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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-16 14:45:28 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-20 12:41:28 +0100
commitd0bd632f89e242a2a217d7e85194589f088f75ea (patch)
tree10ad2a7ba31c1a0a18f8c48c2d915e0fcc33bdb0
parent4c3d2b2a8f6f6249b497776e5513bbadf5c6aa4c (diff)
downloadguix-d0bd632f89e242a2a217d7e85194589f088f75ea.tar
guix-d0bd632f89e242a2a217d7e85194589f088f75ea.tar.gz
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.
-rw-r--r--doc/guix.texi20
-rw-r--r--guix/import/cran.scm103
-rw-r--r--guix/scripts/import/cran.scm9
-rw-r--r--guix/scripts/refresh.scm1
-rw-r--r--tests/cran.scm2
5 files changed, 112 insertions, 23 deletions
diff --git a/doc/guix.texi b/doc/guix.texi
index a3d751a296..2a97516084 100644
--- a/doc/guix.texi
+++ b/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
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 1c30da89c7..f36e9482cf 100644
--- a/guix/import/cran.scm
+++ b/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
diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm
index 8d001ac494..ace1123b90 100644
--- a/guix/scripts/import/cran.scm
+++ b/guix/scripts/import/cran.scm
@@ -42,6 +42,8 @@
(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 (_ "
-V, --version display version information and exit"))
@@ -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))
diff --git a/guix/scripts/refresh.scm b/guix/scripts/refresh.scm
index a5834d12cc..f9e3f31a03 100644
--- a/guix/scripts/refresh.scm
+++ b/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)
diff --git a/tests/cran.scm b/tests/cran.scm
index 0a4a2fdd8f..e4f22353bd 100644
--- a/tests/cran.scm
+++ b/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")