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import: Add Bioconductor importer and updater.

* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.
wip-mediagoblin
Ricardo Wurmus 6 years ago
parent
commit
d0bd632f89
  1. 20
      doc/guix.texi
  2. 103
      guix/import/cran.scm
  3. 9
      guix/scripts/import/cran.scm
  4. 1
      guix/scripts/refresh.scm
  5. 2
      tests/cran.scm

20
doc/guix.texi

@ -4279,11 +4279,12 @@ guix import cpan Acme::Boolean
@item cran
@cindex CRAN
@cindex Bioconductor
Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
central repository for the @uref{http://r-project.org, GNU@tie{}R
statistical and graphical environment}.
Information is extracted from the package's DESCRIPTION file.
Information is extracted from the package's @code{DESCRIPTION} file.
The command command below imports meta-data for the @code{Cairo}
R package:
@ -4292,6 +4293,21 @@ R package:
guix import cran Cairo
@end example
When @code{--archive=bioconductor} is added, meta-data is imported from
@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
packages for for the analysis and comprehension of high-throughput
genomic data in bioinformatics.
Information is extracted from a package's @code{DESCRIPTION} file
published on the web interface of the Bioconductor SVN repository.
The command command below imports meta-data for the @code{GenomicRanges}
R package:
@example
guix import cran --archive=bioconductor GenomicRanges
@end example
@item nix
Import meta-data from a local copy of the source of the
@uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This
@ -4490,6 +4506,8 @@ the updater for GNOME packages;
the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
@item cran
the updater for @uref{http://cran.r-project.org/, CRAN} packages;
@item bioconductor
the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
@item pypi
the updater for @uref{https://pypi.python.org, PyPI} packages.
@end table

