AlignDB-ToXLSX

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lib/AlignDB/ToXLSX.pm  view on Meta::CPAN

            num_format => 'yyyy-mm-dd hh:mm',
            %font,
        ),
        URL       => $workbook->add_format( color => 'blue', underline => 1, %font, ),
        URLHEADER => $workbook->add_format( color => 'blue', underline => 1, %header, %font, ),
    };
    $self->{format} = $format;

    return;
}

sub increase_row {
    my $self = shift;
    my $step = shift || 1;

    $self->{row} += $step;
}

sub increase_column {
    my $self = shift;
    my $step = shift || 1;

    $self->{column} += $step;
}

#@returns Excel::Writer::XLSX::Worksheet
sub write_header {
    my $self       = shift;
    my $sheet_name = shift;
    my $opt        = shift;

    # init
    #@type Excel::Writer::XLSX::Workbook
    my $workbook = $self->{workbook};

    #@type Excel::Writer::XLSX::Worksheet
    my $sheet  = $workbook->add_worksheet($sheet_name);
    my $format = $self->{format};

    my $header     = $opt->{header};
    my $query_name = $opt->{query_name};

    # create table header
    for ( my $i = 0; $i < $self->{column}; $i++ ) {
        $sheet->write( $self->{row}, $i, $query_name, $format->{HEADER} );
    }
    for ( my $i = 0; $i < scalar @{$header}; $i++ ) {
        $sheet->write( $self->{row}, $i + $self->{column}, $header->[$i], $format->{HEADER} );
    }
    $sheet->freeze_panes( 1, 0 );    # freeze table

    $self->increase_row;
    return $sheet;
}

sub sql2names {
    my $self = shift;
    my $sql  = shift;
    my $opt  = shift;

    # bind value
    my $bind_value = $opt->{bind_value};
    if ( !defined $bind_value ) {
        $bind_value = [];
    }

    #@type DBI
    my $dbh = $self->{dbh};

    #@type DBI
    my $sth = $dbh->prepare($sql);
    $sth->execute( @{$bind_value} );
    my @names = @{ $sth->{'NAME'} };

    return @names;
}

sub write_row {
    my $self = shift;

    #@type Excel::Writer::XLSX::Worksheet
    my $sheet = shift;
    my $opt   = shift;

    # init
    my $format = $self->{format};

    # query name
    my $query_name = $opt->{query_name};
    if ( defined $query_name ) {
        $sheet->write( $self->{row}, $self->{column} - 1, $query_name, $format->{NAME} );
    }

    # array_ref
    my $row = $opt->{row};

    # insert table
    for ( my $i = 0; $i < scalar @$row; $i++ ) {
        $sheet->write( $self->{row}, $i + $self->{column}, $row->[$i], $format->{NORMAL} );
    }

    $self->increase_row;
    return;
}

sub write_column {
    my $self = shift;

    #@type Excel::Writer::XLSX::Worksheet
    my $sheet = shift;
    my $opt   = shift;

    # init
    my $format = $self->{format};

    # query name
    my $query_name = $opt->{query_name};
    if ( defined $query_name ) {
        $sheet->write( $self->{row} - 1, $self->{column}, $query_name, $format->{NAME} );
    }

    # array_ref
    my $column = $opt->{column};

    # insert table
    $sheet->write( $self->{row}, $self->{column}, [$column], $format->{NORMAL} );

    $self->increase_column;
    return;
}

sub write_sql {
    my $self = shift;

    #@type Excel::Writer::XLSX::Worksheet
    my $sheet = shift;
    my $opt   = shift;

    # init
    my $format = $self->{format};

    # query name
    my $query_name = $opt->{query_name};
    if ( defined $query_name ) {
        $sheet->write( $self->{row}, $self->{column} - 1, $query_name, $format->{NAME} );
    }

    # bind value
    my $bind_value = $opt->{bind_value};
    if ( !defined $bind_value ) {
        $bind_value = [];
    }

    # init DBI query
    my $sql_query = $opt->{sql_query};

    #@type DBI
    my $dbh = $self->{dbh};

    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute( @{$bind_value} );

    # init $data
    my $data;
    if ( exists $opt->{data} ) {
        if ( defined $opt->{data} and ref( $opt->{data} ) eq 'ARRAY' ) {
            $data = $opt->{data};
        }
        else {
            $data = [];
            push @{$data}, [] for @{ $sth->{'NAME'} };
        }
    }

