Inheritance diagram for Bio::EnsEMBL::DBSQL::AnalysisAdaptor:

Public Member Functions
public Bio::EnsEMBL::DBSQL::AnalysisAdaptor	new ()

public Listref	fetch_all ()

public Listref	fetch_all_by_feature_class ()

public Bio::EnsEMBL::Analysis	fetch_by_dbID ()

public Bio::EnsEMBL::Analysis	fetch_by_logic_name ()

public Int	store ()

protected	_store_description ()

public Int	update ()

public void	remove ()

public Int	exists ()

protected Bio::EnsEMBL::Analysis	_objFromHashref ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

use Bio::EnsEMBL::Registry;
 
Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);
 
$analysis_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "analysis" );
 
my $analysis = $analysis_adaptor->fetch_by_logic_name('genscan');

Description

  Module to encapsulate all db access for persistent class Analysis.
  There should be just one per application and database connection.

Definition at line 29 of file AnalysisAdaptor.pm.

Member Function Documentation

◆ _objFromHashref()

protected Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::_objFromHashref ( )

◆ _store_description()

protected Bio::EnsEMBL::DBSQL::AnalysisAdaptor::_store_description ( )

Undocumented method

Code:

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◆ exists()

public Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::exists ( )

  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    :

if($adaptor->exists($anal)) #do something

  Description: Tests whether this Analysis already exists in the database
               by checking first if the adaptor and dbID are set and
               secondly by whether it is in this adaptors internal cache.
               Note that this will not actually check the database and will
               not find and analysis which were recently added by other
               processes.  You are better off simply trying to store an
               analysis which will reliably ensure that it is not stored twice
               in the database.
  Returntype : int dbID if analysis is found, otherwise returns undef
  Exceptions : thrown if $anal arg is not an analysis object
  Caller     : store
  Status     : Stable

Code:

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◆ fetch_all()

public Listref Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_all ( )

  Args       : none
  Example    :

my @analysis = @{$analysis_adaptor->fetch_all()};

  Description: fetches all of the Analysis objects from the database and caches
               them internally.
  Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
  Exceptions : none
  Caller     : AnalysisAdaptor::new
  Status     : Stable

Code:

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◆ fetch_all_by_feature_class()

public Listref Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_all_by_feature_class ( )

  Arg [1]    : string $feature_cless - The name of the feature class
  Example    :

my @analyses = @{$analysis_adaptor->fetch_all_by_feature_class('Gene');

  Description: Returns all analyses that correspond to a given 
               feature class; see feature_classes method for a list.
  Returntype : Listref of Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_dbID()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $internal_analysis_id - the database id of the analysis 
               record to retrieve
  Example    :

my $analysis = $analysis_adaptor->fetch_by_dbID(1);

  Description: Retrieves an Analysis object from the database via its internal
               id.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_logic_name()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBSQL::AnalysisAdaptor::fetch_by_logic_name ( )

  Arg [1]    : string $logic_name the logic name of the analysis to retrieve
  Example    :

my $analysis = $a_adaptor->fetch_by_logic_name('Eponine');

  Description: Retrieves an analysis object from the database using its unique
               logic name.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::DBSQL::AnalysisAdaptor Bio::EnsEMBL::DBSQL::AnalysisAdaptor::new ( )

  Args       : Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    :

my $aa = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor();

  Description: Creates a new Bio::EnsEMBL::DBSQL::AnalysisAdaptor object and
               internally loads and caches all the Analysis objects from the 
               database.
  Returntype : Bio::EnsEMBL::DBSQL::AnalysisAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBAdaptor
  Status     : Stable

Code:

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◆ remove()

public void Bio::EnsEMBL::DBSQL::AnalysisAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    :

$adaptor->remove($anal)

  Description: Removes this analysis from the database.  This is not really
               safe to execute in a multi process environment, so programs
               should not remove analysis while out on the farm.
  Returntype : none
  Exceptions : thrown if $anal arg is not an analysis object
  Caller     : ?
  Status     : Stable

Code:

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◆ store()

public Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::store ( )

  Arg [1]    : Bio:EnsEMBL::Analysis $analysis
  Example    :

$analysis_adaptor->store($analysis);

  Description: Stores $analysis in db.  If the analysis is already stored in
               the database its dbID and adaptor are updated, but the analysis
               is not stored a second time.
               Sets created date if not already set. Sets dbID and adaptor
               inside $analysis. Returns dbID.
  Returntype : int - dbID of stored analysis
  Exceptions : throw on incorrect argument
               throw if analysis argument does not have a logic name
  Caller     : general
  Status     : Stable

