[ensembl-dev] local Compara and perl API

[Thomas Derrien]

Hi Stephen,

Thank you for your reply.
With your example, I encounter another error (copy-pasted here):

Could not connect to database XXXX as user XXXX using [DBI:mysql:database=XXXXX;host=XXXX;port=5306] as a locator:
DBI connect(‘database=XXXX;host=genobdd;port=5306’,'XXXX',...) failed: Can't connect to MySQL server on ‘XXXX' (111) at src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 263.

-------------------- EXCEPTION --------------------
MSG: Could not connect to database GENOCOMP as user XXXXX using [DBI:mysql:database=XXXXX;host=XXXX;port=5306] as a locator:
DBI connect(‘database=XXX;host=genobdd;port=5306’,'XXXXX',...) failed: Can't connect to MySQL server on ‘xxxxx' (111) at /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 263.

STACK Bio::EnsEMBL::DBSQL::DBConnection::connect /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:279
STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:676
STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:707
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:176
STACK Bio::EnsEMBL::DBSQL::BaseMetaContainer::list_value_by_key /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm:121
STACK Bio::EnsEMBL::DBSQL::BaseMetaContainer::get_schema_version /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm:77
STACK Bio::EnsEMBL::Registry::version_check /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:2675
STACK Bio::EnsEMBL::Registry::get_adaptor /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:1050
STACK toplevel connect.pl:7
Date (localtime)    = Fri Jul 18 14:27:14 2014
Ensembl API version = 75


For information, a "normal" connection with "mysql -u XXX -h XXXX -D XXXX -p" works well.

Thank you for your help.

Cheers,

Thomas

Le 18 juil. 2014 à 12:23, Stephen Fitzgerald <stephenf at ebi.ac.uk> a écrit :

> Hi Thomas, try using this "reg_conf.pl" file in the same directory as your script:
> 
>> cat reg_conf.pl
> 
> ###
> use strict;
> use Bio::EnsEMBL::Utils::ConfigRegistry;
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Registry;
> 
> my @aliases;
> 
> 
> new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
>        -host => 'xxxx',
>        -user => 'xxxx',
>        -port => 5306,
>        -pass => 'xxxx',
>        -species => 'Multi',
>        -group => 'compara',
>        -dbname => 'xxxx');
> 
> 1;
> 
> 
> 
> and call it explicitly in your script.
> 
> ###
> use strict;
> use warnings;
> use Data::Dumper;
> use Bio::EnsEMBL::Registry;
> 
> Bio::EnsEMBL::Registry->load_all("reg_conf.pl");
> my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'GeneMember');
> print Dumper $member_adaptor;
> ###
> 
> See if this works.
> 
> Cheers,
> Stephen.
> 
> 
> 
> 
> On Fri, 18 Jul 2014, Thomas Derrien wrote:
> 
>> Dear all,
>> I have installed a local version of the compara database named GENOCOMP (without the core(s) databases).
>> Then, I would like to use the perl API to query it.
>> Here is the simple script I used with the ensembl.init file at the end of the email.
>> ###############
>> use strict;
>> use warnings;
>> use Data::Dumper;
>> use Bio::EnsEMBL::Registry;
>> Bio::EnsEMBL::Registry->load_all();
>> my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Compara', 'compara', 'GeneMember');
>> print Dumper $member_adaptor;
>> #################
>> This scripts returns the following error:
>> ------------------- WARNING ----------------------
>> MSG: Compara is not a valid species name (check DB and API version)
>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1198
>> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 983
>> Date (localtime)    = Fri Jul 18 11:04:36 2014
>> Ensembl API version = 75
>> ---------------------------------------------------
>> -------------------- EXCEPTION --------------------
>> MSG: Can not find internal name for species 'Compara'
>> STACK Bio::EnsEMBL::Registry::get_adaptor /home/genouest/umr6061/recomgen/tderrien/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:985
>> STACK toplevel getOrthologAPI_genocomp.pl:65
>> Date (localtime)    = Fri Jul 18 11:04:36 2014
>> Ensembl API version = 75
>> ---------------------------------------------------
>> I also tried with:
>> my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor(‘Multi', 'compara', 'GeneMember');
>> without any success.
>> Any help would be much appreciated.
>> Thanks in advance
>> Thomas
>> PS: My ensembl.init file
>> $ cat ~/.ensembl_init 
>> use strict;
>> use Bio::EnsEMBL::Utils::ConfigRegistry;
>> use Bio::EnsEMBL::DBSQL::DBAdaptor;
>> use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
>> my $host   = 'genobdd';
>> my $user   = 'GENOCOMP';
>> my $port   = 5306;
>> my $dbname = 'GENOCOMP';
>> my $pass = ‘XXXXXXXXX';
>> new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
>>   -host    => $host,
>>   -user    => $user,
>>   -pass   => $pass,
>>   -port    => $port,
>>   -dbname  => $dbname,
>>   -verbose => 1
>> );
>> 1;
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