Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor:

Public Member Functions
public	default_table_name ()

public	default_insertion_method ()

public	default_overflow_limit ()

public	default_input_column_mapping ()

public	do_not_update_columns ()

public	new ()

public	db ()

public	dbc ()

public	prepare ()

public	overflow_limit ()

public	input_column_mapping ()

public	table_name ()

public	insertion_method ()

public	column_set ()

public	primary_key ()

public	updatable_column_list ()

public	autoinc_id ()

protected	_table_info_loader ()

public	count_all ()

public	fetch_all ()

public	primary_key_constraint ()

public	fetch_by_dbID ()

public	remove_all ()

public	remove ()

public	update ()

public	store_or_update_one ()

public	check_object_present_in_db_by_content ()

public	class_specific_execute ()

public	store ()

protected	_multi_column_filter ()

public	DESTROY ()

public	AUTOLOAD ()

Detailed Description

Description

    The base class for all other Object- or NakedTable- adaptors.
    Performs the low-level SQL needed to retrieve and store data in tables.

Definition at line 13 of file BaseAdaptor.pm.

Member Function Documentation

◆ _multi_column_filter()

protected Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::_multi_column_filter ( )

Undocumented method

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◆ _table_info_loader()

protected Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::_table_info_loader ( )

Undocumented method

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◆ autoinc_id()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::autoinc_id ( )

Undocumented method

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◆ AUTOLOAD()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::AUTOLOAD ( )

Undocumented method

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sub AUTOLOAD {
    our $AUTOLOAD;
    if($AUTOLOAD =~ /::fetch(_all)?(?:_by_(\w+?))?(?:_HASHED_FROM_(\w+?))?(?:_TO_(\w+?))?$/) {
        my $all             = $1;
        my $filter_string   = $2;
        my $key_string      = $3;
        my $value_column    = $4;
        my ($self) = @_;
        my $column_set = $self->column_set();
        my $key_components = $key_string && [ split(/_AND_/i, $key_string) ];
        if($key_components) {
            foreach my $column_name ( @$key_components ) {
                unless($column_set->{$column_name}) {
                    throw("unknown column '$column_name'");
                }
            }
        }
        if($value_column && !$column_set->{$value_column}) {
            throw("unknown column '$value_column'");
        }
#        warn "Setting up '$AUTOLOAD' method\n";
        *$AUTOLOAD = sub {
            my $self = shift @_;
            return $self->fetch_all(
                $self->_multi_column_filter($filter_string, \@_, $column_set),
                !$all,
                $key_components,
                $value_column
            );
        };
        goto &$AUTOLOAD;    # restart the new method
    } elsif($AUTOLOAD =~ /::count_all(?:_by_(\w+?))?(?:_HASHED_FROM_(\w+?))?$/) {
        my $filter_string   = $1;
        my $key_string      = $2;
        my ($self) = @_;
        my $column_set = $self->column_set();
        my $key_components = $key_string && [ split(/_AND_/i, $key_string) ];
        if($key_components) {
            foreach my $column_name ( @$key_components ) {
                unless($column_set->{$column_name}) {
                    throw("unknown column '$column_name'");
                }
            }
        }
#        warn "Setting up '$AUTOLOAD' method\n";
        *$AUTOLOAD = sub {
            my $self = shift @_;
            return $self->count_all(
                $self->_multi_column_filter($filter_string, \@_, $column_set),
                $key_components,
            );
        };
        goto &$AUTOLOAD;    # restart the new method
    } elsif($AUTOLOAD =~ /::remove_all_by_(\w+)$/) {
        my $filter_string   = $1;
        my ($self) = @_;
        my $column_set = $self->column_set();
#        warn "Setting up '$AUTOLOAD' method\n";
        *$AUTOLOAD = sub {
            my $self = shift @_;
            return $self->remove_all(
                $self->_multi_column_filter($filter_string, \@_, $column_set),
            );
        };
        goto &$AUTOLOAD;    # restart the new method
    } elsif($AUTOLOAD =~ /::update_(\w+)$/) {
        my @columns_to_update = split(/_AND_/i, $1);
#        warn "Setting up '$AUTOLOAD' method\n";
        *$AUTOLOAD = sub { my ($self, $object) = @_; return $self->update($object, @columns_to_update); };
        goto &$AUTOLOAD;    # restart the new method
    } else {
        warn "sub '$AUTOLOAD' not implemented";
    }
}

