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authorRicardo Wurmus <rekado@elephly.net>2019-08-16 14:59:23 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-08-16 15:07:22 +0200
commit5063deab0800ca3f75fa4671dc544cc212326608 (patch)
tree5e8507c89fc1480fc04ff267934921b34b72dd3d
parentc586f427b4831b9b492e5b900b2226e898b8fcfa (diff)
import: cran: Support experiment and annotation packages.
* guix/import/cran.scm (%bioconductor-packages-list-url): Replace variable... (bioconductor-packages-list-url): ...with this procedure. (bioconductor-packages-list): Accept optional TYPE argument. (latest-bioconductor-package-version): Same. (fetch-description): Determine package type and use it in calls to LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI. (description->package): Pass package type to URI helper procedure; include package type in annotation or experiment packages from Bioconducter.
-rw-r--r--guix/import/cran.scm46
1 files changed, 33 insertions, 13 deletions
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 3240094444..9c964701b1 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -132,14 +132,19 @@ package definition."
;; updated together.
(define %bioconductor-version "3.9")
-(define %bioconductor-packages-list-url
+(define* (bioconductor-packages-list-url #:optional type)
(string-append "https://bioconductor.org/packages/"
- %bioconductor-version "/bioc/src/contrib/PACKAGES"))
-
-(define (bioconductor-packages-list)
+ %bioconductor-version
+ (match type
+ ('annotation "/data/annotation")
+ ('experiment "/data/experiment")
+ (_ "/bioc"))
+ "/src/contrib/PACKAGES"))
+
+(define* (bioconductor-packages-list #:optional type)
"Return the latest version of package NAME for the current bioconductor
release."
- (let ((url (string->uri %bioconductor-packages-list-url)))
+ (let ((url (string->uri (bioconductor-packages-list-url type))))
(guard (c ((http-get-error? c)
(format (current-error-port)
"error: failed to retrieve list of packages from ~s: ~a (~s)~%"
@@ -153,12 +158,12 @@ release."
(description->alist (string-join chunk "\n")))
(chunk-lines (read-lines (http-fetch/cached url)))))))
-(define (latest-bioconductor-package-version name)
+(define* (latest-bioconductor-package-version name #:optional type)
"Return the version string corresponding to the latest release of the
bioconductor package NAME, or #F if the package is unknown."
(and=> (find (lambda (meta)
(string=? (assoc-ref meta "Package") name))
- (bioconductor-packages-list))
+ (bioconductor-packages-list type))
(cut assoc-ref <> "Version")))
;; Little helper to download URLs only once.
@@ -187,8 +192,12 @@ from ~s: ~a (~s)~%"
;; Currently, the bioconductor project does not offer a way to access a
;; package's DESCRIPTION file over HTTP, so we determine the version,
;; download the source tarball, and then extract the DESCRIPTION file.
- (and-let* ((version (latest-bioconductor-package-version name))
- (url (car (bioconductor-uri name version)))
+ (and-let* ((type (or
+ (and (latest-bioconductor-package-version name) #t)
+ (and (latest-bioconductor-package-version name 'annotation) 'annotation)
+ (and (latest-bioconductor-package-version name 'experiment) 'experiment)))
+ (version (latest-bioconductor-package-version name type))
+ (url (car (bioconductor-uri name version type)))
(tarball (download url)))
(call-with-temporary-directory
(lambda (dir)
@@ -198,8 +207,11 @@ from ~s: ~a (~s)~%"
"--strip-components=1"
"-C" dir
"-f" tarball "*/DESCRIPTION"))
- (description->alist (with-input-from-file
- (string-append dir "/DESCRIPTION") read-string))))))))))
+ (and=> (description->alist (with-input-from-file
+ (string-append dir "/DESCRIPTION") read-string))
+ (lambda (meta)
+ (if (boolean? type) meta
+ (cons `(bioconductor-type . ,type) meta))))))))))))
(define (listify meta field)
"Look up FIELD in the alist META. If FIELD contains a comma-separated
@@ -306,7 +318,11 @@ from the alist META, which was derived from the R package's DESCRIPTION file."
(home-page (match (listify meta "URL")
((url rest ...) url)
(_ (string-append base-url name))))
- (source-url (match (uri-helper name version)
+ (source-url (match (apply uri-helper name version
+ (case repository
+ ((bioconductor)
+ (list (assoc-ref meta 'bioconductor-type)))
+ (else '())))
((url rest ...) url)
((? string? url) url)
(_ #f)))
@@ -330,7 +346,11 @@ from the alist META, which was derived from the R package's DESCRIPTION file."
(version ,version)
(source (origin
(method url-fetch)
- (uri (,(procedure-name uri-helper) ,name version))
+ (uri (,(procedure-name uri-helper) ,name version
+ ,@(or (and=> (assoc-ref meta 'bioconductor-type)
+ (lambda (type)
+ (list (list 'quote type))))
+ '())))
(sha256
(base32
,(bytevector->nix-base32-string (file-sha256 tarball))))))