[BioSQL-l] " Lost connection to MySQL server" when I via biosql by using "find_by_unique_key" method

[Hilmar Lapp]

Maybe there's a migration script that you need to run and that comes 
with mysql? Have you checked Mysql FAQs and possibly message 
boards/README/HOWTO for what you need to do when upgrading from 4.0.x 
to 4.1.x?

	-hilmar

On Jun 20, 2004, at 1:51 AM, shenyang wrote:

> Hello-
> 	I updated my mysql from "mysql-standard-4.0.20-sgi-irix6.5-mips" to
>  "mysql-max-4.1.12-sgi-irix6.5-mips".
>
> Then I failed to get richseq object from my sequence database which is 
> biosql schema.
> My perl scripte is "
>
> $db = $db||Bio::DB::BioDB->new(-database   => "biosql",
>                             -printerror => 0,	
>                             -host       => "localhost",
>                             -dbname     => $dbname,
>                             -driver     => "mysql",
>                             -user       => $dbuser,
>                             -pass       => $dbpass,
>                             );
> $seq->namespace($namespace);
> $seq->version($version);
> my $adp = $db->get_object_adaptor($seq);
> my $seqfactor=Bio::Seq::SeqFactory->new(-type=>"Bio::Seq::RichSeq");
> $lseq = $adp->find_by_unique_key(
>    			$seq,
>    			-obj_factory =>$seqfactor,
> );
>
> The error message is "
>
> ------------- EXCEPTION  -------------
>
> MSG: error while executing statement in 
> Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: Lost connection to 
> MySQL server during query
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
> /usr/lib/bioperl-db//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:952
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
> /usr/lib/bioperl-db//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
> STACK toplevel test_get_seq_embl_acc.pl:9
>
> --------------------------------------
>
> and the mysql log file indicated it's a innodb's problem, here is the 
> mysql logs:
>
> "
> 050620 16:32:47  mysqld restarted
> 050620 16:32:49  InnoDB: Database was not shut down normally!
> InnoDB: Starting crash recovery.
> InnoDB: Reading tablespace information from the .ibd files...
> InnoDB: Restoring possible half-written data pages from the doublewrite
> InnoDB: buffer...
> 050620 16:32:50  InnoDB: Starting log scan based on checkpoint at
> InnoDB: log sequence number 0 2237087117.
> InnoDB: Doing recovery: scanned up to log sequence number 0 2237087117
> InnoDB: Last MySQL binlog file position 0 79, file name 
> ./biomed-bin.000022
> 050620 16:32:51  InnoDB: Flushing modified pages from the buffer 
> pool...
> 050620 16:32:51  InnoDB: Started; log sequence number 0 2237087117
> 050620 16:32:51 [Warning] mysql.user table is not updated to new 
> password format; Disabling new password usage until 
> mysql_fix_privilege_tables is run
> 050620 16:32:51 [Warning] Can't open and lock time zone table: Table 
> 'mysql.time_zone_leap_second' doesn't exist trying to live without 
> them
> /database/mysql/bin/mysqld: ready for connections.
> Version: '4.1.12-max-log'  socket: '/tmp/mysql.sock'  port: 3306  
> MySQL Community Edition - Experimental (GPL)"
>
>
> Thanks for any suggestions,
> Yang Shen
>
>
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------