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authorEfraim Flashner2020-09-10 11:33:47 -0500
committerEfraim Flashner2020-09-10 11:33:47 -0500
commitf32421a12989a1bcef2050d614171b91eefe5e2d (patch)
tree953a976a0e1c6fe1a6161dbea10ef4ed5771ea49 /gn/services/ratspub-container.scm
parent36241fc8645ad4069974a8f3a5889029681eb85a (diff)
downloadguix-bioinformatics-f32421a12989a1bcef2050d614171b91eefe5e2d.tar.gz
ratspub: create container
Diffstat (limited to 'gn/services/ratspub-container.scm')
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1 files changed, 108 insertions, 0 deletions
diff --git a/gn/services/ratspub-container.scm b/gn/services/ratspub-container.scm
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+(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