some methods moved into proper Adaptors (extending the Core adaptors)

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm

+=pod
+
+=head1 NAME
+
+  Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor
+
+=head1 SYNOPSIS
+
+  $analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
+
+=head1 DESCRIPTION
+
+  This module extends EnsEMBL Core's AnalysisAdaptor, adding some Hive-specific stuff.
+
+=head1 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
+
+use strict;
+
+use base ('Bio::EnsEMBL::DBSQL::AnalysisAdaptor');
+
+
+=head2 fetch_by_logic_name_or_url
+
+    Description: given a URL gets the analysis from URLFactory, otherwise fetches it from the db
+
+=cut
+
+sub fetch_by_logic_name_or_url {
+    my $self                = shift @_;
+    my $logic_name_or_url   = shift @_;
+
+    if($logic_name_or_url =~ m{^\w+://}) {
+        return Bio::EnsEMBL::Hive::URLFactory->fetch($logic_name_or_url, $self->db);
+    } else {
+        return $self->fetch_by_logic_name($logic_name_or_url);
+    }
+}
+
+
+=head2 fetch_by_url_query
+
+    Description: fetches the analysis either by logic_name or by dbID (either coming from the tail of the URL)
+
+=cut
+
+sub fetch_by_url_query {
+    my ($self, $field_name, $field_value) = @_;
+
+    if(!$field_name or !$field_value) {
+
+        return;
+
+    } elsif($field_name eq 'logic_name') {
+
+        return $self->fetch_by_logic_name($field_value);
+
+    } elsif($field_name eq 'dbID') {
+
+        return $self->fetch_by_dbID($field_value);
+
+    }
+}
+
+
+1;

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -41,17 +41,19 @@ use Bio::EnsEMBL::DBSQL::DBConnection;
 use base ('Bio::EnsEMBL::DBSQL::DBAdaptor');
 
 
-sub get_Queen {
-  my $self = shift;
-
-  return $self->get_QueenAdaptor();
-}
+#sub get_Queen {
+#  my $self = shift;
+#
+#  return $self->get_QueenAdaptor();
+#}
 
 sub get_available_adaptors {
  
     my %pairs =  (
-        'MetaContainer'       => 'Bio::EnsEMBL::DBSQL::MetaContainer',
-        'Analysis'            => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor',
+            # Core adaptors extended with Hive stuff:
+        'MetaContainer'       => 'Bio::EnsEMBL::Hive::DBSQL::MetaContainer',
+        'Analysis'            => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
+            # Hive adaptors:
         'Queen'               => 'Bio::EnsEMBL::Hive::Queen',
         'AnalysisJob'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
         'AnalysisData'        => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
@@ -66,4 +68,3 @@ sub get_available_adaptors {
 }
  
 1;
-

modules/Bio/EnsEMBL/Hive/DBSQL/MetaContainer.pm

+=pod
+
+=head1 NAME
+
+  Bio::EnsEMBL::Hive::DBSQL::MetaContainer
+
+=head1 SYNOPSIS
+
+  $meta_container = $db_adaptor->get_MetaContainer;
+
+=head1 DESCRIPTION
+
+  This module extends EnsEMBL Core's MetaContainer, adding some Hive-specific stuff.
+
+=head1 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::DBSQL::MetaContainer;
+
+use strict;
+use Bio::EnsEMBL::Hive::Utils ('destringify');  # import both functions
+
+use base ('Bio::EnsEMBL::DBSQL::MetaContainer');
+
+=head2 get_param_hash
+
+    Description: returns the content of the 'meta' table as a hash
+
+=cut
+
+sub get_param_hash {
+    my $self = shift @_;
+
+    my %meta_params_hash = ();
+
+        # Here we are assuming that meta_keys are unique.
+        # If they are not, you'll be getting the value with the highest meta_id.
+        #
+    my $sth = $self->prepare("SELECT meta_key, meta_value FROM meta ORDER BY meta_id");
+    $sth->execute();
+    while (my ($meta_key, $meta_value)=$sth->fetchrow_array()) {
+
+        $meta_params_hash{$meta_key} = destringify($meta_value);
+    }
+    $sth->finish();
+
+    return \%meta_params_hash;
+}
+
+1;

modules/Bio/EnsEMBL/Hive/Extensions.pm

@@ -32,7 +32,6 @@ use strict;
 use Bio::EnsEMBL::Utils::Exception;
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::DBSQL::DBConnection;
-use Bio::EnsEMBL::DBSQL::AnalysisAdaptor;
 use Bio::EnsEMBL::Hive::URLFactory;
 #use Bio::EnsEMBL::Pipeline::RunnableDB;
 #use Bio::EnsEMBL::Analysis::RunnableDB;
@@ -130,35 +129,6 @@ sub Bio::EnsEMBL::Analysis::url
   return $url;  
 }
 
-sub Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_logic_name_or_url {
-    my $self                = shift @_;
-    my $logic_name_or_url   = shift @_;
-
-    if($logic_name_or_url =~ m{^\w+://}) {
-        return Bio::EnsEMBL::Hive::URLFactory->fetch($logic_name_or_url, $self->db);
-    } else {
-        return $self->fetch_by_logic_name($logic_name_or_url);
-    }
-}
-
-sub Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_url_query {
-    my ($self, $field_name, $field_value) = @_;
-
-    if(!$field_name or !$field_value) {
-
-        return;
-
-    } elsif($field_name eq 'logic_name') {
-
-        return $self->fetch_by_logic_name($field_value);
-
-    } elsif($field_name eq 'dbID') {
-
-        return $self->fetch_by_dbID($field_value);
-
-    }
-}
-
 
 =head2 Bio::EnsEMBL::Analysis::stats
 

modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm

@@ -54,6 +54,7 @@ package Bio::EnsEMBL::Hive::ProcessWithParams;
 
 use strict;
 use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');  # import both functions
+
 use base ('Bio::EnsEMBL::Hive::Process');
 
 
@@ -91,11 +92,11 @@ sub param_init {    # normally will run automatically on the first execution of
 
         my $defaults_hash    = scalar(@_) ? { @_ } : {};            # module-wide built-in defaults have the lowest precedence (will always be the same for this module)
 
-        my $meta_params_hash = $self->_parse_meta();                # then come the pipeline-wide parameters from the 'meta' table (define things common to all modules in this pipeline)
+        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('parameters');  # analysis-wide 'parameters' are even more specific (can be defined differently for several occurence of the same module)
+        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('input_id');    # job-specific 'input_id' parameters have the highest precedence
+        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 };
     }
@@ -222,15 +223,13 @@ sub csvq { # another example stringification formatter
 =cut
 
 sub _parse_string {
-    my ($self, $method) = @_;
-
-    my $string = $self->$method();
+    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 analysis.$method should evaluate into a {'param'=>'value'} hashref."
+                ."' assumes both analysis.parameters and analysis_job.input_id should evaluate into a {'param'=>'value'} hashref."
                 ." The current value is '$string'\n";
         }
         return $param_hash;
@@ -239,29 +238,4 @@ sub _parse_string {
     }
 }
 
-=head2 _parse_meta
-    
-    Description: this is a private method that deals with parsing of parameters out of 'meta' table.
-
-=cut
-
-sub _parse_meta {            # Unfortunately, MetaContainer is useless for us, as we need to load all the parameters in one go
-    my $self = shift @_;
-
-    my %meta_params_hash = ();
-
-        # Here we are assuming that meta_keys are unique.
-        # If they are not, you'll be getting the value with the highest meta_id.
-        #
-    my $sth = $self->db->dbc()->prepare("SELECT meta_key, meta_value FROM meta ORDER BY meta_id");
-    $sth->execute();
-    while (my ($meta_key, $meta_value)=$sth->fetchrow_array()) {
-
-        $meta_params_hash{$meta_key} = destringify($meta_value);
-    }
-    $sth->finish();
-
-    return \%meta_params_hash;
-}
-
 1;