aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--genenetwork-development.scm685
-rw-r--r--genenetwork/development-helper.scm52
2 files changed, 316 insertions, 421 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index 4fb7c46..8025631 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -92,272 +92,76 @@ be imported into G-expressions."
(((or 'forge 'genenetwork) _ ...) #t)
(name (guix-module-name? name))))
-
-;;;
-;;; Development server configuration
-;;;
-
-;; A development server is a server that is automatically redeployed
-;; on every commit to its git repository. This is used by both the
-;; genenetwork2 and the genenetwork3 development servers. Here, we
-;; abstract out the details.
-
-(define-record-type* <development-server-configuration>
- development-server-configuration make-development-server-configuration
- development-server-configuration?
- (name development-server-configuration-name)
- (git-repository development-server-configuration-git-repository)
- (git-branch development-server-configuration-git-branch)
- (executable-path development-server-configuration-executable-path)
- (runner development-server-configuration-runner)
- (port development-server-configuration-port
- (default 8080)))
-
-(define (development-server-redeploy config)
- "Return a G-expression that provides a function redeploy which
-redeploys the development server specified by CONFIG, a
-<development-server-configuration> object."
- (with-imported-modules (source-module-closure '((genenetwork development-helper)
- (forge build git))
- #:select? import-module?)
- (with-extensions (list guile-gcrypt guile-zlib)
- (with-packages (list git-minimal nss-certs)
- #~(begin
- (use-modules (genenetwork development-helper)
- (forge build git)
- (guix derivations)
- (guix gexp)
- (guix monads)
- (guix store)
- (guix utils)
- (rnrs exceptions))
-
- (define (redeploy)
- (parameterize ((%daemon-socket-uri #$%guix-daemon-uri))
- (switch-symlinks
- #$(development-server-configuration-executable-path config)
- (with-store store
- (run-with-store store
- (mlet* %store-monad ((latest-source
- (latest-git-checkout
- #$(string-append (development-server-configuration-name config)
- "-checkout")
- #$(development-server-configuration-git-repository config)
- #:branch #$(development-server-configuration-git-branch config)))
- (runner-drv
- (gexp->script
- #$(string-append (development-server-configuration-name config)
- "-runner")
- (#$(development-server-configuration-runner config)
- latest-source)
- #:guile (read-derivation-from-file
- #$(raw-derivation-file
- (with-store store
- (package-derivation store guile-3.0)))))))
- (mbegin %store-monad
- (built-derivations (list runner-drv))
- (return (derivation->output-path runner-drv))))))))))))))
-
-(define (development-server-activation config)
- "Return a G-expression that runs the development server specified by
-CONFIG, a <development-server-configuration> object, on startup."
- (let ((executable-path (development-server-configuration-executable-path config)))
- #~(begin
- (use-modules (guix build utils))
-
- (mkdir-p #$(dirname executable-path))
- (chown #$(dirname executable-path)
- (passwd:uid (getpw "laminar"))
- (passwd:gid (getpw "laminar")))
- #$(development-server-redeploy config)
- (redeploy))))
+(define-record-type* <genenetwork-configuration>
+ genenetwork-configuration make-genenetwork-configuration
+ genenetwork-configuration?
+ (gn2-repository genenetwork-configuration-gn2-repository
+ (default "https://github.com/genenetwork/genenetwork2"))
+ (gn3-repository genenetwork-configuration-gn3-repository
+ (default "https://github.com/genenetwork/genenetwork3"))
+ (gn2-port genenetwork-configuration-gn2-port
+ (default 8082))
+ (gn3-port genenetwork-configuration-gn3-port
+ (default 8083))
+ (genotype-files genenetwork-configuration-genotype-files
+ (default "/var/genenetwork/genotype-files"))
+ (xapian-db-path genenetwork-xapian-db-path
+ (default "/var/genenetwork/xapian")))
;;;
-;;; genenetwork2
+;;; genenetwork
;;;
-;; Path to genotype files required by genenetwork2
-(define %genotype-files
- "/export/data/genenetwork/genotype_files")
-
-;; Path to the xapian search index used by genenetwork2
-(define %xapian-db-path
- "/export/data/genenetwork/xapian")
-
-;; Port on which genenetwork2 is listening
-(define %genenetwork2-port
- 9092)
-
-;; Port on which genenetwork3 is listening
-(define %genenetwork3-port
- 9093)
-
-(define (genenetwork2-tests project test-command)
- "Return a G-expression that runs TEST-COMMAND with genenetwork2
-source code. PROJECT is a <forge-project> object describing
-genenetwork2. TEST-COMMAND is a list of strings specifying the command
-to be executed."
