SchemaConversion.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::Utils::SchemaConversion - Utility module for Vega schema conversion script
 
=head1 SYNOPSIS
 
  my $serverroot = '/path/to/ensembl';
  my $conversion =
    Bio::EnsEMBL::Utils::ConversionSupport->new($serverroot);
 
  # parse common options
  $conversion->conv_usage->parse_common_options;
 
  # convert from schema 19 to 20+
  $conversion->do_conversion()
 
=head1 DESCRIPTION
 
This module is a helper module for database conversion, for
both vega-vega and ensembl-vega schemas. It provides a wrapper
around SeqStoreConverter::BasicConverter and the species specific
methods therein. Also provides access to helper functions in
Bio::EnsEMBL::Utils::ConversionSupport
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::Utils::SchemaConversion;
 
use strict;
use warnings;
 
use Bio::EnsEMBL::Utils::ConversionSupport;
use Data::Dumper;
 
=head2 new
 
  Example     : $conversion->Bio::EnsEMBL::Utils::SchemaConversion->new($serverroot);
  Description : Constructor, including an instance of a Bio::EnsEMBL::Utils::ConversionSupport 
                object. Parses input file and checks input with user
  Return type : Bio::EnsEMBL::Utils::SchemaConversion object 
  Exceptions  : thrown if $Siteroot not passed over
  Caller      : $Siteroot/utils/vega_schema_conversion
 
=cut
 
sub new {
    my $class = shift;
    my $support = shift;
    my $self = {};
    bless ($self,$class);
    $self->{config} =  Bio::EnsEMBL::Utils::ConversionSupport->new($support);
    $self->conv_support->parse_common_options;
    $self->conv_support->parse_extra_options('do_vega_sc=s',
                                             'do_ens_sc=s',
                                             'source_db=s',
                                             'core_sql=s',
                                             'vega_sql=s',
                                             'patch_sql=s',
                                             'force=s',
                                             'do_features=s');
 
    #check input and show help
    $self->conv_usage() if ($self->conv_support->param("help"));
    $self->conv_usage("configuration file needed") unless ($self->conv_support->param("conffile"));
    $self->conv_usage("password for database access needed") unless ($self->conv_support->param("pass"));
    $self->conv_usage("can only do conversion to ensembl OR Vega, not both") if ($self->conv_support->param('do_vega_sc') && $self->conv_support->param('do_ens_sc'));
    $self->conv_usage("You need to do vega->veg or ensembl->vega conversion") unless ($self->conv_support->param('do_vega_sc') || $self->conv_support->param('do_ens_sc'));
    
    # ask user to confirm parameters to proceed
    $self->conv_support->allowed_params('conffile',
                                        'do_vega_sc',
                                        'do_ens_sc',
                                        'host',
                                        'port',
                                        'user',
                                        'pass',
                                        'source_db',
                                        'dbname',
                                        'force',
                                        'do_features',
                                        'verbose',
                                        'logpath',
                                        'logfile',
                                        'core_sql',
                                        'vega_sql',
                                        'patch_sql');                                       
    $self->conv_support->confirm_params;
 
    return $self;
}
 
=head2 conv_support
 
  Example     : $conversion->conv_support; 
  Description : Provides access to Bio::EnsEMBL::Utils::ConversionSupport methods
  Return type : Bio::EnsEMBL::Utils::ConversionSuppor object
  Exceptions  : none
  Caller      : general
 
=cut
 
sub conv_support {
    my $self = shift;
    return $self->{config};
}
 
=head2 conv_obj
 
  Example     : $conversion->conv_obj; 
  Description : Provides access to SeqStoreConverter::BasicConverter methods
  Return type : SeqStoreConverter::BasicConverter object
  Exceptions  : none
  Caller      : general
 
=cut
 
sub conv_obj {
    my $self = shift;
    return $self->{'converter_object'};
}
 
 
=head2 species_alias
 
  Example     : $self->species_alias
  Description : examines name of source database to determine which conversion module to use
  Return type : string
  Exceptions  : die if wrong species name used
  Caller      : $self
 
=cut
 
sub species_alias {
    my $self=shift;
    my $name = shift;
    return 'CanisFamiliaris' if $name =~ /canis/;
    return 'HomoSapiens' if $name =~ /homo/;
    return 'MusMusculus' if $name =~ /mus/;
    return 'DanioRerio' if $name =~ /danio/;
    ##hack - should use own modules
    return 'HomoSapiens' if $name =~ /sus/;
    die "invalid name of source database, please check configuration file";
}
 
=head2 choose_conversion_type
 
  Example     : $conversion->choose_conversion_type
  Description : compares conversion type (ensembl or vega) and species type with 
                available modules and chooses that to use for the conversion. Stores
                a converter object within the caller
  Return type : none
  Exceptions  : none
  Caller      : $Siteroot/utils/vega_schema_conversion
 
=cut
 
sub choose_conversion_type {
    my $self = shift;
    my $converter;
    my $species;
 
    $species = $self->species_alias($self->conv_support->param('source_db'));
    if ($self->conv_support->param('do_vega_sc')) {
        $species = "vega::".$species;
        eval "require SeqStoreConverter::$species"; ## no critic
        if($@) {
            warn("Could not require conversion module SeqStoreConverter::$species\ for vega conversion\n" .
                    "Using SeqStoreConverter::BasicConverter instead:\n$@");
            require SeqStoreConverter::BasicConverter;
            $species = "BasicConverter";
        }
        else {
            warn "Using conversion module SeqStoreConverter::$species for vega conversion\n";
        }
    }
    else {
        eval "require SeqStoreConverter::$species"; ## no critic
        if($@) {
            warn("Could not require conversion module SeqStoreConverter::$species for Ensembl conversion\n" .
                    "Using SeqStoreConverter::BasicConverter instead:\n$@");
            require SeqStoreConverter::BasicConverter;
            $species = "BasicConverter";
        }
        else {
            warn "Using conversion module SeqStoreConverter::$species for Ensembl conversion\n";
        }
        $self->conv_support->param('vega_sql',0);
    }
    $converter = "SeqStoreConverter::$species"->new
        ( $self->conv_support->param('user'), 
          $self->conv_support->param('pass'), 
          $self->conv_support->param('host').':'.$self->conv_support->param('port'), 
          $self->conv_support->param('source_db'), 
          $self->conv_support->param('dbname'), 
          $self->conv_support->param('core_sql'), 
          $self->conv_support->param('vega_sql'), 
          $self->conv_support->param('force'), 
          $self->conv_support->param('verbose'),
          '',
        );
 
    $self->{'converter_object'} = $converter;
}
 
=head2 do_conversion
 
  Example     : $conversion->do_conversion
  Description : does the database conversion 
  Return type : none
  Exceptions  : none
  Caller      : $Siteroot/utils/vega_schema_conversion
 
=cut
 
 
sub do_conversion {
    my $self= shift;
    $self->conv_obj->debug( "\n\n*** converting " . $self->conv_obj->source . " to " . 
            $self->conv_obj->target() . " ***");
    $self->conv_obj->transfer_meta();
    $self->conv_obj->create_coord_systems();
    $self->conv_obj->create_seq_regions();
    $self->conv_obj->create_assembly();
    $self->conv_obj->create_attribs();
    $self->conv_obj->set_top_level();
    $self->conv_obj->transfer_dna();
    $self->conv_obj->back_patch_schema();
    $self->conv_obj->transfer_genes();
    $self->conv_obj->transfer_prediction_transcripts();
 
    if ($self->conv_support->param('do_features')) {
        $self->conv_obj->transfer_features();
    }
#use this for both ensembl and vega for now,
#but might need changing when vega gets eg transcript modified dates
    $self->conv_obj->transfer_vega_stable_ids();
    $self->conv_obj->copy_other_tables(); 
    $self->conv_obj->copy_repeat_consensus(); 
    $self->conv_obj->create_meta_coord(); 
    if ($self->conv_support->param('do_vega_sc')) { 
        $self->conv_obj->copy_other_vega_tables(); 
        $self->conv_obj->update_clone_info();
        $self->conv_obj->remove_supercontigs(); 
        $self->conv_obj->copy_internal_clone_names(); 
        $self->conv_obj->copy_assembly_exception; 
    } 
}
 
=head2 make_schema_up_to_date
 
  Example     : $conversion->make_schema_up_to_date
  Description : patches schema to latest version
  Return type : none
  Exceptions  : none
  Caller      : $conversion
 
=cut
 
sub make_schema_up_to_date {
    my $self = shift;
    $self->conv_obj->debug ("\nPatching schema to latest version\n");
    my $user = $self->conv_obj->user;
    my $pass = $self->conv_obj->password;
    my $port = $self->conv_obj->port;
    my $host = $self->conv_obj->host;
    my $target = $self->conv_obj->target;
    my $patch_schema = $self->conv_support->param('patch_sql');
    my $cmd = "/usr/local/mysql/bin/mysql -u $user -p$pass -P $port -h $host $target < $patch_schema";
    system ($cmd);
}
 
 
 
=head2 conv_usage
 
  Example     : $conversion->conv_usage("message")
  Description : prints usage information and exits
  Return type : none
  Exceptions  : none
  Caller      : $Siteroot/utils/vega_schema_conversion
 
=cut
 
sub conv_usage {
    my $self = shift;
    my $msg = shift;
 
    print STDERR "\nMSG: $msg\n" if($msg);
    
    print STDERR <<EOF;
 
** Source and target databases must be on the same mysql instance
 
usage: ./conversion_densities.pl  <options>
 
options: --conf <conf_file>      configuration file (uses conf/Conversion.ini by default):
 
                                   fields:
                                      do_vega_sc (do vega conversion: 0 or 1)
                                      do_ens_sc (do ensembl conversion: 0 or 1)
                                      user (a mysql db user with read/write priveleges)
                                      host (eg ecs3f)
                                      port (eg 3310)
                                      source_db (schema 19 source database)
                                      dbname (schema 20+ target database)
                                      force (overwrite existing target database: 0 or 1)
                                      verbose (print out debug statements: 0 or 1)
                                      logpath (location of log file)
                                      do_features (transfer dna- and protein-align features, for debugging: 0 or 1)
                                      core_sql (location of ensembl schema creation script: ensembl/sql/table.sql)
                                      vega_sql (location of creation script for additional vega tables: ensembl/sql/vega_specific_tables.sql)
                                      patch_sql (location of schema patching script: ensembl/sql/vega_latest_schema.sql)
 
         --log                   name of log_file
         --help                  display this message
 
EOF
  exit;
 
}
 
1;