ensembl-hive
2.6
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Public Member Functions | |
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 () |
This class is a wrapper around DBIs datbase handle. It provides some additional functionality such as the ability to automatically disconnect when inactive and reconnect when needed. Generally this class will be used through one of the object adaptors or the Bio::EnsEMBL::Registry and will not be instantiated directly.
Definition at line 42 of file DBConnection.pm.
protected Bio::EnsEMBL::DBSQL::DBConnection::_driver_object | ( | ) |
public SQLStatement Bio::EnsEMBL::DBSQL::DBConnection::add_limit_clause | ( | ) |
Arg [1] : string $sql Arg [2] : int $max_number Example :
Description: Giving an SQL statement, it adds a limit clause, dependent on the database (in MySQL, should add a LIMIT at the end, MSSQL uses a TOP clause) Returntype : String containing the new valid SQL statement Exceptions : none Caller : general Status : at risk
public void Bio::EnsEMBL::DBSQL::DBConnection::connect | ( | ) |
Example :
Description: Connects to the database using the connection attribute information. Returntype : none Exceptions : none Caller : new, db_handle Status : Stable
public Undef Bio::EnsEMBL::DBSQL::DBConnection::connected | ( | ) |
Example :
Description: Boolean which tells if DBConnection is connected or not. State is set internally, and external processes should not alter state. Returntype : undef or 1 Exceptions : none Caller : db_handle, connect, disconnect_if_idle, user processes Status : Stable
public DBI Bio::EnsEMBL::DBSQL::DBConnection::db_handle | ( | ) |
Arg [1] : DBI Database Handle $value Example :
Description: Getter / Setter for the Database handle used by this database connection. Returntype : DBI Database Handle Exceptions : none Caller : new, DESTROY Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::dbname | ( | ) |
Arg [1] : (optional) string $arg The new value of the database name used by this connection. Example :
Description: Getter/Setter for the name of the database used by this connection. There is currently no point in setting this value after the connection has already been established by the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public Bio::EnsEMBL::DBSQL::DBConnection::disconnect_count | ( | ) |
Undocumented method
public Boolean Bio::EnsEMBL::DBSQL::DBConnection::disconnect_if_idle | ( | ) |
Arg [1] : none Example :
Description: Disconnects from the database if there are no currently active statement handles. It is called automatically by the DESTROY method of the Bio::EnsEMBL::DBSQL::SQL::StatementHandle if the disconect_when_inactive flag is set. Users may call it whenever they want to disconnect. Connection will reestablish on next access to db_handle() Returntype : 1 or 0 1=problem trying to disconnect while a statement handle was still active Exceptions : none Caller : Bio::EnsEMBL::DBSQL::SQL::StatementHandle::DESTROY Bio::EnsEMBL::DBSQL::DBConnection::do Status : Stable
public Boolean Bio::EnsEMBL::DBSQL::DBConnection::disconnect_when_inactive | ( | ) |
Arg [1] : (optional) boolean $newval Example :
Description: Getter/Setter for the disconnect_when_inactive flag. If set to true this DBConnection will continually disconnect itself when there are no active statement handles and reconnect as necessary. Useful for farm environments when there can be many (often inactive) open connections to a database at once. Returntype : boolean Exceptions : none Caller : Pipeline Status : Stable
public Result Bio::EnsEMBL::DBSQL::DBConnection::do | ( | ) |
Arg [1] : string $string the SQL statement to prepare Example :
Description: Executes a SQL statement using the internal DBI database handle. Returntype : Result of DBI dbh do() method Exceptions : thrown if the SQL statement is empty, or if the internal database handle is not present. Caller : Adaptor modules Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::driver | ( | ) |
Arg [1] : (optional) string $arg the name of the driver to use to connect to the database Example :
Description: Getter / Setter for the driver this connection uses. Right now there is no point to setting this value after a connection has already been established in the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public Boolean Bio::EnsEMBL::DBSQL::DBConnection::equals | ( | ) |
Example :
Description: Equality checker for DBConnection objects Returntype : boolean Exceptions : none Caller : new Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::from_date_to_seconds | ( | ) |
Arg [1] : date $date Example :
Description: Giving a string representing a column of type date applies the database function to convert to the number of seconds from 01-01-1970 Returntype : string Exceptions : none Caller : general Status : at risk
public String Bio::EnsEMBL::DBSQL::DBConnection::from_seconds_to_date | ( | ) |
Arg [1] : int $seconds Example :
Description: Giving an int representing number of seconds applies the database function to convert to a date Returntype : string Exceptions : none Caller : general Status : at risk
