[Bioperl-l] [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

[Peter Cock]

Found it, and https://github.com/perl5-dbi/DBD-mysql/issues/423 seems
to answer my question, quoting what I took as the key point:

"DBD::mysql no longer builds against MariaDB. This also removes complexity."

So it looks like adding DBD::MariaDB support to BioPerl is the best
solution?

Peter

On Tue, Sep 3, 2024 at 12:35 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> It sounds to me (as an interested third party observer of BioPerl), that
> there
> is value in adding a MariaDB module to Bio::DB:SeqFeature:Store::DBI
> even if it is as simple as an alias or near copy of the MySQL module?
>
> It also sounds like a bug in DBD::MySQL if it refuses to work with version
> 10 (from MariaDB) by insisting on version 8. Do you know where their
> issue tracker is? I would be surprised if that has not been discussed.
>
> Peter
>
> On Mon, Sep 2, 2024 at 10:56 AM Schlachter, Kai <
> kai.schlachter at dkfz-heidelberg.de> wrote:
>
>> Hello Peter,
>>
>>
>>
>> Thanks for your reply.
>>
>>
>>
>> Updating of the database server process itself was no issue, also the
>> migration of the data in the database was nothing unusual – this is also
>> something I already did many times before in other projects.
>>
>>
>>
>> So the next step I did was trying to install DBD::mysql as per some of
>> the error messages I got from the application, this module was missing
>> (which was correct, as I started with a plain Debian container). So I tried
>> to install, but first I needed to get the mysql-config tool installed:
>>
>> apt-get install libmariadb-dev-compat
>>
>>
>>
>> After that I tried again with:
>>
>> cpanm install DBD::mysql
>>
>>
>>
>> and this failed, with the errors in the log:
>>
>> ….
>>
>> DBD::mysql requires MySQL 8.x or newer for building. Version reported by
>> mysql_config --version
>>
>> : 10.11.6 at Makefile.PL line 451, <PIPE> line 3.
>>
>> -> N/A
>>
>> -> FAIL Configure failed for DBD-mysql-5.008. See
>> /root/.cpanm/work/1725256110.1036/build.log f
>>
>> or details.
>>
>> …..
>>
>>
>>
>> As there is a DBD::MariaDB, I thought: Yes that one would most likely do
>> the trick and I could actually install it. For this to be used I also
>> needed to set the configuration in gbrowse to use the MariaDB Connector
>> (which is ok because this is what I just installed). However this does not
>> work out as gbrowse used Bio::DB:SeqFeature:Store::DBI::mysql and now tries
>> to use Bio::DB:SeqFeature:Store::DBI::MariaDB which is a module that does
>> not exist.
>>
>>
>>
>> It might be that everything just works fine if I install the mysql
>> libraries into the container, sourced from MySQL directly instead of
>> relying on Debian packages that come out of the box. But this feels kind of
>> an ugly workaround.
>>
>>
>>
>> Greetings,
>>
>>
>>
>> Kai
>>
>>
>>
>> *Von: *Peter Cock <p.j.a.cock at googlemail.com>
>> *Datum: *Freitag, 30. August 2024 um 14:29
>> *An: *"Schlachter, Kai" <kai.schlachter at dkfz-heidelberg.de>
>> *Cc: *"bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
>> *Betreff: *[Extern] - Re: [Bioperl-l] Support for MariaDB in
>> Bio::DB:SeqFeature:Store::DBI::
>>
>>
>>
>> Hello Kai,
>>
>> Interesting question (although I'm viewing it from a Python and Biopython
>> perspective).
>>
>>
>>
>> https://mariadb.com/kb/en/upgrading-from-mysql-to-mariadb/ suggests this
>> should
>>
>> just work, with existing MySQL bindings treating MariaDB as a newer
>> version.
>>
>>
>>
>> It sounds like your set is breaking in the Perl module DBD::mysql?
>>
>> https://metacpan.org/dist/DBD-mysql
>>
>>
>>
>> Looking at the change log there are entries from this year, and multiple
>> mentions
>>
>> of MariaDB - so I would expect this to work:
>>
>> https://metacpan.org/release/DVEEDEN/DBD-mysql-5.008/source/Changes
>>
>>
>>
>> Can you take a look at their issue tracker
>> https://github.com/perl5-dbi/DBD-mysql
>>
>> and see if you've hit a known issue?
>>
>>
>>
>> Also can you double check the version of DBD::mysql you have installed?
>>
>>
>>
>> Peter
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Aug 30, 2024 at 12:15 PM Schlachter, Kai <
>> kai.schlachter at dkfz-heidelberg.de> wrote:
>>
>> Hi there,
>>
>>
>>
>> I took over an older project to modernize the underlaying hardware /
>> software.
>>
>> This also involves the use of gbrowse, which in turn relies quite a lot
>> on BioPerl.
>>
>>
>>
>> As our freshly provided servers are all Debian based and we are highly
>> encouraged to use a most recent version of Debian inside of our containers
>> (docker), I ran into the following issue:
>>
>> Debian no longer supports MySQL but has switched to MariaDB, which leads
>> me to the following:
>>
>>
>>
>> I tried to install gbrowse, resolving all the dependencies and stuff that
>> came along. I also was able to compile the DBD::MariaDB as this is the
>> required module for MariaDB-Connections.
>>
>> However I was not able to find a Module in Bio::DB:SeqFeature:Store::DBI
>> called MariaDB, there is only Mysql :(
>>
>> Although both adaptors should share at least some basic functionality, it
>> is not possible to install the Mysql-Version on a recent Debian because
>> DBD::MySQL will refuse to work with mariadb because of a version mismatch
>> (expected 8.x but reported 10.y).
>>
>>
>>
>> Are there any plans / ideas to add mariadb support to the modules?
>>
>> I am not an original perl programmer so I don’t think it’s a good idea to
>> start implementing / contributing with such a complex thing.
>>
>>
>>
>> Greetings,
>>
>>
>>
>> Kai
>>
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