diff options
| -rw-r--r-- | genenetwork-development.scm | 685 | ||||
| -rw-r--r-- | genenetwork/development-helper.scm | 52 |
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()"))))))) |