Code:

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sub store {
  my $self = shift;
  my $analysis = shift;
 
  if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
    throw("Bio::EnsEMBL::Analysis argument expected.");
  }
 
  if($analysis->is_stored($self->db())) {
    return $analysis->dbID();
  }
 
  if(!$analysis->logic_name()) {
    throw("Analysis cannot be stored without a valid logic_name");
  }
    
  my $insert_ignore = $self->insert_ignore_clause();
 
  my $rows_inserted = 0;
  my $sth;
 
  if ( $analysis->created() ) {
 
    # We use insert IGNORE so that this method can be used in a
    # multi-process environment.  If another process has already written
    # this record then there will not be a problem.
 
    $sth = $self->prepare(
      qq{
          ${insert_ignore} INTO analysis
              (created, logic_name, db, db_version, db_file, program, program_version, program_file, parameters, module, module_version, gff_source, gff_feature)
          VALUES  (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
      }
    );
    $sth->bind_param( 1,  $analysis->created(),          SQL_DATETIME );
    $sth->bind_param( 2,  lc( $analysis->logic_name() ), SQL_VARCHAR );
    $sth->bind_param( 3,  $analysis->db(),               SQL_VARCHAR );
    $sth->bind_param( 4,  $analysis->db_version(),       SQL_VARCHAR );
    $sth->bind_param( 5,  $analysis->db_file(),          SQL_VARCHAR );
    $sth->bind_param( 6,  $analysis->program(),          SQL_VARCHAR );
    $sth->bind_param( 7,  $analysis->program_version(),  SQL_VARCHAR );
    $sth->bind_param( 8,  $analysis->program_file(),     SQL_VARCHAR );
    $sth->bind_param( 9,  $analysis->parameters(),       SQL_VARCHAR );
    $sth->bind_param( 10, $analysis->module(),           SQL_VARCHAR );
    $sth->bind_param( 11, $analysis->module_version(),   SQL_VARCHAR );
    $sth->bind_param( 12, $analysis->gff_source(),       SQL_VARCHAR );
    $sth->bind_param( 13, $analysis->gff_feature(),      SQL_VARCHAR );
 
    $rows_inserted = $sth->execute();
 
  } else {
    $sth = $self->prepare(
      qq{
          ${insert_ignore} INTO analysis
              (created, logic_name, db, db_version, db_file, program, program_version, program_file, parameters, module, module_version, gff_source, gff_feature)
          VALUES  (CURRENT_TIMESTAMP, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
      }
    );
 
    $sth->bind_param( 1,  $analysis->logic_name,      SQL_VARCHAR );
    $sth->bind_param( 2,  $analysis->db,              SQL_VARCHAR );
    $sth->bind_param( 3,  $analysis->db_version,      SQL_VARCHAR );
    $sth->bind_param( 4,  $analysis->db_file,         SQL_VARCHAR );
    $sth->bind_param( 5,  $analysis->program,         SQL_VARCHAR );
    $sth->bind_param( 6,  $analysis->program_version, SQL_VARCHAR );
    $sth->bind_param( 7,  $analysis->program_file,    SQL_VARCHAR );
    $sth->bind_param( 8,  $analysis->parameters,      SQL_VARCHAR );
    $sth->bind_param( 9,  $analysis->module,          SQL_VARCHAR );
    $sth->bind_param( 10, $analysis->module_version,  SQL_VARCHAR );
    $sth->bind_param( 11, $analysis->gff_source,      SQL_VARCHAR );
    $sth->bind_param( 12, $analysis->gff_feature,     SQL_VARCHAR );
 
    $rows_inserted = $sth->execute();
 
  } ## end else [ if ( $analysis->created...)]
 
  my $dbID;
  # If we need to fetch the timestamp, or the insert failed due to
  # existance of an existing entry, we need to retrieve the entry from
  # the database.  Note: $sth->execute() may return 0E0 on error which
  # is zero, but true which is why the $rows_inserted clause was added.
  if ( !$analysis->created() || !$rows_inserted || $rows_inserted == 0 )
  {
    my $new_analysis =
      $self->fetch_by_logic_name( $analysis->logic_name );
 
    if ( !$new_analysis ) {
      throw("Could not retrieve just stored analysis from database.\n"
          . "Possibly incorrect db permissions or missing analysis table\n"
      );
    }
 
