From e38de2d91f0fcfab8e165dd992e8e6a7cc99c9f5 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 4 Feb 2014 13:03:02 +0000
Subject: [PATCH] Storable->new() now performs setting of all parameters
without the use of rearrange (NB: change of call format!)
---
modules/Bio/EnsEMBL/Hive/Accumulator.pm | 19 +----
modules/Bio/EnsEMBL/Hive/Analysis.pm | 28 +------
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm | 30 +------
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 68 +++++----------
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm | 42 +---------
.../Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm | 4 +-
modules/Bio/EnsEMBL/Hive/DataflowRule.pm | 36 +-------
modules/Bio/EnsEMBL/Hive/NakedTable.pm | 18 +---
.../Hive/PipeConfig/HiveGeneric_conf.pm | 84 +++++++++----------
modules/Bio/EnsEMBL/Hive/ResourceClass.pm | 19 +----
.../Bio/EnsEMBL/Hive/ResourceDescription.pm | 20 +----
modules/Bio/EnsEMBL/Hive/Storable.pm | 17 ++--
modules/Bio/EnsEMBL/Hive/URLFactory.pm | 12 +--
modules/Bio/EnsEMBL/Hive/Worker.pm | 31 +------
scripts/seed_pipeline.pl | 6 +-
scripts/standaloneJob.pl | 6 +-
16 files changed, 95 insertions(+), 345 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Accumulator.pm b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
index dfad3f988..2e3935cd9 100644
--- a/modules/Bio/EnsEMBL/Hive/Accumulator.pm
+++ b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
@@ -32,25 +32,10 @@
package Bio::EnsEMBL::Hive::Accumulator;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-use Bio::EnsEMBL::Hive::Utils ('stringify');
-
-use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
-
-
-sub new {
- my $class = shift @_;
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($struct_name, $signature_template) =
- rearrange([qw(struct_name signature_template) ], @_);
-
- $self->struct_name($struct_name) if(defined($struct_name));
- $self->signature_template($signature_template) if(defined($signature_template));
+use Bio::EnsEMBL::Hive::Utils ('stringify');
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
sub struct_name {
diff --git a/modules/Bio/EnsEMBL/Hive/Analysis.pm b/modules/Bio/EnsEMBL/Hive/Analysis.pm
index 740b98cd3..70180898c 100644
--- a/modules/Bio/EnsEMBL/Hive/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Hive/Analysis.pm
@@ -37,37 +37,11 @@ package Bio::EnsEMBL::Hive::Analysis;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-
use Bio::EnsEMBL::Hive::Utils ('stringify');
-use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
- );
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($logic_name, $module, $parameters, $resource_class_id, $failed_job_tolerance, $max_retry_count, $can_be_empty, $priority, $meadow_type, $analysis_capacity) =
- rearrange([qw(logic_name module parameters resource_class_id failed_job_tolerance max_retry_count can_be_empty priority meadow_type analysis_capacity) ], @_);
-
- $self->logic_name($logic_name) if($logic_name);
- $self->module($module) if($module);
- $self->parameters($parameters) if($parameters);
- $self->resource_class_id($resource_class_id) if($resource_class_id);
- $self->failed_job_tolerance($failed_job_tolerance) if($failed_job_tolerance);
- $self->max_retry_count($max_retry_count) if($max_retry_count);
- $self->can_be_empty($can_be_empty) if($can_be_empty);
- $self->priority($priority) if($priority);
- $self->meadow_type($meadow_type) if($meadow_type);
- $self->analysis_capacity($analysis_capacity) if( defined($analysis_capacity) );
-
- return $self;
-}
-
-
sub logic_name {
my $self = shift;
$self->{'_logic_name'} = shift if(@_);
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
index 0e0cafb7f..72839cb74 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
@@ -42,39 +42,13 @@
package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
+
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::Extensions;
