Explicitly write to gn{2,3,-auth}.conf files.

Make this files editable for local development, instead of interning them at
the store.

1 files changed, 111 insertions, 91 deletions

diff --git a/genenetwork-local-container.scm b/genenetwork-local-container.scm
index 2e3eafb..14403ab 100644
--- a/genenetwork-local-container.scm
+++ b/genenetwork-local-container.scm
@@ -83,74 +83,86 @@
 server described by CONFIG, a <genenetwork-configuration> object."
   (match-record config <genenetwork-configuration>
     (gn2-port gn2-secrets gn3-port gn-auth-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))
-
-            ;; Override the genenetwork3 used by genenetwork2.
-            (setenv "GN3_PYTHONPATH" "/genenetwork3")
-            ;; Set other environment variables required by
-            ;; genenetwork2.
-            (setenv "GN2_PROFILE" #$(profile
-                                     (content (package->development-manifest genenetwork2))
-                                     (allow-collisions? #t)))
-            (setenv
-             "GN2_SETTINGS"
-             #$(mixed-text-file "gn2.conf"
-                                "GN2_SECRETS=\"" gn2-secrets "\"\n"
-                                "AI_SEARCH_ENABLED=True\n"
-                                "TEST_FEATURE_SWITCH=True\n"
-                                "GN3_LOCAL_URL=\""
-                                (string-append "http://localhost:"
-                                               (number->string gn3-port))
-                                "\"\n"
-                                "GN_SERVER_URL=\""
-                                (string-append "http://localhost:"
-                                               (number->string gn3-port))
-                                "/api/\"\n"
-                                "AUTH_SERVER_URL=\""
-                                (string-append "http://localhost:"
-                                               (number->string gn-auth-port))
-                                "\"\n"
-                                "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock&charset=utf8\"\n"
-                                "SSL_PRIVATE_KEY=\"/etc/genenetwork/conf/gn2/private.pem\"\n"
-                                "AUTH_SERVER_SSL_PUBLIC_KEY=\"/etc/genenetwork/conf/gn-auth/clients-public-keys/gn-auth.pem\"\n"))
+      (with-packages
+       (list coreutils git-minimal gunicorn nss-certs)
+       (with-imported-modules '((guix build utils))
+         #~(begin
+             (use-modules (guix build utils)
+                          (ice-9 ftw)
+                          (ice-9 match))
 
-            ;; Start genenetwork2.
-            (with-directory-excursion "/genenetwork2"
-              (invoke #$(file-append bash "/bin/sh")
-                      "bin/genenetwork2" "gn2/default_settings.py" "-gunicorn-dev")))))))
+             ;; Override the genenetwork3 used by genenetwork2.
+             (setenv "GN3_PYTHONPATH" "/genenetwork3")
+             (setenv "GN2_PROFILE" #$(profile
+                                      (content (package->development-manifest genenetwork2))
+                                      (allow-collisions? #t)))
+             (unless (file-exists? "/etc/genenetwork/conf/gn2.conf")
+               (with-output-to-file "/etc/genenetwork/conf/gn2.conf"
+                 (lambda ()
+                   (display #$(string-append
+                               "GN2_SECRETS=\"" gn2-secrets "\"\n"
+                               "AI_SEARCH_ENABLED=True\n"
+                               "TEST_FEATURE_SWITCH=True\n"
+                               "GN3_LOCAL_URL=\"http://localhost:" (number->string gn3-port) "\"\n"
+                               "GN_SERVER_URL=\"http://localhost:" (number->string gn3-port) "/api/\"\n"
+                               "AUTH_SERVER_URL=\"http://localhost:" (number->string gn-auth-port) "\"\n"
+                               "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock&charset=utf8\"\n"
+                               "SSL_PRIVATE_KEY=\"/etc/genenetwork/conf/gn2/private.pem\"\n"
+                               "AUTH_SERVER_SSL_PUBLIC_KEY=\"/etc/genenetwork/conf/gn-auth/clients-public-keys/gn-auth.pem\"\n"))
+                   ;; We actually set here twice so that we can refer to it
+                   ;; when running things manually.
+                   (display "GN2_PROFILE=\"")
+                   (display #$(file-append (profile
+                                            (content (package->development-manifest genenetwork2))
+                                            (allow-collisions? #t))
+                                           "\"\n")))))
+             (setenv "GN2_SETTINGS" "/etc/genenetwork/conf/gn2.conf")
+             ;; Start genenetwork2.
+             (with-directory-excursion "/genenetwork2"
+               (invoke #$(file-append bash "/bin/sh")
+                       "bin/genenetwork2" "gn2/default_settings.py" "-gunicorn-dev")))))))
 
