new 'hive_meta' table to keep hive_sql_schema_version (=number of patches),...

new 'hive_meta' table to keep hive_sql_schema_version (=number of patches), hive_pipeline_name and hive_use_triggers

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

@@ -71,7 +71,7 @@ sub hive_use_triggers {  # getter only, not setter
     my $self = shift @_;
 
     unless( defined($self->{'_hive_use_triggers'}) ) {
-        my ($hive_use_triggers) = @{ $self->get_MetaContainer->list_value_by_key( 'hive_use_triggers' ) };
+        my $hive_use_triggers = $self->get_MetaAdaptor->fetch_by_meta_key( 'hive_use_triggers' );
         $self->{'_hive_use_triggers'} = $hive_use_triggers || 0;
     } 
     return $self->{'_hive_use_triggers'};
@@ -82,23 +82,24 @@ sub get_available_adaptors {
  
     my %pairs =  (
             # Core adaptors extended with Hive stuff:
-        'MetaContainer'       => 'Bio::EnsEMBL::Hive::DBSQL::MetaContainer',
+        'MetaContainer'         => 'Bio::EnsEMBL::Hive::DBSQL::MetaContainer',
 
             # "new" Hive adaptors (sharing the same fetching/storing code inherited from the BaseAdaptor class) :
-        'AnalysisCtrlRule'    => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor',
-        'DataflowRule'        => 'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor',
-        'ResourceDescription' => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
-        'ResourceClass'       => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
-        'LogMessage'          => 'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor',
-        'NakedTable'          => 'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor',
-        'Analysis'            => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
-        'Queen'               => 'Bio::EnsEMBL::Hive::Queen',
-        'AnalysisData'        => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
+        'AnalysisCtrlRule'      => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor',
+        'DataflowRule'          => 'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor',
+        'ResourceDescription'   => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
+        'ResourceClass'         => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
+        'LogMessage'            => 'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor',
+        'NakedTable'            => 'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor',
+        'Analysis'              => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
+        'Queen'                 => 'Bio::EnsEMBL::Hive::Queen',
+        'AnalysisData'          => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
+        'Accumulator'           => 'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor',
+        'Meta'                  => 'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor',
 
             # "old" Hive adaptors (having their own fetching/storing code) :
-        'AnalysisJob'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
-        'AnalysisStats'       => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor',
-        'Accumulator'         => 'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor',
+        'AnalysisJob'           => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
+        'AnalysisStats'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor',
     );
     return \%pairs;
 }

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

+=pod
+
+=head1 NAME
+
+    Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor
+
+=head1 SYNOPSIS
+
+    $dba->get_MetaAdaptor->store( \@rows );
+
+=head1 DESCRIPTION
+
+    This is currently an "objectless" adaptor for storing and fetching metadata
+
+=head1 CONTACT
+
+    Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+
+package Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor;
+
+use strict;
+
+use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
+
+
+sub default_table_name {
+    return 'hive_meta';
+}
+
+
+sub store_pair {
+    my ($self, $meta_key, $meta_value) = @_;
+
+    return $self->store( { 'meta_key' => $meta_key, 'meta_value' => $meta_value } );
+}
+
+1;
+

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -150,7 +150,6 @@ sub pipeline_create_commands {
 sub pipeline_wide_parameters {
     my ($self) = @_;
     return {
-        'pipeline_name'  => $self->o('pipeline_name'),       # name the pipeline to differentiate the submitted processes
     };
 }
 
@@ -205,6 +204,14 @@ sub beekeeper_extra_cmdline_options {
 # ---------------------------------[now comes the interfacing stuff - feel free to call but not to modify]--------------------
 
 
+sub hive_meta_table {
+    my ($self) = @_;
+
+    return {
+        'hive_pipeline_name' => $self->o('pipeline_name'),
+    };
+}
+
 sub pre_options {
     my $self = shift @_;
 
@@ -326,7 +333,7 @@ sub process_options {
     $self->{'_extra_options'} = $self->load_cmdline_options( $self->pre_options() );
     $self->root()->{'pipeline_db'}{'-driver'} = $self->{'_extra_options'}{'hive_driver'} || 'mysql';
 
-    $self->use_cases( [ 'pipeline_create_commands', 'pipeline_wide_parameters', 'resource_classes', 'pipeline_analyses', 'beekeeper_extra_cmdline_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();
 }
 
