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Commit c665fbfc authored by Leo Gordon's avatar Leo Gordon
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inherit Job,Worker,DFR,RC from Bio::EnsEMBL::Storable, reuse some code

parent cb325115
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Showing with 71 additions and 132 deletions
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
View file @ c665fbfc
......@@ -27,23 +27,24 @@
package Bio::EnsEMBL::Hive::AnalysisJob;
use strict;
use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use base ('Bio::EnsEMBL::Hive::Params');
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
'Bio::EnsEMBL::Hive::Params', # inherit param management functionality
);
sub new {
my $class = shift @_;
my $self = bless {}, $class;
my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
my($dbID, $analysis_id, $input_id, $worker_id, $status, $retry_count, $completed, $runtime_msec, $query_count, $semaphore_count, $semaphored_job_id, $adaptor) =
rearrange([qw(dbID analysis_id input_id worker_id status retry_count completed runtime_msec query_count semaphore_count semaphored_job_id adaptor) ], @_);
my($analysis_id, $input_id, $worker_id, $status, $retry_count, $completed, $runtime_msec, $query_count, $semaphore_count, $semaphored_job_id) =
rearrange([qw(analysis_id input_id worker_id status retry_count completed runtime_msec query_count semaphore_count semaphored_job_id) ], @_);
$self->dbID($dbID) if(defined($dbID));
$self->analysis_id($analysis_id) if(defined($analysis_id));
$self->input_id($input_id) if(defined($input_id));
$self->worker_id($worker_id) if(defined($worker_id));
......@@ -54,28 +55,10 @@ sub new {
$self->query_count($query_count) if(defined($query_count));
$self->semaphore_count($semaphore_count) if(defined($semaphore_count));
$self->semaphored_job_id($semaphored_job_id) if(defined($semaphored_job_id));
$self->adaptor($adaptor) if(defined($adaptor));
return $self;
}
sub adaptor {
my $self = shift @_;
if(@_) {
$self->{'_adaptor'} = shift @_;
weaken $self->{'_adaptor'};
}
return $self->{'_adaptor'};
}
sub dbID {
my $self = shift;
$self->{'_dbID'} = shift if(@_);
return $self->{'_dbID'};
}
sub input_id {
my $self = shift;
......@@ -83,6 +66,7 @@ sub input_id {
return $self->{'_input_id'};
}
sub dataflow_rules { # if ever set will prevent the Job from fetching rules from the DB
my $self = shift @_;
my $branch_name_or_code = shift @_;
......@@ -96,12 +80,14 @@ sub dataflow_rules { # if ever set will prevent the Job from fetching rules f
: $self->adaptor->db->get_DataflowRuleAdaptor->fetch_all_by_from_analysis_id_and_branch_code($self->analysis_id, $branch_code);
}
sub worker_id {
my $self = shift;
$self->{'_worker_id'} = shift if(@_);
return $self->{'_worker_id'};
}
sub analysis_id {
my $self = shift;
$self->{'_analysis_id'} = shift if(@_);
......
