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

Class Summary

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.

Available Methods
protected	_columns ()
protected	_default_where_clause ()
protected	_final_clause ()
protected	_left_join ()
protected	_list_dbIDs ()
protected Bio::EnsEMBL::Analysis	_objFromHashref ()
protected	_objs_from_sth ()
protected	_straight_join ()
protected	_tables ()
public Listref	bind_param_generic_fetch ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dump_data ()
public Int	exists ()
public List	feature_classes ()
public Listref	fetch_all ()
public Listref	fetch_all_by_dbID_list ()
public Listref	fetch_all_by_feature_class ()
public Bio::EnsEMBL::Analysis	fetch_by_dbID ()
public Bio::EnsEMBL::Analysis	fetch_by_logic_name ()
public Listref	generic_fetch ()
public	get_dumped_data ()
public Boolean	is_multispecies ()
public Scalar	last_insert_id ()
public Bio::EnsEMBL::DBSQL::AnalysisAdaptor	new ()
public DBI::StatementHandle	prepare ()
public void	remove ()
public Int	species_id ()
public Int	store ()
public Int	update ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_columns ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_left_join ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

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

  Arg [1]    : hashref $rowHash
  Description: Private helper function generates an Analysis object from a 
               mysql row hash reference.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::AnalsisAdaptor::fetch_* methods
  Status     : Stable

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_objs_from_sth ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables ( ) [inherited]

Undocumented method

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]

 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :  $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
              $adaptor->generic_fetch();
 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

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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

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public List Bio::EnsEMBL::DBSQL::AnalysisAdaptor::feature_classes ( )

  Arg [1]    : NONE
  Example    : my @fclasses = $analysis_adaptor->feature_classes;
  Description: Returns a list of the different classes of Ensembl feature 
               object that have an analysis
  Returntype : List of feature classes
  Exceptions : none
  Caller     : general
  Status     : Stable

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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

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]

  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

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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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

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

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

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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable

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sub generic_fetch {
  my ($self, $constraint, $mapper, $slice) = @_;

  my @tabs = $self->_tables();

  my $extra_default_where;

  # Hack for feature types that needs to be restricted to species_id (in
  # coord_system).
  if (    $self->is_multispecies()
       && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
  {
    # We do a check to see if there is already seq_region
    # and coord_system defined to ensure we get the right
    # alias.  We then do the extra query irrespectively of
    # what has already been specified by the user.
    my %thash = map { $_->[0] => $_->[1] } @tabs;

    my $sr_alias =
      ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
    my $cs_alias =
      ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );

    if ( !exists( $thash{seq_region} ) ) {
      push( @tabs, [ 'seq_region', $sr_alias ] );
    }
    if ( !exists( $thash{coord_system} ) ) {
      push( @tabs, [ 'coord_system', $cs_alias ] );
    }

    $extra_default_where = sprintf(
                      '%s.seq_region_id = %s.seq_region_id '
                        . 'AND %s.coord_system_id = %s.coord_system_id '
                        . 'AND %s.species_id = ?',
                      $tabs[0]->[1], $sr_alias, $sr_alias,
                      $cs_alias,     $cs_alias );

    $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
  } ## end if ( $self->is_multispecies...)

  my $columns = join(', ', $self->_columns());

  my $db = $self->db();

  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
  my @left_join_list = $self->_left_join();
  my $left_join_prefix = '';
  my $left_join = '';
  my @tables;
  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
    while(my $t = shift @tabs) {
        my $t_alias = $t->[0] . " " . $t->[1];
      if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
        my $condition = $left_join_hash{ $t->[0] };
        $condition ||= $left_join_hash{$t_alias};
        my $syn = $t->[1];
        $left_join .=
          "\n  LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
        $left_join_prefix .= '(';
      } else {
        push @tables, $t;
      }
    }
  } else {
    @tables = @tabs;
  }

  my $straight_join = '';

  if($self->_straight_join()) {
    $straight_join = "STRAIGHT_JOIN";
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql =
      "SELECT $straight_join $columns\n"
    . "FROM $left_join_prefix ($tablenames) $left_join";

  my $default_where = $self->_default_where_clause();
  my $final_clause = $self->_final_clause;

  if ($extra_default_where) {
    if ($default_where) {
      $default_where .= "\n AND $extra_default_where";
    } else {
      $default_where = $extra_default_where;
    }
  }

