Inheritance diagram for Bio::EnsEMBL::IdMapping::BaseObject:

Public Member Functions
public $this	new ()

public Filehandle	get_filehandle ()

public Boolean	file_exists ()

public SQLStatement	fetch_value_from_db ()

public Int	dump_table_to_file ()

public Int	upload_file_into_table ()

public Bio::EnsEMBL::Utils::Logger	logger ()

public Bio::EnsEMBL::Utils::ConfParser	conf ()

public Bio::EnsEMBL::IdMapping::Cache	cache ()

Detailed Description

Synopsis

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

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...

Definition at line 25 of file BaseObject.pm.

Member Function Documentation

◆ cache()

public Bio::EnsEMBL::IdMapping::Cache Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ conf()

public Bio::EnsEMBL::Utils::ConfParser Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ dump_table_to_file()

public Int Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ fetch_value_from_db()

public SQLStatement Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ file_exists()

public Boolean Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ get_filehandle()

public Filehandle Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ logger()

public Bio::EnsEMBL::Utils::Logger Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ new()

public $this Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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◆ upload_file_into_table()

public Int Bio::EnsEMBL::IdMapping::BaseObject::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

Code:

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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

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/IdMapping/BaseObject.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ cache()

◆ conf()

◆ dump_table_to_file()

◆ fetch_value_from_db()

◆ file_exists()

◆ get_filehandle()

◆ logger()

◆ new()

◆ upload_file_into_table()