Bio::EnsEMBL::Hive::RunnableDB::SqlCmd Class Reference

Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::SqlCmd:

Public Member Functions
public	param_defaults ()
public	run ()
protected	_exec_sql ()
public	write_output ()
Public Member Functions inherited from Bio::EnsEMBL::Hive::Process
public	new ()
public	life_cycle ()
public	say_with_header ()
public	enter_status ()
public	warning ()
public	param_defaults ()
public	fetch_input ()
public	run ()
public	write_output ()
public Bio::EnsEMBL::Hive::Worker	worker ()
public	execute_writes ()
public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::Hive::DBSQL::DBConnection	dbc ()
public Bio::EnsEMBL::Hive::DBSQL::DBConnection	data_dbc ()
public Returns	run_system_command ()
public Bio::EnsEMBL::Hive::AnalysisJob	input_job ()
public	input_id ()
public	param ()
public	param_required ()
public	param_exists ()
public	param_is_defined ()
public	param_substitute ()
public	dataflow_output_id ()
public	dataflow_output_ids_from_json ()
public	throw ()
public This	complete_early ()
public Int	debug ()
public	worker_temp_directory ()
public	cleanup_worker_temp_directory ()

Detailed Description

Synopsis

standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::SqlCmd --db_conn mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2912/lg4_compara_families_64 \
                    --sql "INSERT INTO meta(meta_key,meta_value) VALUES ('Hello', 'world')"
 
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::SqlCmd --db_conn mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2913/lg4_compara_homology_merged_64 \
                    --sql "[ 'CREATE TABLE meta_foo LIKE meta', 'INSERT INTO meta_foo SELECT * FROM meta' ]"

Description

    This RunnableDB module acts as a wrapper for an SQL command
    run against either the current hive database (default) or against one specified by 'db_conn' parameter
    (--db_conn becomes obligatory in standalone mode, because there is no hive_db).

    The Sql command must be stored in the parameters() as the value corresponding to the 'sql' key.
    It allows to pass in other parameters and use the parameter substitution mechanism in its full glory.

    The Sql command(s) can be wrapped in a global transaction if the "wrap_in_transaction" flag is switched on (off by default)

Definition at line 27 of file SqlCmd.pm.

Member Function Documentation

_exec_sql()

protected Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::_exec_sql

(

)

    Description : Actually run the sql command(s).  If a list of commands is given, they are run in succession within the same session
                  (so you can create a temporary tables and use it in another command within the same sql command list).

    param('sql'): Either a scalar SQL command or an array of SQL commands.

    param('db_conn'): An optional hash to pass in connection parameters to the database upon which the sql command(s) will have to be run.

    param('*'):   Any other parameters can be freely used for parameter substitution.

Code:

param_defaults()

public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::param_defaults

(

)

Undocumented method

Code:

run()

public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::run

(

)

    Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process that is used to perform the main bulk of the job (minus input and output).
                  Here it is a simple decision step based on the "wrap_in_transaction" parameter. If the latter is set, call _exec_sql() in a transaction,
                  otherwise call it directly.

    param('wrap_in_transaction'): Whether or not run the commands in a global transaction

Code:

write_output()

public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::write_output

(

)

    Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
                  Here we only flow out the insert_ids.

Code:

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

• modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm