Public Member Functions
public	run ()

public	args ()

public	logging ()

public	check ()

public	defaults ()

public	dry ()

public	process ()

public	sql ()

public	modify_sql ()

public	data ()

public	checksum ()

public	dbh ()

public	dbc_params ()

public	clear_dbh ()

public	is_view ()

public	tables ()

public	clear_tables ()

public	file ()

public	current_dir ()

public	clear_current_dir ()

public	opts ()

public	compress ()

public	permissions ()

public	v ()

protected	_setup_dir ()

protected	_set_opts_from_hostname ()

protected	_hostname_opts_from_config ()

protected	_host ()

protected	_all_dbs ()

protected	_cmd_line_to_array ()

public	args ()

public	run ()

public	defaults ()

public	logging ()

public	process ()

public	delete_tables ()

public	v ()

public	dbh ()

public	clear_dbh ()

public	is_view ()

public	tables ()

public	clear_tables ()

protected	_cmd_line_to_array ()

Detailed Description

Definition at line 9 of file dump_mysql.pl.

Member Function Documentation

◆ _all_dbs()

protected Script::_all_dbs ( )

Undocumented method

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◆ _cmd_line_to_array() [1/2]

protected Script::_cmd_line_to_array ( )

◆ _cmd_line_to_array() [2/2]

protected Script::_cmd_line_to_array ( )

Undocumented method

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◆ _host()

protected Script::_host ( )

Undocumented method

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◆ _hostname_opts_from_config()

protected Script::_hostname_opts_from_config ( )

Undocumented method

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◆ _set_opts_from_hostname()

protected Script::_set_opts_from_hostname ( )

Undocumented method

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◆ _setup_dir()

protected Script::_setup_dir ( )

Undocumented method

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◆ args() [1/2]

public Script::args ( )

◆ args() [2/2]

public Script::args ( )

Undocumented method

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Undocumented method

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◆ check()

public Script::check ( )

Undocumented method

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◆ checksum()

public Script::checksum ( )

Undocumented method

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◆ clear_current_dir()

public Script::clear_current_dir ( )

Undocumented method

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◆ clear_dbh() [1/2]

public Script::clear_dbh ( )

◆ clear_dbh() [2/2]

public Script::clear_dbh ( )

Undocumented method

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◆ clear_tables() [1/2]

public Script::clear_tables ( )

◆ clear_tables() [2/2]

public Script::clear_tables ( )

Undocumented method

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◆ compress()

public Script::compress ( )

Undocumented method

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◆ current_dir()

public Script::current_dir ( )

Undocumented method

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◆ data()

public Script::data ( )

Undocumented method

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◆ dbc_params()

public Script::dbc_params ( )

Undocumented method

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◆ dbh() [1/2]

public Script::dbh ( )

◆ dbh() [2/2]

public Script::dbh ( )

Undocumented method

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◆ defaults() [1/2]

public Script::defaults ( )

◆ defaults() [2/2]

public Script::defaults ( )

Undocumented method

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sub defaults {
  my ($self) = @_;
  my $o = $self->opts();
 
  #Processing -opt 1 -opt 2,3 into opt => [1,2,3]
  $self->_cmd_line_to_array('databases') if $o->{databases};
  $self->_cmd_line_to_array('groups')    if $o->{groups};
  $self->_cmd_line_to_array('species')   if $o->{species};
  
  my $original_databases_args = $o->{databases}; 
 
  #Tables
  if ($o->{tables} && !$o->{sql}) {
    $self->_cmd_line_to_array('tables');
    $self->v(q{Will work with the tables [%s]}, join(q{,}, @{ $o->{tables} }));
  }
  
  if ($o->{defaults}) {
    $self->_set_opts_from_hostname();
  } else {
    $o->{port} = 3306 if !$o->{port};
    if ($o->{pattern}) {
      my $p = $o->{pattern};
      $p = qr/$p/;
      $o->{databases} = $self->_all_dbs($p);
    }
    $o->{directory} = File::Spec->rel2abs($o->{directory});
  }
  
    if(! $o->{username}) {
    pod2usage(
      -msg     => 'No -username given on the command line or in the configuration file',
      -exitval => 1,
      -verbose => 0
    );
  }
 
  $self->v(q{Using the database server %s@%s:%d},
           map { $o->{$_} } qw/username host port/);
 
  #Filter for those on the specified server; sometimes redundant
  my %dbs = map { $_ => 1 } @{ $self->_all_dbs() };
  my @final_dbs;
  foreach my $db (@{$o->{databases}}) {
    if($dbs{$db}) {
      push(@final_dbs, $db);
    }
    else {
      $self->v('DB %s is not available from the specified server', $db);
    }
  }
  $o->{databases} = \@final_dbs;
 
  #Filtering DBs based on groups & species
  if ($o->{groups}) {
    my %dbs;
    foreach my $group (@{ $o->{groups} }) {
      $self->v('Filtering for group %s', $group);
      %dbs = map { $_ => 1 } grep { / _ $group _ /xms } @{ $o->{databases} };
    }
    $o->{databases} = [ keys %dbs ];
  }
  if ($o->{species}) {
    my %dbs;
    foreach my $species (@{ $o->{species} }) {
      $self->v('Filtering for species %s', $species);
      %dbs = map { $_ => 1 } grep { / $species _ /xms } @{ $o->{databases} };
    }
    $o->{databases} = [ keys %dbs ];
  }
 