-use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
-
-
-=head2 new
-
- Title : new
- Usage : ...AnalysisCtrlRule->new;
- Function: Constructor for empty AnalysisCtrlRule object
- Returns : Bio::EnsEMBL::Hive::AnalysisCtrlRule
- Args : none
-
-=cut
-
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ( $condition_analysis_url, $ctrled_analysis_id ) =
- rearrange( [ qw (CONDITION_ANALYSIS_URL CTRLED_ANALYSIS_ID) ], @_ );
-
- # simple scalars:
- $self->condition_analysis_url( $condition_analysis_url ) if(defined($condition_analysis_url));
- $self->ctrled_analysis_id( $ctrled_analysis_id ) if(defined($ctrled_analysis_id));
-
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
=head2 ctrled_analysis_id
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 43f186860..e19a6fd17 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -38,43 +38,15 @@ package Bio::EnsEMBL::Hive::AnalysisJob;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-
use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
-use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
'Bio::EnsEMBL::Hive::Params', # inherit param management functionality
);
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my($prev_job_id, $analysis_id, $input_id, $param_id_stack, $accu_id_stack, $worker_id, $status, $retry_count, $completed, $runtime_msec, $query_count, $semaphore_count, $semaphored_job_id) =
- rearrange([qw(prev_job_id analysis_id input_id param_id_stack accu_id_stack worker_id status retry_count completed runtime_msec query_count semaphore_count semaphored_job_id) ], @_);
-
- $self->prev_job_id($prev_job_id) if(defined($prev_job_id));
- $self->analysis_id($analysis_id) if(defined($analysis_id));
- $self->input_id($input_id) if(defined($input_id));
- $self->param_id_stack($param_id_stack) if(defined($param_id_stack));
- $self->accu_id_stack($accu_id_stack) if(defined($accu_id_stack));
- $self->worker_id($worker_id) if(defined($worker_id));
- $self->status($status) if(defined($status));
- $self->retry_count($retry_count) if(defined($retry_count));
- $self->completed($completed) if(defined($completed));
- $self->runtime_msec($runtime_msec) if(defined($runtime_msec));
- $self->query_count($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));
-
- return $self;
-}
-
-
sub prev_job_id {
my $self = shift;
$self->{'_prev_job_id'} = shift if(@_);
@@ -352,12 +324,12 @@ sub dataflow_output_id {
my $fan_cache_this_branch = $self->fan_cache()->{$funnel_dataflow_rule_id} ||= [];
push @$fan_cache_this_branch, map { Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => $self->dbID,
- -analysis_id => $target_analysis_or_table->dbID, # expecting an Analysis
- -input_id => $_,
- -param_id_stack => $param_id_stack,
- -accu_id_stack => $accu_id_stack,
- # -semaphored_job_id => to be set when the $funnel_job has been stored
+ 'prev_job_id' => $self->dbID,
+ 'analysis_id' => $target_analysis_or_table->dbID, # expecting an Analysis
+ 'input_id' => $_,
+ 'param_id_stack' => $param_id_stack,
+ 'accu_id_stack' => $accu_id_stack,
+ # semaphored_job_id => to be set when the $funnel_job has been stored
) } @$output_ids_for_this_rule;
} else { # either a semaphored funnel or a non-semaphored dataflow:
@@ -373,13 +345,13 @@ sub dataflow_output_id {
} else {
my $funnel_job = Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => $self->dbID,
- -analysis_id => $target_analysis_or_table->dbID, # expecting an Analysis
- -input_id => $output_ids_for_this_rule->[0],
- -param_id_stack => $param_id_stack,
- -accu_id_stack => $accu_id_stack,
- -semaphore_count => scalar(@$fan_jobs), # "pre-increase" the semaphore count before creating the dependent jobs
- -semaphored_job_id => $self->semaphored_job_id(), # propagate parent's semaphore if any
+ 'prev_job_id' => $self->dbID,
+ 'analysis_id' => $target_analysis_or_table->dbID, # expecting an Analysis
+ 'input_id' => $output_ids_for_this_rule->[0],
