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Bio::EnsEMBL::Hive::AnalysisJob Class Reference
Inheritance diagram for Bio::EnsEMBL::Hive::AnalysisJob:

List of all members.


Class Summary

Description

  An AnalysisJob is the link between the input_id control data, the analysis and
  the rule system.  It also tracks the state of the job as it is processed
 

Definition at line 13 of file AnalysisJob.pm.

Available Methods

protected _subst_one_hashpair ()
public adaptor ()
public analysis_id ()
public Boolean autoflow ()
public completed ()
public csvq ()
public dataflow_output_id ()
public dataflow_rules ()
public dbID ()
public fan_cache ()
public incomplete ()
public input_id ()
public lethal_for_worker ()
public mysql_conn ()
public mysql_dbname ()
public new ()
public Any param ()
public param_init ()
public param_substitute ()
public print_job ()
public query_count ()
public retry_count ()
public runtime_msec ()
public semaphore_count ()
public semaphored_job_id ()
public status ()
public stderr_file ()
public stdout_file ()
public transient_error ()
public update_status ()
public warning ()
public worker_id ()

Method Documentation

protected Bio::EnsEMBL::Hive::Params::_subst_one_hashpair ( ) [inherited]
    
    Description: this is a private method that performs one substitution. Called by param_substitute().
 
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public Bio::EnsEMBL::Hive::AnalysisJob::adaptor ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::analysis_id ( )

Undocumented method

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public Boolean Bio::EnsEMBL::Hive::AnalysisJob::autoflow ( )
    Title   :  autoflow
    Function:  Gets/sets flag for whether the job should
               be automatically dataflowed on branch 1 when the job completes.
               If the subclass manually sends a job along branch 1 with dataflow_output_id,
               the autoflow will turn itself off.
    Returns :  boolean (1=default|0)
 
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public Bio::EnsEMBL::Hive::AnalysisJob::completed ( )

Undocumented method

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public Bio::EnsEMBL::Hive::Params::csvq ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::dataflow_output_id ( )
    Title        :  dataflow_output_id
    Arg[1](req)  :  <string> $output_id 
    Arg[2](opt)  :  <int> $branch_name_or_code (optional, defaults to 1)
    Usage        :  $self->dataflow_output_id($output_id, $branch_name_or_code);
    Function:  
      If a RunnableDB(Process) needs to create jobs, this allows it to have jobs 
      created and flowed through the dataflow rules of the workflow graph.
      This 'output_id' becomes the 'input_id' of the newly created job at
      the ends of the dataflow pipes.  The optional 'branch_name_or_code' determines
      which dataflow pipe(s) to flow the job through.
 
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public Bio::EnsEMBL::Hive::AnalysisJob::dataflow_rules ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::dbID ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::fan_cache ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::incomplete ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::input_id ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::lethal_for_worker ( )

Undocumented method

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public Bio::EnsEMBL::Hive::Params::mysql_conn ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Hive::Params::mysql_dbname ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::new ( )

Undocumented method

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public Any Bio::EnsEMBL::Hive::Params::param ( ) [inherited]
    Arg [1]    : string $param_name
    Arg [2]    : (optional) $param_value
    Description: A getter/setter method for a job's parameters that are initialized through 4 levels of precedence (see param_init() )
    Example 1  : my $source = $self->param('source'); # acting as a getter
    Example 2  : $self->param('binpath', '/software/ensembl/compara');  # acting as a setter
    Example 3  : my $all_params = $self-param();    # get the whole hash in one piece
    Returntype : any Perl structure or object that you dared to store
 
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public Bio::EnsEMBL::Hive::Params::param_init ( ) [inherited]
    Description: Parses the parameters from all sources in the reverse precedence order (supply the lowest precedence hash first).
 
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public Bio::EnsEMBL::Hive::Params::param_substitute ( ) [inherited]
    Arg [1]    : Perl structure $string_with_templates
    Description: Performs parameter substitution on strings that contain templates like " \#param_name\# followed by \#another_param_name\# " .
    Returntype : *another* Perl structure with matching topology (may be more complex as a result of substituting a substructure for a term)
 
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public Bio::EnsEMBL::Hive::AnalysisJob::print_job ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::query_count ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::retry_count ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::runtime_msec ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::semaphore_count ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::semaphored_job_id ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::status ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::stderr_file ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::stdout_file ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::transient_error ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::update_status ( )

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::warning ( )
    Description:    records a non-error message in 'job_message' table linked to the current job
 
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public Bio::EnsEMBL::Hive::AnalysisJob::worker_id ( )

Undocumented method

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