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

-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

Member Function Documentation

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:
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protected Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::_validate_tests ( )
    Description : Checks that the tests are properly defined, and parses the "expected_size"
 
Code:
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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:
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public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::param_defaults ( )

Undocumented method

Code:
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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: