From d55b35d119592ee5aa452f7f1e98a885f5ed5fa9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 28 Apr 2020 05:44:52 -0500
Subject: WIP ratspub service

---
 gn/services/ratspub-container.scm | 94 +++++++++++++++++++++++++++++++++++++++
 gn/services/ratspub.service       | 13 ++++++
 2 files changed, 107 insertions(+)
 create mode 100644 gn/services/ratspub-container.scm
 create mode 100644 gn/services/ratspub.service

diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
new file mode 100644
index 0000000..c026247
--- /dev/null
+++ b/gn/services/ratspub-container.scm
@@ -0,0 +1,94 @@
+(define-module (gn services ratspub-container))
+
+(use-modules (gnu)
+             (gn packages ratspub)
+             (gn packages bioinformatics)
+             (guix modules)
+             (guix records)
+             (ice-9 match))
+(use-service-modules networking shepherd)
+(use-package-modules certs)
+
+(define-record-type* <ratspub-configuration>
+  ratspub-configuration
+  make-ratspub-configuration
+  ratspub-configuration?
+  (package          ratspub-configuration-package       ; package
+                    (default ratspub))
+  (deploy-directory ratspub-configuration-deploy-directory
+                    (default "/srv/http")))
+
+(define ratspub-activation
+  (match-lambda
+    (($ <ratspub-configuration> package deploy-directory)
+     #~(begin
+         (use-modules (guix build utils))
+         (when (directory-exists? #$deploy-directory)
+           ;; Not 'delete-file-recursively' because the directory might be empty.
+           (and (string-append #$coreutils "/bin/rm" "-r " #$deploy-directory "/*")
+                (delete-file #$deploy-directory)))
+         (mkdir-p #$deploy-directory)
+         (copy-recursively #$package #$deploy-directory)))))
+
+(define ratspub-shepherd-service
+  (match-lambda
+    (($ <ratspub-configuration> package deploy-directory)
+     (with-imported-modules (source-module-closure
+                              '((gnu build shepherd)
+                                (gnu system file-systems)))
+       (list (shepherd-service
+               (provision '(ratspub))
+               (requirement '(networking))
+               (modules '((gnu build shepherd)
+                          (gnu system file-systems)))
+               (start #~(make-forkexec-constructor
+                          '("./server.py")
+                          #:directory "/srv/http"
+                          #:environment-variables
+                          '("EDIRECT_PUBMED_MASTER=/export2/PubMed"
+                            "NLTK_DATA=/export2/PubMed/nltk_data"
+                            "PERL_LWP_SSL_CA_FILE=/run/current-system/profile/etc/ssl/certs/ca-certificates.crt"
+                            ;"PATH=/run/current-system/profile/bin"
+                            )
+                          #:mappings (list (file-system-mapping
+                                             (source "/export2/PubMed")
+                                             (target source)
+                                             (writable? #t))
+                                           )
+                          ))
+               (stop  #~(make-kill-destructor))))))))
+
+(define ratspub-service-type
+  (service-type
+    (name 'ratspub)
+    (extensions
+      (list
+        (service-extension activation-service-type
+                           ratspub-activation)
+        (service-extension shepherd-root-service-type
+                           ratspub-shepherd-service)
+        ;; Make sure RatsPub doesn't get garbage collected.
+        (service-extension profile-service-type
+                           (compose list ratspub-configuration-package))))
+    (default-value (ratspub-configuration))
+    (description
+     "Run a RatsPub Webserver.")))
+
+(operating-system
+  ;(host-name "ratspub")
+  (host-name "penguin2") ; hardcoded in ratspub.py
+  (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 '())
+  (packages (list edirect-gn sed nss-certs))
+
+  (services (list (service dhcp-client-service-type)
+                  (service ratspub-service-type))))
diff --git a/gn/services/ratspub.service b/gn/services/ratspub.service
new file mode 100644
index 0000000..91b9509
--- /dev/null
+++ b/gn/services/ratspub.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=Rats.pub web server
+
+[Service]
+ExecStart=/home/gn-rshiny/run_ratspub.sh
+#WorkingDirectory=/home/gn-shiny/ratspub
+#ExecStartPre='/bin/cp -r $(/var/guix/profiles/per-user/efraimf/current-guix/bin/guix build ratspub)/* /home/gn-shiny/ratspub'
+#ExecStop='/bin/rm -rf /home/gn-shiny/ratspub/*'
+Environment="EDIRECT_PUBMED_MASTER=/export2/PubMed" "NLTK_DATA=/export2/PubMed/nltk_data" "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt"
+Restart=always
+
+[Install]
+WantedBy=multi-user.target
-- 
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