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

[Peter Cock]

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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