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Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer Class Reference
+ Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer:
+ Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer:

Public Member Functions

public param_defaults ()
 
public fetch_input ()
 
public run ()
 
public write_output ()
 
public get_row_count ()
 
public mysql_conn_from_dbc ()
 
- Public Member Functions inherited from Bio::EnsEMBL::Hive::Process
public new ()
 
public life_cycle ()
 
public say_with_header ()
 
public enter_status ()
 
public warning ()
 
public strict_hash_format ()
 
public param_defaults ()
 
public fetch_input ()
 
public run ()
 
public write_output ()
 
public Bio::EnsEMBL::Hive::Worker worker ()
 
public Boolean 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
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
 
public input_id ()
 
public param ()
 
public param_required ()
 
public param_is_defined ()
 
public param_substitute ()
 
public dataflow_output_id ()
 
public throw ()
 
public complete_early ()
 
public Int debug ()
 
public worker_temp_directory ()
 
public worker_temp_directory_name ()
 
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.

Member Function Documentation

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.
 
Code:
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public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::get_row_count ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::mysql_conn_from_dbc ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::param_defaults ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::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 the actual data transfer is attempted.
 
Code:
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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: