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 ()

protected String	_interval_seconds_sql ()

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 ()

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

public void	connect ()

public Undef	connected ()

public	disconnect_count ()

public	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 DBI	prepare_cached ()

public void	reconnect ()

public Result	do ()

public Any	work_with_db_handle ()

public void	prevent_disconnect ()

public ArrayRef	quote_identifier ()

public Boolean	disconnect_if_idle ()

public SQLStatement	add_limit_clause ()

public String	from_date_to_seconds ()

public String	from_seconds_to_date ()

public Bio::EnsEMBL::Utils::SqlHelper	sql_helper ()

public Hash	to_hash ()

protected	_driver_object ()

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 20 of file DBConnection.pm.

Member Function Documentation

◆ _interval_seconds_sql()

protected String Bio::EnsEMBL::Hive::DBSQL::DBConnection::_interval_seconds_sql ( )

  Argument[1] : String. Name of the column for the start of the interval
  Argument[2] : String, optional. Name of the column for the end of the interval
  Example     :

$self->dbc->_interval_seconds_sql();

  Description : Returns an SQL expression to compute the number of seconds betwen both columns.
                If the second column name is missing, compute the number of seconds until now instead.
  Returntype  : String
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

click to view

◆ _optional_pair()

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

Undocumented method

Code:

click to view

◆ connect()

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

Undocumented method

Code:

click to view

◆ 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:

click to view

sub has_write_access {
    my $self = shift;
    if ($self->driver eq 'mysql') {
        my $current_user = $self->selectrow_arrayref('SELECT CURRENT_USER()');
        # munge grantee - user and host specification need single quoting
        my $grantee = join '@', map { qq{'$_'} } split /@/, @$current_user[0];
        # instance wide privileges
        my $access_sql =
            q{SELECT COUNT(*)
                FROM information_schema.user_privileges
               WHERE PRIVILEGE_TYPE IN ('INSERT', 'DELETE', 'UPDATE')
                 AND GRANTEE = ?};
        my $user_entries =
            $self->selectall_arrayref($access_sql, undef, $grantee);
        # schema specific privileges
        $access_sql =
            q{SELECT COUNT(*)
                FROM information_schema.schema_privileges
               WHERE PRIVILEGE_TYPE IN ('INSERT', 'DELETE', 'UPDATE')
                 AND DATABASE() LIKE TABLE_SCHEMA
                 AND GRANTEE = ?};
        my $schema_entries =
            $self->selectall_arrayref($access_sql, undef, $grantee);
        my $has_write_access_from_some_host = 0;
        foreach my $entry (@$user_entries, @$schema_entries) {
            $has_write_access_from_some_host ||= !!(3 == @$entry[0]);
        }
        return $has_write_access_from_some_host;
    } elsif ($self->driver eq 'pgsql') {
        my $access_sql =
            q{SELECT COUNT(*)
                FROM (SELECT DISTINCT PRIVILEGE_TYPE
                        FROM information_schema.table_privileges
                       WHERE PRIVILEGE_TYPE IN ('INSERT', 'DELETE', 'UPDATE')
                         AND GRANTEE = current_user
                         AND TABLE_CATALOG = current_database()) AS temp};
        my $user_entries =
            $self->selectall_arrayref($access_sql, undef);
        my $has_write_access_from_some_host = 0;
        foreach my $entry (@$user_entries) {
            $has_write_access_from_some_host ||= !!(3 == @$entry[0]);
        }
        return $has_write_access_from_some_host;
    } else {
        # TODO: implement this for other drivers
        return 1;
    }
}

◆ new()

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

Undocumented method

Code:

click to view

◆ protected_prepare_execute()

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

Undocumented method

Code:

click to view

◆ 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:

click to view

◆ 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:

click to view

◆ to_cmd()

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

Undocumented method

Code:

click to view

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:

click to view

◆ 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:

click to view

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

◆ _interval_seconds_sql()

◆ _optional_pair()

◆ connect()

◆ has_write_access()

◆ new()

◆ protected_prepare_execute()

◆ requires_write_access()

◆ run_in_transaction()

◆ to_cmd()

◆ to_url_hash()

◆ url()