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Commit 94f98c8b authored by Leo Gordon's avatar Leo Gordon
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added support for -pipeline_url as an input parameter (no need to supply... 

added support for -pipeline_url as an input parameter (no need to supply hive_driver or password in this case)
parent 5be9b1de
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Showing with 30 additions and 26 deletions
modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
View file @ 94f98c8b
......@@ -11,7 +11,7 @@ Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password <mypass>
# Example 2: specifying the mandatory options as well as overriding some defaults:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -pipeline_db -host <myhost> -pipeline_db -dbname <mydbname> -password <mypass>
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -host <myhost> -dbname <mydbname> -password <mypass>
=head1 DESCRIPTION
......@@ -52,6 +52,7 @@ use Bio::EnsEMBL::ApiVersion ();
use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::Utils::URL;
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
......@@ -89,6 +90,7 @@ sub default_options {
'hive_root_dir' => $ENV{'EHIVE_ROOT_DIR'} # this value is set up automatically if this code is run by init_pipeline.pl
|| $self->o('ensembl_cvs_root_dir').'/ensembl-hive', # otherwise we have to rely on other means
'hive_driver' => 'mysql',
'host' => 'localhost', # BEWARE that 'localhost' for mysql driver usually means a UNIX socket, not a TCPIP socket!
# If you need to connect to TCPIP socket, set -host => '127.0.0.1' instead.
'port' => undef,
......@@ -102,13 +104,13 @@ sub default_options {
'hive_force_init' => 0, # setting it to 1 will drop the database prior to creation (use with care!)
'pipeline_db' => {
-driver => $self->o('hive_driver'),
-host => $self->o('host'),
-port => $self->o('port'),
-user => $self->o('user'),
-pass => $self->o('password'),
-dbname => $self->o('dbowner').'_'.$self->o('pipeline_name'), # example of a linked definition (resolved via saturation)
},
};
}
......@@ -122,10 +124,12 @@ sub default_options {
sub pipeline_create_commands {
my $self = shift @_;
my $db_conn = shift @_ || 'pipeline_db';
my $driver = $self->o($db_conn, '-driver');
my $db_cmd_prefix = 'db_cmd.pl -url '.$self->dbconn_2_url( $db_conn );
my $pipeline_url = $self->pipeline_url();
my $parsed_url = Bio::EnsEMBL::Hive::Utils::URL::parse( $pipeline_url );
my $driver = $parsed_url ? $parsed_url->{'driver'} : '';
my $db_cmd_prefix = "db_cmd.pl -url $pipeline_url";
return [
$self->o('hive_force_init') ? ( $db_cmd_prefix." -sql 'DROP DATABASE IF EXISTS'" ) : (),
......@@ -229,7 +233,7 @@ sub pre_options {
'help!' => '',
'job_topup!' => '',
'analysis_topup!' => '',
'hive_driver' => '',
'pipeline_url' => '',
# 'hive_use_triggers' => '',
};
}
......@@ -237,7 +241,7 @@ sub pre_options {
=head2 dbconn_2_mysql
Description : A convenience method used to stringify a connection-parameters hash into a parameter string that both mysql and beekeeper.pl can understand
Description : Deprecated method. Please use db_cmd.pl with a pipeline_url
=cut
......@@ -254,7 +258,7 @@ sub dbconn_2_mysql { # will save you a lot of typing
=head2 dbconn_2_pgsql
Description : A convenience method used to stringify a connection-parameters hash into a parameter string that pgsql can understand
Description : Deprecated method. Please use db_cmd.pl with a pipeline_url
=cut
......@@ -269,7 +273,7 @@ sub dbconn_2_pgsql { # will save you a lot of typing
=head2 db_connect_command
Description : A convenience method used to stringify a command to connect to the db OR pipe an sql file into it.
Description : Deprecated method. Please use db_cmd.pl with a pipeline_url
=cut
......@@ -288,7 +292,7 @@ sub db_connect_command {
=head2 db_execute_command
Description : A convenience method used to stringify a command to connect to the db OR pipe an sql file into it.