+ 'param_id_stack' => $param_id_stack,
+ 'accu_id_stack' => $accu_id_stack,
+ 'semaphore_count' => scalar(@$fan_jobs), # "pre-increase" the semaphore count before creating the dependent jobs
+ 'semaphored_job_id' => $self->semaphored_job_id(), # propagate parent's semaphore if any
);
my ($funnel_job_id) = @{ $job_adaptor->store_jobs_and_adjust_counters( [ $funnel_job ], 0) };
@@ -393,12 +365,12 @@ sub dataflow_output_id {
}
} else { # non-semaphored dataflow (but potentially propagating any existing semaphores)
my @non_semaphored_jobs = map { Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => $self->dbID,
- -analysis_id => $target_analysis_or_table->dbID, # expecting an Analysis
- -input_id => $_,
- -param_id_stack => $param_id_stack,
- -accu_id_stack => $accu_id_stack,
- -semaphored_job_id => $self->semaphored_job_id(), # propagate parent's semaphore if any
+ 'prev_job_id' => $self->dbID,
+ 'analysis_id' => $target_analysis_or_table->dbID, # expecting an Analysis
+ 'input_id' => $_,
+ 'param_id_stack' => $param_id_stack,
+ 'accu_id_stack' => $accu_id_stack,
+ 'semaphored_job_id' => $self->semaphored_job_id(), # propagate parent's semaphore if any
) } @$output_ids_for_this_rule;
push @output_job_ids, @{ $job_adaptor->store_jobs_and_adjust_counters( \@non_semaphored_jobs, 0) };
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
index fe3103c88..3843afbc6 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
@@ -37,11 +37,10 @@ package Bio::EnsEMBL::Hive::AnalysisStats;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Analysis;
-use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
## Minimum amount of time in msec that a worker should run before reporting
@@ -50,45 +49,6 @@ sub min_batch_time {
return 2*60*1000;
}
-
-sub new {
- my $class = shift;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ( $analysis_id, $batch_size, $hive_capacity, $status,
- $total_job_count, $semaphored_job_count, $ready_job_count, $done_job_count, $failed_job_count, $num_running_workers, $num_required_workers,
- $behaviour, $input_capacity, $output_capacity, $avg_msec_per_job, $avg_input_msec_per_job, $avg_run_msec_per_job, $avg_output_msec_per_job,
- $seconds_since_last_update, $sync_lock) =
- rearrange([qw(analysis_id batch_size hive_capacity status
- total_job_count semaphored_job_count ready_job_count done_job_count failed_job_count num_running_workers num_required_workers
- behaviour input_capacity output_capacity avg_msec_per_job avg_input_msec_per_job avg_run_msec_per_job avg_output_msec_per_job
- seconds_since_last_update sync_lock ) ], @_);
- $self->analysis_id($analysis_id) if(defined($analysis_id));
- $self->batch_size($batch_size) if(defined($batch_size));
- $self->hive_capacity($hive_capacity) if(defined($hive_capacity));
- $self->status($status) if(defined($status));
- $self->total_job_count($total_job_count) if(defined($total_job_count));
- $self->semaphored_job_count($semaphored_job_count) if(defined($semaphored_job_count));
- $self->ready_job_count($ready_job_count) if(defined($ready_job_count));
- $self->done_job_count($done_job_count) if(defined($done_job_count));
- $self->failed_job_count($failed_job_count) if(defined($failed_job_count));
- $self->num_running_workers($num_running_workers) if(defined($num_running_workers));
- $self->num_required_workers($num_required_workers) if(defined($num_required_workers));
- $self->behaviour($behaviour) if(defined($behaviour));
- $self->input_capacity($input_capacity) if(defined($input_capacity));
- $self->output_capacity($output_capacity) if(defined($output_capacity));
- $self->avg_msec_per_job($avg_msec_per_job) if(defined($avg_msec_per_job));
- $self->avg_input_msec_per_job($avg_input_msec_per_job) if(defined($avg_input_msec_per_job));
- $self->avg_run_msec_per_job($avg_run_msec_per_job) if(defined($avg_run_msec_per_job));
- $self->avg_output_msec_per_job($avg_output_msec_per_job) if(defined($avg_output_msec_per_job));
- $self->seconds_since_last_update($seconds_since_last_update)if(defined($seconds_since_last_update)); # NB: this is an input_column_mapped field
- $self->sync_lock($sync_lock) if(defined($sync_lock));
-
- return $self;
-}
-
-
## pre-settable storable object's getters/setters:
sub analysis_id { # an alias
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
index 75c16822a..c93bb1016 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
@@ -69,7 +69,7 @@ sub objectify { # turn the hashref into an object (if only we could inline in Pe
my $autoinc_id = $self->autoinc_id();
- return $self->object_class()->new( -adaptor => $self, map { ('-'.uc( ($_ eq $autoinc_id) ? 'dbID' : $_ ) => $hashref->{$_}) } keys %$hashref );
+ return $self->object_class()->new( 'adaptor' => $self, map { ( ($_ eq $autoinc_id) ? 'dbID' : $_ ) => $hashref->{$_} } keys %$hashref );
}
@@ -90,7 +90,7 @@ sub create_new {
? pop @_ # extra 'odd' parameter that would disrupt the hash integrity anyway
: 0; # do not check by default
- my $object = $self->object_class()->new( -adaptor => $self, @_ );
+ my $object = $self->object_class()->new( 'adaptor' => $self, @_ );
return $self->store( $object, $check_presence_in_db_first );
}
diff --git a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
index 48e809b98..4c95dfc41 100644
--- a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
@@ -53,46 +53,12 @@ package Bio::EnsEMBL::Hive::DataflowRule;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
-use base ( 'Bio::EnsEMBL::Hive::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);
- Function: Constructor for DataflowRule object
- Returns : Bio::EnsEMBL::Hive::DataflowRule
- Args : a rearrange-compatible hash
-
-=cut
-
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($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));
- $self->to_analysis( $toAnalysis ) if(defined($toAnalysis));
-
- # simple scalars:
- $self->from_analysis_id($from_analysis_id) if(defined($from_analysis_id));
- $self->to_analysis_url($to_analysis_url) if(defined($to_analysis_url));
- $self->branch_code($branch_code) if(defined($branch_code));
- $self->funnel_dataflow_rule_id($funnel_dataflow_rule_id) if(defined($funnel_dataflow_rule_id));
- $self->input_id_template($input_id_template) if(defined($input_id_template));
-
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
=head2 branch_code
diff --git a/modules/Bio/EnsEMBL/Hive/NakedTable.pm b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
index ca6b36737..a267e1a9a 100644
--- a/modules/Bio/EnsEMBL/Hive/NakedTable.pm
+++ b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
@@ -32,24 +32,8 @@
package Bio::EnsEMBL::Hive::NakedTable;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
-
-
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($table_name, $insertion_method) =
- rearrange([qw(table_name insertion_method) ], @_);
-
- $self->table_name($table_name) if(defined($table_name));
- $self->insertion_method($insertion_method) if(defined($insertion_method));
-
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
sub table_name {
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
index 5b0c2e48a..a26f62ebd 100644
--- a/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
@@ -495,8 +495,8 @@ sub run {
}
my ($rc, $rc_newly_created) = $resource_class_adaptor->create_new(
- defined($rc_id) ? (-DBID => $rc_id) : (),
- -NAME => $rc_name,
+ defined($rc_id) ? ('dbID' => $rc_id) : (),
+ 'name' => $rc_name,
1 # check whether this ResourceClass was already present in the database
);
$rc_id = $rc->dbID();
@@ -511,16 +511,16 @@ sub run {
$resource_param_list = [ $resource_param_list ] unless(ref($resource_param_list)); # expecting either a scalar or a 2-element array
$resource_description_adaptor->create_new(
- -resource_class_id => $rc_id,
