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

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:
- Hive/AnalysisJob.pm