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Bio::EnsEMBL::Compara::RunnableDB::HealthCheck Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::HealthCheck:

List of all members.


Class Summary

Definition at line 6 of file HealthCheck.pm.

Available Methods

protected _run_compare_to_previous_db_test ()
protected _run_conservation_jobs_test ()
protected _run_conservation_scores_test ()
protected _run_left_and_right_links_in_gat_test ()
protected _run_pairwise_gabs_test ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public void deprecate ()
public DESTROY ()
public fetch_input ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public test_table ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

protected Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::_run_compare_to_previous_db_test ( )
  Arg[1]      : string representing a hashref of options.
                Possible options are:
                  previous_db_url => url of the previous database. Must be
                  defined.
                  previous_method_link_species_set_id => method_link_species_set
                  id for the pairwise alignments in the previous database.
                  current_method_link_species_set_id => method_link_species_set
                  id for the pairwise alignments in the current (this) database.
                  method_link_type => method_link_type for pairwise segment
                  current_genome_db_ids => array of genome_db_ids for current
                  (this) database
                  max_percentage_diff => the percentage difference between the
                  number of genomic_align_blocks in the query and the target
                  databases before being flaged as an error. Default 20.
  Example     : $self->_run_compare_to_previous_db_test("{previous_db_url=\>'mysql://anonymous\@ensembldb.ensembl.org:3306/ensembl_compara_47', previous_method_link_species_set_id=\>123, current_method_link_species_set_id=\>123, max_percentage_diff=\>20}");
 Example      : $self->_run_compare_to_previous_db_test("{previous_db_url=\>\\'mysql://anonymous\\\@ensembldb.ensembl.org\\',method_link_type=\>\\'BLASTZ_NET\\',current_genome_db_ids=\>\\'[25,22,]\\'}")
  Description : Tests whether there are genomic_align_blocks, genomic_aligns
                and method_link_species_sets in the tables and whether the
                total number of genomic_align_blocks between 2 databases are
                within a certain percentage of each other.
  Returntype  :
  Exceptions  : die on failure
  Caller      : general
 
Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::_run_conservation_jobs_test ( )
  Arg[1]      : string representing a hashref of options.
                Possible options are:
                  logic_name => Logic name for the Conservation Score
                      analysis. Default: Gerp
                  method_link_type => corresponds to the multiple
                      alignments. Default: PECAN
  Example     : $self->_run_conservation_jobs_test();
  Example     : $self->_run_conservation_jobs_test("{logic_name=\>'GERP',
                    method_link_type=\>'PECAN'}");
  Description : Tests whether there is one conservation job per multiple
                alignment or not. This test only look at the number of jobs.
  Returntype  :
  Exceptions  : die on failure
  Caller      : general
 
Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::_run_conservation_scores_test ( )
  Arg[1]      : string representing a hashref of options.
                Possible options are:
                  method_link_species_set_id => method_link_species_set_id
                      for the conservation scores
  Example     : $self->_run_conservation_scores_test();
  Example     : $self->_run_conservation_scores_test(
                    "{method_link_species_set_id=\>123}");
  Description : Tests whether there are conservation scores in the table, whether
                these correspond to existing genomic_align_blocks, whether the
                right gerp_XXX entry exists in the meta table and whether there
                are no alignments with more than 3 seqs and no scores.
  Returntype  :
  Exceptions  : die on failure
  Caller      : general
 
Code:
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protected Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::_run_left_and_right_links_in_gat_test ( )
  Arg[1]      : -none-
  Example     : $self->_run_left_and_right_links_in_gat_test();
  Description : Tests whether all the trees in the genomic_align_tree table
                are linked to other trees via their left and right node ids.
  Returntype  :
  Exceptions  : die on failure
  Caller      : general
 
protected Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::_run_pairwise_gabs_test ( )
  Arg[1]      : string representing a hashref of options.
                Possible options are:
                  method_link_species_set_id => method_link_species_set id for
                  the pairwise alignment.
                  method_link_type => method_link_type for pairwise segment
                  genome_db_ids => array of genome_db_ids
  Example     : $self->_run_pairwise_gabs_test();
  Example     : $self->_run_pairwise_gabs_test("{method_link_species_set_id=\>123}");
  Example     : self->_run_pairwise_gabs_test("{method_link_type=\>'BLASTZ_NET', genome_db_ids=\>'[1,2]'}");
  Description : Tests whether the genomic_align_block and genomic_align tables
                are not empty, whether there are twice as many genomic_aligns
                as genomic_align_blocks and whether each genomic_align_block
                has two genomic_aligns.
  Returntype  :
  Exceptions  : die on failure
  Caller      : general
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( ) [inherited]
    Description: this is an intelligent setter/getter of a Compara DBA. Resorts to magic in order to figure out how to connect.
    Example 1:   my $family_adaptor = $self->compara_dba()->get_FamilyAdaptor();    # implicit initialization and hashing
    Example 2:   my $external_foo_adaptor = $self->compara_dba( $self->param('db_conn') )->get_FooAdaptor();    # explicit initialization and hashing
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::fetch_input ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( ) [inherited]
    Description: this is a method that tries lots of different ways to find connection parameters
                 from a given object/hash and returns a Compara DBA. Does not hash anything, just does the detective magic.
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::run ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::test_table ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::RunnableDB::HealthCheck::write_output ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.


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