Package ca.corefacility.bioinformatics.irida.model.workflow.submission

Class AnalysisSubmission.Builder

java.lang.Object

ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission.Builder

Enclosing class:

AnalysisSubmission

public static class AnalysisSubmission.Builder
extends java.lang.Object

Used to build up an AnalysisSubmission.

Constructor Summary

Constructors

Constructor	Description
Builder(AnalysisSubmissionTemplate template)	Create a new AnalysisSubmission.Builder from the given AnalysisSubmissionTemplate
Builder(java.util.UUID workflowId)	Creates a new AnalysisSubmission.Builder with a workflow id.

Method Summary

Modifier and Type	Method	Description
AnalysisSubmission.Builder	analysisDescription(java.lang.String analysisDescription)	Sets the description of the analysis run
AnalysisSubmission.Builder	automated(boolean automated)	Sets whether this pipeline is being run as part of an automated process
AnalysisSubmission	build()	Build the analysis submission from the set parameters
AnalysisSubmission.Builder	emailPipelineResultCompleted(boolean emailPipelineResultCompleted)	Sets if user should be emailed on pipeline completion
AnalysisSubmission.Builder	emailPipelineResultError(boolean emailPipelineResultError)	Sets if user should be emailed on pipeline error
AnalysisSubmission.Builder	inputFiles(java.util.Set<SequencingObject> inputFiles)	Sets the inputFilesPaired for this submission.
AnalysisSubmission.Builder	inputParameter(java.lang.String name, java.lang.String value)	Adds an individual input parameter.
AnalysisSubmission.Builder	inputParameters(java.util.Map<java.lang.String,java.lang.String> inputParameters)	Sets the input parameters for this submission.
AnalysisSubmission.Builder	name(java.lang.String name)	Sets a name for this submission.
AnalysisSubmission.Builder	priority(AnalysisSubmission.Priority priority)	Sets the AnalysisSubmission.Priority of the analysis run
AnalysisSubmission.Builder	referenceFile(ReferenceFile referenceFile)	Sets the referenceFile for this submission.
AnalysisSubmission.Builder	submitter(User submitter)	Set the user who submitted the pipeline
AnalysisSubmission.Builder	updateSamples(boolean updateSamples)	Turns on/off updating of samples from results for this analysis submission.
AnalysisSubmission.Builder	withNamedParameters(IridaWorkflowNamedParameters parameters)	Use the specified set of named parameters to run this workflow.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Builder

public Builder(java.util.UUID workflowId)

Creates a new AnalysisSubmission.Builder with a workflow id.

Parameters:

workflowId - The workflow id for this submission.

Builder

public Builder(AnalysisSubmissionTemplate template)

Create a new AnalysisSubmission.Builder from the given AnalysisSubmissionTemplate

Parameters:

template - an AnalysisSubmissionTemplate to build an AnalysisSubmission

Method Detail

name

public AnalysisSubmission.Builder name(java.lang.String name)

Sets a name for this submission.

Parameters:

name - A name for this submission.

Returns:

A AnalysisSubmission.Builder.

inputFiles

public AnalysisSubmission.Builder inputFiles(java.util.Set<SequencingObject> inputFiles)

Sets the inputFilesPaired for this submission.

Parameters:

inputFiles - The inputFilesPaired for this submission.

Returns:

A AnalysisSubmission.Builder.

referenceFile

public AnalysisSubmission.Builder referenceFile(ReferenceFile referenceFile)

Sets the referenceFile for this submission.

Parameters:

referenceFile - The referenceFile for this submission.

Returns:

A AnalysisSubmission.Builder.

inputParameters

public AnalysisSubmission.Builder inputParameters(java.util.Map<java.lang.String,java.lang.String> inputParameters)

Sets the input parameters for this submission.

Parameters:

inputParameters - A map of parameters for this submission.

Returns:

A AnalysisSubmission.Builder.

inputParameter

public AnalysisSubmission.Builder inputParameter(java.lang.String name,
                                                 java.lang.String value)

Adds an individual input parameter.

Parameters:

name - The name of the parameter.

value - The value of the parameter.

Returns:

A AnalysisSubmission.Builder.

withNamedParameters

public AnalysisSubmission.Builder withNamedParameters(IridaWorkflowNamedParameters parameters)

Use the specified set of named parameters to run this workflow.

Parameters:

parameters - the named parameters to use.

Returns:

A AnalysisSubmission.Builder.

analysisDescription

public AnalysisSubmission.Builder analysisDescription(java.lang.String analysisDescription)

Sets the description of the analysis run

Parameters:

analysisDescription - description of the analysis

Returns:

A AnalysisSubmission.Builder

priority

public AnalysisSubmission.Builder priority(AnalysisSubmission.Priority priority)

Sets the AnalysisSubmission.Priority of the analysis run

Parameters:

priority - the priority of the analysis

Returns:

a AnalysisSubmission.Builder

updateSamples

public AnalysisSubmission.Builder updateSamples(boolean updateSamples)

Turns on/off updating of samples from results for this analysis submission.

Parameters:

updateSamples - Turn on/off updating samples.

Returns:

A AnalysisSubmission.Builder

automated

public AnalysisSubmission.Builder automated(boolean automated)

Sets whether this pipeline is being run as part of an automated process

Parameters:

automated - whether this is an automated pipeline

Returns:

a AnalysisSubmission.Builder

emailPipelineResultCompleted

public AnalysisSubmission.Builder emailPipelineResultCompleted(boolean emailPipelineResultCompleted)

Sets if user should be emailed on pipeline completion

Parameters:

emailPipelineResultCompleted - If user should be emailed or not

Returns:

A AnalysisSubmission.Builder

emailPipelineResultError

public AnalysisSubmission.Builder emailPipelineResultError(boolean emailPipelineResultError)

Sets if user should be emailed on pipeline error

Parameters:

emailPipelineResultError - If user should be emailed or not

Returns:

A AnalysisSubmission.Builder

submitter

public AnalysisSubmission.Builder submitter(User submitter)

Set the user who submitted the pipeline

Parameters:

submitter - User who submitted the pipeline

Returns:

a AnalysisSubmission.Builder

build

public AnalysisSubmission build()

Build the analysis submission from the set parameters

Returns:

the new AnalysisSubmission