added analysis_data table and adaptor.

Estentially a mini filesystem so that data that would normally be stored in
NFS files and referenced via a path, can now be stored in the database and
referenced via a dbID. Data is a LONGTEXT.
Can be used to store configuration data, paramater strings,
BLOSSUM matrix data, uuencode of binary data .....

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

+# Perl module for Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
+#
+# Date of creation: 22.03.2004
+# Original Creator : Jessica Severin <jessica@ebi.ac.uk>
+#
+# Copyright EMBL-EBI 2004
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+  Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
+
+=head1 SYNOPSIS
+  $dataDBA = $db_adaptor->get_AnalysisDataAdaptor;
+
+=head1 DESCRIPTION
+   analysis_data table holds LONGTEXT data for use by the analysis system.
+   This data is general purpose and it's up to each analysis to
+   determine how to use it.
+   This Adaptor module is used to access/store this data.
+
+=head1 CONTACT
+  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
+  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
+
+=head1 APPENDIX
+  The rest of the documentation details each of the object methods.
+  Internal methods are preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Compara::DBSQL::AnalysisDataAdaptor;
+
+use strict;
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+sub fetch_by_dbID {
+  my ($self, $data_id) = @_;
+
+  my $sql = "SELECT data FROM analysis_datae WHERE analysis_data_id = ?";
+  my $sth = $self->prepare($sql);
+  $sth->execute($sequence_id);
+
+  my ($sequence) = $sth->fetchrow_array();
+  $sth->finish();
+  return $sequence;
+}
+
+
+#
+# STORE METHODS
+#
+################
+
+sub store {
+  my ($self, $data) = @_;
+  my $data_id;
+  
+  return 0 unless($data);
+
+  my $sth = $self->prepare("SELECT analysis_data_id FROM analysis_data WHERE data = ?");
+  $sth->execute($data);
+  ($seqID) = $sth->fetchrow_array();
+  $sth->finish;
+
+  if($data_id) {
+    # print("sequence already stored as id $seqID\n");
+    return $data_id;
+  }
+
+  my $sth2 = $self->prepare("INSERT INTO analysis_data (data) VALUES (?)");
+  $sth2->execute($data);
+  $data_id = $sth2->{'mysql_insertid'};
+  $sth2->finish;
+
+  return $data_id;
+}
+
+
+1;
+
+
+
+
+

sql/tables.sql

@@ -190,6 +190,28 @@ CREATE TABLE analysis_job_file (
 );
 
 
+------------------------------------------------------------------------------------
+--
+-- Table structure for table 'analysis_data'
+--
+-- overview:
+--   Table which holds LONGTEXT data for use by the analysis system.
+--   This data is general purpose and it's up to each analysis to
+--   determine how to use it
+--
+-- semantics:
+--   analysis_data_id   - primary id
+--   data               - text blob which holds the data
+
+CREATE TABLE analysis_data (
+  analysis_data_id  int(10) NOT NULL auto_increment,
+  data              longtext,
+
+  PRIMARY KEY (analysis_data_id),
+  KEY data (data(7))
+);
+
+
 ------------------------------------------------------------------------------------
 --
 -- Table structure for table 'analysis_stats'
@@ -220,4 +242,3 @@ CREATE TABLE analysis_stats (
   UNIQUE KEY   (analysis_id)
 );
 
-