gn: genecup testing

1 files changed, 129 insertions, 0 deletions

diff --git a/gn/services/genecup-container.scm b/gn/services/genecup-container.scm
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+++ b/gn/services/genecup-container.scm
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+(define-module (gn services genecup-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* <genecup-configuration>
+  genecup-configuration
+  make-genecup-configuration
+  genecup-configuration?
+  (package  genecup-configuration-package   ; package
+            (default genecup)))
+
+(define %punkt.zip
+  (origin
+    (method url-fetch)
+    (uri "https://github.com/nltk/nltk_data/raw/b63a469d2f83a3cc9a2efcfe36915839d4e11d42/packages/tokenizers/punkt.zip")
+    (sha256
+     (base32 "0i01c5qzn1p8dxyrpx4hry2n6x6b8rgcq1sck091n0jp036f6x4s"))))
+
+(define genecup-activation
+  (match-lambda
+    (($ <genecup-configuration> package)
+     #~(begin
+         (let ((nltk_data "/var/cache/nltk_data/tokenizers")
+               (data_dir "/export/ratspub"))
+           (unless (file-exists? "/export2/PubMed")
+             (mkdir-p "/export2/PubMed"))
+           (unless (file-exists? nltk_data)
+             (begin
+               ;; The correct way would be to use python-nltk to download the data
+               ;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt
+               (mkdir-p nltk_data)
+               (chdir nltk_data)
+               (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip)))
+           (unless (file-exists? (string-append data_dir "/userspub.sqlite"))
+             (begin
+               (install-file #$(file-append package "/userspub.sqlite") data_dir)
+               (chmod (string-append data_dir "/userspub.sqlite") #o554))))))))
+
+(define genecup-shepherd-service
+  (match-lambda
+    (($ <genecup-configuration> package)
+     (with-imported-modules (source-module-closure
+                              '((gnu build shepherd)
+                                (gnu system file-systems)))
+       (list (shepherd-service
+               (provision '(genecup))
+               (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/genecup.log"
+                          ;; We don't need to set TMPDIR because we're inside a container.
+                          #:environment-variables
+                          '("EDIRECT_PUBMED_MASTER=/export2/PubMed"
+                            "NLTK_DATA=/var/cache/nltk_data"
+                            "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/nltk_data")
+                                             (target source))
+                                           (file-system-mapping
+                                             (source "/etc/ssl/certs")
+                                             (target source)))))
+               (stop  #~(make-kill-destructor))))))))
+
+(define genecup-service-type
+  (service-type
+    (name 'genecup)
+    (extensions
+      (list
+        (service-extension shepherd-root-service-type
+                           genecup-shepherd-service)
+        (service-extension activation-service-type
+                           genecup-activation)
+        ;; Make sure we get all the dependencies of RatsPub.
+        (service-extension profile-service-type
+                           (compose list genecup-configuration-package))))
+    (default-value (genecup-configuration))
+    (description
+     "Run a GeneCup Webserver.")))
+
+(operating-system
+  (host-name "genecup")
+  (timezone "Etc/UTC")
+  (locale "en_US.utf8")
+
+  (bootloader (bootloader-configuration
+               (bootloader grub-bootloader)
+               (target "does-not-matter")))
+  (file-systems (list (file-system
+                        (device "does-not-matter")
+                        (mount-point "/")
+                        (type "does-not-matter"))))
+  ;; TODO: A more minimal kernel for use in a docker image
+  ;; (kernel linux-libre-vm)
+  ;; No firmware for VMs.
+  (firmware '())
+  (packages (cons nss-certs %base-packages)) ;(list nss-certs))
+
+  (services (list (service genecup-service-type
+                           (genecup-configuration
+                             ;; genecup for docker, genecup-with-tensorflow-native for architecture specific speed optimizations.
+                             ;(package genecup))))))
+                             (package genecup-with-tensorflow-native))))))
+
+;; guix system container -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network --share=/export2/PubMed=/export2/PubMed --share=/export/ratspub=/export/ratspub
+;; For docker it isn't necessary to list the shared folders at build time.
+;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/genecup-container.scm --network
+;; Docker instructions:
+;; docker load --input genecup-docker-image.tar.gz
+;; docker run -d --privileged --net=host --name genecup --volume /path/to/PubMed:/export2/PubMed guix