103
guix/import/cran.scm

@ -29,12 +29,14 @@
#:use-module (guix base32)
#:use-module ((guix download) #:select (download-to-store))
#:use-module (guix import utils)
#:use-module ((guix build-system r) #:select (cran-uri))
#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
#:use-module (guix upstream)
#:use-module (guix packages)
#:use-module (gnu packages)
#:export (cran->guix-package
%cran-updater))
bioconductor->guix-package
%cran-updater
%bioconductor-updater))
;;; Commentary:
;;;
@ -108,6 +110,15 @@ package definition."
`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "http://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.2. Bioconductor packages should be
;; updated together.
(define %bioconductor-svn-url
(string-append "https://readonly:readonly@"
"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/"
"madman/Rpacks/"))
(define (fetch-description base-url name)
"Return an alist of the contents of the DESCRIPTION file for the R package
@ -136,24 +147,31 @@ empty list when the FIELD cannot be found."
(string-any char-set:whitespace item)))
(map string-trim-both items))))))
(define (description->package meta)
"Return the `package' s-expression for a CRAN package from the alist META,
which was derived from the R package's DESCRIPTION file."
(define (description->package repository meta)
"Return the `package' s-expression for an R package published on REPOSITORY
from the alist META, which was derived from the R package's DESCRIPTION file."
(define (guix-name name)
(if (string-prefix? "r-" name)
(string-downcase name)
(string-append "r-" (string-downcase name))))
(let* ((name (assoc-ref meta "Package"))
(let* ((base-url (case repository
((cran) %cran-url)
((bioconductor) %bioconductor-url)))
(uri-helper (case repository
((cran) cran-uri)
((bioconductor) bioconductor-uri)))
(name (assoc-ref meta "Package"))
(synopsis (assoc-ref meta "Title"))
(version (assoc-ref meta "Version"))
(license (string->license (assoc-ref meta "License")))
;; Some packages have multiple home pages. Some have none.
(home-page (match (listify meta "URL")
((url rest ...) url)
(_ (string-append %cran-url name))))
(source-url (match (cran-uri name version)
(_ (string-append base-url name))))
(source-url (match (uri-helper name version)
((url rest ...) url)
((? string? url) url)
(_ #f)))
(tarball (with-store store (download-to-store store source-url)))
(sysdepends (map string-downcase (listify meta "SystemRequirements")))
@ -167,26 +185,32 @@ which was derived from the R package's DESCRIPTION file."
(version ,version)
(source (origin
(method url-fetch)
(uri (cran-uri ,name version))
(uri (,(procedure-name uri-helper) ,name version))
(sha256
(base32
,(bytevector->nix-base32-string (file-sha256 tarball))))))
(properties ,`(,'quasiquote ((,'upstream-name . ,name))))
,@(if (not (equal? (string-append "r-" name)
(guix-name name)))
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
'())
(build-system r-build-system)
,@(maybe-inputs sysdepends)
,@(maybe-inputs propagate 'propagated-inputs)
(home-page ,(if (string-null? home-page)
(string-append %cran-url name)
(string-append base-url name)
home-page))
(synopsis ,synopsis)
(description ,(beautify-description (assoc-ref meta "Description")))
(license ,license))))
(define (cran->guix-package package-name)
"Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
`package' s-expression corresponding to that package, or #f on failure."
(let ((module-meta (fetch-description %cran-url package-name)))
(and=> module-meta description->package)))
(define* (cran->guix-package package-name #:optional (repo 'cran))
"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
s-expression corresponding to that package, or #f on failure."
(let* ((url (case repo
((cran) %cran-url)
((bioconductor) %bioconductor-svn-url)))
(module-meta (fetch-description url package-name)))
(and=> module-meta (cut description->package repo <>))))
;;;
@ -212,7 +236,7 @@ which was derived from the R package's DESCRIPTION file."
(_ #f)))
(_ #f)))))
(define (latest-release package)
(define (latest-cran-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
@ -229,16 +253,55 @@ which was derived from the R package's DESCRIPTION file."
(version version)
(urls (cran-uri upstream-name version))))))
(define (latest-bioconductor-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
(package->upstream-name (specification->package package)))
(define meta
(fetch-description %bioconductor-svn-url upstream-name))
(and meta
(let ((version (assoc-ref meta "Version")))
;; Bioconductor does not provide signatures.
(upstream-source
(package package)
(version version)
(urls (bioconductor-uri upstream-name version))))))
(define (cran-package? package)
"Return true if PACKAGE is an R package from CRAN."
;; Assume all R packages are available on CRAN.
(string-prefix? "r-" (package-name package)))
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)
((? string? uri)
(string-prefix? "mirror://cran" uri))
((? list? uris)
(any (cut string-prefix? "mirror://cran" <>) uris))
(_ #f))))
(define (bioconductor-package? package)
"Return true if PACKAGE is an R package from Bioconductor."
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)
((? string? uri)
(string-prefix? "http://bioconductor.org" uri))
((? list? uris)
(any (cut string-prefix? "http://bioconductor.org" <>) uris))
(_ #f))))
(define %cran-updater
(upstream-updater
(name 'cran)
(description "Updater for CRAN packages")
(pred cran-package?)
(latest latest-release)))
(latest latest-cran-release)))
(define %bioconductor-updater
(upstream-updater
(name 'bioconductor)
(description "Updater for Bioconductor packages")
(pred bioconductor-package?)
(latest latest-bioconductor-release)))
;;; cran.scm ends here

9
guix/scripts/import/cran.scm

@ -41,6 +41,8 @@
(define (show-help)
(display (_ "Usage: guix import cran PACKAGE-NAME
Import and convert the CRAN package for PACKAGE-NAME.\n"))
(display (_ "
-a, --archive=ARCHIVE specify the archive repository"))
(display (_ "
-h, --help display this help and exit"))
(display (_ "
@ -57,6 +59,10 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
(option '(#\V "version") #f #f
(lambda args
(show-version-and-exit "guix import cran")))
(option '(#\a "archive") #t #f
(lambda (opt name arg result)
(alist-cons 'repo (string->symbol arg)
(alist-delete 'repo result))))
%standard-import-options))
@ -82,7 +88,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
(reverse opts))))
(match args
((package-name)
(let ((sexp (cran->guix-package package-name)))
(let ((sexp (cran->guix-package package-name
(or (assoc-ref opts 'repo) 'cran))))
(unless sexp
(leave (_ "failed to download description for package '~a'~%")
package-name))

1
guix/scripts/refresh.scm

@ -195,6 +195,7 @@ unavailable optional dependencies such as Guile-JSON."
%gnome-updater
%elpa-updater
%cran-updater
%bioconductor-updater
((guix import pypi) => %pypi-updater)))
(define (lookup-updater name)

2
tests/cran.scm

@ -107,7 +107,7 @@ Date/Publication: 2015-07-14 14:15:16
("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
"source")
(_ (error "Unexpected URL: " url))))))))
(match ((@@ (guix import cran) description->package) description-alist)
(match ((@@ (guix import cran) description->package) 'cran description-alist)
(('package
('name "r-my-example")
('version "1.2.3")

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