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

Public Member Functions
public	new ()

protected	_optional_pair ()

public	to_url_hash ()

public String	url ()

public	connect ()

public	protected_prepare_execute ()

public	to_cmd ()

public	run_in_transaction ()

public Boolean	has_write_access ()

public void	requires_write_access ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::DBSQL::CoreDBConnection
public Bio::EnsEMBL::DBSQL::DBConnection	new ()

public void	connect ()

public Undef	connected ()

public	disconnect_count ()

public	wait_timeout ()

public	query_count ()

public Boolean	equals ()

public String	driver ()

public String	port ()

public String	dbname ()

public String	username ()

public String	user ()

public String	host ()

public String	hostname ()

public String	password ()

public String	pass ()

public Boolean	disconnect_when_inactive ()

public Boolean	reconnect_when_lost ()

public String	locator ()

public DBI	db_handle ()

public DBI	prepare ()

public void	reconnect ()

public Any	work_with_db_handle ()

public void	prevent_disconnect ()

public Boolean	disconnect_if_idle ()

public	do ()

public	AUTOLOAD ()

public	DESTROY ()

Detailed Description

Synopsis

my $url = $dbc->url();

Description

    Extends the functionality of Bio::EnsEMBL::Hive::DBSQL::CoreDBConnection with things needed by the Hive

Definition at line 19 of file DBConnection.pm.

Member Function Documentation

◆ _optional_pair()

protected Bio::EnsEMBL::Hive::DBSQL::DBConnection::_optional_pair ( )

Undocumented method

Code:

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◆ connect()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection::connect ( )

Undocumented method

Code:

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◆ has_write_access()

public Boolean Bio::EnsEMBL::Hive::DBSQL::DBConnection::has_write_access ( )

  Example     :

my $can_do = $dbc->has_write_access();

  Description : Tells whether the underlying database connection has write access to the database
  Returntype  : Boolean
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

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◆ new()

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

Undocumented method

Code:

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◆ protected_prepare_execute()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection::protected_prepare_execute ( )

Undocumented method

Code:

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◆ requires_write_access()

public void Bio::EnsEMBL::Hive::DBSQL::DBConnection::requires_write_access ( )

  Example     :

$dbc->requires_write_access();

  Description : See Exceptions
  Returntype  : none
  Exceptions  : Throws if the current user hasn't write access to the database
  Caller      : general
  Status      : Stable

Code:

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◆ run_in_transaction()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection::run_in_transaction ( )

    Description : Wrapper that first sets AutoCommit to 0, runs some user code, and at the end issues a commit() / rollback()
                  It also has to temporarily set disconnect_when_inactive() to 1 because a value of 0 would cause the
                  DBConnection object to disconnect early, which would rollback the transaction.
                  NB: This is essentially a trimmed copy of Ensembl's Utils::SqlHelper::transaction()

Code:

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◆ to_cmd()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection::to_cmd ( )

Undocumented method

Code:

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sub to_cmd {
    my ($self, $executable, $prepend, $append, $sqlcmd, $hide_password_in_env) = @_;
    my $driver = $self->driver || 'mysql';
    my $dbname = $self->dbname;
    if($sqlcmd) {
        if($sqlcmd =~ /(DROP\s+DATABASE(?:\s+IF\s+EXISTS)?\s*?)(?:\s+(\w+))?/i) {
            $dbname = $2 if $2;
            if($driver eq 'sqlite') {
                return ['rm', '-f', $dbname];
            } else {
                if (not $dbname) {
                    die "'DROP DATABASE' needs a database name\n";
                }
                if ($driver eq 'mysql') {
                    $sqlcmd = "$1 \`$dbname\`" unless $2;
                } else {
                    $sqlcmd = "$1 $dbname" unless $2;
                }
                $dbname = '';
            }
        } elsif($sqlcmd =~ /(CREATE\s+DATABASE(?:\s+IF\s+NOT\s+EXISTS)?\s*?)(?:\s+(\w+))?/i ) {
            $dbname = $2 if $2;
            if($driver eq 'sqlite') {
                return ['touch', $dbname];
            } else {
                if (not $dbname) {
                    die "'CREATE DATABASE' needs a database name\n";
                }
                my %limits = ( 'mysql' => 64, 'pgsql' => 63 );
                if (length($dbname) > $limits{$driver}) {
                    die "Database name '$dbname' is too long (> $limits{$driver}). Cannot create the database\n";
                }
                if ($driver eq 'mysql') {
                    $sqlcmd = "$1 \`$dbname\`" unless $2;
                } else {
                    $sqlcmd = "$1 $dbname" unless $2;
                }
                $dbname = '';
            }
        }
    }
    my @cmd;
    my $hidden_password;
    if ($self->password) {
        if ($hide_password_in_env) {
            my $pass_variable = "EHIVE_TMP_PASSWORD_${pass_internal_counter}";
            $pass_internal_counter++;
            $ENV{$pass_variable} = $self->password;
            $hidden_password = '$'.$pass_variable;
        } else {
            $hidden_password = $self->password;
        }
    }
    if($driver eq 'mysql') {
        $executable ||= 'mysql';
        push @cmd, ('env', 'MYSQL_PWD='.$hidden_password)  if ($self->password);
        push @cmd, $executable;
        push @cmd, @$prepend                        if ($prepend && @$prepend);
        push @cmd, '--host='.$self->host            if $self->host;
        push @cmd, '--port='.$self->port            if $self->port;
        push @cmd, '--user='.$self->username        if $self->username;
#        push @cmd, '--password='.$hidden_password   if $self->password;
        push @cmd, ('-e', $sqlcmd)                  if $sqlcmd;
        push @cmd, $dbname                          if $dbname;
    } elsif($driver eq 'pgsql') {
        $executable ||= 'psql';
        push @cmd, ('env', 'PGPASSWORD='.$hidden_password)  if ($self->password);
        push @cmd, $executable;
        push @cmd, @$prepend                if ($prepend && @$prepend);
        push @cmd, ('-h', $self->host)      if defined($self->host);
        push @cmd, ('-p', $self->port)      if defined($self->port);
        push @cmd, ('-U', $self->username)  if defined($self->username);
        push @cmd, ('-c', $sqlcmd)          if $sqlcmd;
        push @cmd, $dbname                  if $dbname;
    } elsif($driver eq 'sqlite') {
        $executable ||= 'sqlite3';
        die "sqlite requires a database (file) name\n" unless $dbname;
        push @cmd, $executable;
        push @cmd, @$prepend                if ($prepend && @$prepend);
        push @cmd, $dbname;
        push @cmd, $sqlcmd                  if $sqlcmd;
    }
    push @cmd, @$append                 if ($append && @$append);
    return \@cmd;
}

◆ to_url_hash()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection::to_url_hash ( )

Undocumented method

Code:

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◆ url()

public String Bio::EnsEMBL::Hive::DBSQL::DBConnection::url ( )

    Arg [1]    : String $environment_variable_name_to_store_password_in (optional)
    Example    :

$url = $dbc->url;

    Description: Constructs a URL string for this database connection.
    Returntype : string of format  mysql://<user>:<pass><host>:<port>/<dbname>
                               or  sqlite:///<dbname>
    Exceptions : none
    Caller     : general

Code:

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _optional_pair()

◆ connect()

◆ has_write_access()

◆ new()

◆ protected_prepare_execute()

◆ requires_write_access()

◆ run_in_transaction()

◆ to_cmd()

◆ to_url_hash()

◆ url()