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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
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