From 6e54a8444097f14ea905584fcc51d40ed22ef5d7 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 3 Jul 2024 17:55:07 -0500
Subject: Generalise index-genenetwork cron gexp

Pass in the configuration to the gexp building function to make the
builder function work across environments.
---
 genenetwork/services/genenetwork.scm | 78 +++++++++++++++++++++++++++++++++++-
 1 file changed, 77 insertions(+), 1 deletion(-)

(limited to 'genenetwork/services/genenetwork.scm')

diff --git a/genenetwork/services/genenetwork.scm b/genenetwork/services/genenetwork.scm
index 48dfcc8..6c08703 100644
--- a/genenetwork/services/genenetwork.scm
+++ b/genenetwork/services/genenetwork.scm
@@ -22,10 +22,11 @@
 (define-module (genenetwork services genenetwork)
   #:use-module ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-uploader))
   #:use-module ((gnu packages web) #:select (nginx))
-  #:use-module ((gnu packages admin) #:select (shadow))
+  #:use-module ((gnu packages admin) #:select (shadow shepherd))
   #:use-module ((gnu packages python) #:select (python))
   #:use-module (gnu services)
   #:use-module (gnu services web)
+  #:use-module (gnu services mcron)
   #:use-module (gnu system file-systems)
   #:use-module (gnu system shadow)
   #:use-module (guix build python-build-system)
@@ -132,6 +133,81 @@
          (home-directory "/var/empty")
          (shell (file-append shadow "/sbin/nologin")))))
 
+(define (build-xapian-index-cron-gexp config)
+  (let* ((sql-uri (genenetwork-configuration-sql-uri config))
+         (genenetwork3 (genenetwork-configuration-genenetwork3 config))
+         (xapian-directory (genenetwork-configuration-xapian-db config))
+         (sparql-endpoint (genenetwork-configuration-sparql-endpoint config))
+         (xapian-build-directory (string-append xapian-directory "/build"))
+         (herd (file-append shepherd "/bin/herd"))
+         (index-genenetwork (file-append genenetwork3 "/bin/index-genenetwork"))
+         (gn3-profile (profile
+                              (content (package->development-manifest genenetwork3))
+                              (allow-collisions? #t)))
+         (python3-version (python-version (package-version python))))
+    (with-imported-modules '((guix build utils))
+      #~(begin
+          (use-modules (guix build utils)
+                       (srfi srfi-26))
+
+          ;; Use GN3 in container, not newly cloned GN3 to avoid
+          ;; inconsistencies between versions
+          (setenv "PYTHONPATH"
+                  (string-append #$(file-append genenetwork3
+                                                "/lib/python"
+                                                python3-version
+                                                "/site-packages")
+                                 ":"
+                                 #$gn3-profile
+                                 "/lib/python"
+                                 #$python3-version
+                                 "/site-packages"))
+
+          (when (and
+                 ;; not currently building an index
+                 (not (file-exists? #$xapian-build-directory))
+                 ;; data has been modified
+                 (zero? (status:exit-val (system* #$index-genenetwork
+                                                  "is-data-modified"
+                                                  #$xapian-directory
+                                                  #$sql-uri
+                                                  #$sparql-endpoint))))
+            (dynamic-wind
+              (const #t)
+              ;; build the index
+              (lambda ()
+                (invoke #$index-genenetwork
+                        "create-xapian-index"
+                        #$xapian-build-directory
+                        #$sql-uri
+                        #$sparql-endpoint)
+                (dynamic-wind
+                  ;; stop GN3: Here there is magic!!!
+                  ;;     The name `gunicorn-genenetwork' is magical. It is not set
+                  ;;     here nor at the point of call, rather, it is set in a
+                  ;;     dependency of the system (forge), thereby creating a
+                  ;;     coupling between this g-expression and whatever forge
+                  ;;     is doing. We need to figure out a way to pass in the
+                  ;;     service name as part of the call to break that coupling
+                  (cut invoke #$herd "stop" "gunicorn-genenetwork3")
+                  ;;replace old index
+                  (lambda ()
+                    (for-each (lambda (file)
+                                (rename-file file
+                                             (string-append #$xapian-directory
+                                                            "/"
+                                                            (basename file))))
+                              (find-files #$xapian-build-directory)))
+                  ;; restart GN3
+                  (cut invoke #$herd "start" "gunicorn-genenetwork3")))
+              (lambda ()
+                ;; delete build directory
+                (delete-file-recursively #$xapian-build-directory)
+                ;; set up correct permissions
+                (for-each (lambda (file)
+                            (chmod file #o644))
+                          (find-files #$xapian-directory)))))))))
+
 (define (genenetwork-activation config)
   (match-record config <genenetwork-configuration>
     (gn2-secrets gn3-secrets gn-auth-secrets auth-db)
-- 
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