◆ check_object_present_in_db_by_content()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::check_object_present_in_db_by_content ( )

Undocumented method

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◆ class_specific_execute()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::class_specific_execute ( )

Undocumented method

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◆ column_set()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::column_set ( )

Undocumented method

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◆ count_all()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::count_all ( )

Undocumented method

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◆ db()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::db ( )

Undocumented method

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◆ dbc()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::dbc ( )

Undocumented method

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◆ default_input_column_mapping()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_input_column_mapping ( )

Undocumented method

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◆ default_insertion_method()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_insertion_method ( )

Undocumented method

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◆ default_overflow_limit()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_overflow_limit ( )

Undocumented method

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◆ default_table_name()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_table_name ( )

Undocumented method

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◆ DESTROY()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::DESTROY ( )

Undocumented method

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◆ do_not_update_columns()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::do_not_update_columns ( )

Undocumented method

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◆ fetch_all()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::fetch_all ( )

Undocumented method

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sub fetch_all {
    my ($self, $constraint, $one_per_key, $key_list, $value_column) = @_;
    
    my $table_name              = $self->table_name();
    my $input_column_mapping    = $self->input_column_mapping();
    my $sql = 'SELECT ' . join(', ', map { $input_column_mapping->{$_} // "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name";
    if($constraint) { 
            # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
        $sql .= (($constraint=~/\bJOIN\b/i or $constraint=~/^LIMIT|ORDER|GROUP/) ? ' ' : ' WHERE ') . $constraint;
    }
    # warn "SQL: $sql\n";
    my $sth = $self->prepare($sql);
    $sth->execute;  
    my @overflow_columns = keys %{ $self->overflow_limit() };
    my $overflow_adaptor = scalar(@overflow_columns) && $self->db->get_AnalysisDataAdaptor();
    my $result_struct;  # will be autovivified to the correct data structure
    while(my $hashref = $sth->fetchrow_hashref) {
        foreach my $overflow_key (@overflow_columns) {
            if($hashref->{$overflow_key} =~ /^_ext(?:\w+)_data_id (\d+)$/) {
                $hashref->{$overflow_key} = $overflow_adaptor->fetch_by_analysis_data_id_TO_data($1);
            }
        }
        my $pptr = \$result_struct;
        if($key_list) {
            foreach my $syll (@$key_list) {
                $pptr = \$$pptr->{$hashref->{$syll}};   # using pointer-to-pointer to enforce same-level vivification
            }
        }
        my $object = $value_column
            ? ( (ref($value_column) eq 'ARRAY')
                    ? { map { ($_ => $hashref->{$_}) } @$value_column } # project to a subhash
                    : $hashref->{$value_column}                         # project to just one field
              )
            : $self->objectify($hashref);                               # keep the whole object
        if($one_per_key) {
            $$pptr = $object;                                           # just return the one value (either the key_list is unique or override)
        } else {
            push @$$pptr, $object;                                      # return a list of values that potentially share the same key_list
        }
    }
    $sth->finish;  
    unless(defined($result_struct)) {
        if($key_list and scalar(@$key_list)) {
            $result_struct = {};
        } elsif(!$one_per_key) {
            $result_struct = [];
        }
    }
    return $result_struct;  # either listref or hashref is returned, depending on the call parameters
}

◆ fetch_by_dbID()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::fetch_by_dbID ( )

Undocumented method

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◆ input_column_mapping()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::input_column_mapping ( )

Undocumented method

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◆ insertion_method()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::insertion_method ( )

Undocumented method

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◆ new()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::new ( )

Undocumented method

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◆ overflow_limit()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::overflow_limit ( )

Undocumented method

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◆ prepare()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::prepare ( )

Undocumented method

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◆ primary_key()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::primary_key ( )

Undocumented method

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◆ primary_key_constraint()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::primary_key_constraint ( )

Undocumented method

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◆ remove()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::remove ( )

Undocumented method

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◆ remove_all()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::remove_all ( )

