diff options
Diffstat (limited to 'genenetwork-development.scm')
| -rw-r--r-- | genenetwork-development.scm | 107 |
1 files changed, 62 insertions, 45 deletions
diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 87d8c20..4d290b1 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -481,7 +481,7 @@ genenetwork3 source from the latest commit of @var{project}." "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 gn2-secrets genotype-files gn-guile-port) + (gn2-repository gn3-repository gn2-port gn3-port gn2-secrets genotype-files gn-guile-port repositories) (with-packages (list coreutils git-minimal gunicorn nss-certs) (with-imported-modules '((guix build utils)) #~(begin @@ -499,18 +499,20 @@ server described by CONFIG, a <genenetwork-configuration> object." (invoke "git" "log" "--max-count" "1") (hline)) - ;; Clone the latest genenetwork2 and genenetwork3 + ;; Clone the latest genenetwork2 ;; 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)) + (with-directory-excursion + #$repositories + (when (file-exists? "genenetwork2") + (delete-file-recursively "genenetwork2")) + (invoke "git" "clone" "--depth" "1" #$gn2-repository) + (with-directory-excursion + (string-append #$repositories "/genenetwork2") + (show-head-commit))) ;; Override the genenetwork3 used by genenetwork2. (setenv "GN3_PYTHONPATH" - (string-append (getcwd) "/genenetwork3")) + (string-append #$repositories "/genenetwork3")) ;; Set other environment variables required by ;; genenetwork2. (setenv "GN2_PROFILE" #$(profile @@ -540,15 +542,16 @@ server described by CONFIG, a <genenetwork-configuration> object." "AUTH_SERVER_SSL_PUBLIC_KEY=\"" gn2-secrets "/gn-auth-ssl-public-key.pem\"\n")) ;; Start genenetwork2. - (with-directory-excursion "genenetwork2" - (invoke #$(file-append bash "/bin/sh") - "bin/genenetwork2" "gn2/default_settings.py" "-gunicorn-prod"))))))) + (with-directory-excursion + (string-append #$repositories "/genenetwork2") + (invoke #$(file-append bash "/bin/sh") + "bin/genenetwork2" "gn2/default_settings.py" "-gunicorn-dev"))))))) (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 gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path lmdb-data-path) + (gn3-repository gn3-port gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path lmdb-data-path repositories) (with-manifest (package->development-manifest genenetwork3) (with-packages (list git-minimal nss-certs) (with-imported-modules '((guix build utils)) @@ -567,9 +570,7 @@ server described by CONFIG, a <genenetwork-configuration> object." (invoke "git" "log" "--max-count" "1") (hline)) - ;; Clone the latest genenetwork3 repository. - (invoke "git" "clone" "--depth" "1" #$gn3-repository) - (setenv "GN3_PROFILE" #$(profile + (setenv "GN3_PROFILE" #$(profile (content (package->development-manifest genenetwork3)) (allow-collisions? #t))) (setenv "REQUESTS_CA_BUNDLE" (string-append @@ -592,23 +593,32 @@ server described by CONFIG, a <genenetwork-configuration> object." (content (package->development-manifest genenetwork3)) (allow-collisions? #t)) "/bin/Rscript")) - ;; Run genenetwork3. - (with-directory-excursion "genenetwork3" - (show-head-commit) - (invoke #$(file-append gunicorn "/bin/gunicorn") - "-b" #$(string-append "localhost:" (number->string gn3-port)) - "--workers" "8" - "gn3.app:create_app()" - ;; gunicorn's default 30 second timeout is - ;; insufficient for Fahamu AI endpoints and - ;; results in worker timeout errors. - "--timeout" "1200")))))))) + + (with-directory-excursion + #$repositories + ;; Clone the latest genenetwork3 repository. + (when (file-exists? (string-append #$repositories "/genenetwork3")) + (delete-file-recursively (string-append #$repositories "/genenetwork3"))) + (invoke "git" "clone" "--depth" "1" #$gn3-repository)) + + (with-directory-excursion + (string-append #$repositories "/genenetwork3") + (show-head-commit) + ;; Run genenetwork3. + (invoke #$(file-append gunicorn "/bin/gunicorn") + "-b" #$(string-append "localhost:" (number->string gn3-port)) + "--workers" "8" + "gn3.app:create_app()" + ;; gunicorn's default 30 second timeout is + ;; insufficient for Fahamu AI endpoints and + ;; results in worker timeout errors. + "--timeout" "1200")))))))) (define (gn-auth-cd-gexp config) "Return a G-expression that runs the latest gn-auth development server described by CONFIG, a <genenetwork-configuration> object." (match-record config <genenetwork-configuration> - (gn-auth-repository gn-auth-port auth-db-path gn-auth-secrets) + (gn-auth-repository gn-auth-port auth-db-path gn-auth-secrets repositories) (with-manifest (package->development-manifest gn-auth) (with-packages (list git-minimal nss-certs) (with-imported-modules '((guix build utils)) @@ -626,9 +636,13 @@ server described by CONFIG, a <genenetwork-configuration> object." (hline) (invoke "git" "log" "--max-count" "1") (hline)) + (with-directory-excursion + #$repositories + ;; Clone the latest gn-auth repository. + (when (file-exists? "gn-auth") + (delete-file-recursively "gn-auth")) + (invoke "git" "clone" "--depth" "1" #$gn-auth-repository)) - ;; Clone the latest gn-auth repository. - (invoke "git" "clone" "--depth" "1" #$gn-auth-repository) ;; Configure gn-auth. (setenv "GN_AUTH_PROFILE" #$(profile (content (package->development-manifest gn-auth)) @@ -646,7 +660,7 @@ server described by CONFIG, a <genenetwork-configuration> object." (setenv "HOME" "/tmp") (setenv "AUTHLIB_INSECURE_TRANSPORT" "true") ;; Run gn-auth. - (with-directory-excursion "gn-auth" + (with-directory-excursion (string-append #$repositories "/gn-auth") (show-head-commit) (invoke #$(file-append gunicorn "/bin/gunicorn") "-b" #$(string-append "localhost:" (number->string gn-auth-port)) @@ -691,22 +705,25 @@ server described by CONFIG, a <genenetwork-configuration> object." (setenv "CURL_CA_BUNDLE" (getenv "SSL_CERT_FILE")) (setenv "REQUESTS_CA_BUNDLE" (getenv "SSL_CERT_FILE")) - (let ((current-repo-path (string-append (getcwd) "/gn-docs"))) + (let ((current-repo-path "/export/data/repositories/gn-docs")) (when (file-exists? current-repo-path) (delete-file-recursively current-repo-path)) - (setenv "CURRENT_REPO_PATH" current-repo-path) - (invoke #$(file-append git-minimal "/bin/git") - "clone" "--depth" "1" (getenv "CGIT_REPO_PATH"))) - (invoke "git" "clone" "--depth" "1" "https://git.genenetwork.org/gn-guile") - - ;; We have a gn-guile-dev wrapper script that sets a "./" in the - ;; GN_GUILE_LOAD_PATH hence allowing this to be run from the gn-guile - ;; directory. This allows gn-guile to be run from the latest - ;; upstream commits without pinning to guix. - (with-directory-excursion "gn-guile" - (show-head-commit) - (invoke #$(file-append gn-guile "/bin/gn-guile-dev") - (number->string #$gn-guile-port))))))) + (setenv "CURRENT_REPO_PATH" current-repo-path) + (with-directory-excursion + "/export/data/repositories" + (invoke #$(file-append git-minimal "/bin/git") + "clone" "--depth" "1" (getenv "CGIT_REPO_PATH") current-repo-path) + (when (file-exists? "gn-guile") + (delete-file-recursively "gn-guile")) + (invoke "git" "clone" "--depth" "1" "https://git.genenetwork.org/gn-guile") + ;; We have a gn-guile-dev wrapper script that sets a "./" in the + ;; GN_GUILE_LOAD_PATH hence allowing this to be run from the gn-guile + ;; directory. This allows gn-guile to be run from the latest + ;; upstream commits without pinning to guix. + (with-directory-excursion "gn-guile" + (show-head-commit) + (invoke #$(file-append gn-guile "/bin/gn-guile-dev") + (number->string #$gn-guile-port))))))))) (define (genenetwork-shepherd-services config) "Return shepherd services to run the genenetwork development server |