Bio::EnsEMBL::Hive::AnalysisJob Class Reference

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

List of all members.

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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 ()

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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().

Code:

public Bio::EnsEMBL::Hive::AnalysisJob::adaptor

(

)

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::analysis_id

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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)

Code:

public Bio::EnsEMBL::Hive::AnalysisJob::completed

(

)

Undocumented method

Code:

public Bio::EnsEMBL::Hive::Params::csvq

(

)

[inherited]

Undocumented method

Code:

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.

Code:

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

Code:

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

(

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Undocumented method

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public Bio::EnsEMBL::Hive::Params::mysql_conn

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Hive::Params::mysql_dbname

(

)

[inherited]

Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::new

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)

Undocumented method

Code:

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

Code:

public Bio::EnsEMBL::Hive::Params::param_init

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)

[inherited]

    Description: Parses the parameters from all sources in the reverse precedence order (supply the lowest precedence hash first).

Code:

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)

Code:

public Bio::EnsEMBL::Hive::AnalysisJob::print_job

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::query_count

(

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::retry_count

(

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::runtime_msec

(

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::semaphore_count

(

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::semaphored_job_id

(

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::status

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::stderr_file

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::stdout_file

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::transient_error

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Undocumented method

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public Bio::EnsEMBL::Hive::AnalysisJob::update_status

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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

Code:

public Bio::EnsEMBL::Hive::AnalysisJob::worker_id

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)

Undocumented method

Code:

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

• Hive/AnalysisJob.pm