Undocumented method

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◆ store()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::store ( )

Undocumented method

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sub store {
    my ($self, $object_or_list) = @_;
    my $objects = (ref($object_or_list) eq 'ARRAY')     # ensure we get an array of objects to store
        ? $object_or_list
        : [ $object_or_list ];
    return ([], 0) unless(scalar(@$objects));
    my $table_name              = $self->table_name();
    my $autoinc_id              = $self->autoinc_id();
    my $all_storable_columns    = [ grep { $_ ne $autoinc_id } keys %{ $self->column_set() } ];
    my $driver                  = $self->dbc->driver();
    my $insertion_method        = $self->insertion_method;  # INSERT, INSERT_IGNORE or REPLACE
    $insertion_method           =~ s/_/ /g;
    if($driver eq 'sqlite') {
        $insertion_method =~ s/INSERT IGNORE/INSERT OR IGNORE/ig;
    } elsif($driver eq 'pgsql') {
        # Rules have been created to mimic the behaviour INSERT IGNORE / REPLACE
        # Here we can do fall-back to a standard INSERT
        $insertion_method = 'INSERT';
    }
    my %hashed_sth = ();  # do not prepare statements until there is a real need
    my $stored_this_time        = 0;
    foreach my $object (@$objects) {
            my ($columns_being_stored, $column_key) = $self->keys_to_columns($object);
            # warn "COLUMN_KEY='$column_key'\n";
            my $this_sth;
                # only prepare (once!) if we get here:
            unless($this_sth = $hashed_sth{$column_key}) {
                    # By using question marks we can insert true NULLs by setting corresponding values to undefs:
                my $sql = "$insertion_method INTO $table_name (".join(', ', @$columns_being_stored).') VALUES ('.join(',', (('?') x scalar(@$columns_being_stored))).')';
                # warn "STORE: $sql\n";
                $this_sth = $hashed_sth{$column_key} = $self->prepare( $sql ) or throw("Could not prepare statement: $sql");
            }
            # warn "STORED_COLUMNS: ".stringify($columns_being_stored)."\n";
            my $values_being_stored = $self->slicer( $object, $columns_being_stored );
            # warn "STORED_VALUES: ".stringify($values_being_stored)."\n";
            my $return_code = $self->class_specific_execute($object, $this_sth, $values_being_stored )
                    # using $return_code in boolean context allows to skip the value '0E0' ('no rows affected') that Perl treats as zero but regards as true:
                or throw("Could not store fields\n\t{$column_key}\nwith data:\n\t(".join(',', @$values_being_stored).')');
            if($return_code > 0) {     # <--- for the same reason we have to be explicitly numeric here
                # FIXME: does this work if the "MySQL server has gone away" ?
                my $liid = $autoinc_id && $self->dbc->db_handle->last_insert_id(undef, undef, $table_name, $autoinc_id);
                $self->mark_stored($object, $liid );
                ++$stored_this_time;
            }
    }
    foreach my $sth (values %hashed_sth) {
        $sth->finish();
    }
    return ($object_or_list, $stored_this_time);
}

◆ store_or_update_one()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::store_or_update_one ( )

Undocumented method

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◆ table_name()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::table_name ( )

Undocumented method

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◆ updatable_column_list()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::updatable_column_list ( )

Undocumented method

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◆ update()

public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::update ( )

Undocumented method

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

modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ _multi_column_filter()

◆ _table_info_loader()

◆ autoinc_id()

◆ AUTOLOAD()

◆ check_object_present_in_db_by_content()

◆ class_specific_execute()

◆ column_set()

◆ count_all()

◆ db()

◆ dbc()

◆ default_input_column_mapping()

◆ default_insertion_method()

◆ default_overflow_limit()

◆ default_table_name()

◆ DESTROY()

◆ do_not_update_columns()

◆ fetch_all()

◆ fetch_by_dbID()

◆ input_column_mapping()

◆ insertion_method()

◆ new()

◆ overflow_limit()

◆ prepare()

◆ primary_key()

◆ primary_key_constraint()

◆ remove()

◆ remove_all()

◆ store()

◆ store_or_update_one()

◆ table_name()

◆ updatable_column_list()

◆ update()