From dab19f78848da9c176238cc1eec486964a54dfca Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 19 Oct 2023 13:32:19 +0100
Subject: Remove bh20-seq-resource.

The package is broken, some of its inputs have been removed from
upstream Guix, and we no longer need this package.

* gn/packages/bioinformatics.scm (bh20-seq-resource): Delete variable.
* gn/services/bh20-seq-resource-container.scm: Delete file.
---
 gn/services/bh20-seq-resource-container.scm | 110 ----------------------------
 1 file changed, 110 deletions(-)
 delete mode 100644 gn/services/bh20-seq-resource-container.scm

(limited to 'gn/services/bh20-seq-resource-container.scm')

diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm
deleted file mode 100644
index e0eccf7..0000000
--- a/gn/services/bh20-seq-resource-container.scm
+++ /dev/null
@@ -1,110 +0,0 @@
-(define-module (gn services bh20-seq-resource-container))
-
-(use-modules (gnu)
-             (gn packages bioinformatics)
-             (guix modules)
-             ((guix packages) #:select (package-source))
-             (guix records)
-             (guix build-system python) ; for python-version from guix/build/python-build-system.scm
-             (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-for-service))
-  (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
-                          ;(let (pyversion (python-version (@ (gnu packages python) python)))
-                          '("TMPDIR=/export/tmp"
-                            "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages")
-                          ;  (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/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/python3.9/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))))
-
-;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network
-- 
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