[DAS] entry_points trouble (was mysql.sock trouble)
Steve Chervitz
sac@bioperl.org
Mon, 20 May 2002 15:07:59 -0700 (PDT)
I just tried /usr/etc, but still no luck. The symlink will do.
BTW, in running through the server test in the LDasServer README, all of the
commands work as advertised with the exception of the entry_points command. I
get an empty ENTRY_POINTS element:
http://siena/cgi-bin/das/dicty/entry_points
<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
<DASEP>
<ENTRY_POINTS href="http://siena/cgi-bin/das/dicty/entry_points" version="1.0">
</ENTRY_POINTS>
</DASEP>
Output from "ldasdump.pl --database dicty" looks fine, so I know data was
loaded OK.
Why might the server show no entry points?
Steve
--- Lincoln Stein <lstein@cshl.org> wrote:
> Urrrgh. I bet that the RedHat RPM wants my.cnf to be in
> some weird place like /usr/etc.
>
> Lincoln
>
> On Monday 20 May 2002 16:04, Steve Chervitz wrote:
> > Thanks for the replies. The symlink trick works. The /etc/my.cnf file
> > didn't work. I stopped mysqld, created the /etc/my.cnf file, re-started
> > mysqld, but ldas_load.pl still throws a DBI->connect error complaining that
> > it can't connect via /tmp/mysql.sock. If I then create symlink and re-try,
> > it's happy.
> >
> > I also tried uninstalling and re-installing mysql (from rpms) with the
> > /etc/my.cnf file in place. Still no go.
> >
> > Steve
> >
> > --- Lincoln Stein <lstein@cshl.org> wrote:
> > > I think this has been addressed already (I'm reading my e-mail
> > > backwards), but the best of all solution to is set the socket path
> > > correctly in /etc/my.cnf:
> > >
> > > [client]
> > > port = 3306
> > > socket = /var/lib/mysql/mysql.sock
> > >
> > > [mysqld]
> > > datadir=/var/lib/mysql
> > > socket=/var/lib/mysql/mysql.sock
> > >
> > > These two stanzas tell both the client and the server to use the same
> > > socket.
> > >
> > > Lincoln
> > >
> > > On Saturday 18 May 2002 00:01, Leonardo Marino-Ramirez wrote:
> > > > Steve,
> > > >
> > > > I think that I found something that could be useful to you:
> > > >
> > > > http://www.mysql.com/doc/C/a/Can_not_connect_to_server.html and
> > > > http://www.mysql.com/doc/P/r/Problems_with_mysql.sock.html
> > > >
> > > > in synthesis you can try to symlink it: "ln -s
> > > > /var/lib/mysql/mysql.sock /tmp"
> > > >
> > > > I hope it works for you.
> > > >
> > > > Leonardo
> > > >
> > > > On Fri, 17 May 2002, Steve Chervitz wrote:
> > > > > DAS folks,
> > > > >
> > > > > This may be more of a mysql issue than a DAS issue, and is more of an
> > > > > FYI since I have a mostly satisfactory resolution, but I was getting
> > > > > a connection error when using the ldas_load.pl script:
> > > > >
> > > > > $ ldas_load.pl --create --database dicty test.das
> > > > > DBI->connect(dicty) failed: Can't connect to local MySQL server
> > > > > through socket '/tmp/mysql.sock' (111) at
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > > >i/ca ching_handle.pm line 140
> > > > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > > > MSG: Can't connect to database: Can't connect to local MySQL server
> > > > > through socket '/tmp/mysql.sock' (111)
> > > > > STACK: Error::throw
> > > > > STACK: Bio::Root::Root::throw
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/Root/Root.pm:315
> > > > > STACK: Bio::DB::GFF::Adaptor::dbi::caching_handle::new
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > > >i/ca ching_handle.pm:90 STACK: Bio::DB::GFF::Adaptor::dbi::new
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > > >i.pm
> > > > >
> > > > >:74 STACK: Bio::DB::GFF::Adaptor::dbi::mysql::new
> > > > >
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > > >i/my sql.pm:253 STACK: Bio::DB::GFF::Adaptor::dbi::mysqlopt::new
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF/Adaptor/db
> > > > >i/my sqlopt.pm:149 STACK: Bio::DB::GFF::new
> > > > > /nfs/linux/pkg/perl/build-1/lib/site_perl/5.6.1/Bio/DB/GFF.pm:550
> > > > > STACK: /usr/local/bin/ldas_load.pl:50
> > > > > -----------------------------------------------------------
> > > > >
> > > > > I could succesfully connect to the dicty database using mysql on the
> > > > > command-line, so my mysql setup appeared OK.
> > > > >
> > > > > My /tmp/mysql.sock was apparently defunct, probably from an old mysql
> > > > > install that I did over a year ago. The real socket from the latest
> > > > > mysql installation was at /var/lib/mysql/mysql.sock and wasn't been
> > > > > recognized. I tried deleting /tmp/mysql.sock and re-installing
> > > > > LDasServer, but still no go.
> > > > >
> > > > > Problem was solved by restarting mysqld with --socket=/tmp/mysql.sock
> > > > >
> > > > > This however created another annoyance in that the mysqladmin now
> > > > > requires that I specify the --socket, since it defaults to
> > > > > /var/lib/mysql/mysql.sock.
> > > > >
> > > > > So it seems I have to use /tmp/mysql.sock to appease the LDasServer,
> > > > > but it complicates my mysql installation. Any suggestions from the
> > > > > mysql jocks out there?
> > > > >
> > > > > Here's my version info:
> > > > > mysqladmin Ver 8.23 Distrib 3.23.49a, for pc-linux-gnu on i686
> > > > >
> > > > > Steve
> > > > >
> > > > >
> > > > > =====
> > > > > Steve Chervitz
> > > > > sac@bioperl.org
> > > > >
> > > > > __________________________________________________
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> > =====
> > Steve Chervitz
> > sac@bioperl.org
> >
> > __________________________________________________
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=====
Steve Chervitz
sac@bioperl.org
__________________________________________________
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