BaseObject.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::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;
 
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);
 
  # initialise
  $self->logger($logger);
  $self->conf($conf);
  $self->cache($cache);
  
  return $self;
}
 
 
=head2 get_filehandle 
 
  Arg[1]      : String $filename - filename for filehandle
  Arg[2]      : String $path_append - append subdirectory name to basedir
  Arg[3]      : String $mode - filehandle mode (<|>|>>)
  Example     : my $fh = $object->get_filehandle('mapping_stats.txt', 'stats',
                  '>');
                print $fh "Stats:\n";
  Description : Returns a filehandle to a file for reading or writing. The file
                is qualified with the basedir defined in the configuration and
                an optional subdirectory name.
  Return type : filehandle
  Exceptions  : thrown on missing filename
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub get_filehandle {
  my $self = shift;
  my $filename = shift;
  my $path_append = shift;
  my $mode = shift;
 
  throw("Need a filename for this filehandle.") unless (defined($filename));
  
  my $path = $self->conf->param('basedir');
  $path = path_append($path, $path_append) if (defined($path_append));
 
  $mode ||= '>';
  
  open(my $fh, $mode, "$path/$filename") or
    throw("Unable to open $path/$filename: $!");
 
  return $fh;
}
 
 
=head2 file_exists
 
  Arg[1]      : String $filename - filename to test
  Arg[2]      : Boolean $path_append - turn on pre-pending of basedir
  Example     : unless ($object->file_exists('gene_mappings.ser', 1)) {
                  $object->do_gene_mapping;
                }
  Description : Tests if a file exists and has non-zero size.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub file_exists {
  my $self = shift;
  my $filename = shift;
  my $path_append = shift;
 
  my $path = $self->conf->param('basedir');
  $path = path_append($path, $path_append) if (defined($path_append));
 
  return (-s "$path/$filename");
}
 
 
=head2 fetch_value_from_db 
 
  Arg[1]      : DBI::db $dbh - a DBI database handle
  Arg[2]      : String $sql - SQL statement to execute
  Example     : my $num_genes = $object->fetch_value_from_db($dbh,
                  'SELECT count(*) FROM gene');
  Description : Executes an SQL statement on a db handle and returns the first
                column of the first row returned. Useful for queries returning a
                single value, like table counts.
  Return type : Return type of SQL statement
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
=cut
 
sub fetch_value_from_db {
  my $self = shift;
  my $dbh = shift;
  my $sql = shift;
 
  throw("Need a db handle.") unless ($dbh and $dbh->isa('DBI::db'));
  throw("Need an SQL query to execute.") unless ($sql);
 
  my $sth = $dbh->prepare($sql);
  $sth->execute;
  my ($retval) = $sth->fetchrow_array;
 
  return $retval;
}
 
 
=head2 dump_table_to_file 
 
  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to dump
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $check_existing - turn on test for existing dump
  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'};
}
 
 
1;