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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::IdMapping::BaseObject - base object for IdMapping objects

=head1 SYNOPSIS

  # this object isn't instantiated directly but rather extended
  use Bio::EnsEMBL::IdMapping::BaseObject;
  our @ISA = qw(Bio::EnsEMBL::IdMapping::BaseObject);

=head1 DESCRIPTION

This is the base object for some of the objects used in the IdMapping
application. An object that extends BaseObject will have a ConfParser,
Logger and Cache object. BaseObject also implements some useful utility
functions related to file and db access.

This isn't very clean OO design but it's efficient and easy to use...

=head1 METHODS

  new
  get_filehandle
  file_exists
  fetch_value_from_db
  dump_table_to_file
  upload_file_into_table
  logger
  conf
  cache

=cut


package Bio::EnsEMBL::IdMapping::BaseObject;
$Bio::EnsEMBL::IdMapping::BaseObject::VERSION = '114.0.0';
use strict;
use warnings;
no warnings 'uninitialized';

use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);


=head2 new

  Arg [LOGGER]: Bio::EnsEMBL::Utils::Logger $logger - a logger object
  Arg [CONF]  : Bio::EnsEMBL::Utils::ConfParser $conf - a configuration object
  Arg [CACHE] : Bio::EnsEMBL::IdMapping::Cache $cache - a cache object
  Example     : my $object = Bio::EnsEMBL::IdMapping::BaseObjectSubclass->new(
                  -LOGGER => $logger,
                  -CONF   => $conf,
                  -CACHE  => $cache
                );
  Description : Constructor
  Return type : implementing subclass type
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;

  my ($logger, $conf, $cache) = rearrange(['LOGGER', 'CONF', 'CACHE'], @_);

  unless ($logger and ref($logger) and
          $logger->isa('Bio::EnsEMBL::Utils::Logger')) {
    throw("You must provide a Bio::EnsEMBL::Utils::Logger for logging.");
  }
  
  unless ($conf and ref($conf) and
          $conf->isa('Bio::EnsEMBL::Utils::ConfParser')) {
    throw("You must provide configuration as a Bio::EnsEMBL::Utils::ConfParser object.");
  }
  
  unless ($cache and ref($cache) and
          $cache->isa('Bio::EnsEMBL::IdMapping::Cache')) {
    throw("You must provide configuration as a Bio::EnsEMBL::IdMapping::Cache object.");
  }
  
  my $self = {};
  bless ($self, $class);

lib/Bio/EnsEMBL/IdMapping/BaseObject.pm  view on Meta::CPAN

  Example     : my $rows_dumped = $object->dump_table_to_file('source',
                  'stable_id_event', 'stable_id_event_existing.txt');
  Description : Dumps the contents of a db table to a tab-delimited file. The
                dump file will be written to a subdirectory called 'tables'
                under the basedir from your configuration.
  Return type : Int - the number of rows dumped
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub dump_table_to_file {
  my $self = shift;
  my $dbtype = shift;
  my $table = shift;
  my $filename = shift;
  my $check_existing = shift;

  # argument check
  unless (($dbtype eq 'source') or ($dbtype eq 'target')) {
    throw("Missing or unknown db type: $dbtype.");
  }
  throw("Need a table name.") unless ($table);
  throw("Need a filename.") unless ($filename);

  # conditionally check if table was already dumped
  if ($check_existing and $self->file_exists($filename, 'tables')) {
    $self->logger->info("$filename exists, won't dump again.\n");
    return 0;
  }
  
  my $fh = $self->get_filehandle($filename, 'tables');

  my $dba = $self->cache->get_DBAdaptor($dbtype);
  my $dbh = $dba->dbc->db_handle;
  my $sth = $dbh->prepare("SELECT * FROM $table");
  $sth->execute;

  my $i = 0;

  while (my @row = $sth->fetchrow_array) {
    $i++;

    # use '\N' for NULL values
    for (my $j = 0; $j < scalar(@row); $j++) {
      $row[$j] = '\N' unless (defined($row[$j]));
    }
    
    print $fh join("\t", @row);
    print $fh "\n";
  }

  $sth->finish;
  
  return $i;
}


=head2 upload_file_into_table

  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to upload the data to
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $no_check_empty - don't check if table is empty
  Example     : my $rows_uploaded = $object->upload_file_into_table('target',
                  'stable_id_event', 'stable_id_event_new.txt');
  Description : Uploads a tab-delimited data file into a db table. The data file
                will be taken from a subdirectory 'tables' under your configured
                basedir. If the db table isn't empty and $no_check_empty isn't
                set, no data is uploaded (and a warning is issued).
  Return type : Int - the number of rows uploaded
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub upload_file_into_table {
  my $self           = shift;
  my $dbtype         = shift;
  my $table          = shift;
  my $filename       = shift;
  my $no_check_empty = shift;

  # argument check
  unless ( ( $dbtype eq 'source' ) or ( $dbtype eq 'target' ) ) {
    throw("Missing or unknown db type: $dbtype.");
  }
  throw("Need a table name.") unless ($table);
  throw("Need a filename.")   unless ($filename);

  # sanity check for dry run
  if ( $self->conf->param('dry_run') ) {
    $self->logger->warning(
                       "dry_run - skipping db upload for $filename.\n");
    return;
  }

  my $file =
    join( '/', $self->conf->param('basedir'), 'tables', $filename );
  my $r = 0;

  if ( -s $file ) {

    $self->logger->debug( "$file -> $table\n", 1 );

    my $dba = $self->cache->get_DBAdaptor($dbtype);
    my $dbh = $dba->dbc->db_handle;

    my $idtable = 0;
    if ( $table =~ /^([^_]+)_stable_id/ ) {
      # This is a stable_id table we're working with.
      $idtable = 1;
      $table   = $1;
    }

    # check table is empty
    my ( $sql, $sth );
    unless ($no_check_empty) {
      if ($idtable) {
        $sql =
          qq(SELECT count(*) FROM $table WHERE stable_id IS NOT NULL);
      }
      else {
        $sql = qq(SELECT count(*) FROM $table);
      }
      $sth = $dbh->prepare($sql);
      $sth->execute;
      my ($c) = $sth->fetchrow_array;
      $sth->finish;

      if ( $c > 0 ) {
        if ($idtable) {
          $self->logger->warning(
                               "Table $table contains $c stable IDs.\n",
                               1 );
        }
        else {
          $self->logger->warning(
                          "Table $table not empty: found $c entries.\n",
                          1 );
        }
        $self->logger->info( "Data not uploaded!\n", 1 );
        return $r;
      }
    } ## end unless ($no_check_empty)

    # now upload the data
    if ($idtable) {
      # Create a temporary table, upload the data into it, and then
      # update the main table.
      $dbh->do(
        qq( CREATE TABLE stable_id_$$ (  object_id INTEGER UNSIGNED,
                                             stable_id VARCHAR(255),
                                             version SMALLINT UNSIGNED,
                                             created_date DATETIME,
                                             modified_date DATETIME,
                                             PRIMARY KEY(object_id) ) )
      );

      $dbh->do(
            qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE stable_id_$$));

      $dbh->do(
        qq(
      UPDATE $table, stable_id_$$
      SET $table.stable_id=stable_id_$$.stable_id,
          $table.version=stable_id_$$.version,
          $table.created_date=stable_id_$$.created_date,
          $table.modified_date=stable_id_$$.modified_date
      WHERE $table.${table}_id = stable_id_$$.object_id )
      );

      $dbh->do(qq(DROP TABLE stable_id_$$));
    } ## end if ($idtable)
    else {
      $dbh->do(qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE $table));
    }
    $dbh->do(qq(OPTIMIZE TABLE $table));

  } ## end if ( -s $file )
  else {
    $self->logger->warning( "No data found in file $filename.\n", 1 );
  }

  return $r;
} ## end sub upload_file_into_table


=head2 logger

  Arg[1]      : (optional) Bio::EnsEMBL::Utils::Logger - the logger to set
  Example     : $object->logger->info("Starting ID mapping.\n");
  Description : Getter/setter for logger object
  Return type : Bio::EnsEMBL::Utils::Logger
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development

=cut

sub logger {
  my $self = shift;
  $self->{'_logger'} = shift if (@_);
  return $self->{'_logger'};
}


=head2 conf

  Arg[1]      : (optional) Bio::EnsEMBL::Utils::ConfParser - the configuration
                to set
  Example     : my $basedir = $object->conf->param('basedir');
  Description : Getter/setter for configuration object
  Return type : Bio::EnsEMBL::Utils::ConfParser
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development

=cut

sub conf {
  my $self = shift;
  $self->{'_conf'} = shift if (@_);
  return $self->{'_conf'};
}


=head2 cache

  Arg[1]      : (optional) Bio::EnsEMBL::IdMapping::Cache - the cache to set
  Example     : $object->cache->read_from_file('source');
  Description : Getter/setter for cache object
  Return type : Bio::EnsEMBL::IdMapping::Cache
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development

=cut

sub cache {
  my $self = shift;
  $self->{'_cache'} = shift if (@_);
  return $self->{'_cache'};