Public Member Functions
public	new ()

public	tmp_dir ()

public	source_dbh ()

public	target_dbh ()

public	close_dbh ()

public	transfer ()

public	check_possible_transfer ()

public	standard_table_transfer ()

public	read_dbs ()

public	table_rename ()

public	table_skip ()

public	column_rename ()

public	column_skip ()

public	custom_select ()

public	set_row_modifier ()

public	clear_target ()

public	big_table ()

public	do_first ()

Detailed Description

Definition at line 3 of file SchemaConverter.pm.

Member Function Documentation

◆ big_table()

public SchemaConverter::big_table ( )

Undocumented method

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◆ check_possible_transfer()

public SchemaConverter::check_possible_transfer ( )

Undocumented method

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◆ clear_target()

public SchemaConverter::clear_target ( )

Undocumented method

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◆ close_dbh()

public SchemaConverter::close_dbh ( )

Undocumented method

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◆ column_rename()

public SchemaConverter::column_rename ( )

Undocumented method

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◆ column_skip()

public SchemaConverter::column_skip ( )

Undocumented method

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◆ custom_select()

public SchemaConverter::custom_select ( )

Undocumented method

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◆ do_first()

public SchemaConverter::do_first ( )

Undocumented method

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◆ new()

public SchemaConverter::new ( )

Undocumented method

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◆ read_dbs()

public SchemaConverter::read_dbs ( )

Undocumented method

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◆ set_row_modifier()

public SchemaConverter::set_row_modifier ( )

Undocumented method

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◆ source_dbh()

public SchemaConverter::source_dbh ( )

Undocumented method

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◆ standard_table_transfer()

public SchemaConverter::standard_table_transfer ( )

Undocumented method

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sub standard_table_transfer {
  my ( $self, $sourcetable, $targettable, $tmpfile ) = @_;
  
  my $sourcedb = $self->source_dbh();
  my $targetdb = $self->target_dbh();
 
  # look for custom select
  my $select = "";
  if( exists $self->{targetdb}{tables}{$targettable}{select} ) {
    $select = $self->{targetdb}{tables}{$targettable}{select};
  } else {
    # check if all columns have matching names
    my @newcols = @{$self->{targetdb}{tables}{$targettable}{columns}};
    my @oldcols = @{$self->{sourcedb}{tables}{$sourcetable}{columns}};
    
    my %rename;
 
    if( exists $self->{targetdb}{tables}{$targettable}{columnrename} ) {
      %rename = %{$self->{targetdb}{tables}{$targettable}{columnrename}};
    } else {
      %rename = ();
    }
 
    # find all source columns and build select statement 
 
    for my $colname ( @newcols ) {
      my $selname;
 
      if( exists $rename{$colname} ) {
    $selname = $rename{$colname};
    if( $selname eq "" ) {
      $selname = "NULL";
    }
      } else {
    my $colExists = 0;
    for my $oldcol ( @oldcols ) {
      if(  $oldcol eq $colname ) {
        $selname = $colname;
        $colExists = 1;
        last;
      }
    }
    if( ! $colExists ) {
      die "Couldnt fill $targettable.$colname\n";
    }
      }
 
      $select .= " $selname,";
    }
    chop( $select );
    $select = "SELECT $select from $sourcetable";
  }    
           
  # MySQL specific ...
  # DBD doesn't use cursors; loads whole table during execute()
  # problem for large tables - "mysql_use_result" gets around this
  my $sth;
  if (defined $self->{targetdb}{tables}{$targettable}{its_a_big_un}) {
    $sth = $self->source_dbh()->prepare( $select , { mysql_use_result => 1 } );
  }
  else {
    $sth = $self->source_dbh()->prepare( $select );
  }
  $sth->execute();
  
  my $row;
  if( exists $self->{targetdb}{tables}{$targettable}{row_modify} ) {
    my $rowmod = $self->{targetdb}{tables}{$targettable}{row_modify};
 
    while( my $arref = $sth->fetchrow_arrayref() ) {
 
      $row = &{$rowmod}($arref);
 
      print $tmpfile ( join( "\t",@{$row} ),"\n" );
    }
  } else {
    while( my $arref = $sth->fetchrow_arrayref() ) {
      $row = join( "\t", @$arref );
      print $tmpfile "$row\n";
    }
  }
}

◆ table_rename()

public SchemaConverter::table_rename ( )

Undocumented method

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◆ table_skip()

public SchemaConverter::table_skip ( )

Undocumented method

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◆ target_dbh()

public SchemaConverter::target_dbh ( )

Undocumented method

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◆ tmp_dir()

public SchemaConverter::tmp_dir ( )

Undocumented method

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◆ transfer()

public SchemaConverter::transfer ( )

Undocumented method

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sub transfer {
  my $self = shift;
  
  local *FH;
  my $tmpdir;
 
  if( ! defined $self->tmp_dir() ) {
    $self->close_dbh();
    die( "No tmp_dir specified" );
  } else {
    $tmpdir = $self->tmp_dir();
  }
 
  # first we should check if all standard trnasfers can go
  # otherwise testing this is a pain
  $self->check_possible_transfer();
  my @ordered_tables = $self->{targetdb}{dofirst};
  my %all_tables = %{$self->{targetdb}{tables}};
  for my $tablename ( @ordered_tables ) {
    delete $all_tables{$tablename};
  }
  for my $tablename ( keys %all_tables ) {
    push( @ordered_tables, $tablename );
  }
 
  for my $tablename ( @ordered_tables ) {
    my $skip = 0;
    print STDERR "Transfer $tablename ";
 
    open( FH, ">$tmpdir/$tablename.txt" ) or die "cant open dumpfile";
    
    if( exists $self->{targetdb}{tables}{$tablename}{transfer} ) {
      my $transfunc = $self->{targetdb}{tables}{$tablename}{transfer};
      &$transfunc( $self->source_dbh(), $self->target_dbh(), $tablename, \*FH );
    } else {
      my $sourcetable;
      if( exists $self->{targetdb}{tables}{$tablename}{link} ) {
    $sourcetable = $self->{targetdb}{tables}{$tablename}{link};
    if( $sourcetable eq "" ) {
      # skip this table
      $skip = 1;
    }
      } else {
    # find the sourcetable
    if( exists $self->{targetdb}{tables}{$tablename}{select} ) {
 
      # if we have custom select, sourcetable doesnt make sense
      $sourcetable = undef;
 
    } elsif( ! exists $self->{sourcedb}{tables}{$tablename} ) {
 
      die "Couldnt find source for $tablename. Enter empty sourcetable.";
 
    } else {
      $sourcetable = $tablename;
    }
      }
      if( ! $skip ) {
    $self->standard_table_transfer( $sourcetable, $tablename, \*FH );
      }
    }
 
    close FH;
 
    if( ! $skip ) {
      $self->target_dbh->do( "load data infile '$tmpdir/$tablename.txt' into table $tablename" );
    }
 
    # upload ?
    unlink "$tmpdir/$tablename.txt";
    print STDERR " finished\n";
  }
 
  # close databases
  
}

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

ensembl/misc-scripts/surgery/SchemaConverter.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ big_table()

◆ check_possible_transfer()

◆ clear_target()

◆ close_dbh()

◆ column_rename()

◆ column_skip()

◆ custom_select()

◆ do_first()

◆ new()

◆ read_dbs()

◆ set_row_modifier()

◆ source_dbh()

◆ standard_table_transfer()

◆ table_rename()

◆ table_skip()

◆ target_dbh()

◆ tmp_dir()

◆ transfer()