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(define-module (gn services bh20-seq-resource-container))
(use-modules (gnu)
(gn packages bioinformatics)
(guix modules)
((guix packages) #:select (package-source))
(guix records)
(ice-9 match))
(use-service-modules shepherd)
(use-package-modules compression python python-web)
(define-record-type* <covid19-pubseq-configuration>
covid19-pubseq-configuration
make-covid19-pubseq-configuration
covid19-pubseq-configuration?
(package covid19-pubseq-configuration-package ; package
(default bh20-seq-resource))
(deploy-directory covid19-pubseq-deploy-directory ; string
(default "/srv/http"))
(port covid19-pubseq-configuration-port ; string
(default "5000")))
(define covid19-pubseq-activation-service
(match-lambda
(($ <covid19-pubseq-configuration> package deploy-directory port)
#~(begin
(let ((pkg-src #$(package-source package)))
(when (file-exists? #$deploy-directory)
(delete-file-recursively (mkdir-p #$deploy-directory)))
(mkdir-p #$deploy-directory)
(if (file-is-directory? pkg-src)
(copy-recursively pkg-src #$deploy-directory)
(begin
(copy-file pkg-src #$(string-append deploy-directory
"/src.tar.xz"))
(with-directory-excursion #$deploy-directory
(invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz")
(invoke #$(file-append tar "/bin/tar") "xvf" "src.tar"
"--strip-components=1")))))))))
(define covid19-pubseq-shepherd-service
(match-lambda
(($ <covid19-pubseq-configuration> package deploy-directory port)
(with-imported-modules (source-module-closure
'((gnu build shepherd)
(gnu system file-systems)))
(list (shepherd-service
(provision '(covid19-pubseq))
(requirement '(networking))
(modules '((gnu build shepherd)
(gnu system file-systems)))
;(start #~(make-forkexec-constructor/container
(start #~(make-forkexec-constructor
(list
#$(file-append gunicorn "/bin/gunicorn")
(string-append "-blocalhost:" #$port)
"bh20simplewebuploader.main:app")
#:directory #$deploy-directory
#:log-file "/var/log/covid19-pubseq.log"
#:environment-variables
'("TMPDIR=/export/tmp"
;; TODO: Don't hardcode python version!
"PYTHONPATH=/run/current-system/profile/lib/python3.8/site-packages")
;#:mappings
;(list (file-system-mapping
; (source "/export/tmp")
; (target source)
; (writable? #t))
; (file-system-mapping
; ;; TODO: Don't hardcode python version!
; (source "/run/current-system/profile/lib/python3.8/site-packages")
; (target source)))
))
(stop #~(make-kill-destructor))))))))
(define covid19-pubseq-service-type
(service-type
(name 'covid19-pubseq)
(extensions
(list
(service-extension shepherd-root-service-type
covid19-pubseq-shepherd-service)
(service-extension activation-service-type
covid19-pubseq-activation-service)
(service-extension profile-service-type
(compose list
covid19-pubseq-configuration-package))))
(default-value (covid19-pubseq-configuration))
(description
"Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver.")))
(operating-system
(host-name "covid19-pubseq")
(timezone "Etc/UTC")
(locale "en_US.utf8")
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())
;; We don't need any packages inside the container.
(packages '())
(services (list (service covid19-pubseq-service-type))))