 (define (genenetwork3-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-port gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path)
+    (gn3-port gn3-secrets gn-auth-port sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path)
     (with-manifest (package->development-manifest genenetwork3)
       (with-imported-modules '((guix build utils))
         #~(begin
-            (use-modules (guix build utils)
-                         (ice-9 match))
-
+            (use-modules (guix build utils))
             ;; Configure genenetwork3.
-            (setenv "GN3_CONF"
-                    #$(mixed-text-file "gn3.conf"
-                                       "SPARQL_ENDPOINT=\"" sparql-endpoint "\"\n"
-                                       "DATA_DIR=\"" data-directory "\"\n"
-                                       "AUTH_SERVER_URL=\"http://localhost:8084/\"\n"
-                                       "XAPIAN_DB_PATH=\"" xapian-db-path "\"\n"
-                                       "AUTH_DB=\"" auth-db-path "\"\n"
-                                       "LLM_DB_PATH=\"" llm-db-path "\"\n"))
-            (setenv "GN3_SECRETS" #$gn3-secrets)
-            (setenv "HOME" "/tmp")
-            (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock")
             (setenv "RSCRIPT" #$(file-append
                                  (profile
                                   (content (package->development-manifest genenetwork3))
                                   (allow-collisions? #t))
                                  "/bin/Rscript"))
+            (unless (file-exists? "/etc/genenetwork/conf/gn3.conf")
+              (with-output-to-file "/etc/genenetwork/conf/gn3.conf"
+                (lambda ()
+                  (display #$(string-append
+                              "SPARQL_ENDPOINT=\"" sparql-endpoint "\"\n"
+                              "DATA_DIR=\"" data-directory "\"\n"
+                              "AUTH_SERVER_URL=\"http://localhost:8084/\"\n"
+                              "XAPIAN_DB_PATH=\"" xapian-db-path "\"\n"
+                              "AUTH_DB=\"" auth-db-path "\"\n"
+                              "LLM_DB_PATH=\"" llm-db-path "\"\n"))
+                  (display "GN3_PROFILE=\"")
+                  (display #$(file-append (profile
+                                           (content (package->development-manifest genenetwork3))
+                                           (allow-collisions? #t))
+                                          "\"\n"))
+                  (display "R_SCRIPT=\"")
+                  (display #$(file-append
+                              (profile
+                               (content (package->development-manifest genenetwork3))
+                               (allow-collisions? #t))
+                              "/bin/Rscript\"\n")))))
+            (setenv "GN3_CONF" "/etc/genenetwork/conf/gn3.conf")
+            (setenv "GN3_SECRETS" #$gn3-secrets)
+            (setenv "HOME" "/tmp")
+            (setenv "SQL_URI" "mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock")
+
             (setenv "FLASK_ENV" "development")
             (setenv "FLASK_DEBUG" "1")
             ;; Run genenetwork3.
@@ -168,18 +180,24 @@ server described by CONFIG, a <genenetwork-configuration> object."
       (with-packages (list git-minimal nss-certs)
         (with-imported-modules '((guix build utils))
           #~(begin
-              (use-modules (guix build utils)
-                           (ice-9 match))
+              (use-modules (guix build utils))
               ;; Configure gn-auth.
-              (setenv "GN_AUTH_CONF"
-                      #$(mixed-text-file
-                         "gn-auth.conf"
+              (unless (file-exists? "/etc/genenetwork/conf/gn-auth.conf")
+              (with-output-to-file "/etc/genenetwork/conf/gn-auth.conf"
+                (lambda ()
+                  (display #$(string-append
                          "LOGLEVEL=\"DEBUG\"\n"
                          "SQL_URI=\"mysql://webqtlout:webqtlout@localhost/db_webqtl?unix_socket=/run/mysqld/mysqld.sock\"\n"
                          "AUTH_DB=\"" auth-db-path "\"\n"
                          "GN_AUTH_SECRETS=\"" gn-auth-secrets "\"\n"
                          "CLIENTS_SSL_PUBLIC_KEYS_DIR=\"/etc/genenetwork/conf/gn-auth/clients-public-keys/\"\n"
                          "SSL_PRIVATE_KEY=\"/etc/genenetwork/conf/gn-auth/private.pem\"\n"))
+                  (display "GN_AUTH_PROFILE=\"")
+                  (display #$(file-append (profile
+                                           (content (package->development-manifest gn-auth))
+                                           (allow-collisions? #t))
+                                          "\"\n")))))
+              (setenv "GN_AUTH_CONF" "/etc/genenetwork/conf/gn-auth.conf")
               (setenv "HOME" "/tmp")
               (setenv "AUTHLIB_INSECURE_TRANSPORT" "true")
               ;; Run gn-auth.
@@ -190,40 +208,42 @@ server described by CONFIG, a <genenetwork-configuration> object."
                         "gn_auth.wsgi:app"))))))))
 
