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

Modifier and Type	Field and Description
static String	EXE_RSCRIPT Config property "exe.Rscript" defines the command line executable to call RScript
protected static String	P_VAL_CUTOFF Config property "r.pvalCutoff" defines the p-value cutoff for significance
protected static String	R_COLOR_BASE Config property "r.colorBase" defines the base label color
protected static String	R_COLOR_HIGHLIGHT Config property "r.colorHighlight" defines the highlight label color
protected static String	R_COLOR_PALETTE Config property "r.colorPalette" defines the color palette for PDF plots
protected static String	R_COLOR_POINT Config property "r.colorPoint" defines the pch point colors for PDF plots
protected static String	R_DEBUG Config boolean property "r.debug" sets the debug log function endabled
protected static String	R_FUNCTION_LIB This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"
protected static String	R_MAIN_SCRIPT This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"
protected static String	R_PCH Config property "r.pch" defines the plot point shape for PDF plots
protected static String	R_RARE_OTU_THRESHOLD Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in reports
protected static String	R_SAVE_R_DATA Config boolean property "r.saveRData" enables the .RData file to save.
protected static String	R_TIMEOUT Config property "r.timeout" defines the number of minutes before R script fails due to timeout.

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.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
R_Module()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildDockerBashScript() Run R script in docker.
List<List<String>>	buildScript(List<File> files) Not needed for R script modules.
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
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.
String[]	getJobParams() If running Docker, run the Docker bash script, otherwise: Run Config."exe.Rscript" command on the generated R Script: ScriptModuleImpl.getMainScript().
static File	getMainR() Get the main R script
protected String	getMetaMergedModule() Get correct meta-merged BioModule type for the give module.
File	getModuleScript() Get the Module script
List<String>	getPreRequisiteModules() Require combined count-metadata tables as input.
File	getPrimaryScript() Get the primary R script
static String	getRTemplateDir() Get the BioLockJ resource R directory.
protected List<String>	getStatPreReqs() Add R_CalculateStats to standard getPreRequisiteModules()
String	getSummary() Produce summary file counts for each file extension in the output directory and the number of log files in the temp directory.
Integer	getTimeout() The R Script should run quickly, timeout = 10 minutes appears to work well.
List<String>	getWorkerScriptFunctions() This method generates the bash function that calls the R script: runScript.
static void	writeNewScript(String path, String rCode) This method generates an R script with the given rCode saved to the given path.
protected void	writePrimaryScript() Initialize the R script by creating the MAIN R script that calls source on the BaseScript and adds the R code for the runProgarm() method.
protected static void	writeScript(BufferedWriter writer, String rCode) This method formats the rCode to indent code blocks surround by curly-braces "{ }"

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, isValidInputModule, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.BioModule

cleanUp, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, isValidInputModule

Field Detail

EXE_RSCRIPT

public static final String EXE_RSCRIPT

Config property "exe.Rscript" defines the command line executable to call RScript

See Also:

Constant Field Values

P_VAL_CUTOFF

protected static final String P_VAL_CUTOFF

Config property "r.pvalCutoff" defines the p-value cutoff for significance

See Also:

Constant Field Values

R_COLOR_BASE

protected static final String R_COLOR_BASE

Config property "r.colorBase" defines the base label color

See Also:

Constant Field Values

R_COLOR_HIGHLIGHT

protected static final String R_COLOR_HIGHLIGHT

Config property "r.colorHighlight" defines the highlight label color

See Also:

Constant Field Values

R_COLOR_PALETTE

protected static final String R_COLOR_PALETTE

Config property "r.colorPalette" defines the color palette for PDF plots

See Also:

Constant Field Values

R_COLOR_POINT

protected static final String R_COLOR_POINT

Config property "r.colorPoint" defines the pch point colors for PDF plots

See Also:

Constant Field Values

R_DEBUG

protected static final String R_DEBUG

Config boolean property "r.debug" sets the debug log function endabled

See Also:

Constant Field Values

R_FUNCTION_LIB

protected static final String R_FUNCTION_LIB

This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"

See Also:

Constant Field Values

R_MAIN_SCRIPT

protected static final String R_MAIN_SCRIPT

This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"

See Also:

Constant Field Values

R_PCH

protected static final String R_PCH

Config property "r.pch" defines the plot point shape for PDF plots

See Also:

Constant Field Values

R_RARE_OTU_THRESHOLD

protected static final String R_RARE_OTU_THRESHOLD

Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in reports

See Also:

Constant Field Values

R_SAVE_R_DATA

protected static final String R_SAVE_R_DATA

Config boolean property "r.saveRData" enables the .RData file to save.

See Also:

Constant Field Values

R_TIMEOUT

protected static final String R_TIMEOUT

Config property "r.timeout" defines the number of minutes before R script fails due to timeout. If undefined, no timeout is used.

See Also:

Constant Field Values

Constructor Detail

R_Module

public R_Module()

Method Detail

buildDockerBashScript

public List<List<String>> buildDockerBashScript()

Run R script in docker.

Returns:

Bash script lines for the docker script

buildScript

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

Not needed for R script modules.

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

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

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

getJobParams

public String[] getJobParams()
                      throws Exception

If running Docker, run the Docker bash script, otherwise:
Run Config."exe.Rscript" command on the generated R Script: ScriptModuleImpl.getMainScript().

Specified by:

getJobParams in interface ScriptModule

Overrides:

getJobParams in class ScriptModuleImpl

Returns:

Runtime.exec(String) parameters

Throws:

Exception - if unable to build the job parameters

getModuleScript

public File getModuleScript()
                     throws Exception

Get the Module script

Returns:

Module R script

Throws:

Exception - if errors occur

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Require combined count-metadata tables as input.

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getPrimaryScript

public File getPrimaryScript()

Get the primary R script

Returns:

File (R script)

getSummary

public String getSummary()
                  throws Exception

Produce summary file counts for each file extension in the output directory and the number of log files in the temp directory. Any R Script errors detected during execution will also be printed. also contain details of R script errors, if any.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getTimeout

public Integer getTimeout()

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

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the bash function that calls the R script: runScript.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getMetaMergedModule

protected String getMetaMergedModule()
                              throws Exception

Get correct meta-merged BioModule type for the give module. This is determined by examining previous configured modules to see what type of raw count tables are generated.

Returns:

MetaMerged BioModule

Throws:

Exception - if errors occur

getStatPreReqs

protected List<String> getStatPreReqs()
                               throws Exception

Add R_CalculateStats to standard getPreRequisiteModules()

Returns:

Statistics Module prerequisite if needed

Throws:

Exception - if errors occur determining eligibility

writePrimaryScript

protected void writePrimaryScript()
                           throws Exception

Initialize the R script by creating the MAIN R script that calls source on the BaseScript and adds the R code for the runProgarm() method.

Throws:

Exception - if unable to build the R script stub

getMainR

public static File getMainR()
                     throws Exception

Get the main R script

Returns:

Main R script

Throws:

Exception - if errors occur

getRTemplateDir

public static String getRTemplateDir()
                              throws Exception

Get the BioLockJ resource R directory.

Returns:

System file path

Throws:

Exception - if errors occur

writeNewScript

public static void writeNewScript(String path,
                                  String rCode)
                           throws Exception

This method generates an R script with the given rCode saved to the given path.

Parameters:

path - Path to new R Script

rCode - R script code

Throws:

Exception - if I/O errors occur

writeScript

protected static void writeScript(BufferedWriter writer,
                                  String rCode)
                           throws Exception

This method formats the rCode to indent code blocks surround by curly-braces "{ }"

Parameters:

writer - BufferedWriter writes to the file

rCode - R code

Throws:

Exception - if I/O errors occur