GNU bug report logs - #26369
[PATCH] import cran: Fetch DESCRIPTION files from Github mirror.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: guix-patches <at> gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror.
Date: Wed,  5 Apr 2017 15:37:03 +0200

* guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
(bioconductor-mirror-url): New procedure.
(fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
(cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
(latest-cran-release, latest-bioconductor-release): Adjust accordingly.
(bioconductor-package?): Update comment about SVN.
---
 guix/import/cran.scm | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 4d36882cf..8e24f6e17 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -124,17 +124,19 @@ package definition."
 
 ;; The latest Bioconductor release is 3.4.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-svn-url
-  (string-append "https://readonly:readonly@"
-                 "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/"
-                 "madman/Rpacks/"))
+(define (bioconductor-mirror-url name)
+  (string-append "https://raw.githubusercontent.com/Bioconductor-mirror/"
+                 name "/release-3.4"))
 
-
-(define (fetch-description base-url name)
+(define (fetch-description repository name)
   "Return an alist of the contents of the DESCRIPTION file for the R package
-NAME, or #f in case of failure.  NAME is case-sensitive."
+NAME in the given REPOSITORY, or #f in case of failure.  NAME is
+case-sensitive."
   ;; This API always returns the latest release of the module.
-  (let ((url (string-append base-url name "/DESCRIPTION")))
+  (let ((url (string-append (case repository
+                              ((cran)         (string-append %cran-url name))
+                              ((bioconductor) (bioconductor-mirror-url name)))
+                            "/DESCRIPTION")))
     (guard (c ((http-get-error? c)
                (format (current-error-port)
                        "error: failed to retrieve package information \
@@ -290,11 +292,8 @@ from the alist META, which was derived from the R package's DESCRIPTION file."
    (lambda* (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 <>))))))
+     (and=> (fetch-description repo package-name)
+            (cut description->package repo <>)))))
 
 (define* (recursive-import package-name #:optional (repo 'cran))
   "Generate a stream of package expressions for PACKAGE-NAME and all its
@@ -385,7 +384,7 @@ dependencies."
     (package->upstream-name package))
 
   (define meta
-    (fetch-description %cran-url upstream-name))
+    (fetch-description 'cran upstream-name))
 
   (and meta
        (let ((version (assoc-ref meta "Version")))
@@ -402,7 +401,7 @@ dependencies."
     (package->upstream-name package))
 
   (define meta
-    (fetch-description %bioconductor-svn-url upstream-name))
+    (fetch-description 'bioconductor upstream-name))
 
   (and meta
        (let ((version (assoc-ref meta "Version")))
@@ -426,7 +425,10 @@ dependencies."
   "Return true if PACKAGE is an R package from Bioconductor."
   (let ((predicate (lambda (uri)
                      (and (string-prefix? "http://bioconductor.org" uri)
-                          ;; Data packages are not listed in SVN
+                          ;; Data packages are neither listed in SVN nor on
+                          ;; the Github mirror, so we have to exclude them
+                          ;; from the set of bioconductor packages that can be
+                          ;; updated automatically.
                           (not (string-contains uri "/data/annotation/"))))))
     (and (string-prefix? "r-" (package-name package))
          (match (and=> (package-source package) origin-uri)
-- 
2.12.2

Message #8 received at 26369 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 26369 <at> debbugs.gnu.org
Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from
 Github mirror.
Date: Mon, 10 Apr 2017 11:57:35 +0200

Ricardo Wurmus <rekado <at> elephly.net> skribis:

> * guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
> (bioconductor-mirror-url): New procedure.
> (fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
> (cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
> (latest-cran-release, latest-bioconductor-release): Adjust accordingly.
> (bioconductor-package?): Update comment about SVN.

LGTM.

Out of curiosity, what’s the rationale for using the GitHub mirror
instead of the SVN repo?

Thanks,
Ludo’.

Message #11 received at 26369 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 26369 <at> debbugs.gnu.org
Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from
 Github mirror.
Date: Mon, 10 Apr 2017 13:14:22 +0200

Ludovic Courtès <ludo <at> gnu.org> writes:

> Ricardo Wurmus <rekado <at> elephly.net> skribis:
>
>> * guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
>> (bioconductor-mirror-url): New procedure.
>> (fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
>> (cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
>> (latest-cran-release, latest-bioconductor-release): Adjust accordingly.
>> (bioconductor-package?): Update comment about SVN.
>
> LGTM.
>
> Out of curiosity, what’s the rationale for using the GitHub mirror
> instead of the SVN repo?

The Bioconductor people have been planning for a while to retire their
SVN repository and use the Github mirror exclusively.  I heard from
Bioconductor users that this move is going to happen soon.

-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Message #16 received at 26369-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 26369-done <at> debbugs.gnu.org
Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from
 Github mirror.
Date: Tue, 16 May 2017 21:39:41 +0200

Ricardo Wurmus <rekado <at> elephly.net> writes:

> Ludovic Courtès <ludo <at> gnu.org> writes:
>
>> Ricardo Wurmus <rekado <at> elephly.net> skribis:
>>
>>> * guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
>>> (bioconductor-mirror-url): New procedure.
>>> (fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
>>> (cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
>>> (latest-cran-release, latest-bioconductor-release): Adjust accordingly.
>>> (bioconductor-package?): Update comment about SVN.
>>
>> LGTM.
>>
>> Out of curiosity, what’s the rationale for using the GitHub mirror
>> instead of the SVN repo?
>
> The Bioconductor people have been planning for a while to retire their
> SVN repository and use the Github mirror exclusively.  I heard from
> Bioconductor users that this move is going to happen soon.

Pushed to master.

-- 
Ricardo

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