diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 6ebc49b3f1c8d56cdbb851ffb09eaa14bc28443b..804cf00dd6570c0b29b457d7f31a90734572f94b 100755
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -28,9 +28,11 @@ package Bio::EnsEMBL::Hive::AnalysisJob;
use strict;
-use Bio::EnsEMBL::Analysis;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Hive::Worker;
+#use Bio::EnsEMBL::Analysis;
+#use Bio::EnsEMBL::DBSQL::DBAdaptor;
+#use Bio::EnsEMBL::Hive::Worker;
+
+use base ('Bio::EnsEMBL::Hive::Params');
sub new {
my ($class,@args) = @_;
@@ -191,6 +193,81 @@ sub incomplete { # Job should set this to 0 prior to throwing if the
##-----------------[/indicators to the Worker]-------------------------------
+
+=head2 dataflow_output_id
+
+ Title : dataflow_output_id
+ Arg[1](req) : <string> $output_id
+ Arg[2](opt) : <int> $branch_code (optional, defaults to 1)
+ Arg[3](opt) : <hashref> $create_job_options (optional, defaults to {}, options added to the CreateNewJob method)
+ Usage : $self->dataflow_output_id($output_id, $branch_code);
+ Function:
+ If a RunnableDB(Process) needs to create jobs, this allows it to have jobs
+ created and flowed through the dataflow rules of the workflow graph.
+ This 'output_id' becomes the 'input_id' of the newly created job at
+ the ends of the dataflow pipes. The optional 'branch_code' determines
+ which dataflow pipe(s) to flow the job through.
+
+=cut
+
+sub dataflow_output_id {
+ my ($self, $output_ids, $branch_code, $create_job_options) = @_;
+
+ $output_ids ||= [ $self->input_id() ]; # replicate the input_id in the branch_code's output by default
+ $output_ids = [ $output_ids ] unless(ref($output_ids) eq 'ARRAY'); # force previously used single values into an arrayref
+
+ $branch_code ||= 1; # default branch_code is 1
+ $create_job_options ||= {}; # { -block => 1 } or { -semaphore_count => scalar(@fan_job_ids) } or { -semaphored_job_id => $funnel_job_id }
+
+ # this tricky code is responsible for correct propagation of semaphores down the dataflow pipes:
+ my $propagate_semaphore = not exists ($create_job_options->{'-semaphored_job_id'}); # CONVENTION: if zero is explicitly supplied, it is a request not to propagate
+
+ # However if nothing is supplied, semaphored_job_id will be propagated from the parent job:
+ my $semaphored_job_id = $create_job_options->{'-semaphored_job_id'} ||= $self->semaphored_job_id();
+
+ # if branch_code is set to 1 (explicitly or impliticly), turn off automatic dataflow:
+ $self->autoflow(0) if($branch_code==1);
+
+ my @output_job_ids = ();
+ my $rules = $self->adaptor->db->get_DataflowRuleAdaptor->fetch_from_analysis_id_branch_code($self->analysis_id, $branch_code);
+ foreach my $rule (@{$rules}) {
+
+ my $substituted_template;
+ if(my $template = $rule->input_id_template()) {
+ $substituted_template = $self->param_substitute($template);
+ }
+
+ my $target_analysis_or_table = $rule->to_analysis();
+
+ foreach my $output_id ($substituted_template ? ($substituted_template) : @$output_ids) {
+
+ if($target_analysis_or_table->can('dataflow')) {
+
+ my $insert_id = $target_analysis_or_table->dataflow( $output_id );
+
+ } else {
+ if(my $job_id = $self->adaptor->CreateNewJob(
+ -input_id => $output_id,
+ -analysis => $target_analysis_or_table,
+ -input_job_id => $self->dbID, # creator_job's id
+ %$create_job_options
+ )) {
+ if($semaphored_job_id and $propagate_semaphore) {
+ $self->adaptor->increase_semaphore_count_for_jobid( $semaphored_job_id ); # propagate the semaphore
+ }
+ # only add the ones that were indeed created:
+ push @output_job_ids, $job_id;
+
+ } elsif($semaphored_job_id and !$propagate_semaphore) {
+ $self->adaptor->decrease_semaphore_count_for_jobid( $semaphored_job_id ); # if we didn't succeed in creating the job, fix the semaphore
+ }
+ }
+ }
+ }
+ return \@output_job_ids;
+}
+
+
sub print_job {
my $self = shift;
my $logic_name = $self->adaptor()
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index e5f20eeade62f6cb4e1ca69c5ff1ced8ec60eeb5..129686e6bde6f9245da3eaff17a2b00dae0b7bb5 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -40,7 +40,6 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use strict;
use Data::UUID;
-use Sys::Hostname;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
@@ -50,8 +49,6 @@ use Bio::EnsEMBL::Hive::Utils 'stringify'; # import 'stringify()'
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
-# our $max_retry_count = 7;
-
###############################################################################
#
# CLASS methods
diff --git a/modules/Bio/EnsEMBL/Hive/Params.pm b/modules/Bio/EnsEMBL/Hive/Params.pm
new file mode 100644
index 0000000000000000000000000000000000000000..1484e2156e86d32a630e856189984125aa4bf089
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Hive/Params.pm
@@ -0,0 +1,218 @@
+
+=pod
+
+=head1 NAME
+
+Bio::EnsEMBL::Hive::Params
+
+=head1 SYNOPSIS
+
+By inheriting from this module you make your module able to deal with parameters:
+
+ 1) parsing of parameters in the order of precedence, starting with the lowest:
+ #
+ ## general usage:
+ # $self->param_init( $lowest_precedence_hashref, $middle_precedence_hashref, $highest_precedence_hashref );
+ #
+ ## typical usage:
+ # $job->param_init(
+ # $runObj->param_defaults(), # module-wide built-in defaults have the lowest precedence (will always be the same for this module)
+ # $self->db->get_MetaContainer->get_param_hash(), # then come the pipeline-wide parameters from the 'meta' table (define things common to all modules in this pipeline)
+ # $self->analysis->parameters(), # analysis-wide 'parameters' are even more specific (can be defined differently for several occurence of the same module)
+ # $job->input_id(), # job-specific 'input_id' parameters have the highest precedence
+ # );
+
+
+ 2) reading a parameter's value
+ #
+ # my $source = $self->param('source'); )
+
+ 3) dynamically setting a parameter's value
+ #
+ # $self->param('binpath', '/software/ensembl/compara');
+ #
+ Note: It proved to be a convenient mechanism to exchange params
+ between fetch_input(), run(), write_output() and other methods.
+
+=head1 DESCRIPTION
+
+Most of Compara RunnableDB methods work under assumption
+that both analysis.parameters and analysis_job.input_id fields contain a Perl-style parameter hashref as a string.
+
+This module implements a generic param() method that allows to set parameters according to the following parameter precedence rules:
+
+ (1) Job-Specific parameters defined in analysis_job.input_id hash, they have the highest priority and override everything else.
+
+ (2) Analysis-Wide parameters defined in analysis.parameters hash. Can be overridden by (1).
+
+ (3) Pipeline-Wide parameters defined in the 'meta' table. Can be overridden by (1) and (2).
+
+ (4) Module_Defaults that are hard-coded into modules have the lowest precedence. Can be overridden by (1), (2) and (3).
+
+=head1 CONTACT
+
+ Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::Params;
+
+use strict;
+use Bio::EnsEMBL::Hive::Utils ('stringify'); # import stringify()
+
+
+=head2 param_init
+
+ Description: Parses the parameters from all sources in the reverse precedence order (supply the lowest precedence hash first).
+
+=cut
+
+sub param_init {
+
+ my $self = shift @_;
+ my $strict_hash_format = shift @_;
+
+ if( !$self->{'_param_hash'} ) {
+
+ $self->{'_param_hash'} = {};
+
+ foreach my $source (@_) {
+ if(ref($source) ne 'HASH') {
+ if($strict_hash_format or $source=~/^\{.*\}$/) {
+ my $param_hash = eval($source) || {};
+ if($@ or (ref($param_hash) ne 'HASH')) {
+ die "Expected a {'param'=>'value'} hashref, but got the following string instead: '$source'\n";
+ }
+ $source = $param_hash;
+ } else {
+ $source = {};
+ }
+ }
+ while(my ($k,$v) = each %$source ) {
+ $self->{'_param_hash'}{$k} = $v;
+ }
+ }
+ }
+}
+
+
+=head2 param
+
+ Arg [1] : string $param_name
+
+ Arg [2] : (optional) $param_value
+
+ Description: A getter/setter method for a job's parameters that are initialized through 4 levels of precedence (see param_init() )
+
+ Example 1 : my $source = $self->param('source'); # acting as a getter
+
+ Example 2 : $self->param('binpath', '/software/ensembl/compara'); # acting as a setter
+
+ Returntype : any Perl structure or object that you dared to store
+
+=cut
+
+sub param {
+ my $self = shift @_;
+
+ my $param_name = shift @_;
+ if(@_) { # If there is a value (even if undef), then set it!
+ $self->{'_param_hash'}{$param_name} = shift @_;
+ }
+
+ return $self->{'_param_hash'}{$param_name};
+}
+
+=head2 param_substitute
+
+ Arg [1] : Perl structure $string_with_templates
+
+ Description: Performs parameter substitution on strings that contain templates like " #param_name# followed by #another_param_name# " .
+
+ Returntype : *another* Perl structure with matching topology (may be more complex as a result of substituting a substructure for a term)
+
+=cut
+
+sub param_substitute {
+ my ($self, $structure) = @_;
+
+ my $type = ref($structure);
+
+ if(!$type) {
+
+ if($structure=~/^#([^#]*)#$/) { # if the given string is one complete substitution, we don't want to force the output into a string
+
+ return $self->_subst_one_hashpair($1);
+
+ } else {
+
+ $structure=~s/(?:#(.+?)#)/$self->_subst_one_hashpair($1)/eg;
+ return $structure;
+ }
+
+ } elsif($type eq 'ARRAY') {
+ my @substituted_array = ();
+ foreach my $element (@$structure) {
+ push @substituted_array, $self->param_substitute($element);
+ }
+ return \@substituted_array;
+ } elsif($type eq 'HASH') {
+ my %substituted_hash = ();
+ while(my($key,$value) = each %$structure) {
+ $substituted_hash{$self->param_substitute($key)} = $self->param_substitute($value);
+ }
+ return \%substituted_hash;
+ } else {
+ die "Could not substitute parameters in $structure";
+ }
+}
+
+
+sub mysql_conn { # an example stringification formatter (others can be defined here or in a descendent of Params)
+ my ($self, $db_conn) = @_;
+
+ return "--host=$db_conn->{-host} --port=$db_conn->{-port} --user='$db_conn->{-user}' --pass='$db_conn->{-pass}' $db_conn->{-dbname}";
+}
+
+sub mysql_dbname { # another example stringification formatter
+ my ($self, $db_conn) = @_;
+
+ return $db_conn->{-dbname};
+}
+
+sub csvq { # another example stringification formatter
+ my ($self, $list) = @_;
+
+ return join(',', map { "'$_'" } @$list);
+}
+
+#--------------------------------------------[private methods]----------------------------------------------
+
+=head2 _subst_one_hashpair
+
+ Description: this is a private method that performs one substitution. Called by param_substitute().
