[moby] [MOBY-dev] Perl API: MOBY::Central::DUMP_MySQL()

[Pieter Neerincx]

Hi Mark,

On 6-Jul-2005, at 5:09 PM, Mark Wilkinson wrote:

> Hi Pieter,
>
> I didn't realize that the calls were hard-coded!  Ugh!
>
> Thanks for catching that error - please do go ahead and fix the code.

Ok, done.

>
> We will be committing a major change to the organization of SQL in the
> codebase in the next few days, so once you have committed I am  
> going to
> tag this version and make a release before the chaos ensues :-)

Whoops, good luck!

Cheers,

Pieter


>
> M
>
>
> On Wed, 2005-07-06 at 16:50 +0200, Pieter Neerincx wrote:
>
>> Hi all,
>>
>> This message is for those who use Perl and have local MOBY Centrals.
>> I had some problems with the way MOBY::Central::DUMP_MySQL()
>> currently works. Getting a DUMP fails for example with the new
>> central at:
>>
>> URL: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
>> URI: http://mobycentral.icapture.ubc.ca/MOBY/Central
>>
>> Currently DUMP_MySQL() has the mysql username, the path to mysqldump
>> and the lack of a password, host and portnumber hard coded. Hence it
>> ignores whatever you have in your mobycentral.config file. Therefore
>> I propose the code below which uses MOBY::Config->new() to get the
>> connection details from your mobycentral.config. The path to
>> mysqldump is no longer hard coded. Hence if it's not in the path of
>> webserver user, I think it's better to modify the path env var as
>> compared to hard coding it in the perl modules:) Unless anyone has
>> objections against the porposed code I'll merge this with the code in
>> the CVS in a few days...
>>
>> Cheers,
>>
>> Pieter
>>
>> --------------------------------------------------
>> sub DUMP_MySQL {
>>          my ( $pkg ) = @_;
>>          my $config = MOBY::Config->new();
>>          my @dbsections = ('mobycentral', 'mobyobject',
>> 'mobyservice', 'mobynamespace', 'mobyrelationship');
>>          my @response;
>>
>>          foreach my $dbsection (@dbsections)     {
>>                  my $dbname   = ${${$config}{$dbsection}}{'dbname'};
>>                  my $username = ${${$config}{$dbsection}} 
>> {'username'};
>>                  my $password = ${${$config}{$dbsection}} 
>> {'password'};
>>                  my $host     = ${${$config}{$dbsection}}{'url'};
>>                  my $port     = ${${$config}{$dbsection}}{'port'};
>>                  open( IN, "mysqldump -h $host -P $port -u $username
>> --password=$password $dbname|" )
>>                          || die "can't open $dbname for dumping";
>>                  my @dbdump;
>>                  while ( <IN> ) {
>>                          push @dbdump, $_;
>>                  }
>>                  my $dbdump = ( join "", @dbdump );
>>                  push @response, $dbdump;
>>          }
>>          return [@response];
>> }
>> ------------------------------------------------
>>
>>
>>
>> Wageningen University and Research centre (WUR)
>> Laboratory of Bioinformatics
>> Transitorium (building 312) room 1038
>> Dreijenlaan 3
>> 6703 HA Wageningen
>> phone: 0317-484 706
>> fax: 0317-483 584
>> mobile: 06-143 66 783
>> pieter.neerincx at wur.nl
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at biomoby.org
>> http://www.biomoby.org/mailman/listinfo/moby-dev
>>
> -- 
> Mark Wilkinson
> Asst. Professor
> Dept. of Medical Genetics
> University of British Columbia
> PI in Bioinformatics
> iCAPTURE Centre
> St. Paul's Hospital
> Vancouver, BC
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
>


Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1038
Dreijenlaan 3
6703 HA Wageningen
phone: 0317-484 706
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl