Re: [Extern] - Re: Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::
Peter Cock <[email protected]> Tue, 3 Sep 2024 12:50:57 +0100
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <CAKVJ-_6-Pig1RQYKk8CUYz12NeVs6+=GfZOAeSp2w4gX9z_Tzw@mail.gmail.com> |
--===============0867025630484212905== Content-Type: multipart/alternative; boundary="0000000000005a2fd0062135ac5b" --0000000000005a2fd0062135ac5b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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=E2=80=AFPM Peter Cock <[email protected]= om> 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 versio= n > 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 >> 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 tr= ied >> 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 n= ot >> work out as gbrowse used Bio::DB:SeqFeature:Store::DBI::mysql and now tr= ies >> to use Bio::DB:SeqFeature:Store::DBI::MariaDB which is a module that doe= s >> 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 Biopytho= n >> 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 >> 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 containe= rs >> (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 tha= t >> 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, i= t >> 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 mismatc= h >> (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= =99s 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 >> > --0000000000005a2fd0062135ac5b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Found it, and <a href=3D"https://github.com/perl5-dbi= /DBD-mysql/issues/423">https://github.com/perl5-dbi/DBD-mysql/issues/423</a= > seems</div><div>to answer my question, quoting what I took as the key poi= nt:</div><div><br></div><div>"DBD::mysql no longer builds against Mari= aDB. This also removes complexity."</div><div><br></div><div>So it loo= ks like adding DBD::MariaDB support to BioPerl is the best solution?<br></d= iv><div><br></div><div>Peter<br></div></div><br><div class=3D"gmail_quote">= <div dir=3D"ltr" class=3D"gmail_attr">On Tue, Sep 3, 2024 at 12:35=E2=80=AF= PM Peter Cock <<a href=3D"mailto:[email protected]">p.j.a.cock@g= ooglemail.com</a>> wrote:<br></div><blockquote class=3D"gmail_quote" sty= le=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);paddi= ng-left:1ex"><div dir=3D"ltr"><div>It sounds to me (as an interested third = party observer of BioPerl), that there</div><div>is value in adding <span l= ang=3D"EN-US">a MariaDB module to Bio::DB:SeqFeature:Store::DBI</span></div= ><div><span lang=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></di= v><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"EN-US">10 (from MariaDB) by insisting on version 8. Do you kno= w where their</span></div><div><span lang=3D"EN-US">issue tracker is? I wou= ld be surprised 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_a= ttr">On Mon, Sep 2, 2024 at 10:56=E2=80=AFAM Schlachter, Kai <<a href=3D= "mailto:[email protected]" target=3D"_blank">kai.schlachter= @dkfz-heidelberg.de</a>> wrote:<br></div><blockquote class=3D"gmail_quot= e" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204)= ;padding-left:1ex"><div> <div lang=3D"DE"> <div> <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> </blockquote></div> --0000000000005a2fd0062135ac5b-- --===============0867025630484212905== 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 --===============0867025630484212905==--