    $dbID = $new_analysis->dbID();
    $analysis->created( $new_analysis->created() );
  }
  
  $dbID ||= $self->last_insert_id('analysis_id', undef, 'analysis');
  $sth->finish();
 
  # store description and display_label
  if( defined( $analysis->description() ) || defined( $analysis->display_label() )|| defined( $analysis->web_data() )) {
      $self->_store_description($analysis, $dbID);
  }
 
 
  $self->{_cache}->{$dbID} = $analysis;
  $self->{_logic_name_cache}{lc($analysis->logic_name)} = $analysis;
 
  $analysis->adaptor( $self );
  $analysis->dbID( $dbID );
 
  return $dbID;
}

◆ update()

public Int Bio::EnsEMBL::DBSQL::AnalysisAdaptor::update ( )

  Arg [1]    : Bio::EnsEMBL::Analysis $anal
  Example    :

$adaptor->update($anal)

  Description: Updates this analysis in the database
  Returntype : int 1 if update is performed, undef if it is not
  Exceptions : throw if arg is not an analysis object
  Caller     : ?
  Status     : Stable

Code:

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sub update {
  my $self = shift;
  my $a    = shift;
 
  if (!ref($a) || !$a->isa('Bio::EnsEMBL::Analysis')) {
    throw("Expected Bio::EnsEMBL::Analysis argument.");
  }
 
  if(!$a->is_stored($self->db())) {
    return;
  }
 
  my $sth = $self->prepare
    ("UPDATE analysis " .
     "SET created = ?, logic_name = ?, db = ?, db_version = ?, db_file = ?, ".
     "    program = ?, program_version = ?, program_file = ?,  ".
     "    parameters = ?, module = ?, module_version = ?, ".
     "    gff_source = ?, gff_feature = ? " .
     "WHERE analysis_id = ?");
 
 
 
  $sth->bind_param(1,$a->created,SQL_DATETIME);
  $sth->bind_param(2,$a->logic_name,SQL_VARCHAR);
  $sth->bind_param(3,$a->db,SQL_VARCHAR);
  $sth->bind_param(4,$a->db_version,SQL_VARCHAR);
  $sth->bind_param(5,$a->db_file,SQL_VARCHAR);
  $sth->bind_param(6,$a->program,SQL_VARCHAR);
  $sth->bind_param(7,$a->program_version,SQL_VARCHAR);
  $sth->bind_param(8,$a->program_file,SQL_VARCHAR);
  $sth->bind_param(9,$a->parameters,SQL_VARCHAR);
  $sth->bind_param(10,$a->module,SQL_VARCHAR);
  $sth->bind_param(11,$a->module_version,SQL_VARCHAR);
  $sth->bind_param(12,$a->gff_source,SQL_VARCHAR);
  $sth->bind_param(13,$a->gff_feature,SQL_VARCHAR);
  $sth->bind_param(14,$a->dbID,SQL_INTEGER);
 
  $sth->execute();
 
  $sth->finish();
 
  # also update description & display label - may need to create these if
  # not already there
  $sth = $self->prepare("SELECT description FROM analysis_description WHERE analysis_id= ?");
  $sth->execute($a->dbID);
  if ($sth->fetchrow_hashref) { # update if exists
      $sth = $self->prepare
      ("UPDATE analysis_description SET description = ?, display_label = ?, displayable = ?, web_data = ? WHERE analysis_id = ?");
      $sth->bind_param(1,$a->description,SQL_LONGVARCHAR);     
      $sth->bind_param(2,$a->display_label(),SQL_VARCHAR);
      $sth->bind_param(3,$a->displayable,SQL_TINYINT);
      $sth->bind_param(4,$a->web_data,SQL_LONGVARCHAR);
      $sth->bind_param(5,$a->dbID,SQL_INTEGER);
      $sth->execute();
 
  } else { # create new entry
 
    if( $a->description() || $a->display_label() || $a->web_data) {
        $self->_store_description($a, $a->dbID);
    }
 
  }
 
 
    $sth->finish();
 
  # the logic_name cache needs to be re-updated now, since we may have just
  # changed the logic_name
  $self->fetch_all();
 
  return 1;
}

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

ensembl/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _objFromHashref()

◆ _store_description()

◆ exists()

◆ fetch_all()

◆ fetch_all_by_feature_class()

◆ fetch_by_dbID()

◆ fetch_by_logic_name()

◆ new()

◆ remove()

◆ store()

◆ update()