public String Bio::EnsEMBL::DBSQL::DBConnection::host | ( | ) |
Arg [1] : (optional) string $arg The new value of the host used by this connection. Example :
Description: Getter/Setter for the domain name of the database host use by this connection. There is currently no point in setting this value after the connection has already been established by the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::hostname | ( | ) |
Arg [1] : (optional) string $arg The new value of the host used by this connection. Example :
Description: Convenience alias for the host method Returntype : String
public String Bio::EnsEMBL::DBSQL::DBConnection::locator | ( | ) |
Arg [1] : none Example :
Description: Constructs a locator string for this database connection that can, for example, be used by the DBLoader module Returntype : string Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::DBConnection::new | ( | ) |
Arg [DBNAME] : (optional) string The name of the database to connect to. Arg [HOST] : (optional) string The domain name of the database host to connect to. 'localhost' by default. Arg [USER] : string The name of the database user to connect with Arg [PASS] : (optional) string The password to be used to connect to the database Arg [PORT] : (optional) int The port to use when connecting to the database 3306 by default if the driver is mysql. Arg [DRIVER] : (optional) string The type of database driver to use to connect to the DB mysql by default. Arg [DBCONN] : (optional) Open another handle to the same database as another connection If this argument is specified, no other arguments should be specified. Arg [DISCONNECT_WHEN_INACTIVE]: (optional) boolean If set to true, the database connection will be disconnected everytime there are no active statement handles. This is useful when running a lot of jobs on a compute farm which would otherwise keep open a lot of connections to the database. Database connections are automatically reopened when required.Do not use this option together with RECONNECT_WHEN_CONNECTION_LOST. Arg [WAIT_TIMEOUT]: (optional) integer Time in seconds for the wait timeout to happen. Time after which the connection is deleted if not used. By default this is 28800 (8 hours) on most systems. So set this to greater than this if your connection are getting deleted. Only set this if you are having problems and know what you are doing. Arg [RECONNECT_WHEN_CONNECTION_LOST]: (optional) boolean In case you're reusing the same database connection, i.e. DISCONNECT_WHEN_INACTIVE is set to false and running a job which takes a long time to process (over 8hrs), which means that the db connection may be lost, set this option to true. On each prepare or do statement the db handle will be pinged and the database connection will be reconnected if it's lost.
Example :
Description: Constructor for a Database Connection. Any adaptors that require database connectivity should inherit from this class. Returntype : Bio::EnsEMBL::DBSQL::DBConnection Exceptions : thrown if USER or DBNAME are not specified, or if the database cannot be connected to. Caller : Bio::EnsEMBL::Utils::ConfigRegistry ( for newer code using the registry) Bio::EnsEMBL::DBSQL::DBAdaptor ( for old style code) Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::pass | ( | ) |
Arg [1] : (optional) string $arg The new value of the password used by this connection. Example :
Description: Convenience alias for the password method Returntype : String
public String Bio::EnsEMBL::DBSQL::DBConnection::password | ( | ) |
Arg [1] : (optional) string $arg The new value of the password used by this connection. Example :
Description: Getter/Setter for the password of to use for this connection. There is currently no point in setting this value after the connection has already been established by the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public String Bio::EnsEMBL::DBSQL::DBConnection::port | ( | ) |
Arg [1] : (optional) int $arg the TCP or UDP port to use to connect to the database Example :
Description: Getter / Setter for the port this connection uses to communicate to the database daemon. There currently is no point in setting this value after the connection has already been established by the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public DBI Bio::EnsEMBL::DBSQL::DBConnection::prepare | ( | ) |
Arg [1] : string $string the SQL statement to prepare Example :
Description: Prepares a SQL statement using the internal DBI database handle and returns the DBI statement handle. Returntype : DBI statement handle Exceptions : thrown if the SQL statement is empty, or if the internal database handle is not present Caller : Adaptor modules Status : Stable
public DBI Bio::EnsEMBL::DBSQL::DBConnection::prepare_cached | ( | ) |
Arg [1] : string $string the SQL statement to prepare Example :
Description: Prepares a SQL statement using the internal DBI database handle and returns the DBI statement handle. The prepared statement is cached so that it does not have to be prepared again.
