Re: [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::
Peter Cock <[email protected]> Tue, 3 Sep 2024 12:35:50 +0100
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <CAKVJ-_40mDS1ywc2OXaHkj-yj4-VZV9oU4sNm1fHCD3c2vdbMQ@mail.gmail.com> |
--===============2211814553949967900== Content-Type: multipart/alternative; boundary="0000000000004c623406213576f6" --0000000000004c623406213576f6 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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=E2=80=AFAM Schlachter, Kai < [email protected]> 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 =E2=80=93 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 th= e > 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: > > =E2=80=A6. > > 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. > > =E2=80=A6.. > > > > 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 no= t > work out as gbrowse used Bio::DB:SeqFeature:Store::DBI::mysql and now tri= es > 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 <[email protected]> > *Datum: *Freitag, 30. August 2024 um 14:29 > *An: *"Schlachter, Kai" <[email protected]> > *Cc: *"[email protected]" <[email protected]> > *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=E2=80=AFPM Schlachter, Kai < > [email protected]> 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 o= n > 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 container= s > (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=E2=80=99t think it=E2=80=99= s a good idea to > start implementing / contributing with such a complex thing. > > > > Greetings, > > > > Kai > > _______________________________________________ > Bioperl-l mailing list > [email protected] > https://mailman.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > [email protected] > https://mailman.open-bio.org/mailman/listinfo/bioperl-l > --0000000000004c623406213576f6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>It sounds to me (as an interested third party observe= r of BioPerl), that there</div><div>is value in adding <span lang=3D"EN-US"= >a MariaDB module to Bio::DB:SeqFeature:Store::DBI</span></div><div><span l= ang=3D"EN-US">even if it is as simple as an alias or near copy of the MySQL= module?</span></div><div><span lang=3D"EN-US"><br></span></div><div><span = lang=3D"EN-US">It also sounds like a bug in </span><span lang=3D"EN-US">DBD= ::MySQL if it refuses to work with version</span></div><div><span lang=3D"E= N-US">10 (from MariaDB) by insisting on version 8. Do you know where their<= /span></div><div><span lang=3D"EN-US">issue tracker is? I would be surprise= d if that has not been discussed.<br></span></div><div><span lang=3D"EN-US"= ><br></span></div><div><span lang=3D"EN-US">Peter<br></span></div></div><br= ><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Mon, S= ep 2, 2024 at 10:56=E2=80=AFAM Schlachter, Kai <<a href=3D"mailto:kai.sc= [email protected]">[email protected]</a>> wrot= e:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0= .8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=3D= "msg4141255994118379919"> <div lang=3D"DE" style=3D"overflow-wrap: break-word;"> <div class=3D"m_4141255994118379919WordSection1"> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">Hello Pet= er,<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0<u>= </u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">Thanks fo= r your reply.<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0<u>= </u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">Updating = of the database server process itself was no issue, also the migration of t= he data in the database was nothing unusual =E2=80=93 this is also somethin= g I already did many times before in other projects.<u></u><u></u></span></= p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0<u>= </u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">So the ne= xt step I did was trying to install DBD::mysql as per some of the error mes= sages I got from the application, this module was missing (which was correc= t, as I started with a plain Debian container). So I tried to install, but first I needed to get the mysql-config tool ins= talled:<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">apt-get i= nstall libmariadb-dev-compat<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0<u>= </u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">After tha= t I tried again with:<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">cpanm ins= tall DBD::mysql<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0<u>= </u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">and this = failed, with the errors in the log:<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=E2=80=A6= .<u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">DBD::mysq= l requires MySQL 8.x or newer for building. Version reported by mysql_confi= g --version</span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">: 10.11.6= at Makefile.PL line 451, <PIPE> line 3.</span><span style=3D"color:b= lack"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">-> N/A= </span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">-> FAI= L Configure failed for DBD-mysql-5.008. See /root/.cpanm/work/1725256110.10= 36/build.log f</span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">or detail= s.</span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=E2=80=A6= ..</span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0</s= pan><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">As there = is a DBD::MariaDB, I thought: Yes that one would most likely do the trick a= nd I could actually install it. For this to be used I also needed to set th= e configuration in gbrowse to use the MariaDB Connector (which is ok because this is what I just installed). How= ever this does not work out as gbrowse used=C2=A0Bio::DB:SeqFeature:Store::= DBI::mysql and now tries to use Bio::DB:SeqFeature:Store::DBI::MariaDB whic= h is a module that does not exist.</span><span style=3D"color:black"><u></u= ><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0</s= pan><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">It might = be that everything just works fine if I install the mysql libraries into th= e container, sourced from MySQL directly instead of relying on Debian packa= ges that come out of the box. But this feels kind of an ugly workaround.