@@ -359,7 +366,14 @@ sub run {
     my $resource_class_adaptor       = $hive_dba->get_ResourceClassAdaptor;
     
     unless($job_topup) {
-        my $meta_container = $hive_dba->get_MetaContainer;
+        my $meta_adaptor = $hive_dba->get_MetaAdaptor;      # the new adaptor for 'hive_meta' table
+        warn "Loading hive_meta table ...\n";
+        my $hive_meta_table = $self->hive_meta_table;
+        while( my($meta_key, $meta_value) = each %$hive_meta_table ) {
+            $meta_adaptor->store_pair( $meta_key, $meta_value );
+        }
+
+        my $meta_container = $hive_dba->get_MetaContainer;  # adaptor over core's 'meta' table for compatibility with core API
         warn "Loading pipeline-wide parameters ...\n";
 
         my $pipeline_wide_parameters = $self->pipeline_wide_parameters;

scripts/beekeeper.pl

@@ -143,10 +143,7 @@ sub main {
 
     my $queen = $self->{'dba'}->get_Queen;
 
-    my $pipeline_name = destringify(
-            $self->{'dba'}->get_MetaContainer->list_value_by_key("pipeline_name")->[0]
-         || $self->{'dba'}->get_MetaContainer->list_value_by_key("name")->[0]
-    );
+    my $pipeline_name = $self->{'dba'}->get_MetaAdaptor->fetch_by_meta_key( 'hive_pipeline_name' );
 
     unless($pipeline_name) {
         print STDERR "+---------------------------------------------------------------------+\n";

sql/patch_2013-06-25.sql

+    -- create a new, hive-specific table for meta data and start using it for hive_sql_schema_version tracking:
+
+CREATE TABLE hive_meta (
+    meta_key                VARCHAR(80) NOT NULL PRIMARY KEY,
+    meta_value              TEXT
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
+    -- INSERT the 'hive_sql_schema_version' for the first time, then keep UPDATE'ing
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_sql_schema_version', '49');
+
+    -- move 'hive_use_triggers' into hive_meta:
+INSERT IGNORE INTO hive_meta (meta_key, meta_value) SELECT 'hive_use_triggers', COALESCE(MIN(REPLACE(meta_value, '"', '')), 0) FROM meta WHERE meta_key='hive_use_triggers';
+
+    -- move 'pipeline_name' into hive_meta and rename it into 'hive_pipeline_name':
+INSERT IGNORE INTO hive_meta (meta_key, meta_value) SELECT 'hive_pipeline_name', REPLACE(meta_value,'"','') FROM meta WHERE meta_key='pipeline_name' or meta_key='name';
+

sql/tables.mysql

@@ -356,6 +356,25 @@ CREATE TABLE analysis_data (
 ) COLLATE=latin1_swedish_ci ENGINE=InnoDB;
 
 
+/**
+@table  hive_meta
+
+@colour #000000
+
+@desc This table keeps several important hive-specific pipeline-wide key-value pairs
+        such as hive_sql_schema_version, hive_use_triggers and hive_pipeline_name.
+
+@column meta_key        the KEY of KEY-VALUE pairs (primary key)
+@column meta_value      the VALUE of KEY-VALUE pairs
+*/
+
+CREATE TABLE hive_meta (
+    meta_key                VARCHAR(80) NOT NULL PRIMARY KEY,
+    meta_value              TEXT
+
+) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+
+
 /**
 @table  meta
 
@@ -366,8 +385,7 @@ CREATE TABLE analysis_data (
          if we are dealing with core-hive hybrid that is created in the wrong order.
         At the moment meta table is used
             (1) for compatibility with the Core API ('schema_version'),
-            (2) to keep some Hive-specific meta-information ('pipeline_name') and
-            (3) to keep pipeline-wide parameters.
+            (2) to keep pipeline-wide parameters.
 