If only a subset of rows are required, finish() should be called on the object to free up the statement handle.
For further information please consult https://metacpan.org/pod/DBI#prepare_cached Returntype : DBI statement handle Exceptions : thrown if the SQL statement is empty, or if the internal database handle is not present Caller : Adaptor modules Status : Experimental
public void Bio::EnsEMBL::DBSQL::DBConnection::prevent_disconnect | ( | ) |
Arg[1] : CodeRef $callback Example :
Description : A wrapper method which prevents database disconnection for the duration of the callback. This is very useful if you need to make multiple database calls avoiding excessive database connection creation/destruction but still want the API to disconnect after the body of work.
The value of disconnect_when_inactive() is set to 0 no matter what the original value was & after $callback has been executed. If disconnect_when_inactive() was already set to 0 then this method will be an effective no-op. Returntype : None Exceptions : Raised if there are issues with reverting the connection to its default state. Caller : DBConnection methods Status : Beta
public Bio::EnsEMBL::DBSQL::DBConnection::query_count | ( | ) |
Undocumented method
public ArrayRef Bio::EnsEMBL::DBSQL::DBConnection::quote_identifier | ( | ) |
Arg [n] : scalar/ArrayRef Example :
Description: Executes the DBI quote_identifier method which will quote any given string using the database driver's quote character. Returntype : ArrayRef Exceptions : None Caller : General Status : Stable
public void Bio::EnsEMBL::DBSQL::DBConnection::reconnect | ( | ) |
Example :
Description: Reconnects to the database using the connection attribute information if db_handle no longer pingable. Returntype : none Exceptions : none Caller : new, db_handle Status : Stable
public Boolean Bio::EnsEMBL::DBSQL::DBConnection::reconnect_when_lost | ( | ) |
Arg [1] : (optional) boolean $newval Example :
Description: Getter/Setter for the reconnect_when_lost flag. If set to true the db handle will be pinged on each prepare or do statement and the connection will be reestablished in case it's lost. Useful for long running jobs (over 8hrs), which means that the db connection may be lost. Returntype : boolean Exceptions : none Caller : Pipeline Status : Stable
public Bio::EnsEMBL::Utils::SqlHelper Bio::EnsEMBL::DBSQL::DBConnection::sql_helper | ( | ) |
Example :
Description: Lazy generated instance of Bio::EnsEMBL::Utils::SqlHelper which provides useful wrapper methods for interacting with a DBConnection instance. Returntype : Bio::EnsEMBL::Utils::SqlHelper Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::DBSQL::DBConnection::timeout | ( | ) |
Undocumented method
public Hash Bio::EnsEMBL::DBSQL::DBConnection::to_hash | ( | ) |
Example :
Description: Provides a hash which is compatible with the parameters for DBConnection's new() method. This can be useful during serialisation Returntype : Hash Exceptions : none Caller : general Status : New
public String Bio::EnsEMBL::DBSQL::DBConnection::user | ( | ) |
Arg [1] : (optional) string $arg The new value of the username used by this connection. Example :
Description: Convenience alias for the username method Returntype : String
public String Bio::EnsEMBL::DBSQL::DBConnection::username | ( | ) |
Arg [1] : (optional) string $arg The new value of the username used by this connection. Example :
Description: Getter/Setter for the username used by this connection. There is currently no point in setting this value after the connection has already been established by the constructor. Returntype : string Exceptions : none Caller : new Status : Stable
public Any Bio::EnsEMBL::DBSQL::DBConnection::work_with_db_handle | ( | ) |
Arg [1] : CodeRef $callback Example :
Description: Gives access to the DBI handle to execute methods not normally provided by the DBConnection interface Returntype : Any from callback Exceptions : If the callback paramater is not a CodeRef; all other errors are re-thrown after cleanup. Caller : Adaptor modules Status : Stable