biolockj.module

Class ScriptModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

DESeq2, EdgeR, GenMod, Hello_Friends, Hello_World, JavaModuleImpl, MergeQiimeOtuTables, R_Module, Rmarkdown, SeqModuleImpl, SequenceReadArchive, Step1

public abstract class ScriptModuleImpl
extends BioModuleImpl
implements ScriptModule

Superclass for Java BioModules that will be called in separate instances of the application.

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
ScriptModuleImpl()

Method Summary

Modifier and Type	Method and Description
abstract List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
List<List<String>>	buildScriptForPairedReads(List<File> files) The default behavior is the same for paired or unpaired data.
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	executeTask() Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts.
String[]	getJobParams() Many ScriptModules generate bash or R scripts for the Operating System to run as a Processor. The Processor creates a Process using the parameters supplied by this method and executed in the Runtime environment. Parameters typically contain the full script path and script parameters, if needed.
File	getMainScript() Get the main script file in the bioModule script directory, with prefix: "MAIN_".
protected String	getRuntimeParams(List<String> params, String numThreadsParam) Return all collectionProperty values separated by a space.
File	getScriptDir() Returns moduleDir/script which contains all scripts generated by the module.
List<String>	getScriptErrors() This method returns all of the lines from any failure files found in the script directory.
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
Integer	getTimeout() Default behavior is for scripts to run indefinitely (no timeout).
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.
protected boolean	hasScripts() Check if module produced any scripts
Boolean	isValidProp(String property)

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getDockerImageOwner, getDockerImageTag, 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

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

Constructor Detail

ScriptModuleImpl

public ScriptModuleImpl()

Method Detail

buildScript

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

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

Specified by:

buildScript in interface ScriptModule

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

buildScriptForPairedReads

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

The default behavior is the same for paired or unpaired data. This method must be overridden to create separate scripts for paired datasets.

Specified by:

buildScriptForPairedReads in interface ScriptModule

Parameters:

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

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate the script lines

checkDependencies

public void checkDependencies()
                       throws Exception

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

Specified by:

checkDependencies in class BioModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

executeTask

public void executeTask()
                 throws Exception

Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts. PassBioModuleImpl.getInputFiles() to either buildScript(List) or buildScriptForPairedReads(List) based on Config."internal.pairedReads".

Specified by:

executeTask in interface BioModule

Specified by:

executeTask in class BioModuleImpl

Throws:

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

getJobParams

public String[] getJobParams()
                      throws Exception

Description copied from interface: ScriptModule

Many ScriptModules generate bash or R scripts for the Operating System to run as a Processor.
The Processor creates a Process using the parameters supplied by this method and executed in the Runtime environment.
Parameters typically contain the full script path and script parameters, if needed.

Specified by:

getJobParams in interface ScriptModule

Returns:

Runtime.exec(String) parameters

Throws:

Exception

getMainScript

public File getMainScript()

Get the main script file in the bioModule script directory, with prefix: "MAIN_". R_Modules not running in a docker container end in , otherwise must end with

Specified by:

getMainScript in interface ScriptModule

Returns:

Main script file

getScriptDir

public File getScriptDir()

Returns moduleDir/script which contains all scripts generated by the module.

Specified by:

getScriptDir in interface ScriptModule

Returns:

File directory containing all ScriptModule scripts

getScriptErrors

public List<String> getScriptErrors()
                             throws Exception

This method returns all of the lines from any failure files found in the script directory.

Specified by:

getScriptErrors in interface ScriptModule

Returns:

List of script errors

Throws:

Exception - if errors occur reading failure files

getSummary

public String getSummary()
                  throws Exception

Returns summary message to be displayed by Email module so must not contain confidential info. ModuleUtil provides summary metrics on output files

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class BioModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getTimeout

public Integer getTimeout()
                   throws ConfigFormatException

Default behavior is for scripts to run indefinitely (no timeout).

Specified by:

getTimeout in interface ScriptModule

Returns:

Number of minutes before script is cancelled due to timeout

Throws:

ConfigFormatException - if the value is invalid

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

Description copied from interface: ScriptModule

Method returns bash script lines used to build the functions called by the worker scripts.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getRuntimeParams

protected String getRuntimeParams(List<String> params,
                                  String numThreadsParam)
                           throws ConfigException

Return all collectionProperty values separated by a space. If numThreadsParam is not null, append the numThreads param and value.

Parameters:

params - Runtime parameter

numThreadsParam - Number of threads parameter name

Returns:

all runtime parameters

Throws:

ConfigException - if Configuration errors occur

hasScripts

protected boolean hasScripts()

Check if module produced any scripts

Returns:

boolean TRUE if script dir exists

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Overrides:

isValidProp in class BioModuleImpl

Throws:

Exception