Use /home/genenetwork for git cloning.

2 files changed, 35 insertions, 50 deletions

diff --git a/genenetwork-development-deploy.sh b/genenetwork-development-deploy.sh
index 81d7573..d63dcf0 100755
--- a/genenetwork-development-deploy.sh
+++ b/genenetwork-development-deploy.sh
@@ -43,7 +43,6 @@ container_script=$(guix system container --network \
                         --share=/export/data/genenetwork-xapian \
                         --share=/export/data/genenetwork-sqlite \
 			--share=/export/data/lmdb \
-			--share=/export/data/repositories \
                         --share=/var/run/mysqld=/run/mysqld \
 			--share=/export/data/gn-docs/ \
                         genenetwork-development.scm)
diff --git a/genenetwork-development.scm b/genenetwork-development.scm
index fe20ec2..abdb694 100644
--- a/genenetwork-development.scm
+++ b/genenetwork-development.scm
@@ -496,7 +496,7 @@ genenetwork3 source from the latest commit of @var{project}."
   "Return a G-expression that runs the latest genenetwork2 development
 server described by CONFIG, a <genenetwork-configuration> object."
   (match-record config <genenetwork-configuration>
-    (gn2-repository gn3-repository gn2-port gn3-port gn2-secrets genotype-files gn-guile-port repositories)
+    (gn2-repository gn3-repository gn2-port gn3-port gn2-secrets genotype-files gn-guile-port)
     (with-packages (list coreutils git-minimal gunicorn nss-certs)
       (with-imported-modules '((guix build utils))
         #~(begin
@@ -518,17 +518,13 @@ server described by CONFIG, a <genenetwork-configuration> object."
             ;; Clone the latest genenetwork2
             ;; repositories.
 	    (with-directory-excursion
-		#$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)))
+	     "/home/genenetwork"
+	     (when (file-exists? "/home/genenetwork/genenetwork2")
+	       (delete-file-recursively "/home/genenetwork/genenetwork2"))
+	     (invoke "git" "clone" "--depth" "1" #$gn2-repository))
 
             ;; Override the genenetwork3 used by genenetwork2.
-            (setenv "GN3_PYTHONPATH"
-                    (string-append #$repositories "/genenetwork3"))
+            (setenv "GN3_PYTHONPATH" "/home/genenetwork/genenetwork3")
             ;; Set other environment variables required by
             ;; genenetwork2.
             (setenv "GN2_PROFILE" #$(profile
@@ -548,7 +544,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
 	    (setenv "PLINK_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/plink2"))
 	    (setenv "GEMMA_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/gemma"))
 	    (setenv "GEMMA_WRAPPER_COMMAND" (string-append (getenv "GN2_PROFILE") "/bin/gemma-wrapper"))
-	    (setenv "HOME" "/tmp")
+	    (setenv "HOME" "/home/genenetwork")
             (setenv
              "GN2_SETTINGS"
              #$(mixed-text-file "gn2.conf"
@@ -571,21 +567,22 @@ server described by CONFIG, a <genenetwork-configuration> object."
 
             ;; Start genenetwork2.
             (with-directory-excursion
-	     (string-append #$repositories "/genenetwork2")
+	     "/home/genenetwork/genenetwork2"
+	     (show-head-commit)
 	     (invoke #$(file-append gunicorn "/bin/gunicorn")
-               "--bind" (string-append "0.0.0.0:" (number->string #$gn2-port))
-               "--workers" "20"
-               "--keep-alive" "6000"
-               "--max-requests" "100"
-               "--max-requests-jitter" "30"
-               "--timeout" "1200"
-               "gn2.wsgi")))))))
+		     "--bind" (string-append "0.0.0.0:" (number->string #$gn2-port))
+		     "--workers" "20"
+		     "--keep-alive" "6000"
+		     "--max-requests" "100"
+		     "--max-requests-jitter" "30"
+		     "--timeout" "1200"
+		     "gn2.wsgi")))))))
 
 (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 repositories)
+    (gn3-repository gn3-port gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path lmdb-data-path)
     (with-manifest (package->development-manifest genenetwork3)
       (with-packages (list git-minimal nss-certs)
         (with-imported-modules '((guix build utils))
@@ -628,14 +625,14 @@ server described by CONFIG, a <genenetwork-configuration> object."
                                  "/bin/Rscript"))
 
 	      (with-directory-excursion
-	       #$repositories
+	       "/home/genenetwork"
 	       ;; Clone the latest genenetwork3 repository.
-	       (when (file-exists? (string-append #$repositories "/genenetwork3"))
-		 (delete-file-recursively (string-append #$repositories "/genenetwork3")))
+	       (when (file-exists? "/home/genenetwork/genenetwork3")
+		 (delete-file-recursively "/home/genenetwork/genenetwork3"))
 	       (invoke "git" "clone" "--depth" "1" #$gn3-repository))
 
 	      (with-directory-excursion
-	       (string-append #$repositories "/genenetwork3")
+	       "/home/genenetwork/genenetwork3"
 	       (show-head-commit)
 	       ;; Run genenetwork3.
 	       (invoke #$(file-append gunicorn "/bin/gunicorn")
@@ -651,7 +648,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
   "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 repositories)
+    (gn-auth-repository gn-auth-port auth-db-path gn-auth-secrets)
     (with-manifest (package->development-manifest gn-auth)
       (with-packages (list git-minimal nss-certs)
         (with-imported-modules '((guix build utils))
@@ -673,10 +670,10 @@ server described by CONFIG, a <genenetwork-configuration> object."
 	      (setenv "GIT_PAGER" #$(file-append coreutils-minimal "/bin/cat"))
 
