biolockj.module.report.r

Class R_Module

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.report.r.R_Module

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

R_CalculateStats, R_PlotEffectSize, R_PlotMds, R_PlotOtus, R_PlotPvalHistograms

public abstract class R_Module
extends ScriptModuleImpl

This BioModule is the superclass for R script generating modules.

Field Summary

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
R_Module()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
protected int	calcTimeout(List<File> inputs) Use this to estimate the max time needed to process a given list of inputs.
void	checkDependencies() Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled
void	cleanUp() If metadata exists in module output directory, refresh MetaUtil.
void	executeTask() Builds an R script by calling sub-methods to builds the BaseScript and creates the MAIN script shell that sources the BaseScript, calls runProgram(), reportStatus() and main() which can only be implemented in a subclass.
protected String	getCustomScriptProp()
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
protected File	getFunctionLib()
static File	getFunctionLib(BioModule module)
protected abstract String	getModulePrefix() Returns that prefix to use for property names.
protected File	getModuleRScript()
protected abstract String	getModuleRScriptName()
Integer	getTimeout() The R Script should run quickly, timeout = 10 minutes appears to work well.
protected void	grapRUsedProps()
protected Map<String,String>	requiredRPackages()

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getWorkerScriptFunctions, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.BioModule

getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Constructor Detail

R_Module

public R_Module()

Method Detail

executeTask

public void executeTask()
                 throws Exception

Builds an R script by calling sub-methods to builds the BaseScript and creates the MAIN script shell that sources the BaseScript, calls runProgram(), reportStatus() and main() which can only be implemented in a subclass.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Description copied from class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ScriptModuleImpl

Validate module dependencies:

• Require Config. exists
• Require Config. is positive integer
• Require Config. is positive integer
• Verify Config. is positive integer if set
• Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

requiredRPackages

protected Map<String,String> requiredRPackages()

getTimeout

public Integer getTimeout()
                   throws ConfigFormatException

The R Script should run quickly, timeout = 10 minutes appears to work well.

Specified by:

getTimeout in interface ScriptModule

Overrides:

getTimeout in class ScriptModuleImpl

Returns:

Number of minutes before script is cancelled due to timeout

Throws:

ConfigFormatException

calcTimeout

protected int calcTimeout(List<File> inputs)

Use this to estimate the max time needed to process a given list of inputs. Estimate the time that the head node should wait on the module using all inputs; Estimate the wait time for a given worker using only its assigned inputs.

Parameters:

inputs -

Returns:

getFunctionLib

protected File getFunctionLib()
                       throws IOException,
                              BioLockJException

Throws:

IOException

BioLockJException

getFunctionLib

public static File getFunctionLib(BioModule module)
                           throws IOException,
                                  BioLockJException

Throws:

IOException

BioLockJException

getModuleRScript

protected File getModuleRScript()
                         throws IOException,
                                BioLockJException

Throws:

IOException

BioLockJException

getModuleRScriptName

protected abstract String getModuleRScriptName()

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns:

getCustomScriptProp

protected String getCustomScriptProp()

Returns:

The property name that can be used for passing a custom version of the R script used for this module.

getModulePrefix

protected abstract String getModulePrefix()

Returns that prefix to use for property names.

Returns:

cleanUp

public void cleanUp()
             throws Exception

Description copied from class: BioModuleImpl

If metadata exists in module output directory, refresh MetaUtil.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

grapRUsedProps

protected void grapRUsedProps()
                       throws Exception

Throws:

Exception