 (define (genenetwork-activation config)
-  (match-record config <genenetwork-configuration>
-    (gn2-secrets gn3-secrets auth-db-path gn-auth-secrets gn-doc-git-checkout)
+  (match-record
+      config <genenetwork-configuration>
+      (gn2-secrets gn3-secrets gn3-port gn-auth-port  auth-db-path gn-auth-secrets gn-doc-git-checkout)
     (with-imported-modules '((guix build utils))
-      #~(begin
-          (use-modules (guix build utils))
-          ;; Set ownership of files.
-          (for-each (lambda (file)
-                      (when (eq? (stat:type (stat file)) 'directory)
-                        (chmod file #o755))
-                      (chown file
-                             (passwd:uid (getpw "genenetwork"))
-                             (passwd:gid (getpw "genenetwork"))))
-                    (append
-                     '("/etc/genenetwork/conf" "/genenetwork2/flask_session")
-                     (find-files #$(dirname gn-auth-secrets)
-                                 #:directories? #t)
-                     (find-files #$(dirname gn2-secrets)
-                                 #:directories? #t)
-                     (find-files #$(dirname gn3-secrets)
-                                 #:directories? #t)
-                     (find-files #$(dirname auth-db-path)
-                                 #:directories? #t)
-                     (find-files #$(dirname gn-doc-git-checkout)
-                                 #:directories? #t)))
-          ;; Prevent other users from reading secret files.
-          (for-each (lambda (file)
-                      (chmod file #o600))
-                    (append
-                     (find-files #$gn-auth-secrets
-                                 #:directories? #f)
-                     (find-files #$gn2-secrets
-                                 #:directories? #f)
-                     (find-files #$gn3-secrets
-                                 #:directories? #f)))))))
+        #~(begin
+            (use-modules (guix build utils)
+                         (ice-9 ftw))
+            ;; Set ownership of files.
+            (for-each (lambda (file)
+                        (when (eq? (stat:type (stat file)) 'directory)
+                          (chmod file #o755))
+                        (chown file
+                               (passwd:uid (getpw "genenetwork"))
+                               (passwd:gid (getpw "genenetwork"))))
+                      (append
+                       '("/etc/genenetwork/conf" "/genenetwork2/flask_session")
+                       (find-files #$(dirname gn-auth-secrets)
+                                   #:directories? #t)
+                       (find-files #$(dirname gn2-secrets)
+                                   #:directories? #t)
+                       (find-files #$(dirname gn3-secrets)
+                                   #:directories? #t)
+                       (find-files #$(dirname auth-db-path)
+                                   #:directories? #t)
+                       (find-files #$(dirname gn-doc-git-checkout)
+                                   #:directories? #t)))
+            ;; Prevent other users from reading secret files.
+            (for-each (lambda (file)
+                        (chmod file #o600))
+                      (append
+                       (find-files #$gn-auth-secrets
+                                   #:directories? #f)
+                       (find-files #$gn2-secrets
+                                   #:directories? #f)
+                       (find-files #$gn3-secrets
+                                   #:directories? #f)))))))
 
 (define (gn-guile-gexp gn-guile-port)
   (with-imported-modules '((guix build utils))