Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer Class Reference

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

Public Member Functions
public	param_defaults ()
public	fetch_input ()
public	write_output ()
public	get_row_count ()
protected	_assert_same_table_schema ()
Public Member Functions inherited from Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
public	param_defaults ()
public	run ()
public	write_output ()
public Void	complete_early_if_branch_connected ()
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::MySQLTransfer --table meta_foo \
            --src_db_conn mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2913/lg4_compara_homology_merged_64 \
            --dest_db_conn mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2912/lg4_compara_families_64

Description

    This RunnableDB module lets you copy/merge rows from a table in one database into table with the same name in another.
    There are three modes ('overwrite', 'topup' and 'insertignore') that do it very differently.
    Also, 'where' parameter allows to select subset of rows to be copied/merged over.

Definition at line 21 of file MySQLTransfer.pm.

Member Function Documentation

_assert_same_table_schema()

protected Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::_assert_same_table_schema

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)

Undocumented method

Code:

fetch_input()

public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::fetch_input

(

)

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
                  Here it parses parameters, creates up to two database handles and finds the pre-execution row counts filtered by '$where'.

    param('src_db_conn'):   connection parameters to the source database (if different from hive_db)

    param('dest_db_conn'):  connection parameters to the destination database (if different from hive_db - at least one of the two will have to be different)

    param('mode'):          'overwrite' (default), 'topup' or 'insertignore'

    param('where'):         filter for rows to be copied/merged.

    param('table'):         table name to be copied/merged.

    param('lock_tables'):   [boolean] when 1, lock tables when dumping the source database. Default if not set (or set to 0) is to not lock (runs mysqldump with --skip-lock-tables)

Code:

get_row_count()

public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::get_row_count

(

)

Undocumented method

Code:

param_defaults()

public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::param_defaults

(

)

Undocumented method

Code:

write_output()

public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::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 compare the number of rows and detect problems.

Code:

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

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