ratspub: create container

1 files changed, 108 insertions, 0 deletions

diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
new file mode 100644
index 0000000..4ffb3b8
--- /dev/null
+++ b/gn/services/ratspub-container.scm
@@ -0,0 +1,108 @@
+(define-module (gn services ratspub-container))
+
+(use-modules (gnu)
+             (gn packages ratspub)
+             (guix download)
+             (guix modules)
+             (guix packages)
+             (guix records)
+             (ice-9 match))
+(use-service-modules shepherd)
+(use-package-modules certs compression)
+
+(define-record-type* <ratspub-configuration>
+  ratspub-configuration
+  make-ratspub-configuration
+  ratspub-configuration?
+  (package  ratspub-configuration-package   ; package
+            (default ratspub)))
+
+(define %punkt.zip
+  (origin
+    (method url-fetch)
+    (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
+    (sha256
+     (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
+
+;; The correct way would be to use python-nltk to download the data
+;; python3 -m nltk.downloader -d /var/cache/ratspub punkt
+(define ratspub-activation
+  (lambda _
+    #~(begin
+        (let ((nltk_data "/var/cache/ratspub/tokenizers"))
+          (mkdir-p nltk_data)
+          (chdir nltk_data)
+          (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))))
+
+(define ratspub-shepherd-service
+  (match-lambda
+    (($ <ratspub-configuration> package)
+     (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/container
+                          (list #$(file-append package "/server.py"))
+                          ;; Needs to run from the directory it is located in.
+                          #:directory #$package
+                          #:log-file "/var/log/ratspub.log"
+                          #:environment-variables
+                          '("EDIRECT_PUBMED_MASTER=/export2/PubMed"
+                            "NLTK_DATA=/var/cache/ratspub"
+                            "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt")
+                          #:mappings (list (file-system-mapping
+                                             (source "/export2/PubMed")
+                                             (target source)
+                                             (writable? #t))
+                                           (file-system-mapping
+                                             (source "/export/ratspub")
+                                             (target source)
+                                             (writable? #t))
+                                           (file-system-mapping
+                                             (source "/var/cache/ratspub")
+                                             (target source))
+                                           (file-system-mapping
+                                             (source "/etc/ssl/certs")
+                                             (target source)))))
+               (stop  #~(make-kill-destructor))))))))
+
+(define ratspub-service-type
+  (service-type
+    (name 'ratspub)
+    (extensions
+      (list
+        (service-extension shepherd-root-service-type
+                           ratspub-shepherd-service)
+        ;; Setup the NLTK_DATA data.
+        (service-extension activation-service-type
+                           ratspub-activation)
+        ;; Make sure we get all the dependencies of RatsPub.
+        (service-extension profile-service-type
+                           (compose list ratspub-configuration-package))))
+    (default-value (ratspub-configuration))
+    (description
+     "Run a RatsPub Webserver.")))
+
+(operating-system
+  (host-name "ratspub")
+  (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 '())
+  (packages (list nss-certs))
+
+  (services (list (service ratspub-service-type
+                           (ratspub-configuration
+                             ;(package ratspub)
+                             (package ratspub-with-tensorflow-native))))))
+
+;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/ratspub-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub