_EMAIL" "no-reply@git.genenetwork.org"))))
+ #~(make-forkexec-constructor
+ (list #$(least-authority-wrapper
+ (program-file "gn-guile"
+ (gn-guile-gexp gn-guile-port))
+ #:name "gn-guile-pola-wrapper"
+ #:preserved-environment-variables
+ (map first gn-guile-settings)
+ #:mappings (list (file-system-mapping
+ (source gn-doc-git-checkout)
+ (target source)
+ (writable? #t)))
+ #:namespaces (delq 'net %namespaces))
+ "127.0.0.1" #$(number->string gn-guile-port))
+ #:user "genenetwork"
+ #:group "genenetwork"
+ #:environment-variables
+ (map (match-lambda
+ ((spec value)
+ (string-append spec "=" value)))
+ '#$gn-guile-settings)
+ #:log-file "/var/log/cd/gn-guile.log")))
+ (stop #~(make-kill-destructor)))
+ (shepherd-service
(documentation "Run GeneNetwork 2 development server.")
(provision '(genenetwork2))
;; FIXME: The genenetwork2 service should depend on redis.
(requirement '(networking genenetwork3))
- (start #~(make-forkexec-constructor
- (list #$(least-authority-wrapper
- (program-file "genenetwork2"
- (genenetwork2-cd-gexp config))
- #:name "genenetwork2-pola-wrapper"
- ;; If we mapped only the mysqld.sock
- ;; socket file, it would break when the
- ;; external mysqld server is restarted.
- #:mappings (list (file-system-mapping
- (source genotype-files)
- (target source))
- (file-system-mapping
- (source "/run/mysqld")
- (target source)
- (writable? #t))
- (file-system-mapping
- (source gn2-secrets)
- (target source)
- (writable? #t)))
- #:namespaces (delq 'net %namespaces))
- "127.0.0.1" #$(number->string gn2-port))
- #:user "genenetwork"
- #:group "genenetwork"
- #:log-file "/var/log/cd/genenetwork2.log"))
+ (modules '((guix search-paths)
+ (ice-9 match)
+ (srfi srfi-1)))
+ (start
+ (let* ((gn2-manifest (packages->manifest (list genenetwork2)))
+ (gn2-profile (profile
+ (content gn2-manifest)
+ (allow-collisions? #t)))
+ (gn2-settings
+ `(("SERVER_PORT" ,(number->string gn2-port))
+ ("GENENETWORK_FILES" ,genotype-files)
+ ("HOME" "/tmp")
+ ("LC_ALL" "en_US.UTF-8")
+ ("NO_REDIS" "no-redis")
+ ("RUST_BACKTRACE" "1"))))
+ (with-imported-modules (source-module-closure '((guix search-paths)))
+ #~(make-forkexec-constructor
+ (list #$(least-authority-wrapper
+ (program-file "genenetwork2"
+ (genenetwork2-cd-gexp config))
+ #:name "genenetwork2-pola-wrapper"
+ #:preserved-environment-variables
+ (append '("REQUESTS_CA_BUNDLE")
+ (map first gn2-settings)
+ (map search-path-specification-variable
+ (manifest-search-paths gn2-manifest)))
+ ;; If we mapped only the mysqld.sock
+ ;; socket file, it would break when the
+ ;; external mysqld server is restarted.
+ #:mappings (list (file-system-mapping
+ (source genotype-files)
+ (target source))
+ (file-system-mapping
+ (source "/run/mysqld")
+ (target source)
+ (writable? #t))
+ ;; XXXX: FIXME: R/Qtl generates
+ ;; files in "/tmp" and
+ ;; "/tmp/gn2". These files are
+ ;; accessed by gn3 for R/Qtl
+ ;; mapping
+ (file-system-mapping
+ (source "/tmp")
+ (target source)
+ (writable? #t))
+ (file-system-mapping
+ (source gn2-secrets)
+ (target source)
+ (writable? #t)))
+ #:namespaces (delq 'net %namespaces))
+ "127.0.0.1" #$(number->string gn2-port))
+ #:user "genenetwork"
+ #:group "genenetwork"
+ #:environment-variables
+ (append
+ '("REQUESTS_CA_BUNDLE="
+ #$(file-append gn2-profile "/etc/ssl/certs/ca-certificates.crt"))
+ (map (match-lambda
+ ((spec . value)
+ (string-append (search-path-specification-variable spec)
+ "="
+ value)))
+ (evaluate-search-paths
+ (map sexp->search-path-specification
+ '#$(map search-path-specification->sexp
+ (manifest-search-paths gn2-manifest)))
+ (list #$gn2-profile)))
+ (map (match-lambda
+ ((spec value)
+ (string-append spec "=" value)))
+ '#$gn2-settings))
+ #:log-file "/var/log/cd/genenetwork2.log"))))
(stop #~(make-kill-destructor)))
(shepherd-service
(documentation "Run GeneNetwork 3 development server.")
@@ -626,6 +755,15 @@ described by CONFIG, a <genenetwork-configuration> object."
(source "/run/mysqld")
(target source)
(writable? #t))
+ ;; XXXX: FIXME: R/Qtl generates
+ ;; files in "/tmp" and
+ ;; "/tmp/gn2". These files are
+ ;; accessed by gn3 for R/Qtl
+ ;; mapping
+ (file-system-mapping
+ (source "/tmp")
+ (target source)
+ (writable? #t))
(file-system-mapping
(source data-directory)
(target source))
@@ -711,6 +849,8 @@ described by CONFIG, a <genenetwork-configuration> object."
(cons* #$gn3-secrets
(append (find-files #$gn2-secrets
#:directories? #t)
+ (find-files "/export/data/gn-docs"
+ #:directories? #t)
(find-files #$(dirname auth-db-path)
#:directories? #t)
(find-files #$gn-auth-secrets
@@ -744,10 +884,6 @@ described by CONFIG, a <genenetwork-configuration> object."
;;; transform-genenetwork-database
;;;
-;; Path to genenetwork database dump export directory that has lots of
-;; free space
-(define %transform-genenetwork-database-export-directory
- "/export/genenetwork-database-dump")
;; Unreleased version of ccwl that is required by
;; transform-genenetwork-database for its graphql library.
@@ -804,57 +940,54 @@ described by CONFIG, a <genenetwork-configuration> object."
(description "run64 is a SRFI-64 test runner for Scheme.")
(license license:gpl3+)))
-(define (transform-genenetwork-database project)
+;; Connection settings for Virtuoso and MySQL used to load data into Virtuoso
+(define %connection-settings
+ "/etc/genenetwork/conf/gn-transform-database/conn.scm")
+
+;; Path to where the data directory from which virtuoso loads all the files
+(define %virtuoso-data-dir "/var/lib/data")
+
+(define (transform-genenetwork-database-gexp connection-settings virtuoso-data-dir repository)
(with-imported-modules '((guix build utils))
(with-packages (list ccwl git-minimal gnu-make guile-3.0 guile-dbd-mysql
guile-dbi guile-hashing guile-libyaml guile-sparql
- guile-zlib nss-certs virtuoso-ose)
- #~(begin
- (use-modules (guix build utils)
- (srfi srfi-26)
- (ice-9 threads))
-
- (invoke "git" "clone"
- "--depth" "1"
- #$(forge-project-repository project)
- ".")
- (invoke "make" "-j" (number->string (current-processor-count)))
- (let ((connection-settings-file #$(string-append %transform-genenetwork-database-export-directory
- "/conn.scm"))
- (dump-directory #$(string-append %transform-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"
- connection-settings-file
- dump-directory)
- ;; Validate dumped RDF, sending the error output to
- ;; oblivion because we don't want to print out potentially
- ;; sensitive data.
- (with-error-to-file "/dev/null"
- (cut invoke
- #$(file-append raptor2 "/bin/rapper")
- "--input" "turtle"
- "--count"
- (string-append dump-directory "/dump.ttl")))
- ;; Load RDF into virtuoso.
- (invoke "./pre-inst-env" "./load-rdf.scm"
- connection-settings-file
- (string-append dump-directory "/dump.ttl"))
- ;; Visualize schema and archive results.
- (invoke "./pre-inst-env" "./visualize-schema.scm"
- connection-settings-file)
- (invoke #$(file-append graphviz "/bin/dot")
- "-Tsvg" "sql.dot" (string-append "-o" (getenv "ARCHIVE") "/sql.svg"))
- (invoke #$(file-append graphviz "/bin/dot")
- "-Tsvg" "rdf.dot" (string-append "-o" (getenv "ARCHIVE") "/rdf.svg")))))))
+ guile-zlib nss-certs virtuoso-ose raptor2)
+ #~(begin
+ (use-modules (guix build utils)
+ (srfi srfi-26)
+ (ice-9 threads))
+ (setenv "LC_ALL" "en_US.UTF-8")
+ (let ((build-directory (string-append #$virtuoso-data-dir
+ "/build")))
+ ;; Only run this job if the build directory does not
+ ;; exists. This ensures that no other process is
+ ;; running this.
+ (unless (file-exists? build-directory)
+ (invoke "git" "clone" "--depth" "1" #$repository ".")
