From 63646e03a140f2ffd3004d17d32900f9185416a3 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 28 Jun 2020 12:46:12 +0300
Subject: gn: Add bh20-seq-resource service

---
 gn/services/bh20-seq-resource-container.scm | 106 ++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 gn/services/bh20-seq-resource-container.scm

(limited to 'gn/services')

diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm
new file mode 100644
index 0000000..0114625
--- /dev/null
+++ b/gn/services/bh20-seq-resource-container.scm
@@ -0,0 +1,106 @@
+(define-module (gn services bh20-seq-resource-container))
+
+(use-modules (gnu)
+             (gn packages bioinformatics)
+             (guix modules)
+             ((guix packages) #:select (package-source))
+             (guix records)
+             (ice-9 match))
+(use-service-modules shepherd)
+(use-package-modules compression python python-web)
+
+(define-record-type* <covid19-pubseq-configuration>
+  covid19-pubseq-configuration
+  make-covid19-pubseq-configuration
+  covid19-pubseq-configuration?
+  (package          covid19-pubseq-configuration-package    ; package
+                    (default bh20-seq-resource))
+  (deploy-directory covid19-pubseq-deploy-directory         ; string
+                    (default "/srv/http"))
+  (port             covid19-pubseq-configuration-port       ; string
+                    (default "5000")))
+
+(define covid19-pubseq-activation-service
+  (match-lambda
+    (($ <covid19-pubseq-configuration> package deploy-directory port)
+     #~(begin
+         (let ((pkg-src #$(package-source package)))
+           (when (file-exists? #$deploy-directory)
+             (delete-file-recursively (mkdir-p #$deploy-directory)))
+           (mkdir-p #$deploy-directory)
+           (if (file-is-directory? pkg-src)
+             (copy-recursively pkg-src #$deploy-directory)
+             (begin
+               (copy-file pkg-src #$(string-append deploy-directory
+                                                   "/src.tar.xz"))
+               (with-directory-excursion #$deploy-directory
+                 (invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz")
+                 (invoke #$(file-append tar "/bin/tar") "xvf" "src.tar"
+                         "--strip-components=1")))))))))
+
+(define covid19-pubseq-shepherd-service
+  (match-lambda
+    (($ <covid19-pubseq-configuration> package deploy-directory port)
+     (with-imported-modules (source-module-closure
+                              '((gnu build shepherd)
+                                (gnu system file-systems)))
+       (list (shepherd-service
+               (provision '(covid19-pubseq))
+               (requirement '(networking))
+               (modules '((gnu build shepherd)
+                          (gnu system file-systems)))
+               ;(start #~(make-forkexec-constructor/container
+               (start #~(make-forkexec-constructor
+                          (list
+                            #$(file-append gunicorn "/bin/gunicorn")
+                            (string-append "-blocalhost:" #$port)
+                            "bh20simplewebuploader.main:app")
+                          #:directory #$deploy-directory
+                          #:log-file "/var/log/covid19-pubseq.log"
+                          #:environment-variables
+                          '("TMPDIR=/export/tmp"
+                            ;; TODO: Don't hardcode python version!
+                            "PYTHONPATH=/run/current-system/profile/lib/python3.8/site-packages")
+                          ;#:mappings
+                          ;(list (file-system-mapping
+                          ;        (source "/export/tmp")
+                          ;        (target source)
+                          ;        (writable? #t))
+                          ;      (file-system-mapping
+                          ;        ;; TODO: Don't hardcode python version!
+                          ;        (source "/run/current-system/profile/lib/python3.8/site-packages")
+                          ;        (target source)))
+                          ))
+               (stop  #~(make-kill-destructor))))))))
+
+(define covid19-pubseq-service-type
+  (service-type
+    (name 'covid19-pubseq)
+    (extensions
+      (list
+        (service-extension shepherd-root-service-type
+                           covid19-pubseq-shepherd-service)
+        (service-extension activation-service-type
+                           covid19-pubseq-activation-service)
+        (service-extension profile-service-type
+                           (compose list
+                                    covid19-pubseq-configuration-package))))
+    (default-value (covid19-pubseq-configuration))
+    (description
+     "Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver.")))
+
+(operating-system
+  (host-name "covid19-pubseq")
+  (timezone "Etc/UTC")
+  (locale "en_US.utf8")
+
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (target "does-not-matter")))
+  (file-systems %base-file-systems)
+  ;; No firmware for VMs.
+  (firmware '())
+  ;; We don't need any packages inside the container.
+  (packages '())
+
+  (services (list (service covid19-pubseq-service-type))))
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