- -meadow_type => $meadow_type,
- -submission_cmd_args => $resource_param_list->[0],
- -worker_cmd_args => $resource_param_list->[1],
+ resource_class_id => $rc_id,
+ meadow_type => $meadow_type,
+ submission_cmd_args => $resource_param_list->[0],
+ worker_cmd_args => $resource_param_list->[1],
);
}
}
unless(my $default_rc = $resource_class_adaptor->fetch_by_name('default')) {
warn "\tNB:'default' resource class is not in the database (did you forget to inherit from SUPER::resource_classes ?) - creating it for you\n";
- $resource_class_adaptor->create_new(-NAME => 'default');
+ $resource_class_adaptor->create_new('name' => 'default');
}
warn "Done.\n\n";
}
@@ -579,36 +579,36 @@ sub run {
die "'-parameters' has to be a hash" unless(ref($parameters_hash) eq 'HASH');
$analysis = Bio::EnsEMBL::Hive::Analysis->new(
- -logic_name => $logic_name,
- -module => $module,
- -parameters => $parameters_hash,
- -resource_class_id => $rc_id,
- -failed_job_tolerance => $failed_job_tolerance,
- -max_retry_count => $max_retry_count,
- -can_be_empty => $can_be_empty,
- -priority => $priority,
- -meadow_type => $meadow_type,
- -analysis_capacity => $analysis_capacity,
+ 'logic_name' => $logic_name,
+ 'module' => $module,
+ 'parameters' => $parameters_hash,
+ 'resource_class_id' => $rc_id,
+ 'failed_job_tolerance' => $failed_job_tolerance,
+ 'max_retry_count' => $max_retry_count,
+ 'can_be_empty' => $can_be_empty,
+ 'priority' => $priority,
+ 'meadow_type' => $meadow_type,
+ 'analysis_capacity' => $analysis_capacity,
);
$analysis->get_compiled_module_name(); # check if it compiles and is named correctly
$analysis_adaptor->store($analysis);
my $stats = Bio::EnsEMBL::Hive::AnalysisStats->new(
- -analysis_id => $analysis->dbID,
- -batch_size => $batch_size,
- -hive_capacity => $hive_capacity,
- -status => $blocked ? 'BLOCKED' : 'EMPTY', # be careful, as this "soft" way of blocking may be accidentally unblocked by deep sync
- -total_job_count => 0,
- -semaphored_job_count => 0,
- -ready_job_count => 0,
- -done_job_count => 0,
- -failed_job_count => 0,
- -num_running_workers => 0,
- -num_required_workers => 0,
- -behaviour => 'STATIC',
- -input_capacity => 4,
- -output_capacity => 4,
- -sync_lock => 0,
+ 'analysis_id' => $analysis->dbID,
+ 'batch_size' => $batch_size,
+ 'hive_capacity' => $hive_capacity,
+ 'status' => $blocked ? 'BLOCKED' : 'EMPTY', # be careful, as this "soft" way of blocking may be accidentally unblocked by deep sync
+ 'total_job_count' => 0,
+ 'semaphored_job_count' => 0,
+ 'ready_job_count' => 0,
+ 'done_job_count' => 0,
+ 'failed_job_count' => 0,
+ 'num_running_workers' => 0,
+ 'num_required_workers' => 0,
+ 'behaviour' => 'STATIC',
+ 'input_capacity' => 4,
+ 'output_capacity' => 4,
+ 'sync_lock' => 0,
);
$analysis_stats_adaptor->store($stats);
}
@@ -616,9 +616,9 @@ sub run {
# now create the corresponding jobs (if there are any):
if($input_ids) {
my @jobs = map { Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => undef, # these jobs are created by the initialization script, not by another job
- -analysis_id => $analysis->dbID,
- -input_id => $_, # input_ids are now centrally stringified in the AnalysisJob itself
+ 'prev_job_id' => undef, # these jobs are created by the initialization script, not by another job
+ 'analysis_id' => $analysis->dbID,
+ 'input_id' => $_, # input_ids are now centrally stringified in the AnalysisJob itself
) } @$input_ids;
$job_adaptor->store_jobs_and_adjust_counters( \@jobs );
@@ -648,8 +648,8 @@ sub run {
die "Could not fetch analysis '$condition_url' to create a control rule (in '".($analysis->logic_name)."')\n" unless defined $condition_analysis;
}
my $c_rule = Bio::EnsEMBL::Hive::AnalysisCtrlRule->new(
- -condition_analysis_url => $condition_url,
- -ctrled_analysis_id => $analysis->dbID,
+ 'condition_analysis_url' => $condition_url,
+ 'ctrled_analysis_id' => $analysis->dbID,
);
$ctrl_rule_adaptor->store( $c_rule, 1 );