+
+=cut
+
+sub _subst_one_hashpair {
+ my ($self, $inside_hashes) = @_;
+
+ if($inside_hashes=~/^\w+$/) {
+
+ return $self->param($inside_hashes);
+
+ } elsif($inside_hashes=~/^(\w+):(\w+)$/) {
+
+ return $self->$1($self->param($2));
+
+ } elsif($inside_hashes=~/^expr\((.*)\)expr$/) {
+
+ my $expression = $1;
+ $expression=~s/(?:\$(\w+))/stringify($self->param($1))/eg;
+
+ return eval($expression);
+ }
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Hive/Process.pm b/modules/Bio/EnsEMBL/Hive/Process.pm
index 70589193e08a59639fe31cf7e69cf254f75e68fa..52987463c70aaac0f998f8a03ca081a99e3e2c27 100755
--- a/modules/Bio/EnsEMBL/Hive/Process.pm
+++ b/modules/Bio/EnsEMBL/Hive/Process.pm
@@ -107,6 +107,31 @@ sub new {
#
##########################################
+=head2 strict_hash_format
+
+ Title : strict_hash_format
+ Function: if a subclass wants more flexibility in parsing analysis_job.input_id and analysis.parameters,
+ it should redefine this method to return 0
+
+=cut
+
+sub strict_hash_format {
+ return 1;
+}
+
+
+=head2 param_defaults
+
+ Title : param_defaults
+ Function: sublcass can define defaults for all params used by the RunnableDB/Process
+
+=cut
+
+sub param_defaults {
+ return {};
+}
+
+
=head2 fetch_input
Title : fetch_input
@@ -270,85 +295,31 @@ sub input_job {
return $self->{'_input_job'};
}
-=head2 dataflow_output_id
- Title : dataflow_output_id
- Arg[1](req) : <string> $output_id
- Arg[2](opt) : <int> $branch_code (optional, defaults to 1)
- Arg[3](opt) : <hashref> $create_job_options (optional, defaults to {}, options added to the CreateNewJob method)
- Usage : $self->dataflow_output_id($output_id, $branch_code);
- Function:
- If Process needs to create jobs, this allows it to have jobs
- created and flowed through the dataflow rules of the workflow graph.
- This 'output_id' becomes the 'input_id' of the newly created job at
- the ends of the dataflow pipes. The optional 'branch_code' determines
- which dataflow pipe(s) to flow the job through.
+# ##################### subroutines that link through to Job's methods #########################
-=cut
+sub input_id {
+ my $self = shift;
+ return '' unless($self->input_job);
+ return $self->input_job->input_id;
+}
+
+sub param {
+ my $self = shift @_;
+
+ return $self->input_job->param(@_);
+}
+
+sub param_substitute {
+ my $self = shift @_;
+
+ return $self->input_job->param_substitute(@_);
+}
sub dataflow_output_id {
- my ($self, $output_ids, $branch_code, $create_job_options) = @_;
-
- return unless($self->analysis);
- return unless($self->input_job);
-
- $output_ids ||= [ $self->input_id() ]; # replicate the input_id in the branch_code's output by default
- $output_ids = [ $output_ids ] unless(ref($output_ids) eq 'ARRAY'); # force previously used single values into an arrayref
-
- $branch_code ||= 1; # default branch_code is 1
- $create_job_options ||= {}; # { -block => 1 } or { -semaphore_count => scalar(@fan_job_ids) } or { -semaphored_job_id => $funnel_job_id }
-
- # this tricky code is responsible for correct propagation of semaphores down the dataflow pipes:
- my $propagate_semaphore = not exists ($create_job_options->{'-semaphored_job_id'}); # CONVENTION: if zero is explicitly supplied, it is a request not to propagate
-
- # However if nothing is supplied, semaphored_job_id will be propagated from the parent job:
- my $semaphored_job_id = $create_job_options->{'-semaphored_job_id'} ||= $self->input_job->semaphored_job_id();
-
- # if branch_code is set to 1 (explicitly or impliticly), turn off automatic dataflow:
- $self->input_job->autoflow(0) if($branch_code==1);
-
- my @output_job_ids = ();
- my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
- my $rules = $self->db->get_DataflowRuleAdaptor->fetch_from_analysis_id_branch_code($self->analysis->dbID, $branch_code);
- foreach my $rule (@{$rules}) {
-
- my $substituted_template;
- if(my $template = $rule->input_id_template()) {
- if($self->can('param_substitute')) {
- $substituted_template = $self->param_substitute($template);
- } else {
- die "In order to use input_id_template your RunnableDB has to be derived from Bio::EnsEMBL::Hive::ProcessWithParams\n";
- }
- }
-
- my $target_analysis_or_table = $rule->to_analysis();
-
- foreach my $output_id ($substituted_template ? ($substituted_template) : @$output_ids) {
-
- if($target_analysis_or_table->can('dataflow')) {
-
- my $insert_id = $target_analysis_or_table->dataflow( $output_id );
-
- } else {
- if(my $job_id = Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob(
- -input_id => $output_id,
- -analysis => $target_analysis_or_table,
- -input_job_id => $self->input_job->dbID, # creator_job's id
- %$create_job_options
- )) {
- if($semaphored_job_id and $propagate_semaphore) {
- $job_adaptor->increase_semaphore_count_for_jobid( $semaphored_job_id ); # propagate the semaphore
- }
- # only add the ones that were indeed created:
- push @output_job_ids, $job_id;
-
- } elsif($semaphored_job_id and !$propagate_semaphore) {
- $job_adaptor->decrease_semaphore_count_for_jobid( $semaphored_job_id ); # if we didn't succeed in creating the job, fix the semaphore
- }
- }
- }
- }
- return \@output_job_ids;
+ my $self = shift @_;
+
+ return $self->input_job->dataflow_output_id(@_);
}
@@ -432,12 +403,6 @@ sub worker_temp_directory {
#
#################################################
-sub input_id {
- my $self = shift;
- return '' unless($self->input_job);
- return $self->input_job->input_id;
-}
-
sub parameters {
my $self = shift;
return '' unless($self->analysis);
@@ -526,4 +491,3 @@ sub check_if_exit_cleanly {
1;
-
diff --git a/modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm b/modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm
index cbf272cf870bb63f5aa022c7a805d77b340d679c..a1b23e78322d2893e5c7339799503f6964ce4b94 100644
--- a/modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm
+++ b/modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm
@@ -1,49 +1,13 @@
=pod
-=head1 NAME
+=head1 OBSOLETE CLASS
Bio::EnsEMBL::Hive::ProcessWithParams
=head1 SYNOPSIS
-This module extends Bio::EnsEMBL::Hive::Process by implementing the following capabilities:
-
- 1) parsing of parameters in the right order of precedence (including built-in defaults, if supplied).
- This parsing happens automatically and in most cases you should not need to activate it.
- However you may want to provide built-in defaults for your RunnableDB
- by defining your own param_defaults() method that returns a hashref.
-
- 2) reading a parameter's value
- #
- # my $source = $self->param('source'); )
-
- 3) dynamically setting a parameter's value
- #
- # $self->param('binpath', '/software/ensembl/compara');
- #
- Note: It proved to be a convenient mechanism to exchange params
- between fetch_input(), run(), write_output() and other methods.
-
-=head1 DESCRIPTION
-
-Most of Compara RunnableDB methods work under assumption
-that both analysis.parameters and analysis_job.input_id fields contain a Perl-style parameter hashref as a string.
-
-This module extends Bio::EnsEMBL::Hive::Process by implementing a generic param() method that sets module parameters
-accorting to the following parameter precedence rules:
-
- (1) Job-Specific parameters defined in analysis_job.input_id hash, they have the highest priority and override everything else.
-
- (2) Analysis-Wide parameters defined in analysis.parameters hash. Can be overridden by (1).
-
- (3) Pipeline-Wide parameters defined in the 'meta' table. Can be overridden by (1) and (2).
-
- (4) Module_Defaults that are hard-coded into modules have the lowest precedence. Can be overridden by (1), (2) and (3).
-
-=head1 CONTACT
-
- Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+This module is scheduled for removal. Please use Bio::EnsEMBL::Hive::Process instead.
=cut
@@ -51,205 +15,6 @@ accorting to the following parameter precedence rules:
package Bio::EnsEMBL::Hive::ProcessWithParams;
use strict;
-use Bio::EnsEMBL::Hive::Utils ('stringify'); # import stringify()
-
use base ('Bio::EnsEMBL::Hive::Process');
-
-=head2 strict_hash_format
-
- Description: This public virtual method should either return 1 or 0, depending on whether it is expected that input_id() and parameters() contain a hashref or not
-
- Callers : Bio::EnsEMBL::Hive::RunnableDB::ProcessWithParams
-
-=cut
-
-sub strict_hash_format { # This public virtual must be redefined to "return 0;" in all inheriting classes
- # that want more flexibility for the format of parameters() or input_id()
- return 1;
-}
-
-
-=head2 param_defaults
-
- Description: This public virtual method should return a hash of param defaults of the RunnableDB
-
- Callers : Bio::EnsEMBL::Hive::RunnableDB::ProcessWithParams
-
-=cut
-
-sub param_defaults {
-
- return {};
-}
-
-
-=head2 param_init
-
- Description: Parses the parameters from all sources in the correct precedence order.
-
-=cut
-
-sub param_init { # will run automatically on the first execution of $self->param()
-
- my $self = shift @_;
-
- if( !$self->{'_param_hash'} ) {
-
- my $defaults_hash = $self->param_defaults(); # module-wide built-in defaults have the lowest precedence (will always be the same for this module)
-
- my $meta_params_hash = $self->db->get_MetaContainer->get_param_hash(); # then come the pipeline-wide parameters from the 'meta' table (define things common to all modules in this pipeline)
-
- my $parameters_hash = $self->_parse_string( $self->parameters() ); # analysis-wide 'parameters' are even more specific (can be defined differently for several occurence of the same module)
-
- my $input_id_hash = $self->_parse_string( $self->input_id() ); # job-specific 'input_id' parameters have the highest precedence
-
- $self->{'_param_hash'} = { %$defaults_hash, %$meta_params_hash, %$parameters_hash, %$input_id_hash };
- }
-}
-
-
-=head2 param
-
- Arg [1] : string $param_name
-
- Arg [2] : (optional) $param_value
-
- Description: A getter/setter method for a job's parameters that are initialized through 4 levels of precedence (see param_init() )
-
- Example 1 : my $source = $self->param('source'); # acting as a getter
-
- Example 2 : $self->param('binpath', '/software/ensembl/compara'); # acting as a setter
-
- Returntype : any Perl structure or object that you dared to store
-
-=cut
-
-sub param {
- my $self = shift @_;
-
- $self->param_init(); # normally will only run on the first execution
-
- my $param_name = shift @_;
- if(@_) { # If there is a value (even if undef), then set it!
- $self->{'_param_hash'}{$param_name} = shift @_;
- }
-
- return $self->{'_param_hash'}{$param_name};
-}
-
-=head2 param_substitute
-
- Arg [1] : Perl structure $string_with_templates
-
- Description: Performs parameter substitution on strings that contain templates like " #param_name# followed by #another_param_name# " .
-
- Returntype : *another* Perl structure with matching topology (may be more complex as a result of substituting a substructure for a term)
-
-=cut
-
-sub param_substitute {
- my ($self, $structure) = @_;
-
- my $type = ref($structure);
-
- if(!$type) {
-
- if($structure=~/^#([^#]*)#$/) { # if the given string is one complete substitution, we don't want to force the output into a string
-
- return $self->_subst_one_hashpair($1);
-
- } else {
-
- $structure=~s/(?:#(.+?)#)/$self->_subst_one_hashpair($1)/eg;
- return $structure;
- }
-
- } elsif($type eq 'ARRAY') {
- my @substituted_array = ();
- foreach my $element (@$structure) {
- push @substituted_array, $self->param_substitute($element);
- }
- return \@substituted_array;
- } elsif($type eq 'HASH') {
- my %substituted_hash = ();
- while(my($key,$value) = each %$structure) {
- $substituted_hash{$self->param_substitute($key)} = $self->param_substitute($value);
- }
- return \%substituted_hash;
- } else {
- die "Could not substitute parameters in $structure";
- }
-}
-
-
-sub mysql_conn { # an example stringification formatter (others can be defined here, in a descendent of ProcessWithParams, or in the Runnable)
- my ($self, $db_conn) = @_;
-
- return "--host=$db_conn->{-host} --port=$db_conn->{-port} --user='$db_conn->{-user}' --pass='$db_conn->{-pass}' $db_conn->{-dbname}";
-}
-
-sub mysql_dbname { # another example stringification formatter
- my ($self, $db_conn) = @_;
-
- return $db_conn->{-dbname};
-}
-
-sub csvq { # another example stringification formatter
- my ($self, $list) = @_;
-
- return join(',', map { "'$_'" } @$list);
-}
-
-#--------------------------------------------[private methods]----------------------------------------------
-
-=head2 _subst_one_hashpair
-
- Description: this is a private method that performs one substitution. Called by param_substitute().
-
-=cut
-
-sub _subst_one_hashpair {
- my ($self, $inside_hashes) = @_;
-
- if($inside_hashes=~/^\w+$/) {
-
- return $self->param($inside_hashes);
-
- } elsif($inside_hashes=~/^(\w+):(\w+)$/) {
-
- return $self->$1($self->param($2));
-
- } elsif($inside_hashes=~/^expr\((.*)\)expr$/) {
-
- my $expression = $1;
- $expression=~s/(?:\$(\w+))/stringify($self->param($1))/eg;
-
- return eval($expression);
- }
-}
-
-
-=head2 _parse_string
-
- Description: this is a private method that deals with parsing of parameters out of strings.
-
-=cut
-
-sub _parse_string {
- my ($self, $string) = @_;
-
- if($self->strict_hash_format() or $string=~/^\{.*\}$/) {
- my $param_hash = eval($string) || {};
- if($@ or (ref($param_hash) ne 'HASH')) {
- die "The module '".ref($self)."' for analysis '".$self->analysis->logic_name()
- ."' assumes both analysis.parameters and analysis_job.input_id should evaluate into a {'param'=>'value'} hashref."
- ." The current value is '$string'\n";
- }
- return $param_hash;
- } else {
- return {};
- }
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
index 42dbb7ef9cc5fe1f85c0d3bc865b4b1c9d27d642..bfc026658ec9f69d75d48c286ad6fd274a933ec6 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
@@ -50,7 +50,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::FailureTest;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
BEGIN {
# die "Could not compile this nonsense!";
@@ -58,7 +58,7 @@ BEGIN {
=head2 param_defaults
- Description : Implements param_defaults() interface method of Bio::EnsEMBL::Hive::ProcessWithParams that defines module defaults for parameters.
+ Description : Implements param_defaults() interface method of Bio::EnsEMBL::Hive::Process that defines module defaults for parameters.
=cut
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
index 2ae2db903e7c47e46ded2cd7a5224e3eb3bc077f..57da44d597e9b207e90c6f6f3157037dad6b3ee9 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
@@ -42,7 +42,7 @@ use strict;
use DBI;
use Bio::EnsEMBL::Hive::Utils ('dir_revhash'); # import dir_revhash
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
index 8a35ea8dbca16368d0e303e641682dbe513301fd..196f074d6e0fa5264e6f9a4181eba1c63425a4bf 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
@@ -21,7 +21,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
index 13f7489f1e6dc25c97cdc7ebd7899b1167db3d83..73045d84434fc35de670933293c9cc6c1684a8a5 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
@@ -21,7 +21,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/SemaStart.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/SemaStart.pm
index 60f43f898b282539b4297dbf1459ac47e1d4e3c0..cf48aa4dad1c06b308af99b56375737e3ab1e48f 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/SemaStart.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/SemaStart.pm
@@ -27,7 +27,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::LongMult::SemaStart;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
index 16be1d38b50cb3f524a4cf44027e63ab5aa23257..a2c404177c9dc742fad10c590ce8ad8ee799e3fe 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm
@@ -26,7 +26,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::LongMult::Start;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
index ad77a185e460f3bce1fd7a1cf740f6a78902e2a1..9d3e06c6f9d04b40cb3bcb8cdafd502bf382eff6 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
@@ -34,7 +34,7 @@ package Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 fetch_input
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
index 31a16995a16ece8299dce53bb82d7086aebe6461..9dd6b77131c8b1891ec552c3e881506ec12fb48e 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
@@ -42,11 +42,11 @@ package Bio::EnsEMBL::Hive::RunnableDB::SqlCmd;
use strict;
use DBI;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 strict_hash_format
- Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::ProcessWithParams that is used to set the strictness level of the parameters' parser.
+ Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::Process that is used to set the strictness level of the parameters' parser.
Here we return 0 in order to indicate that neither input_id() nor parameters() is required to contain a hash.
=cut
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
index dcb7e3ff3950321f99fee3ea17b60c3bb588a494..0c279744e7fed51c7aca0ee56cba5fa64024d7f0 100755
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
@@ -38,11 +38,11 @@ The command can be given using two different syntaxes:
package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
use strict;
-use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
+use base ('Bio::EnsEMBL::Hive::Process');
=head2 strict_hash_format
- Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::ProcessWithParams that is used to set the strictness level of the parameters' parser.
+ Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::Process that is used to set the strictness level of the parameters' parser.
Here we return 0 in order to indicate that neither input_id() nor parameters() is required to contain a hash.
=cut
diff --git a/modules/Bio/EnsEMBL/Hive/Utils.pm b/modules/Bio/EnsEMBL/Hive/Utils.pm
index 0aec846f587f403b8c39257dc7ab94edaa2743ce..723b3614c67344ca36a0cba119f1b54e19e8c70d 100755
--- a/modules/Bio/EnsEMBL/Hive/Utils.pm
+++ b/modules/Bio/EnsEMBL/Hive/Utils.pm
@@ -75,7 +75,7 @@ sub stringify {
If it seems to contain a hash/array/quoted_string, the contents is evaluated, otherwise it is returned "as is".
This function is mainly used to read values from 'meta' table that may represent Perl structures, but generally don't have to.
- Callers : Bio::EnsEMBL::Hive::ProcessWithParams # destringification of general 'meta' params
+ Callers : Bio::EnsEMBL::Hive::DBSQL::MetaContainer # destringification of general 'meta' params
beekeeper.pl script # destringification of the 'pipeline_name' meta param
=cut
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index a456d07cb8e39e9e412cd4e8fbb1b22c67c1e254..064050b519aaf3940eeddcd1e0aa9872cbe1f6ea 100755
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -647,7 +647,6 @@ sub run_module_with_job {
my $native_hive_process = $runObj->isa("Bio::EnsEMBL::Hive::Process");
my $job_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new()->restart();
-
$self->queen->dbc->query_count(0);
#pass the input_id from the job into the Process object
@@ -656,7 +655,10 @@ sub run_module_with_job {
$runObj->queen($self->queen);
$runObj->worker($self);
$runObj->debug($self->debug);
+
$job->autoflow(1);
+ $job->param_init( $runObj->strict_hash_format(), $runObj->param_defaults(), $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() );
+
} else {
$runObj->input_id($job->input_id);
$runObj->db($self->db);