* [bug#41980] [PATCH] rshiny service
2020-06-21 13:31 [bug#41980] [PATCH] rshiny service Efraim Flashner
@ 2020-06-21 13:34 ` Efraim Flashner
2020-06-22 22:12 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Efraim Flashner @ 2020-06-21 13:34 UTC (permalink / raw)
To: 41980; +Cc: Ricardo Wurmus
[-- Attachment #1.1: Type: text/plain, Size: 1137 bytes --]
On Sun, Jun 21, 2020 at 04:31:12PM +0300, Efraim Flashner wrote:
> I created this for Pjotr but Ricardo said he was interested in a shiny
> service too so I figured I'd see about documenting it. Currently we
> don't have any packages in Guix which would work with this so I have a
> link¹ to one. I'm not sure if this fits well in Guix or if I should keep
> it in the guix-bioinformatics channel.
>
> I feel like the documentation as I've written it so far is weak. Also,
> I've tried to run it inside a make-forkexec-command/container Guix
> Service but I ran into problems, as I documented elsewhere².
>
>
> ¹ http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/branch/master/gn/packages/bioinformatics.scm#L716
> ² http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/branch/master/gn/services/rshiny.scm#L41
>
And of course I forgot to attach the patch ...
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
[-- Attachment #1.2: 0001-services-Add-rshiny-service.patch --]
[-- Type: text/plain, Size: 5290 bytes --]
From 88567daa3e9d952e1723078ef13b088ef111b1bd Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 21 Jun 2020 16:20:16 +0300
Subject: [PATCH] services: Add rshiny service.
* gnu/services/science.scm: New file.
(<rshiny-configuration>): New record.
(rshiny-shepherd-service-type): New variable.
* doc/guix.texi (Miscellaneous Services): Document it.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
doc/guix.texi | 49 ++++++++++++++++++++++++++++++++++
gnu/local.mk | 1 +
gnu/services/science.scm | 57 ++++++++++++++++++++++++++++++++++++++++
3 files changed, 107 insertions(+)
create mode 100644 gnu/services/science.scm
diff --git a/doc/guix.texi b/doc/guix.texi
index 5b854ccbd4..996122483d 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -26612,6 +26612,55 @@ setuid-root (@pxref{Setuid Programs}) such that unprivileged users can invoke
@command{singularity run} and similar commands.
@end defvr
+@cindex rshiny
+@subsubheading R-Shiny service
+
+The @code{(gnu services science)} module provides the following service.
+
+@defvr {Scheme Variable} rshiny-service-type
+
+This is a type of service which is used to run a webapp created with
+@code{r-shiny}. This service sets the @code{R_LIBS_USER} environment
+variable and runs the provided script to call @code{runApp}.
+
+@deftp {Data Type} rshiny-configuration
+This is the data type representing the configuration of rshiny.
+
+@table @asis
+
+@item @code{package} (default: @code{r-shiny})
+The package to use.
+
+@item @code{binary} (defaunlt @code{"rshiny"})
+The name of the binary or shell script located at @code{package/bin/} to
+run when the service is run.
+
+The common way to create this file is as follows:
+
+@lisp
+@dots{}
+(let* ((out (assoc-ref %outputs "out"))
+ (targetdir (string-append out "/share/" ,name))
+ (app (string-append out "/bin/" ,name))
+ (Rbin (string-append (assoc-ref %build-inputs "r-min")
+ "/bin/Rscript")))
+@dots{}
+ (mkdir-p (string-append out "/bin"))
+ (call-with-output-file app
+ (lambda (port)
+ (format port
+"#!~a
+library(shiny)
+setwd(\"~a\")
+runApp(launch.browser=0, port=4202)~%\n"
+ Rbin targetdir)))
+@dots{}
+@end lisp
+
+@end table
+@end deftp
+@end defvr
+
@cindex Nix
@subsubheading Nix service
diff --git a/gnu/local.mk b/gnu/local.mk
index 347d4bbb17..6b76500172 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -597,6 +597,7 @@ GNU_SYSTEM_MODULES = \
%D%/services/nix.scm \
%D%/services/nfs.scm \
%D%/services/pam-mount.scm \
+ %D%/services/science.scm \
%D%/services/security-token.scm \
%D%/services/shepherd.scm \
%D%/services/sound.scm \
diff --git a/gnu/services/science.scm b/gnu/services/science.scm
new file mode 100644
index 0000000000..94ff0f36f2
--- /dev/null
+++ b/gnu/services/science.scm
@@ -0,0 +1,57 @@
+(define-module (gnu services science)
+ #:export (<rshiny-configuration>
+ rshiny-configuration
+ rshiny-configuration?
+ rshiny-configuration-package
+ rshiny-configuration-binary
+ rshiny-shepherd-service
+ rshiny-service-type))
+
+(use-modules (gnu)
+ (guix records)
+ (ice-9 match))
+(use-service-modules shepherd)
+(use-package-modules cran)
+
+(define-record-type* <rshiny-configuration>
+ rshiny-configuration
+ make-rshiny-configuration
+ rshiny-configuration?
+ (package rshiny-configuration-package ; package
+ (default r-shiny))
+ (binary rshiny-configuration-binary ; string
+ (default "rshiny")))
+
+(define rshiny-shepherd-service
+ (match-lambda
+ (($ <rshiny-configuration> package binary)
+ (list
+ (shepherd-service
+ (documentation (string-append "R-Shiny service for " binary))
+ (provision (list (symbol-append 'rshiny- (string->symbol
+ (string-take binary 9)))))
+ (requirement '(networking))
+ (start
+ #~(exec-command
+ (list
+ #$(string-append "/run/current-system/profile/bin/" binary))
+ ;#:log-file #$(string-append "/var/log/" binary ".log") ; kills shepherd
+ #:environment-variables
+ (list "R_LIBS_USER=/run/current-system/profile/site-library/")))
+ (stop #~(make-kill-destructor)))))))
+
+(define rshiny-service-type
+ (service-type
+ (name 'rshiny)
+ (extensions
+ (list
+ (service-extension shepherd-root-service-type
+ rshiny-shepherd-service)
+ (service-extension profile-service-type
+ ;; We want the package installed so that it
+ ;; pulls in the propagated inputs as well.
+ (lambda (config)
+ (list
+ (rshiny-configuration-package config))))))
+ (description
+ "Run an R-Shiny webapp as a Guix Service.")))
--
2.26.2
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]
^ permalink raw reply related [flat|nested] 4+ messages in thread