    # insert table rows
    while ( my @row = $sth->fetchrow_array ) {
        for ( my $i = 0; $i < scalar @row; $i++ ) {
            if ( exists $opt->{data} ) {
                push @{ $data->[$i] }, $row[$i];
            }
            $sheet->write( $self->{row}, $i + $self->{column}, $row[$i], $format->{NORMAL} );
        }
        $self->increase_row;
    }

    return $data;
}

sub make_combine {
    my $self = shift;
    my $opt  = shift;

    # init parameters
    my $sql_query  = $opt->{sql_query};
    my $threshold  = $opt->{threshold};
    my $standalone = $opt->{standalone};

    # bind value
    my $bind_value = $opt->{bind_value};
    unless ( defined $bind_value ) {
        $bind_value = [];
    }

    # merge_last
    my $merge_last = $opt->{merge_last};
    unless ( defined $merge_last ) {
        $merge_last = 0;
    }

    # init DBI query
    #@type DBI
    my $dbh = $self->{dbh};

    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute(@$bind_value);

    my @row_count = ();
    while ( my @row = $sth->fetchrow_array ) {
        push @row_count, \@row;
    }

    my @combined;    # return these
    my @temp_combined = ();
    my $temp_count    = 0;
    foreach my $row_ref (@row_count) {
        if ( List::MoreUtils::PP::any { $_ eq $row_ref->[0] } @{$standalone} ) {
            push @combined, [ $row_ref->[0] ];
        }
        elsif ( $temp_count < $threshold ) {
            push @temp_combined, $row_ref->[0];
            $temp_count += $row_ref->[1];

            if ( $temp_count < $threshold ) {
                next;
            }
            else {
                push @combined, [@temp_combined];
                @temp_combined = ();
                $temp_count    = 0;
            }
        }
        else {
            warn "Errors occured in calculating combined distance.\n";
        }
    }

    # Write the last weighted row which COUNT might
    #   be smaller than $threshold
    if ( $temp_count > 0 ) {
        if ($merge_last) {
            if ( @combined == 0 ) {
                @combined = ( [] );
            }
            push @{ $combined[-1] }, @temp_combined;
        }
        else {
            push @combined, [@temp_combined];
        }
    }

    return \@combined;
}

sub make_combine_piece {
    my ( $self, $opt ) = @_;

    #@type DBI
    my $dbh = $self->{dbh};

    # init parameters
    my $sql_query = $opt->{sql_query};
    my $piece     = $opt->{piece};

    # bind value
    my $bind_value = $opt->{bind_value};
    unless ( defined $bind_value ) {
        $bind_value = [];
    }

    # init DBI query
    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute(@$bind_value);

    my @row_count = ();
    while ( my @row = $sth->fetchrow_array ) {
        push @row_count, \@row;
    }

    my $sum;
    $sum += $_->[1] for @row_count;
    my $small_chunk = $sum / $piece;

    my @combined;    # return these
    my @temp_combined = ();
    my $temp_count    = 0;
    for my $row_ref (@row_count) {
        if ( $temp_count < $small_chunk ) {
            push @temp_combined, $row_ref->[0];
            $temp_count += $row_ref->[1];

            if ( $temp_count >= $small_chunk ) {
                push @combined, [@temp_combined];
                @temp_combined = ();
                $temp_count    = 0;
            }
        }
        else {
            warn "Errors occured in calculating combined distance.\n";
        }
    }

    # Write the last weighted row which COUNT might
    #   be smaller than $threshold
    if ( $temp_count > 0 ) {
        push @combined, [@temp_combined];
    }

    return \@combined;
}

sub make_last_portion {
    my ( $self, $opt ) = @_;

    #@type DBI
    my $dbh = $self->{dbh};

    # init parameters
    my $sql_query = $opt->{sql_query};
    my $portion   = $opt->{portion};

    # init DBI query
    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute;

    my @row_count = ();
    while ( my @row = $sth->fetchrow_array ) {
        push @row_count, \@row;
    }

    my @last_portion;    # return @last_portion
    my $all_length = 0;  # return $all_length
    foreach (@row_count) {
        $all_length += $_->[2];
    }
    my @rev_row_count = reverse @row_count;
    my $temp_length   = 0;
    foreach (@rev_row_count) {
        push @last_portion, $_->[0];
        $temp_length += $_->[2];
        if ( $temp_length >= $all_length * $portion ) {
            last;
        }
    }

    return ( $all_length, \@last_portion );
}

sub excute_sql {
    my ( $self, $opt ) = @_;

    # bind value
    my $bind_value = $opt->{bind_value};
    unless ( defined $bind_value ) {
        $bind_value = [];
    }

    # init DBI query
    my $sql_query = $opt->{sql_query};

    #@type DBI
    my $dbh = $self->{dbh};

    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute( @{$bind_value} );
}

sub check_column {
    my ( $self, $table, $column ) = @_;

    # init
    #@type DBI
    my $dbh = $self->{dbh};

    {    # check table existing
        my @table_names = $dbh->tables( '', '', '' );

        # table names are quoted by ` (back-quotes) which is the
        #   quote_identifier
        my $table_name = "`$table`";
        unless ( List::MoreUtils::PP::any { $_ =~ /$table_name/i } @table_names ) {
            print " " x 4, "Table $table does not exist\n";
            return 0;
        }
    }

    {    # check column existing
        my $sql_query = qq{
            SHOW FIELDS
            FROM $table
            LIKE "$column"
        };

        #@type DBI
        my $sth = $dbh->prepare($sql_query);
        $sth->execute();
        my ($field) = $sth->fetchrow_array;

        if ( not $field ) {
            print " " x 4, "Column $column does not exist\n";
            return 0;
        }
    }

    {    # check values in column
        my $sql_query = qq{
            SELECT COUNT($column)
            FROM $table
        };

        #@type DBI
        my $sth = $dbh->prepare($sql_query);
        $sth->execute;
        my ($count) = $sth->fetchrow_array;

        if ( not $count ) {
            print " " x 4, "Column $column has no records\n";
        }

        return $count;
    }
}

sub quantile {
    my ( $self, $data, $part_number ) = @_;

    my $stat = Statistics::Descriptive::Full->new();

    $stat->add_data(@$data);

    my $min = $stat->min;
    my @quantiles;
    my $base = 100 / $part_number;
    for ( 1 .. $part_number - 1 ) {
        my $percentile = $stat->percentile( $_ * $base );
        push @quantiles, $percentile;
    }
    my $max = $stat->max;

    return [ $min, @quantiles, $max, ];
}

sub quantile_sql {
    my ( $self, $opt, $part_number ) = @_;

    #@type DBI
    my $dbh = $self->{dbh};

    # bind value
    my $bind_value = $opt->{bind_value};
    unless ( defined $bind_value ) {
        $bind_value = [];
    }

    # init DBI query
    my $sql_query = $opt->{sql_query};

    #@type DBI
    my $sth = $dbh->prepare($sql_query);
    $sth->execute(@$bind_value);

    my @data;

    while ( my @row = $sth->fetchrow_array ) {
        push @data, $row[0];
    }

    return $self->quantile( \@data, $part_number );
}

sub calc_threshold {
    my $self = shift;

    my ( $combine, $piece );

    #@type DBI
    my $dbh = $self->{dbh};

    #@type DBI
    my $sth = $dbh->prepare(
        q{
        SELECT SUM(FLOOR(align_comparables / 500) * 500)
        FROM align
        }
    );
    $sth->execute;
    my ($total_length) = $sth->fetchrow_array;

    if ( $total_length <= 5_000_000 ) {
        $piece = 10;
    }
    elsif ( $total_length <= 10_000_000 ) {
        $piece = 10;
    }
    elsif ( $total_length <= 100_000_000 ) {
        $piece = 20;
    }
    elsif ( $total_length <= 1_000_000_000 ) {
        $piece = 50;
    }
    else {
        $piece = 100;
    }

    if ( $total_length <= 1_000_000 ) {
        $combine = 100;
    }
    elsif ( $total_length <= 5_000_000 ) {
        $combine = 500;
    }
    else {
        $combine = 1000;
    }

    return ( $combine, $piece );
}

# See HACK #7 in OReilly.Excel.Hacks.2nd.Edition.
sub add_index_sheet {
    my $self = shift;



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