ensembl-hive  2.1
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Bio::EnsEMBL::Hive::AnalysisJob Class Reference
+ Inheritance diagram for Bio::EnsEMBL::Hive::AnalysisJob:
+ Collaboration diagram for Bio::EnsEMBL::Hive::AnalysisJob:

Public Member Functions

public input_id ()
 
public param_id_stack ()
 
public accu_id_stack ()
 
public role_id ()
 
public status ()
 
public retry_count ()
 
public completed ()
 
public runtime_msec ()
 
public query_count ()
 
public semaphore_count ()
 
public semaphored_job_id ()
 
public set_and_update_status ()
 
public dataflow_rules ()
 
public stdout_file ()
 
public stderr_file ()
 
public accu_hash ()
 
public Boolean autoflow ()
 
public lethal_for_worker ()
 
public transient_error ()
 
public incomplete ()
 
public died_somewhere ()
 
public fan_cache ()
 
public dataflow_output_id ()
 
public toString ()
 
- Public Member Functions inherited from Bio::EnsEMBL::Hive::Storable
public Bio::EnsEMBL::Hive::Storable new ()
 
public Int dbID ()
 
public
Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor 
adaptor ()
 
public DESTROY ()
 
public AUTOLOAD ()
 
- Public Member Functions inherited from Bio::EnsEMBL::Hive::Params
public new ()
 
public param_init ()
 
protected _param_possibly_overridden ()
 
protected _param_silent ()
 
public Any param_required ()
 
public Boolean param_exists ()
 
public Boolean param_is_defined ()
 
public Any param ()
 
public param_substitute ()
 
public mysql_conn ()
 
public mysql_dbname ()
 
public csvq ()
 
protected _subst_one_hashpair ()
 

Detailed Description

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

Member Function Documentation

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

Undocumented method

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

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::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::died_somewhere ( )

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::AnalysisJob::param_id_stack ( )

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::role_id ( )

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::set_and_update_status ( )

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::toString ( )

Undocumented method

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

Undocumented method

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