 	      (with-directory-excursion
-	       #$repositories
+	       "/home/genenetwork/"
 	       ;; Clone the latest gn-auth repository.
-	       (when (file-exists? "gn-auth")
-		 (delete-file-recursively "gn-auth"))
+	       (when (file-exists? "/home/genenetwork/gn-auth")
+		 (delete-file-recursively "/home/genenetwork/gn-auth"))
                (invoke "git" "clone" "--depth" "1" #$gn-auth-repository))
 
               ;; Configure gn-auth.
@@ -696,7 +693,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
               (setenv "HOME" "/tmp")
               (setenv "AUTHLIB_INSECURE_TRANSPORT" "true")
               ;; Run gn-auth.
-              (with-directory-excursion (string-append #$repositories "/gn-auth")
+              (with-directory-excursion "/home/genenetwork/gn-auth"
                 (show-head-commit)
                 (invoke #$(file-append gunicorn "/bin/gunicorn")
                         "-b" #$(string-append "localhost:" (number->string gn-auth-port))
@@ -741,10 +738,10 @@ server described by CONFIG, a <genenetwork-configuration> object."
          (setenv "CURL_CA_BUNDLE" (getenv "SSL_CERT_FILE"))
          (setenv "REQUESTS_CA_BUNDLE" (getenv "SSL_CERT_FILE"))
 	 (setenv "GIT_PAGER" #$(file-append coreutils-minimal "/bin/cat"))
-         (let ((current-repo-path "/export/data/repositories/gn-docs"))
+         (let ((current-repo-path "/home/genenetwork/gn-docs"))
 	   (setenv "CURRENT_REPO_PATH" current-repo-path)
 	   (with-directory-excursion
-	    "/export/data/repositories"
+	    "/home/genenetwork/gn-docs"
 	    ;; All edits go to the current-repo-path; so we need it to
 	    ;; be persistent.
 	    (unless (file-exists? current-repo-path)
@@ -767,7 +764,7 @@ server described by CONFIG, a <genenetwork-configuration> object."
   "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 lmdb-data-path gn-doc-git-checkout gn-guile-port repositories)
+    (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 lmdb-data-path gn-doc-git-checkout gn-guile-port)
     (list (shepherd-service
            (documentation "Run gn-guile server.")
            (provision '(gn-guile))
@@ -792,7 +789,7 @@ described by CONFIG, a <genenetwork-configuration> object."
                                             (target source)
                                             (writable? #t))
 					   (file-system-mapping
-                                            (source repositories)
+                                            (source "/home/genenetwork")
                                             (target source)
                                             (writable? #t)))
                           #:namespaces (delq 'net %namespaces))
@@ -843,7 +840,7 @@ described by CONFIG, a <genenetwork-configuration> object."
                                               (source genotype-files)
                                               (target source))
 					     (file-system-mapping
-                                              (source repositories)
+                                              (source "/home/genenetwork")
                                               (target source)
                                               (writable? #t))
                                              (file-system-mapping
@@ -904,7 +901,7 @@ described by CONFIG, a <genenetwork-configuration> object."
                                                 (target source)
                                                 (writable? #t))
 					       (file-system-mapping
-						(source repositories)
+						(source "/home/genenetwork")
 						(target source)
 						(writable? #t))
                                                (file-system-mapping
@@ -961,7 +958,7 @@ described by CONFIG, a <genenetwork-configuration> object."
                                                 (target source)
                                                 (writable? #t))
 					       (file-system-mapping
-						(source repositories)
+						(source "/home/genenetwork")
 						(target source)
 						(writable? #t))
                                                (file-system-mapping
@@ -996,7 +993,7 @@ described by CONFIG, a <genenetwork-configuration> object."
 
 (define (genenetwork-activation config)
   (match-record config <genenetwork-configuration>
-    (gn2-secrets gn3-secrets auth-db-path gn-auth-secrets gn-doc-git-checkout repositories)
+    (gn2-secrets gn3-secrets auth-db-path gn-auth-secrets gn-doc-git-checkout)
     (with-imported-modules '((guix build utils))
       #~(begin
           (use-modules (guix build utils)
@@ -1008,9 +1005,7 @@ described by CONFIG, a <genenetwork-configuration> object."
                              (passwd:uid (getpw "genenetwork"))
                              (passwd:gid (getpw "genenetwork"))))
                     (cons* #$gn3-secrets
-                           (append (find-files #$repositories
-                                               #:directories? #t)
-				   (find-files #$gn2-secrets
+                           (append (find-files #$gn2-secrets
                                                #:directories? #t)
                                    (find-files gn-doc-git-checkout
                                                #:directories? #t)
@@ -1018,15 +1013,6 @@ described by CONFIG, a <genenetwork-configuration> object."
                                                #:directories? #t)
                                    (find-files #$gn-auth-secrets
                                                #:directories? #t))))
-	  ;; Here we need to set the top-level directories for the
-	  ;; repositories to 0775 so that they are editable by the
-	  ;; "genenetwork" user/group.  Otherwise, we get:
-	  ;; guix/build/syscalls.scm:1231:10: In procedure unshare:
-	  ;; 268566528: Invalid argument
-	  (for-each (lambda (dir)
-		      (chmod dir #o775))
-		    (scandir #$repositories
-			     (lambda (name) (not (member name '("." ".."))))))
 
           ;; Prevent other users from reading secret files.
           (for-each (lambda (file)