[Biojava-dev] ongoing release - mediawiki woes

[Peter Cock]

Hi Spencer,

I've replied in more detail on root-l, but yes, migration is a long-term
solution, so if you can help with the current MediaWiki instance for
the short-term that will have immediate practical benefits for BioJava,
BioPerl, Biopython, etc.

Thanks,

Peter

On Fri, Mar 11, 2016 at 10:00 AM, Spencer Bliven
<spencer.bliven at gmail.com> wrote:
> Migrating sounds like a long-term solution. For now, I'm going to try to get
> logins working for Biojava and try out the oauth2 plugin. It's not great
> timing with the release today, but I think it had better be done. If I have
> to switch back to password logins then I'll disable new user accounts
> temporarily.
>
> -Spencer
>
> On Fri, Mar 11, 2016 at 10:30 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> On Fri, Mar 11, 2016 at 5:03 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi,
>> >
>> > Jose and I worked on the release today. Everything went well with Maven
>> > Central, and the code is already available from there.  However it turns
>> > out
>> > that the MediaWiki instance on biojava.org is fundamentally broken and
>> > it is
>> > almost impossible to login (both Google and Yahoo open id login are
>> > broken).
>> > I managed to login just by chance (long story). I am in the process of
>> > updating the wiki pages. We will finalize and write the announce email
>> > tomorrow (Friday).
>> >
>> > The bottom line is, we will need to migrate away from MediaWiki soon,
>> > since
>> > it is not maintainable. I suggest we move to GitHub markdown pages.
>> >
>> > https://help.github.com/articles/using-a-custom-domain-with-github-pages/
>> >
>> > Andreas
>>
>> Hello Andreas & the BioJava developers,
>>
>> I said much of this directly on root-l, but it is worth stating openly as
>> for any migration more eyes are especially welcome. I have deliberately
>> CC'd the cross-project open-bio-l mailing list (a public list) plus also
>> root-l (our closed mailing list for SysAdmin stuff).
>>
>> Brian Osborne has been driving the BioPerl Wiki migration to GitHub
>> pages, using pandoc to migrate to markdown, with a lot of fine tuning:
>>
>> http://bioperl.github.io/
>> https://github.com/bioperl/bioperl.github.io
>>
>> Presumably at some point www.bioperl.org will point there instead, perhaps
>> after all the non-BioPerl content like file format pages has been moved to
>> wikipedia or elsewhere - anyone curious can follow up on the BioPerl-l
>> mailing list.
>>
>> Before that I had started looking at migrating MediaWiki to GitHub pages
>> using pandoc for the markdown conversion while preserving the history:
>>
>> https://github.com/peterjc/mediawiki_to_git_md/
>>
>> There are a few niggles like dealing with categories and sub-folders
>> messing up the URL mapping, which meant this isn't yet good enough
>> to use for the www.open-bio.org wiki (most of the BOSC URLs break),
>> nor for the www.bioperl.org wiki (lots of templates and other advanced
>> features) but looks more promising for the simpler biopython.org wiki.
>>
>> https://OBF.github.io
>> https://github.com/OBF/OBF.github.io
>>
>> https://biopython.github.io
>> https://github.com/biopython/biopython.github.io
>>
>> Once the migration is working nicely preserving functional content,
>> I plan to copy all the nice styling work from Brian to make the pages
>> look nice.
>>
>> If you would like to try this migration script on the BioJava wiki, please
>> let me know - You'll need the XML dump from MediaWiki which Andreas
>> can probably get - if not I could, or another root-l mailing list
>> volunteer.
>>
>> Regards,
>>
>> Peter
>> Biopython developer, OBF secretary, BOSC co-chair, etc.
>> _______________________________________________
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>> biojava-dev at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>
>