</span><span style=3D"color:black"><u></u= ><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0</s= pan><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">Greetings= ,</span><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">=C2=A0</s= pan><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"color:black">Kai</span= ><span style=3D"color:black"><u></u><u></u></span></p> <p class=3D"MsoNormal"><span><u></u>=C2=A0<u></u></span></p> <div style=3D"border-width:1pt medium medium;border-style:solid none none;b= order-color:rgb(181,196,223) currentcolor currentcolor;padding:3pt 0cm 0cm"= > <p class=3D"MsoNormal"><b><span style=3D"font-size:12pt;color:black">Von: <= /span></b><span style=3D"font-size:12pt;color:black">Peter Cock <<a href= =3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock@googlema= il.com</a>><br> <b>Datum: </b>Freitag, 30. August 2024 um 14:29<br> <b>An: </b>"Schlachter, Kai" <<a href=3D"mailto:kai.schlachter= @dkfz-heidelberg.de" target=3D"_blank">[email protected]</a= >><br> <b>Cc: </b>"<a href=3D"mailto:[email protected]" target=3D"_blank"= >[email protected]</a>" <<a href=3D"mailto:[email protected]= g" target=3D"_blank">[email protected]</a>><br> <b>Betreff: </b>[Extern] - Re: [Bioperl-l] Support for MariaDB in Bio::DB:S= eqFeature:Store::DBI::<u></u><u></u></span></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <div> <p class=3D"MsoNormal">Hello Kai,<br> <br> Interesting question (although I'm viewing it from a Python and Biopyth= on perspective).<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal"><a href=3D"https://mariadb.com/kb/en/upgrading-from-= mysql-to-mariadb/" target=3D"_blank">https://mariadb.com/kb/en/upgrading-fr= om-mysql-to-mariadb/</a> suggests this should<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">just work, with existing MySQL bindings treating Mar= iaDB as a newer version.<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">It sounds like your set is breaking in the Perl modu= le DBD::mysql?<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><a href=3D"https://metacpan.org/dist/DBD-mysql" targ= et=3D"_blank">https://metacpan.org/dist/DBD-mysql</a><u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">Looking at the change log there are entries from thi= s year, and multiple mentions<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">of MariaDB - so I would expect this to work:<u></u><= u></u></p> </div> <div> <p class=3D"MsoNormal"><a href=3D"https://metacpan.org/release/DVEEDEN/DBD-= mysql-5.008/source/Changes" target=3D"_blank">https://metacpan.org/release/= DVEEDEN/DBD-mysql-5.008/source/Changes</a><u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">Can you take a look at their issue tracker <a href= =3D"https://github.com/perl5-dbi/DBD-mysql" target=3D"_blank"> https://github.com/perl5-dbi/DBD-mysql</a><u></u><u></u></p> </div> <div> <p class=3D"MsoNormal">and see if you've hit a known issue?<u></u><u></= u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">Also can you double check the version of DBD::mysql = you have installed?<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal">Peter<u></u><u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> <div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> </div> </div> <p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p> <div> <div> <p class=3D"MsoNormal">On Fri, Aug 30, 2024 at 12:15=E2=80=AFPM Schlachter,= Kai <<a href=3D"mailto:[email protected]" target=3D"_bl= ank">[email protected]</a>> wrote:<u></u><u></u></p> </div> <blockquote style=3D"border-width:medium medium medium 1pt;border-style:non= e none none solid;border-color:currentcolor currentcolor currentcolor rgb(2= 04,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <div> <p class=3D"MsoNormal">Hi there,<u></u><u></u></p> <p class=3D"MsoNormal">=C2=A0<u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">I took over an older project to= modernize the underlaying hardware / software.</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">This also involves the use of g= browse, which in turn relies quite a lot on BioPerl.</span><u></u><u></u></= p> <p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">As our freshly provided servers= are all Debian based and we are highly encouraged to use a most recent ver= sion of Debian inside of our containers (docker), I ran into the following issue:</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">Debian no longer supports MySQL= but has switched to MariaDB, which leads me to the following:</span><u></u= ><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">I tried to install gbrowse, res= olving all the dependencies and stuff that came along. I also was able to c= ompile the DBD::MariaDB as this is the required module for MariaDB-Connections.</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">However I was not able to find = a Module in Bio::DB:SeqFeature:Store::DBI called MariaDB, there is only Mys= ql :(</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">Although both adaptors should s= hare at least some basic functionality, it is not possible to install the M= ysql-Version on a recent Debian because DBD::MySQL will refuse to work with mariadb because of a version mismatch (expected 8.x bu= t reported 10.y).</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">Are there any plans / ideas to = add mariadb support to the modules?</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">I am not an original perl progr= ammer so I don=E2=80=99t think it=E2=80=99s a good idea to start implementi= ng / contributing with such a complex thing.</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">Greetings,</span><u></u><u></u>= </p> <p class=3D"MsoNormal"><span lang=3D"EN-US">=C2=A0</span><u></u><u></u></p> <p class=3D"MsoNormal"><span lang=3D"EN-US">Kai</span><u></u><u></u></p> </div> </div> <p class=3D"MsoNormal">_______________________________________________<br> Bioperl-l mailing list<br> <a href=3D"mailto:[email protected]" target=3D"_blank">Bioperl-l@bioper= l.org</a><br> <a href=3D"https://mailman.open-bio.org/mailman/listinfo/bioperl-l" target= =3D"_blank">https://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><u><= /u><u></u></p> </div> </blockquote> </div> </div> </div> _______________________________________________<br> Bioperl-l mailing list<br> <a href=3D"mailto:[email protected]" target=3D"_blank">Bioperl-l@bioper= l.org</a><br> <a href=3D"https://mailman.open-bio.org/mailman/listinfo/bioperl-l" rel=3D"= noreferrer" target=3D"_blank">https://mailman.open-bio.org/mailman/listinfo= /bioperl-l</a><br> </div></blockquote></div> --0000000000004c623406213576f6-- --===============2211814553949967900== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Bioperl-l mailing list [email protected] https://mailman.open-bio.org/mailman/listinfo/bioperl-l --===============2211814553949967900==--