biolockj.module.diy

Class ForEachLoop

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.diy.GenMod

biolockj.module.diy.ForEachLoop

All Implemented Interfaces:

ApiModule, BioModule, InputDataModule, ScriptModule, Comparable<BioModule>

public class ForEachLoop
extends GenMod

Field Summary

Fields inherited from class biolockj.module.diy.GenMod

CODE_LINE, LAUNCHER, PARAM, RESOURCES, SCRIPT

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
ForEachLoop()

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.
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
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getDetails() A extension of getDescription.
List<File>	getInputFiles() Supply a list with the correct number of files to match the number of inputs.
protected List<String>	getLoopElements()
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.diy.GenMod

getDockerImageName, getDockerImageOwner, getDockerImageTag, getInputDataTypes, getLauncher, getScriptParams, isValidProp, transferResources, transferScript

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, getWorkerScriptFunctions, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, 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.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias

Constructor Detail

ForEachLoop

public ForEachLoop()

Method Detail

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 GenMod

Throws:

Exception - thrown if missing or invalid dependencies are found

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

Overrides:

buildScript in class GenMod

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

getLoopElements

protected List<String> getLoopElements()
                                throws ConfigNotFoundException

Throws:

ConfigNotFoundException

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Overrides:

getDescription in class GenMod

Returns:

getDetails

public String getDetails()
                  throws API_Exception

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class GenMod

Returns:

Throws:

API_Exception

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Overrides:

getCitationString in class GenMod

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Overrides:

version in class GenMod

Returns:

getInputFiles

public List<File> getInputFiles()

Supply a list with the correct number of files to match the number of inputs. These are not files that actually exist; but this list allows for correct worker assignment. TODO: revisit this when worker assignment is a little smarter.

Specified by:

getInputFiles in interface BioModule

Overrides:

getInputFiles in class BioModuleImpl

Returns:

Input files