@@ -704,11 +704,11 @@ sub run {
foreach my $input_id_template (@$input_id_template_list) {
my $df_rule = Bio::EnsEMBL::Hive::DataflowRule->new(
- -from_analysis => $analysis,
- -to_analysis_url => $heir_url,
- -branch_code => $branch_name_or_code,
- -input_id_template => $input_id_template,
- -funnel_dataflow_rule_id => $funnel_dataflow_rule_id,
+ 'from_analysis' => $analysis,
+ 'to_analysis_url' => $heir_url,
+ 'branch_code' => $branch_name_or_code,
+ 'input_id_template' => $input_id_template,
+ 'funnel_dataflow_rule_id' => $funnel_dataflow_rule_id,
);
$dataflow_rule_adaptor->store( $df_rule, 1 );
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
index 4756ef78a..69603215b 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
@@ -39,26 +39,9 @@ package Bio::EnsEMBL::Hive::ResourceClass;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-
-use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
- );
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($name) =
- rearrange([qw(name) ], @_);
-
- $self->name($name) if($name);
-
- return $self;
-}
-
-
sub name {
my $self = shift @_;
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
index 0bc99694c..cc247607f 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
@@ -40,26 +40,8 @@
package Bio::EnsEMBL::Hive::ResourceDescription;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-use base ( 'Bio::EnsEMBL::Hive::Storable' ); # inherit dbID(), adaptor() and new() methods
-
-
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my ($resource_class_id, $meadow_type, $submission_cmd_args, $worker_cmd_args) =
- rearrange([qw(resource_class_id meadow_type submission_cmd_args worker_cmd_args) ], @_);
-
- $self->resource_class_id($resource_class_id);
- $self->meadow_type($meadow_type);
- $self->submission_cmd_args($submission_cmd_args);
- $self->worker_cmd_args($worker_cmd_args);
-
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
sub resource_class_id {
diff --git a/modules/Bio/EnsEMBL/Hive/Storable.pm b/modules/Bio/EnsEMBL/Hive/Storable.pm
index f08d088d3..3d19da53f 100644
--- a/modules/Bio/EnsEMBL/Hive/Storable.pm
+++ b/modules/Bio/EnsEMBL/Hive/Storable.pm
@@ -44,15 +44,13 @@ package Bio::EnsEMBL::Hive::Storable;
use strict;
use warnings;
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken);
=head2 new
- Arg [-ADAPTOR] : Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor
- Arg [-dbID] : database internal id
- Caller : internal calls
+ Args : pairs of ($method_name, $value)
+ Caller : ObjectAdaptor, AnalysisJob, URLFactory.pm, HiveGeneric_conf, seed_pipeline.pl, standaloneJob.pl
Description : create a new Storable object
Returntype : Bio::EnsEMBL::Hive::Storable
Exceptions : Adaptor not a Bio::EnsEMBL::DBSQL::BaseAdaptor
@@ -61,14 +59,15 @@ use Scalar::Util qw(weaken);
=cut
sub new {
- my $caller = shift;
- my $class = ref($caller) || $caller;
+ my $class = shift @_;
my $self = bless {}, $class;
- my ($adaptor, $dbID) = rearrange(['ADAPTOR', 'dbID'], @_);
- $self->dbID( $dbID ) if defined( $dbID );
- $self->adaptor($adaptor) if defined( $adaptor );
+ while(my ($method,$value) = splice(@_,0,2)) {
+ if(defined($value)) {
+ $self->$method($value);
+ }
+ }
return $self;
}
diff --git a/modules/Bio/EnsEMBL/Hive/URLFactory.pm b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
index 3d096186a..bf8466e7a 100644
--- a/modules/Bio/EnsEMBL/Hive/URLFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
@@ -118,17 +118,17 @@ sub fetch {
} elsif($table_name eq 'accu') {
return Bio::EnsEMBL::Hive::Accumulator->new(
- -adaptor => $dba->get_AccumulatorAdaptor,
- -struct_name => $tparam_name,
- -signature_template => $tparam_value,
+ adaptor => $dba->get_AccumulatorAdaptor,
+ struct_name => $tparam_name,
+ signature_template => $tparam_value,
);
} else {
return Bio::EnsEMBL::Hive::NakedTable->new(
- -adaptor => $dba->get_NakedTableAdaptor,
- -table_name => $table_name,
- $tparam_value ? (-insertion_method => $tparam_value) : ()
+ adaptor => $dba->get_NakedTableAdaptor,
+ table_name => $table_name,
+ $tparam_value ? (insertion_method => $tparam_value) : ()
);
}
}
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index 11ef740a1..f5e1f1b47 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -74,8 +74,6 @@ package Bio::EnsEMBL::Hive::Worker;
use strict;
use POSIX;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-
use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::AnalysisStats;
use Bio::EnsEMBL::Hive::Extensions;
@@ -89,34 +87,7 @@ use Bio::EnsEMBL::Hive::Utils::RedirectStack;
use Bio::EnsEMBL::Hive::Utils::Stopwatch;
use Bio::EnsEMBL::Hive::Utils ('stringify');
-use base ( 'Bio::EnsEMBL::Hive::Storable', # inherit dbID(), adaptor() and new() methods
- );
-
-
-sub new {
- my $class = shift @_;
-
- my $self = $class->SUPER::new( @_ ); # deal with Storable stuff
-
- my($analysis_id, $meadow_type, $meadow_name, $host, $process_id, $resource_class_id, $work_done, $status, $born, $last_check_in, $died, $cause_of_death, $log_dir) =
- rearrange([qw(analysis_id meadow_type meadow_name host process_id resource_class_id work_done status born last_check_in died cause_of_death log_dir) ], @_);
-
- $self->analysis_id($analysis_id) if(defined($analysis_id));
- $self->meadow_type($meadow_type) if(defined($meadow_type));
- $self->meadow_name($meadow_name) if(defined($meadow_name));
- $self->host($host) if(defined($host));
- $self->process_id($process_id) if(defined($process_id));
- $self->resource_class_id($resource_class_id) if(defined($resource_class_id));
- $self->work_done($work_done) if(defined($work_done));
- $self->status($status) if(defined($status));
- $self->born($born) if(defined($born));
- $self->last_check_in($last_check_in) if(defined($last_check_in));
- $self->died($died) if(defined($died));
- $self->cause_of_death($cause_of_death) if(defined($cause_of_death));
- $self->log_dir($log_dir) if(defined($log_dir));
-
- return $self;
-}
+use base ( 'Bio::EnsEMBL::Hive::Storable' );
sub init {
diff --git a/scripts/seed_pipeline.pl b/scripts/seed_pipeline.pl
index 108a1ea9b..51b14d378 100755
--- a/scripts/seed_pipeline.pl
+++ b/scripts/seed_pipeline.pl
@@ -91,9 +91,9 @@ sub main {
}
my $job = Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => undef, # this job has been created by the initialization script, not by another job
- -analysis_id => $analysis->dbID,
- -input_id => destringify( $input_id ), # Make sure all job creations undergo re-stringification to avoid alternative "spellings" of the same input_id hash
+ 'prev_job_id' => undef, # this job has been created by the initialization script, not by another job
+ 'analysis_id' => $analysis->dbID,
+ 'input_id' => destringify( $input_id ), # Make sure all job creations undergo re-stringification to avoid alternative "spellings" of the same input_id hash
);
my ($job_id) = @{ $hive_dba->get_AnalysisJobAdaptor->store_jobs_and_adjust_counters( [ $job ] ) };
diff --git a/scripts/standaloneJob.pl b/scripts/standaloneJob.pl
index bfa766767..99038c82f 100755
--- a/scripts/standaloneJob.pl
+++ b/scripts/standaloneJob.pl
@@ -47,7 +47,7 @@ $runnable_object->debug($debug) if($debug);
$runnable_object->execute_writes(not $no_write);
-my $job = Bio::EnsEMBL::Hive::AnalysisJob->new( -dbID => -1 );
+my $job = Bio::EnsEMBL::Hive::AnalysisJob->new( 'dbID' => -1 );
unless($input_id) {
my ($param_hash, $param_list) = parse_cmdline_options();
$input_id = stringify($param_hash);
@@ -74,8 +74,8 @@ foreach my $branch_code (keys %$flow_into) {
foreach my $input_id_template (@$input_id_template_list) {
push @dataflow_rules, Bio::EnsEMBL::Hive::DataflowRule->new(
- -to_analysis_url => $heir_url,
- -input_id_template => $input_id_template,
+ 'to_analysis_url' => $heir_url,
+ 'input_id_template' => $input_id_template,
);
}
}
--
GitLab