  #append a where clause if it was defined
  if ($constraint) {
    $sql .= "\n WHERE $constraint ";
    if ($default_where) {
      $sql .= " AND\n       $default_where ";
    }
  } elsif ($default_where) {
    $sql .= "\n WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= "\n$final_clause";


  # FOR DEBUG:
  #printf(STDERR "SQL:\n%s\n", $sql);
  
  
  my $sth = $db->dbc->prepare($sql);
  my $bind_parameters = $self->bind_param_generic_fetch();
  if (defined $bind_parameters){
      #if we have bind the parameters, call the DBI to bind them
      my $i = 1;
      foreach my $param (@{$bind_parameters}){
        $sth->bind_param($i,$param->[0],$param->[1]);
        $i++;
      }
      #after binding parameters, undef for future queries
      $self->{'_bind_param_generic_fetch'} = ();
  }
  eval { $sth->execute() };
  if ($@) {
    throw("Detected an error whilst executing SQL '${sql}': $@");
  }

  my $res = $self->_objs_from_sth($sth, $mapper, $slice);
  $sth->finish();
  return $res;
}

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

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public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]

  Arg [1]    : (optional) boolean $arg
  Example    : if ($adaptor->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]

  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();
  Returntype  : Scalar or undef

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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

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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]

  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

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

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public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]

  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

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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 $insertion_method = (lc($self->dbc->driver) eq 'sqlite') ? 'INSERT OR IGNORE' : 'INSERT IGNORE';

  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{
          $insertion_method 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{
          $insertion_method 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 ||= $sth->{'mysql_insertid'};
  $sth->finish();

  # store description and display_label
  if( defined( $analysis->description() ) || defined( $analysis->display_label() )|| defined( $analysis->web_data() )) {
      $sth = $self->prepare( "INSERT IGNORE INTO analysis_description (analysis_id, display_label, description, displayable, web_data) VALUES (?,?,?,?, ?)");

      $sth->bind_param(1,$dbID,SQL_INTEGER);
      $sth->bind_param(2,$analysis->display_label(),SQL_VARCHAR);
      $sth->bind_param(3,$analysis->description,SQL_LONGVARCHAR);
      $sth->bind_param(4,$analysis->displayable,SQL_TINYINT);
      #$sth->bind_param(5,$analysis->web_data(),SQL_LONGVARCHAR);
      my $web_data;
      $web_data = $self->dump_data($analysis->web_data()) if ($analysis->web_data());
      $sth->bind_param(5,$web_data,SQL_LONGVARCHAR);
      $sth->execute();

      $sth->finish();
  }
  


  $self->{_cache}->{$dbID} = $analysis;
  $self->{_logic_name_cache}{lc($analysis->logic_name)} = $analysis;

  $analysis->adaptor( $self );
  $analysis->dbID( $dbID );

  return $dbID;
}

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:

click to view

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 undef;
  }

  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);
  my $web_data; #this is an anonymous reference to a hash, will have to be dumped into string before writing to db
  if ($sth->fetchrow_hashref) { # update if exists
      $web_data = $self->dump_data($a->web_data()) if ($a->web_data());
      $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);
      #      print "after $web_data\n";
      $sth->bind_param(4,$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) {
    $web_data = $self->dump_data($a->web_data()) if ($a->web_data());
      #my $web_data = $self->dump_data($a->web_data());
      $sth = $self->prepare( "INSERT IGNORE INTO analysis_description (analysis_id, display_label, description, displayable, web_data) VALUES (?,?,?,?,?)");
    $sth->bind_param(1,$a->dbID,SQL_INTEGER);   
    $sth->bind_param(2,$a->display_label(),SQL_VARCHAR);
    $sth->bind_param(3,$a->description,SQL_LONGVARCHAR);     
    $sth->bind_param(4,$a->displayable,SQL_TINYINT);
    #my $web_data = $self->dump_data($a->web_data());
    $sth->bind_param(5,$web_data,SQL_LONGVARCHAR);
    $sth->execute();

    }

  }


    $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:

Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation