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

[Mark Wilkinson]

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.

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 :-)

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
> 
> 
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-- 
Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Vancouver, BC