  #Do we have any DBs left to process?
  my $db_count = scalar(@{ $o->{databases} });
  if ($db_count == 0) {
    my $msg = 'No databases found on the server ' . $o->{host};
    if($original_databases_args && $o->{defaults}) {
      my $version  = $o->{version} || '-NONE';
      $msg .= qq{. You specified the -database arg and -defaults. Are you on the correct server or did  -version '$version' excluded this DB?};
    }
    pod2usage(-msg => $msg, -exitval => 1, -verbose => 0);
  }
  $self->v(q{Working %d database(s)}, $db_count);
 
  $o->{databases} = [ sort { $a cmp $b } @{ $o->{databases} } ];
  
  $o->{verbose} = 1 if $o->{dry};
 
  return;
}

Undocumented method

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◆ delete_tables()

public Script::delete_tables ( )

Undocumented method

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◆ dry()

public Script::dry ( )

Undocumented method

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◆ file()

public Script::file ( )

Undocumented method

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◆ is_view() [1/2]

public Script::is_view ( )

◆ is_view() [2/2]

public Script::is_view ( )

Undocumented method

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◆ logging() [1/2]

public Script::logging ( )

Undocumented method

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◆ logging() [2/2]

public Script::logging ( )

◆ modify_sql()

public Script::modify_sql ( )

Undocumented method

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◆ opts()

public Script::opts ( )

Undocumented method

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◆ permissions()

public Script::permissions ( )

Undocumented method

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◆ process() [1/2]

public Script::process ( )

◆ process() [2/2]

public Script::process ( )

Undocumented method

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sub process {
  my ($self) = @_;
  
  
  my $test_case = $self->opts()->{testcompatible}; 
  
  $self->v('Producing test case compatible dumps') if $test_case;
  
  my $databases = $self->opts()->{databases};
  foreach my $db (@{$databases}) {
    $self->v('Working with database %s', $db);
 
    #Setup connection
    $self->dbh($db);
 
    $self->_setup_dir($db);
 
    #Get all tables
    my @tables = keys %{ $self->tables() };
 
    #Do data dumps if we didn't ask for just SQL
    if (!$self->opts()->{sql}) {
      my @tables_to_process;
      if ($self->opts()->{tables}) {
        my %lookup;
        %lookup = map { $_ => 1 } @{ $self->opts()->{tables} };
        @tables_to_process = grep { $lookup{$_} } @tables;
      } else {
        @tables_to_process = @tables;
      }
      foreach my $table (sort { $a cmp $b } @tables_to_process) {
        next if $self->is_view($table);
        $self->data($table, $db);
      }
    } else {
      $self->v('-sql mode is on so no data dumping will occur');
    }
 
    #Do SQL
    my $sql_file;
    my $fh;
    if($test_case) {
      $sql_file = $self->file('table.sql');
      unlink $sql_file if -f $sql_file;
      open $fh, '>', $sql_file or croak "Cannot open filehandle to $sql_file: $!"; 
    }
    else {
      $sql_file = $self->file($db . '.sql.gz');
      unlink $sql_file if -f $sql_file;
      $fh = IO::Compress::Gzip->new($sql_file) or croak "Cannot create gzip stream to $sql_file: $GzipError";
    }
    
    my $writer = sub {
      my (@tabs) = @_;
      foreach my $table (sort { $a cmp $b } @tabs) {
        my $sql = $self->sql($table);
        print $fh $sql, ';', "\n" x 2;
      }
    };
    $writer->(grep { !$self->is_view($_) } @tables);
    $writer->(grep { $self->is_view($_) } @tables);
    $fh->close();
    $self->permissions($sql_file);
    
    #Checksum the DB's files
    $self->checksum() if ! $test_case;
 
    #Reset everything
    $self->clear_dbh();
    $self->clear_current_dir();
    $self->clear_tables();
 
    $self->v('Finished with database %s', $db);
  }
  return;
}

Undocumented method

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◆ run() [1/2]

public Script::run ( )

Undocumented method

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Undocumented method

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◆ run() [2/2]

public Script::run ( )

◆ sql()

public Script::sql ( )

Undocumented method

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◆ tables() [1/2]

public Script::tables ( )

◆ tables() [2/2]

public Script::tables ( )

Undocumented method

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◆ v() [1/2]

public Script::v ( )

◆ v() [2/2]

public Script::v ( )

Undocumented method

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

ensembl/misc-scripts/db/dump_mysql.pl
ensembl/misc-scripts/db/remove_mysqldb.pl

Public Member Functions

Detailed Description

Member Function Documentation

◆ _all_dbs()

◆ _cmd_line_to_array() [1/2]

◆ _cmd_line_to_array() [2/2]

◆ _host()

◆ _hostname_opts_from_config()

◆ _set_opts_from_hostname()

◆ _setup_dir()

◆ args() [1/2]

◆ args() [2/2]

◆ check()

◆ checksum()

◆ clear_current_dir()

◆ clear_dbh() [1/2]

◆ clear_dbh() [2/2]

◆ clear_tables() [1/2]

◆ clear_tables() [2/2]

◆ compress()

◆ current_dir()

◆ data()

◆ dbc_params()

◆ dbh() [1/2]

◆ dbh() [2/2]

◆ defaults() [1/2]

◆ defaults() [2/2]

◆ delete_tables()

◆ dry()

◆ file()

◆ is_view() [1/2]

◆ is_view() [2/2]

◆ logging() [1/2]

◆ logging() [2/2]

◆ modify_sql()

◆ opts()

◆ permissions()

◆ process() [1/2]

◆ process() [2/2]

◆ run() [1/2]

◆ run() [2/2]

◆ sql()

◆ tables() [1/2]

◆ tables() [2/2]

◆ v() [1/2]

◆ v() [2/2]