Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck Class Reference

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

Public Member Functions
public	param_defaults ()
public	fetch_input ()
protected	_validate_tests ()
public	run ()
protected	_run_test ()
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::SqlHealthcheck \
                -db_conn mysql://ensro@compara1/mm14_compara_homology_71 \
                -description 'We expect at least 20,000 human genes' \
                -query 'SELECT * FROM member WHERE genome_db_id = 90 AND source_name = "ENSEMBLGENE"' \
                -expected_size '>= 20000'

Description

    This is a generic RunnableDB module for testing the size of the resultset of any SQL query.

    The query is passed by the parameter 'inputquery' (param substituted)
    The expected size is passed by the parameter 'expected_size' as a string "CONDITION VALUE" (CONDITION defaults to equality, VALUE defaults to 0).
    Currently, CONDITION is one of: = == < <= > >= <> !=

    TODO: implement a "expected_value" test

Definition at line 26 of file SqlHealthcheck.pm.

Member Function Documentation

_run_test()

protected Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::_run_test

(

)

    Description : Runs a single test, defined in a hash with the following keys:
                   description, query, reference_size, logical_test

Code:

_validate_tests()

protected Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::_validate_tests

(

)

    Description : Checks that the tests are properly defined, and parses the "expected_size"

Code:

fetch_input()

public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::fetch_input

(

)

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.

Code:

param_defaults()

public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::param_defaults

(

)

Undocumented method

Code:

run()

public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::run

(

)

    Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process
                  Iterate through the tests and run them all. Report the failed tests at the end

Code:

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

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