- (with-imported-modules '((guix build utils))
- (with-packages (list bash coreutils git-minimal nss-certs)
- #~(begin
- (use-modules (guix build utils))
-
- (define (hline)
- "Print a horizontal line 50 '=' characters long."
- (display (make-string 50 #\=))
- (newline)
- (force-output))
-
- (define (show-head-commit)
- (hline)
- (invoke "git" "log" "--max-count" "1")
- (hline))
-
- (invoke "git" "clone" "--depth" "1"
- "https://github.com/genenetwork/genenetwork3")
- (with-directory-excursion "genenetwork3"
- (show-head-commit))
- (invoke "git" "clone" "--depth" "1"
- "--branch" #$(forge-project-repository-branch project)
- #$(forge-project-repository project))
- (with-directory-excursion "genenetwork2"
- (show-head-commit))
- (setenv "SERVER_PORT" "8080")
- ;; Use a profile with all dependencies except genenetwork3.
- (setenv "GN2_PROFILE"
- #$(profile
- (content (package->development-manifest genenetwork2))
- (allow-collisions? #t)))
- ;; Set GN3_PYTHONPATH to the latest genenetwork3.
- (setenv "GN3_PYTHONPATH"
- (string-append (getcwd) "/genenetwork3"))
- (setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
- (setenv "GN3_LOCAL_URL" (string-append "http://localhost:" (number->string #$%genenetwork3-port)))
- (setenv "GENENETWORK_FILES" #$%genotype-files)
- (setenv "HOME" "/tmp")
- (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl")
- (chdir "genenetwork2")
- (apply invoke '#$test-command)))))
-
-(define (genenetwork2-project config)
- "Return a forge project describing genenetwork2. CONFIG is a
-<development-server-configuration> object describing genenetwork2."
- (forge-project
- (name "genenetwork2")
- (repository (development-server-configuration-git-repository config))
- (repository-branch (development-server-configuration-git-branch config))
- (ci-jobs (list (forge-laminar-job
- (name "genenetwork2")
- (run (genenetwork2-tests
- this-forge-project
- (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
- "-c" "-m" "pytest")))
- ;; If unit tests pass, redeploy genenetwork2 and
- ;; trigger Mechanical Rob.
- (after #~(begin
- (use-modules (guix build utils))
- #$(development-server-redeploy config)
- (when (string=? (getenv "RESULT") "success")
- (redeploy)
- ;; We cannot refer to sudo in the
- ;; store since that sudo does not have
- ;; the setuid bit set. See "(guix)
- ;; Setuid Programs".
- (invoke "/run/setuid-programs/sudo"
- #$(file-append shepherd "/bin/herd")
- "restart" "genenetwork2")
- (invoke #$(file-append laminar "/bin/laminarc")
- "queue" "genenetwork2-mechanical-rob")))))
- (forge-laminar-job
- (name "genenetwork2-mechanical-rob")
- (run (genenetwork2-tests
- this-forge-project
- (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
- "-c" "../test/requests/test-website.py"
- "--all" (string-append "http://localhost:" (number->string %genenetwork2-port)))))
- (trigger? #f))))
- (ci-jobs-trigger 'webhook)))
-
-(define (genenetwork2-shepherd-service config)
- "Return a shepherd service to run the genenetwork2 development
-server. CONFIG is a <development-server-configuration> object
-describing genenetwork2."
- (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 #$(least-authority-wrapper
- (development-server-configuration-executable-path config)
- #:name "genenetwork2-pola-wrapper"
- #:mappings (list (file-system-mapping
- (source (development-server-configuration-executable-path config))
- (target source))
- (file-system-mapping
- (source %genotype-files)
- (target source))
- (file-system-mapping
- (source "/run/mysqld/mysqld.sock")
- (target source)
- (writable? #t))
- %store-mapping)
- #:namespaces (delq 'net %namespaces))
- "127.0.0.1" #$(number->string (development-server-configuration-port config)))
- #:user "genenetwork"
- #:group "genenetwork"
- #:log-file "/var/log/cd/genenetwork2.log"))
- (stop #~(make-kill-destructor))))
-
-(define %default-genenetwork2-configuration
- (development-server-configuration
- (name "genenetwork2")
- (git-repository "https://github.com/genenetwork/genenetwork2")
- (git-branch "testing")
- (executable-path "/laminar/bin/genenetwork2")
- (runner (with-imported-modules (source-module-closure '((genenetwork development-helper))
- #:select? import-module?)
- #~(lambda (latest-gn2-source)
- ((@@ (genenetwork development-helper) genenetwork2-runner-gexp)
- latest-gn2-source
- #$(profile
- (content (package->development-manifest genenetwork2))
- (allow-collisions? #t))
- #$%genenetwork3-port
- #$%genotype-files))))))
-
-(define %genenetwork-accounts
- (list (user-group
- (name "genenetwork")
- (system? #t))
- (user-account
- (name "genenetwork")
- (group "genenetwork")
- (system? #t)
- (comment "GeneNetwork user")
- (home-directory "/var/empty")
- (shell (file-append shadow "/sbin/nologin")))))
-
-(define genenetwork2-service-type
- (service-type
- (name 'genenetwork2)
- (description "Run GeneNetwork 2 development server and CI.")
- (extensions
- (list (service-extension account-service-type
- (const %genenetwork-accounts))
- (service-extension activation-service-type
- development-server-activation)
- (service-extension shepherd-root-service-type
- (compose list genenetwork2-shepherd-service))
- (service-extension forge-service-type
- (compose list genenetwork2-project))))
- (default-value %default-genenetwork2-configuration)))
-
-
-;;;
-;;; genenetwork3
-;;;
+(define (genenetwork2-tests config test-command)
+ "Return a G-expression that runs TEST-COMMAND for genenetwork2
+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>
+ (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))
+
+ (define (hline)
+ "Print a horizontal line 50 '=' characters long."
+ (display (make-string 50 #\=))
+ (newline)
+ (force-output))
+
+ (define (show-head-commit)
+ (hline)
+ (invoke "git" "log" "--max-count" "1")
+ (hline))
+
+ (invoke "git" "clone" "--depth" "1" gn3-repository)
+ (with-directory-excursion "genenetwork3"
+ (show-head-commit))
+ (invoke "git" "clone" "--depth" "1" gn2-repository)
+ (with-directory-excursion "genenetwork2"
+ (show-head-commit))
+ ;; This is a dummy SERVER_PORT to placate
+ ;; bin/genenetwork2. TODO: Fix bin/genenetwork2 so that
+ ;; this is not needed.
+ (setenv "SERVER_PORT" "8080")
+ ;; Use a profile with all dependencies except
+ ;; genenetwork3.
+ (setenv "GN2_PROFILE"
+ #$(profile
+ (content (package->development-manifest genenetwork2))
+ (allow-collisions? #t)))
+ ;; Set GN3_PYTHONPATH to the latest genenetwork3.
+ (setenv "GN3_PYTHONPATH"
+ (string-append (getcwd) "/genenetwork3"))
+ (setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
+ (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")
+ (chdir "genenetwork2")
+ (apply invoke '#$test-command))))))
(define (genenetwork3-tests tests-command manifest)
"Return a G-expression running TESTS-COMMAND in a profile described
@@ -396,109 +200,251 @@ command to be executed."
(manifest-cons python-mypy
(package->development-manifest genenetwork3))))
-(define (genenetwork3-project config)
- (forge-project
- (name "genenetwork3")
- (repository (development-server-configuration-git-repository config))
- (repository-branch (development-server-configuration-git-branch config))
- (ci-jobs (list (forge-laminar-job
- (name "genenetwork3")
- (run (derivation-job-gexp
- this-forge-project
- this-forge-laminar-job
- genenetwork3-unit-tests
- #:guix-daemon-uri %guix-daemon-uri))
- ;; If unit tests pass, redeploy genenetwork3 and
- ;; trigger genenetwork2 tests.
- (after #~(begin
- (use-modules (guix build utils))
- #$(development-server-redeploy config)
- (when (string=? (getenv "RESULT") "success")
- (redeploy)
- ;; We cannot refer to sudo in the
- ;; store since that sudo does not have
- ;; the setuid bit set. See "(guix)
- ;; Setuid Programs".
- (invoke "/run/setuid-programs/sudo"
- #$(file-append shepherd "/bin/herd")
- "restart" "genenetwork3")
- (invoke #$(file-append laminar "/bin/laminarc")
- "queue" "genenetwork2")))))
- (forge-laminar-job
- (name "genenetwork3-pylint")
- (run (derivation-job-gexp
- this-forge-project
- this-forge-laminar-job
- genenetwork3-pylint
- #:guix-daemon-uri %guix-daemon-uri)))
- (forge-laminar-job
- (name "genenetwork3-mypy")
- (run (derivation-job-gexp
- this-forge-project
- this-forge-laminar-job
- genenetwork3-mypy
- #:guix-daemon-uri %guix-daemon-uri)))))
- (ci-jobs-trigger 'webhook)))
+(define (genenetwork-projects config)
+ "Return forge projects for genenetwork described by CONFIG, a
+<genenetwork-configuration> object."
+ (match-record config <genenetwork-configuration>
+ (gn2-repository gn3-repository gn2-port)
+ (list (forge-project
+ (name "genenetwork2")
+ (repository gn2-repository)
+ (ci-jobs (list (forge-laminar-job
+ (name "genenetwork2")
+ (run (genenetwork2-tests
+ config
+ (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
+ "-c" "-m" "pytest")))
+ ;; If unit tests pass, redeploy genenetwork2 and
+ ;; trigger Mechanical Rob.
+ (after #~(begin
+ (use-modules (guix build utils))
+ (when (string=? (getenv "RESULT") "success")
+ ;; We cannot refer to sudo in the
+ ;; store since that sudo does not have
+ ;; the setuid bit set. See "(guix)
+ ;; Setuid Programs".
+ (invoke "/run/setuid-programs/sudo"
+ #$(file-append shepherd "/bin/herd")
+ "restart" "genenetwork2")
+ (invoke #$(file-append laminar "/bin/laminarc")
+ "queue" "genenetwork2-mechanical-rob")))))
+ (forge-laminar-job
+ (name "genenetwork2-mechanical-rob")
+ (run (genenetwork2-tests
+ config
+ (list "sh" "bin/genenetwork2" "./etc/default_settings.py"
+ "-c" "../test/requests/test-website.py"
+ "--all" (string-append "http://localhost:" (number->string gn2-port)))))
+ (trigger? #f))))
+ (ci-jobs-trigger 'webhook))
+ (forge-project
+ (name "genenetwork3")
+ (repository gn3-repository)
+ (ci-jobs (list (forge-laminar-job
+ (name "genenetwork3")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-unit-tests
+ #:guix-daemon-uri %guix-daemon-uri))
+ ;; If unit tests pass, redeploy genenetwork3 and
+ ;; trigger genenetwork2 tests.
+ (after #~(begin
+ (use-modules (guix build utils))
+ (when (string=? (getenv "RESULT") "success")
+ ;; We cannot refer to sudo in the
+ ;; store since that sudo does not have
+ ;; the setuid bit set. See "(guix)
+ ;; Setuid Programs".
+ (invoke "/run/setuid-programs/sudo"
+ #$(file-append shepherd "/bin/herd")
+ "restart" "genenetwork3")
+ (invoke #$(file-append laminar "/bin/laminarc")
+ "queue" "genenetwork2")))))
+ (forge-laminar-job
+ (name "genenetwork3-pylint")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-pylint
+ #:guix-daemon-uri %guix-daemon-uri)))
+ (forge-laminar-job
+ (name "genenetwork3-mypy")
+ (run (derivation-job-gexp
+ this-forge-project
+ this-forge-laminar-job
+ genenetwork3-mypy
+ #:guix-daemon-uri %guix-daemon-uri)))))
+ (ci-jobs-trigger 'webhook)))))
+
+(define (genenetwork2-cd-gexp config)
+ "Return a G-expression that runs the latest genenetwork2 development
+server described by CONFIG, a <genenetwork-configuration> object."
+ (match-record config <genenetwork-configuration>
+ (gn2-repository gn3-repository gn2-port gn3-port genotype-files)
+ (with-packages (list coreutils git-minimal gunicorn nss-certs)
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils)
+ (ice-9 match))
+
+ (define (hline)
+ "Print a horizontal line 50 '=' characters long."
+ (display (make-string 50 #\=))
+ (newline)
+ (force-output))
+
+ (define (show-head-commit)
+ (hline)
+ (invoke "git" "log" "--max-count" "1")
+ (hline))
+
+ ;; Clone the latest genenetwork2 and genenetwork3
+ ;; repositories.
+ (invoke "git" "clone" "--depth" "1" #$gn2-repository)
+ (with-directory-excursion "genenetwork2"
+ (show-head-commit))
+ (invoke "git" "clone" "--depth" "1" #$gn3-repository)
+ (with-directory-excursion "genenetwork3"
+ (show-head-commit))
+
+ ;; Override the genenetwork3 used by genenetwork2.
+ (setenv "GN3_PYTHONPATH"
+ (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_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
+ (setenv "GN_SERVER_URL" "/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")
+
+ ;; Start genenetwork2.
+ (with-directory-excursion "genenetwork2"
+ (invoke #$(file-append bash "/bin/sh")
+ "bin/genenetwork2" "etc/default_settings.py" "-gunicorn-prod")))))))
+
+(define (genenetwork3-cd-gexp config)
+ "Return a G-expression that runs the latest genenetwork3 development
+server described by CONFIG, a <genenetwork-configuration> object."
+ (match-record config <genenetwork-configuration>
+ (gn3-repository gn3-port xapian-db-path)
+ (with-manifest (package->development-manifest genenetwork3)
+ (with-packages (list git-minimal nss-certs)
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils)
+ (ice-9 match))
+
+ (define (hline)
+ "Print a horizontal line 50 '=' characters long."
+ (display (make-string 50 #\=))
+ (newline)
+ (force-output))
+
+ (define (show-head-commit)
+ (hline)
+ (invoke "git" "log" "--max-count" "1")
+ (hline))
+
+ ;; Clone the latest genenetwork3 repository.
+ (invoke "git" "clone" "--depth" "1" #$gn3-repository)
+ ;; Configure genenetwork3.
+ (setenv "GN3_CONF"
+ #$(mixed-text-file "gn3.conf"
+ "XAPIAN_DB_PATH=\"" xapian-db-path "\"\n"))
+ (setenv "HOME" "/tmp")
+ ;; Run genenetwork3.
+ (with-directory-excursion "genenetwork3"
+ (show-head-commit)
+ (invoke #$(file-append gunicorn "/bin/gunicorn")
+ "-b" #$(string-append "localhost:" (number->string gn3-port))
+ "gn3.app:create_app()"))))))))
+
+(define (genenetwork-shepherd-services config)
+ "Return shepherd services to run the genenetwork development server
+described by CONFIG, a <genenetwork-configuration> object."
+ (match-record config <genenetwork-configuration>
+ (gn2-port gn3-port genotype-files xapian-db-path)
+ (list (shepherd-service
+ (documentation "Run GeneNetwork 2 development server.")
+ (provision '(genenetwork2))
+ ;; FIXME: The genenetwork2 service should depend on redis.
+ (requirement '(networking genenetwork3))
+ (start #~(make-forkexec-constructor
+ (list #$(least-authority-wrapper
+ (program-file "genenetwork2"
+ (genenetwork2-cd-gexp config))
+ #:name "genenetwork2-pola-wrapper"
+ #:mappings (list (file-system-mapping
+ (source genotype-files)
+ (target source))
+ (file-system-mapping
+ (source "/run/mysqld/mysqld.sock")
+ (target source)
+ (writable? #t)))
+ #:namespaces (delq 'net %namespaces))
+ "127.0.0.1" #$(number->string gn2-port))
+ #:user "genenetwork"
+ #:group "genenetwork"
+ #:log-file "/var/log/cd/genenetwork2.log"))
+ (stop #~(make-kill-destructor)))
+ (shepherd-service
+ (documentation "Run GeneNetwork 3 development server.")
+ (provision '(genenetwork3))
+ (requirement '(networking))
+ (start #~(make-forkexec-constructor
+ (list #$(least-authority-wrapper
+ (program-file "genenetwork3"
+ (genenetwork3-cd-gexp config))
+ #:name "genenetwork3-pola-wrapper"
+ #:mappings (list (file-system-mapping
+ (source "/run/mysqld/mysqld.sock")
+ (target source)
+ (writable? #t))
+ (file-system-mapping
+ (source xapian-db-path)
+ (target source)))
+ #:namespaces (delq 'net %namespaces))
+ "127.0.0.1" #$(number->string gn3-port))
+ #:user "genenetwork"
+ #:group "genenetwork"
+ #:log-file "/var/log/cd/genenetwork3.log"))
+ (stop #~(make-kill-destructor))))))
+
+(define %genenetwork-accounts
+ (list (user-group
+ (name "genenetwork")
+ (system? #t))
+ (user-account
+ (name "genenetwork")
+ (group "genenetwork")
+ (system? #t)
+ (comment "GeneNetwork user")
+ (home-directory "/var/empty")
+ (shell (file-append shadow "/sbin/nologin")))))
-(define (genenetwork3-shepherd-service config)
- (shepherd-service
- (documentation "Run GeneNetwork 3.")
- (provision '(genenetwork3))
- (requirement '(networking))
- (start #~(make-forkexec-constructor
- (list #$(least-authority-wrapper
- (development-server-configuration-executable-path config)
- #:name "genenetwork3-pola-wrapper"
- #:mappings (list (file-system-mapping
- (source (development-server-configuration-executable-path config))
- (target source))
- (file-system-mapping
- (source "/run/mysqld/mysqld.sock")
- (target source)
- (writable? #t))
- (file-system-mapping
- (source %xapian-db-path)
- (target source))
- %store-mapping)
- #:namespaces (delq 'net %namespaces))
- "127.0.0.1" #$(number->string (development-server-configuration-port config)))
- #:user "genenetwork"
- #:group "genenetwork"
- #:log-file "/var/log/cd/genenetwork3.log"))
- (stop #~(make-kill-destructor))))
-
-(define %default-genenetwork3-configuration
- (development-server-configuration
- (name "genenetwork3")
- (git-repository "https://github.com/genenetwork/genenetwork3")
- (git-branch "main")
- (executable-path "/laminar/bin/genenetwork3")
- (runner (with-imported-modules (source-module-closure '((genenetwork development-helper))
- #:select? import-module?)
- #~(lambda (latest-gn3-source)
- ((@@ (genenetwork development-helper) genenetwork3-runner-gexp)
- latest-gn3-source
- #$(mixed-text-file "gn3.conf"
- "XAPIAN_DB_PATH=\"" %xapian-db-path "\"\n")
- #$(profile
- (content (manifest-cons gunicorn
- (package->development-manifest genenetwork3)))
- (allow-collisions? #t))))))))
-
-(define genenetwork3-service-type
+(define genenetwork-service-type
(service-type
- (name 'genenetwork3)
- (description "Run GeneNetwork 3.")
+ (name 'genenetwork)
+ (description "Run GeneNetwork development servers and CI.")
(extensions
(list (service-extension account-service-type
(const %genenetwork-accounts))
- (service-extension activation-service-type
- development-server-activation)
(service-extension shepherd-root-service-type
- (compose list genenetwork3-shepherd-service))
+ genenetwork-shepherd-services)
(service-extension forge-service-type
- (compose list genenetwork3-project))))
- (default-value %default-genenetwork3-configuration)))
+ genenetwork-projects)))
+ (default-value (genenetwork-configuration))))
;;;
@@ -775,10 +721,6 @@ on."
(number->string gn3-port) ";")
"proxy_set_header Host $host;")))))))
-;; Port on which webhook is listening
-(define %webhook-port
- 9091)
-
(define (laminar-reverse-proxy-server-block listen laminar-bind-http webhook-port published-channel-names)
"Return an <nginx-server-configuration> object to reverse proxy
laminar. The nginx server will listen on LISTEN and reverse proxy to
@@ -825,6 +767,13 @@ reverse proxy tissue."
(body (list "proxy_pass http://unix:/var/run/tissue/socket:;"
"proxy_set_header Host $host;")))))))
+;; Port on which webhook is listening
+(define %webhook-port 9091)
+;; Port on which genenetwork2 is listening
+(define %genenetwork2-port 9092)
+;; Port on which genenetwork3 is listening
+(define %genenetwork3-port 9093)
+
(operating-system
(host-name "genenetwork-development")
(timezone "UTC")
@@ -868,14 +817,12 @@ reverse proxy tissue."
(virtuoso-configuration
(server-port 8891)
(http-server-port 8892)))
- (service genenetwork2-service-type
- (development-server-configuration
- (inherit %default-genenetwork2-configuration)
- (port %genenetwork2-port)))
- (service genenetwork3-service-type
- (development-server-configuration
- (inherit %default-genenetwork3-configuration)
- (port %genenetwork3-port)))
+ (service genenetwork-service-type
+ (genenetwork-configuration
+ (gn2-port %genenetwork2-port)
+ (gn3-port %genenetwork3-port)
+ (genotype-files "/export/data/genenetwork/genotype_files")
+ (xapian-db-path "/export/data/genenetwork/xapian")))
(simple-service 'set-dump-genenetwork-database-export-directory-permissions
activation-service-type
(with-imported-modules '((guix build utils))
diff --git a/genenetwork/development-helper.scm b/genenetwork/development-helper.scm
index 9bf737d..e65f9da 100644
--- a/genenetwork/development-helper.scm
+++ b/genenetwork/development-helper.scm
@@ -101,55 +101,3 @@ with genenetwork3 dependencies."
(find-files "." shell-script?))
(invoke "pylint" "gn3"))
(mkdir-p #$output)))))
-
-(define (genenetwork2-runner-gexp genenetwork2-source profile gn3-port
- genotype-files)
- "Return a G-expression that runs the genenetwork2 server for
-GENENETWORK2-SOURCE in PROFILE. GENENETWORK2-SOURCE is a checkout of
-the genenetwork2 source code. PROFILE is a profile with genenetwork2
-dependencies. GN3-PORT is the port on which a local instance of
-genenetwork3 is listening. GENOTYPE-FILES is the path to genotype
-files."
- (with-imported-modules '((guix build utils))
- (with-profile profile
- #~(begin
- (use-modules (guix build utils)
- (ice-9 match))
-
- (chdir #$genenetwork2-source)
- (match (command-line)
- ((_ ip port)
- (setenv "SERVER_PORT" port)
- (setenv "GN2_PROFILE" #$profile)
- (setenv "GN_PROXY_URL" "http://genenetwork.org/gn3-proxy/")
- (setenv "GN_SERVER_URL" "/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")
- (invoke "sh" "bin/genenetwork2" "etc/default_settings.py" "-gunicorn-prod")))))))
-
-(define (genenetwork3-runner-gexp genenetwork3-source config-file profile)
- "Return a G-expression that runs the genenetwork3 server for
-GENENETWORK3-SOURCE in PROFILE. GENENETWORK3-SOURCE is a checkout of
-the genenetwork3 source code. CONFIG-FILE is a file containing
-configuration settings for genenetwork3. PROFILE is a profile with
-genenetwork3 dependencies."
- (with-imported-modules '((guix build utils))
- (with-profile profile
- #~(begin
- (use-modules (guix build utils)
- (ice-9 match))
-
- (chdir #$genenetwork3-source)
- (setenv "GN3_CONF" #$config-file)
- (setenv "HOME" "/tmp")
- (match (command-line)
- ((_ ip port)
- (invoke "gunicorn"
- "-b" (string-append ip ":" port)
- "gn3.app:create_app()")))))))