Description : Deprecated method. Please use db_cmd.pl with a pipeline_url
=cut
......@@ -314,7 +318,7 @@ sub db_execute_command {
=head2 dbconn_2_url
Description : A convenience method used to stringify a connection-parameters hash into a 'url' that beekeeper.pl will undestand
Description : A convenience method used to stringify a connection-parameters hash into a 'pipeline_url' that beekeeper.pl will undestand
=cut
......@@ -336,7 +340,7 @@ sub dbconn_2_url {
sub pipeline_url {
my $self = shift @_;
return $self->dbconn_2_url('pipeline_db'); # used to force vivification of the whole 'pipeline_db' structure (used in run() )
return $self->root()->{'pipeline_url'} || $self->dbconn_2_url('pipeline_db', 1); # used to force vivification of the whole 'pipeline_db' structure (used in run() )
}
......@@ -358,7 +362,7 @@ sub process_options {
# pre-patch definitely_used_options:
$self->{'_extra_options'} = $self->load_cmdline_options( $self->pre_options() );
$self->root()->{'pipeline_db'}{'-driver'} = $self->{'_extra_options'}{'hive_driver'} || 'mysql';
$self->root()->{'pipeline_url'} = $self->{'_extra_options'}{'pipeline_url'};
$self->use_cases( [ 'pipeline_create_commands', 'pipeline_wide_parameters', 'resource_classes', 'pipeline_analyses', 'beekeeper_extra_cmdline_options', 'pipeline_url', 'hive_meta_table' ] );
return $self->SUPER::process_options();
......@@ -390,7 +394,7 @@ sub run {
}
Bio::EnsEMBL::Registry->no_version_check(1);
my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( %{$self->o('pipeline_db')}, -no_sql_schema_version_check => 1 );
my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $self->pipeline_url(), -no_sql_schema_version_check => 1 );
my $resource_class_adaptor = $hive_dba->get_ResourceClassAdaptor;
unless($job_topup) {
......@@ -650,33 +654,33 @@ sub run {
}
}
my $url = $self->dbconn_2_url('pipeline_db');
my $pipeline_url = $self->pipeline_url();
print "\n\n# --------------------[Useful commands]--------------------------\n";
print "\n";
print " # It is convenient to store the pipeline url in a variable:\n";
print "\texport HIVE_URL=$url\t\t\t# bash version\n";
print "\texport EHIVE_URL=$pipeline_url\t\t\t# bash version\n";
print "(OR)\n";
print "\tsetenv HIVE_URL $url\t\t\t# [t]csh version\n";
print "\tsetenv EHIVE_URL $pipeline_url\t\t\t# [t]csh version\n";
print "\n";
print " # Add a new job to the pipeline (usually done once before running, but pipeline can be \"topped-up\" at any time) :\n";
print "\tseed_pipeline.pl -url $url -logic_name <analysis_name> -input_id <param_hash>\n";
print "\tseed_pipeline.pl -url $pipeline_url -logic_name <analysis_name> -input_id <param_hash>\n";
print "\n";
print " # Synchronize the Hive (should be done before [re]starting a pipeline) :\n";
print "\tbeekeeper.pl -url $url -sync\n";
print "\tbeekeeper.pl -url $pipeline_url -sync\n";
print "\n";
print " # Run the pipeline (can be interrupted and restarted) :\n";
print "\tbeekeeper.pl -url $url ".$self->beekeeper_extra_cmdline_options()." -loop\t\t# run in looped automatic mode (a scheduling step performed every minute)\n";
print "\tbeekeeper.pl -url $pipeline_url ".$self->beekeeper_extra_cmdline_options()." -loop\t\t# run in looped automatic mode (a scheduling step performed every minute)\n";
print "(OR)\n";
print "\tbeekeeper.pl -url $url ".$self->beekeeper_extra_cmdline_options()." -run \t\t# run one scheduling step of the pipeline and exit (useful for debugging/learning)\n";
print "\tbeekeeper.pl -url $pipeline_url ".$self->beekeeper_extra_cmdline_options()." -run \t\t# run one scheduling step of the pipeline and exit (useful for debugging/learning)\n";
print "(OR)\n";
print "\trunWorker.pl -url $url ".$self->beekeeper_extra_cmdline_options()." \t\t# run exactly one Worker locally (useful for debugging/learning)\n";
print "\trunWorker.pl -url $pipeline_url ".$self->beekeeper_extra_cmdline_options()." \t\t# run exactly one Worker locally (useful for debugging/learning)\n";
print "\n";
print " # At any moment during or after execution you can request a pipeline diagram in an image file (desired format is set via extension) :\n";
print "\tgenerate_graph.pl -url $url -out diagram.png\n";
print "\tgenerate_graph.pl -url $pipeline_url -out diagram.png\n";
print "\n";
print " # Peek into your pipeline database with a database client (useful to have open while the pipeline is running) :\n";
print "\tdb_cmd.pl -url $url\n\n";
print "\tdb_cmd.pl -url $pipeline_url\n\n";
}
1;
......
modules/Bio/EnsEMBL/Hive/PipeConfig/LongMultSt_conf.pm
View file @ 94f98c8b
......@@ -96,7 +96,7 @@ sub pipeline_create_commands {
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables' creation
# additional tables needed for long multiplication pipeline's operation:
'db_cmd.pl -url '.$self->dbconn_2_url('pipeline_db').' -sql '
'db_cmd.pl -url '.$self->pipeline_url().' -sql '
."'CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'",
];
}
......
modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm
View file @ 94f98c8b
......@@ -94,7 +94,7 @@ sub pipeline_create_commands {
@{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables' creation
# additional tables needed for long multiplication pipeline's operation:
'db_cmd.pl -url '.$self->dbconn_2_url('pipeline_db').' -sql '
'db_cmd.pl -url '.$self->pipeline_url().' -sql '
."'CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'",
];
}
......
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