modules/Bio/EnsEMBL/Hive/DataflowRule.pm
View file @ c665fbfc
......@@ -50,13 +50,16 @@
package Bio::EnsEMBL::Hive::DataflowRule;
use strict;
use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils ('stringify'); # import 'stringify()'
use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
);
=head2 new
Usage : Bio::EnsEMBL::Hive::DataflowRule->new(-from_analysis => $fromAnalysis, -to_analysis => $toAnalysis, -branch_code => $branch_code);
......@@ -68,14 +71,11 @@ use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
sub new {
my $class = shift @_;
my $self = bless {}, $class;
my ( $dbID, $adaptor, $fromAnalysis, $toAnalysis, $from_analysis_id, $branch_code, $funnel_dataflow_rule_id, $to_analysis_url, $input_id_template ) =
rearrange( [ qw (DBID ADAPTOR FROM_ANALYSIS TO_ANALYSIS FROM_ANALYSIS_ID BRANCH_CODE FUNNEL_DATAFLOW_RULE_ID TO_ANALYSIS_URL INPUT_ID_TEMPLATE) ], @_ );
my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
# database persistence:
$self->dbID( $dbID ) if(defined($dbID));
$self->adaptor( $adaptor ) if(defined($adaptor));
my ($fromAnalysis, $toAnalysis, $from_analysis_id, $branch_code, $funnel_dataflow_rule_id, $to_analysis_url, $input_id_template ) =
rearrange( [ qw (FROM_ANALYSIS TO_ANALYSIS FROM_ANALYSIS_ID BRANCH_CODE FUNNEL_DATAFLOW_RULE_ID TO_ANALYSIS_URL INPUT_ID_TEMPLATE) ], @_ );
# from objects:
$self->from_analysis( $fromAnalysis ) if(defined($fromAnalysis));
......@@ -91,38 +91,6 @@ sub new {
return $self;
}
=head2 dbID
Function: getter/setter method for the dbID of the dataflow rule
=cut
sub dbID {
my $self = shift @_;
if(@_) { # setter mode
$self->{'_dbID'} = shift @_;
}
return $self->{'_dbID'};
}
=head2 adaptor
Function: getter/setter method for the adaptor of the dataflow rule
=cut
sub adaptor {
my $self = shift @_;
if(@_) {
$self->{'_adaptor'} = shift @_;
weaken $self->{'_adaptor'};
}
return $self->{'_adaptor'};
}
=head2 branch_code
......@@ -139,6 +107,7 @@ sub branch_code {
return $self->{'_branch_code'};
}
=head2 funnel_dataflow_rule_id
Function: getter/setter method for the funnel_dataflow_rule_id of the dataflow rule
......@@ -154,6 +123,7 @@ sub funnel_dataflow_rule_id {
return $self->{'_funnel_dataflow_rule_id'};
}
=head2 input_id_template
Function: getter/setter method for the input_id_template of the dataflow rule
......@@ -170,6 +140,7 @@ sub input_id_template {
return $self->{'_input_id_template'};
}
=head2 from_analysis_id
Arg[1] : (optional) int $dbID
......
modules/Bio/EnsEMBL/Hive/Process.pm
View file @ c665fbfc
......@@ -175,7 +175,7 @@ sub enter_status {
}
if($worker) {
$worker->status( $status );
$worker->queen->check_in_worker( $worker );
$worker->adaptor->check_in_worker( $worker );
}
}
......
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @ c665fbfc
......@@ -212,6 +212,8 @@ sub create_new_worker {
my $worker = $self->fetch_by_dbID($worker_id);
$worker=undef unless($worker and $worker->analysis);
$worker->init;
if($worker and $analysisStats) {
$analysisStats->update_status('WORKING');
}
......@@ -1060,10 +1062,11 @@ sub _objs_from_sth {
my @workers = ();
while ($sth->fetch()) {
my $worker = Bio::EnsEMBL::Hive::Worker->new();
$worker->init;
my $worker = Bio::EnsEMBL::Hive::Worker->new( # will be passed to Storable's new()
-adaptor => $self,
-dbID => $column{'worker_id'},
);
$worker->dbID($column{'worker_id'});
$worker->meadow_type($column{'meadow_type'});
$worker->meadow_name($column{'meadow_name'});
$worker->host($column{'host'});
......@@ -1074,7 +1077,6 @@ sub _objs_from_sth {
$worker->last_check_in($column{'last_check_in'});
$worker->died($column{'died'});
$worker->cause_of_death($column{'cause_of_death'});
$worker->queen($self);
$worker->db($self->db);
if($column{'analysis_id'} and $self->db->get_AnalysisAdaptor) {
......
modules/Bio/EnsEMBL/Hive/ResourceClass.pm
View file @ c665fbfc
......@@ -26,49 +26,26 @@
package Bio::EnsEMBL::Hive::ResourceClass;
use strict;
use Scalar::Util ('weaken');
use Bio::EnsEMBL::Utils::Argument; # import 'rearrange()'
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
);
sub new {
my $class = shift @_;
my $self = bless {}, $class;
my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
my ($adaptor, $dbID, $name) =
rearrange([qw(adaptor dbID name) ], @_);
my ($name) =
rearrange([qw(name) ], @_);
$self->adaptor($adaptor) if(defined($adaptor));
$self->dbID($dbID);
$self->name($name);
$self->name($name) if($name);
return $self;
}
sub adaptor {
my $self = shift @_;
if(@_) {
$self->{'_adaptor'} = shift @_;
weaken $self->{'_adaptor'};
}
return $self->{'_adaptor'};
}
sub dbID {
my $self = shift @_;
if(@_) {
$self->{'_resource_class_id'} = shift @_;
}
return $self->{'_resource_class_id'};
}
sub name {
my $self = shift @_;
......