 @column meta_id         auto-incrementing primary key, not really used per se
 @column species_id      always 1, kept for compatibility with the Core API
@@ -571,6 +589,9 @@ CREATE TABLE monitor (
 ) COLLATE=latin1_swedish_ci ENGINE=InnoDB;
 
 
--- Auto add schema version to database (should be overridden by Compara's table.sql)
+-- Auto add core schema_version to core meta table - for compatibility with core API. Could be overridden by Compara's table.sql
 INSERT IGNORE INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'schema_version', '72');
 
+-- Auto add hive_sql_schema_version to hive_meta table
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_sql_schema_version', '49');
+

sql/tables.pgsql

@@ -359,6 +359,25 @@ CREATE TABLE analysis_data (
 CREATE INDEX ON analysis_data (data);
 
 
+/**
+@table  hive_meta
+
+@colour #000000
+
+@desc This table keeps several important hive-specific pipeline-wide key-value pairs
+        such as hive_sql_schema_version, hive_use_triggers and hive_pipeline_name.
+
+@column meta_key        the KEY of KEY-VALUE pairs (primary key)
+@column meta_value      the VALUE of KEY-VALUE pairs
+*/
+
+CREATE TABLE hive_meta (
+    meta_key                VARCHAR(80) NOT NULL PRIMARY KEY,
+    meta_value              TEXT
+
+);
+
+
 /**
 @table  meta
 
@@ -369,8 +388,7 @@ CREATE INDEX ON analysis_data (data);
          if we are dealing with core-hive hybrid that is created in the wrong order.
         At the moment meta table is used
             (1) for compatibility with the Core API ('schema_version'),
-            (2) to keep some Hive-specific meta-information ('pipeline_name') and
-            (3) to keep pipeline-wide parameters.
+            (2) to keep pipeline-wide parameters.
 
 @column meta_id         auto-incrementing primary key, not really used per se
 @column species_id      always 1, kept for compatibility with the Core API
@@ -573,6 +591,9 @@ CREATE TABLE monitor (
 );
 
 
--- Auto add schema version to database (should be overridden by Compara's table.sql)
+-- Auto add core schema_version to core meta table - for compatibility with core API. Could be overridden by Compara's table.sql
 INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'schema_version', '72');
 
+-- Auto add hive_sql_schema_version to hive_meta table
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_sql_schema_version', '49');
+

sql/tables.sqlite

@@ -350,6 +350,25 @@ CREATE TABLE analysis_data (
 CREATE        INDEX analysis_data_idx ON analysis_data (data);
 
 
+/**
+@table  hive_meta
+
+@colour #000000
+
+@desc This table keeps several important hive-specific pipeline-wide key-value pairs
+        such as hive_sql_schema_version, hive_use_triggers and hive_pipeline_name.
+
+@column meta_key        the KEY of KEY-VALUE pairs (primary key)
+@column meta_value      the VALUE of KEY-VALUE pairs
+*/
+
+CREATE TABLE hive_meta (
+    meta_key                VARCHAR(80) NOT NULL PRIMARY KEY,
+    meta_value              TEXT
+
+);
+
+
 /**
 @table  meta
 
@@ -360,8 +379,7 @@ CREATE        INDEX analysis_data_idx ON analysis_data (data);
          if we are dealing with core-hive hybrid that is created in the wrong order.
         At the moment meta table is used
             (1) for compatibility with the Core API ('schema_version'),
-            (2) to keep some Hive-specific meta-information ('pipeline_name') and
-            (3) to keep pipeline-wide parameters.
+            (2) to keep pipeline-wide parameters.
 
 @column meta_id         auto-incrementing primary key, not really used per se
 @column species_id      always 1, kept for compatibility with the Core API
@@ -559,6 +577,9 @@ CREATE TABLE monitor (
 );
 
 
--- Auto add schema version to database (should be overridden by Compara's table.sql)
+-- Auto add core schema_version to core meta table - for compatibility with core API. Could be overridden by Compara's table.sql
 INSERT OR IGNORE INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'schema_version', '72');
 
+-- Auto add hive_sql_schema_version to hive_meta table
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_sql_schema_version', '49');
+

sql/triggers.mysql

@@ -61,5 +61,5 @@ FOR EACH ROW
       AND NEW.status =  'DEAD';
 
 
-    # inform the runtime part of the system that triggers are in place:
-INSERT INTO meta (meta_key, meta_value) VALUES ('hive_use_triggers', '1');
+    -- inform the runtime part of the system that triggers are in place:
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_use_triggers', '1');

sql/triggers.sqlite

@@ -65,4 +65,4 @@ END;
 
 
     -- inform the runtime part of the system that triggers are in place:
-INSERT INTO meta (meta_key, meta_value) VALUES ('hive_use_triggers', '1');
+INSERT INTO hive_meta (meta_key, meta_value) VALUES ('hive_use_triggers', '1');