+ (invoke "make" "-j" (number->string (current-processor-count)))
+ (invoke "./generate-ttl-files.scm" "--settings"
+ #$connection-settings "--output" build-directory)
+ ;; First clear all the files in our virtuoso directory
+ (for-each (lambda (file)
+ (unless (string-suffix? "build" (dirname file))
+ (delete-file file)))
+ (find-files #$virtuoso-data-dir ".ttl"))
+ ;; Move data into the container's virtuoso data directory
+ (copy-recursively build-directory #$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
(forge-project
(name "transform-genenetwork-database")
- (repository "/home/git/public/gn-transform-databases/")
+ (repository "/home/git/public/gn-transform-databases")
(ci-jobs (list (forge-laminar-job
(name "transform-genenetwork-database-tests")
(run (guix-channel-job-gexp
@@ -866,7 +999,10 @@ described by CONFIG, a <genenetwork-configuration> object."
#:guix-daemon-uri %guix-daemon-uri)))
(forge-laminar-job
(name "transform-genenetwork-database")
- (run (transform-genenetwork-database this-forge-project)))))))
+ (run (transform-genenetwork-database-gexp
+ %connection-settings
+ %virtuoso-data-dir
+ "https://git.genenetwork.org/gn-transform-databases")))))))
;;;
@@ -884,6 +1020,7 @@ described by CONFIG, a <genenetwork-configuration> object."
#~(begin
(use-modules (guix build utils))
+ (setenv "LC_ALL" "en_US.UTF-8")
(invoke #$(file-append tissue "/bin/tissue")
"pull" "issues.genenetwork.org"))))))))
(ci-jobs-trigger 'webhook)))
@@ -1137,6 +1274,20 @@ gn-auth."
";")
"proxy_set_header Host $host;")))))))
+(define set-build-directory-permissions-gexp
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+
+ (for-each (lambda (file)
+ (chown file
+ (passwd:uid (getpw "laminar"))
+ (passwd:gid (getpw "laminar"))))
+ (append (find-files #$%xapian-directory
+ #:directories? #t)
+ (find-files #$%virtuoso-data-dir
+ #:directories? #t))))))
+
;; Port on which webhook is listening
(define %webhook-port 9091)
;; Port on which genenetwork2 is listening
@@ -1194,6 +1345,15 @@ gn-auth."
(jobs (list #~(job '(next-hour)
#$(program-file "build-xapian-index-cron"
build-xapian-index-cron-gexp)
+ #:user "laminar")
+ ;; Run cron once a week at midnight on Sunday morning
+ ;; Verify using: https://crontab.guru/#0_0_*_*_0
+ #~(job "0 0 * * 0"
+ #$(program-file "update-virtuoso"
+ (transform-genenetwork-database-gexp
+ %connection-settings
+ %virtuoso-data-dir
+ "https://git.genenetwork.org/gn-transform-databases"))
#:user "laminar")))))
(simple-service 'install-laminar-template
activation-service-type
@@ -1212,7 +1372,7 @@ gn-auth."
(number-of-buffers 4000000)
(maximum-dirty-buffers 3000000)
(server-port 9081)
- (dirs-allowed "/var/lib/data")
+ (dirs-allowed (list "/var/lib/data"))
(http-server-port %virtuoso-sparql-port)))
(service genenetwork-service-type
(genenetwork-configuration
@@ -1230,18 +1390,7 @@ gn-auth."
(xapian-db-path %xapian-directory)))
(simple-service 'set-build-directory-permissions
activation-service-type
- (with-imported-modules '((guix build utils))
- #~(begin
- (use-modules (guix build utils))
-
- (for-each (lambda (file)
- (chown file
- (passwd:uid (getpw "laminar"))
- (passwd:gid (getpw "laminar"))))
- (append (find-files #$%xapian-directory
- #:directories? #t)
- (find-files #$%transform-genenetwork-database-export-directory
- #:directories? #t))))))
+ set-build-directory-permissions-gexp)
(service tissue-service-type
(tissue-configuration
(socket
@@ -1250,8 +1399,12 @@ gn-auth."
(hosts
(list (tissue-host
(name "issues.genenetwork.org")
- (user "laminar")
- (upstream-repository "https://github.com/genenetwork/gn-gemtext-threads"))))))
+ (projects (list (tissue-project
+ (name "issues.genenetwork.org")
+ (user "laminar")
+ (base-path "/")
+ (upstream-repository
+ "https://github.com/genenetwork/gn-gemtext-threads")))))))))
(service forge-nginx-service-type
(forge-nginx-configuration
(http-listen (forge-ip-socket
generated by cgit v1.2.3 (git 2.47.1) at 2025-07-12 04:56:03 +0000