diff options
| -rw-r--r-- | guix/import/cran.scm | 46 |
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)))))) |