modules/Bio/EnsEMBL/Hive/Worker.pm
View file @ c665fbfc
......@@ -64,67 +64,75 @@
package Bio::EnsEMBL::Hive::Worker;
use strict;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils::Stopwatch;
use POSIX;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Hive::Process;
use Bio::EnsEMBL::Hive::Utils::Stopwatch;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Hive::Process;
use Bio::EnsEMBL::Hive::Utils::RedirectStack;
use Bio::EnsEMBL::Hive::Utils ('dir_revhash'); # import dir_revhash
use base ( 'Bio::EnsEMBL::Storable', # inherit dbID(), adaptor() and new() methods
);
sub new {
my ($class,@args) = @_;
my $self = bless {}, $class;
return $self;
my $class = shift @_;
my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
return $self;
}
sub init {
my $self = shift;
my $self = shift;
my $lifespan_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new();
$lifespan_stopwatch->_unit(1); # count in seconds (default is milliseconds)
$lifespan_stopwatch->restart;
$self->lifespan_stopwatch( $lifespan_stopwatch );
my $lifespan_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new();
$lifespan_stopwatch->_unit(1); # count in seconds (default is milliseconds)
$lifespan_stopwatch->restart;
$self->lifespan_stopwatch( $lifespan_stopwatch );
$self->debug(0);
return $self;
return $self;
}
sub queen {
my $self = shift;
$self->{'_queen'} = shift if(@_);
return $self->{'_queen'};
}
sub db {
my $self = shift;
$self->{'_db'} = shift if(@_);
return $self->{'_db'};
}
sub meadow_type {
my $self = shift;
$self->{'_meadow_type'} = shift if(@_);
return $self->{'_meadow_type'};
}
sub meadow_name {
my $self = shift;
$self->{'_meadow_name'} = shift if(@_);
return $self->{'_meadow_name'};
}
sub debug {
my $self = shift;
$self->{'_debug'} = shift if(@_);
$self->{'_debug'}=0 unless(defined($self->{'_debug'}));
return $self->{'_debug'};
}
sub execute_writes {
my $self = shift;
$self->{'_execute_writes'} = shift if(@_);
......@@ -132,6 +140,7 @@ sub execute_writes {
return $self->{'_execute_writes'};
}
=head2 analysis
Arg [1] : (optional) Bio::EnsEMBL::Analysis $value
......@@ -284,12 +293,6 @@ sub prev_job_error {
}
sub dbID {
my( $self, $value ) = @_;
$self->{'_worker_id'} = $value if($value);
return $self->{'_worker_id'};
}
sub host {
my( $self, $value ) = @_;
$self->{'_host'} = $value if($value);
......@@ -583,7 +586,7 @@ sub run {
}
}
$self->queen->register_worker_death($self);
$self->adaptor->register_worker_death($self);
$self->analysis->stats->print_stats if($self->debug);
......@@ -603,8 +606,8 @@ sub run_one_batch {
my $max_retry_count = $self->analysis->stats->max_retry_count(); # a constant (as the Worker is already specialized by the Queen) needed later for retrying jobs
$self->queen->check_in_worker( $self );
$self->queen->safe_synchronize_AnalysisStats($self->analysis->stats);
$self->adaptor->check_in_worker( $self );
$self->adaptor->safe_synchronize_AnalysisStats($self->analysis->stats);
$self->cause_of_death('NO_WORK') unless(scalar @{$jobs});
......@@ -715,7 +718,7 @@ sub enter_status {
$job->update_status( $status );
}
$self->status( $status );
$self->queen->check_in_worker( $self );
$self->adaptor->check_in_worker( $self );
}
......
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