biolockj.module.classifier

Class ClassifierModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

All Implemented Interfaces:

BioModule, ClassifierModule, DatabaseModule, ScriptModule, SeqModule, Comparable<BioModule>

Direct Known Subclasses:

Humann2Classifier, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, QiimeClassifier, RdpClassifier

public abstract class ClassifierModuleImpl
extends SeqModuleImpl
implements ClassifierModule, DatabaseModule

This is the superclass for all WGS and 16S biolockj.module.classifier BioModules.

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
ClassifierModuleImpl()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Call getClassifierExe() to verify the executable Call getClassifierParams() to verify the runtime parameters are valid Call validateModuleOrder() to validate module configuration order.
abstract String	getClassifierExe() Get the executable required to classify your samples.
abstract List<String>	getClassifierParams() Get optional list of parameters to append whenever the classifier executable is called.
protected String	getClassifierType() This method returns the classifier class name in lower case, after "classifier" is removed. The remaining text should uniquely identify the name of the program. The basic deployment will return one of: (rdp, qiime, kraken, metaphlan2, or humann2).
abstract File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.
protected File	getDbCache() DB directory path getter
List<String>	getPostRequisiteModules() This method returns the corresponding Parser module associated with the classifier.
String	getSummary() Add database info if module is a DatabaseModule
protected void	setDbCache(File db) Set DB cache directory path on 1st access
protected void	validateModuleOrder() Validate that no biolockj.module.seq modules run after this classifier unless a new classifier branch is started.

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScript, buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

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

Constructor Detail

ClassifierModuleImpl

public ClassifierModuleImpl()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies:

• Call getClassifierExe() to verify the executable
• Call getClassifierParams() to verify the runtime parameters are valid
• Call validateModuleOrder() to validate module configuration order.
• Call BioModule.checkDependencies() to validate script dependencies.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getClassifierExe

public abstract String getClassifierExe()
                                 throws ConfigException

Description copied from interface: ClassifierModule

Get the executable required to classify your samples.

Specified by:

getClassifierExe in interface ClassifierModule

Returns:

Command to execute classifier program

Throws:

ConfigException - if Configuration errors are thrown

getClassifierParams

public abstract List<String> getClassifierParams()
                                          throws ConfigException,
                                                 DockerVolCreationException

Description copied from interface: ClassifierModule

Get optional list of parameters to append whenever the classifier executable is called.

Specified by:

getClassifierParams in interface ClassifierModule

Returns:

Runtime parameters

Throws:

ConfigException - if Configuration errors are thrown

DockerVolCreationException

getDB

public abstract File getDB()
                    throws ConfigPathException,
                           ConfigNotFoundException,
                           DockerVolCreationException

Description copied from interface: DatabaseModule

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Specified by:

getDB in interface DatabaseModule

Returns:

Database directory

Throws:

ConfigPathException - if path is defined but does not exists

ConfigNotFoundException - if DB property is undefined and the default DB is not included in the module runtime env

DockerVolCreationException

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

This method returns the corresponding Parser module associated with the classifier. The Parser module name is built using the same prefix used in the Classifier module

For example RdpClassifier, will return the RdpParser.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class BioModuleImpl

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

getSummary

public String getSummary()
                  throws Exception

Description copied from class: SeqModuleImpl

Add database info if module is a DatabaseModule

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getClassifierType

protected String getClassifierType()

This method returns the classifier class name in lower case, after "classifier" is removed.
The remaining text should uniquely identify the name of the program.
The basic deployment will return one of: (rdp, qiime, kraken, metaphlan2, or humann2).

Returns:

String - options { rdp, qiime, kraken, kraken2, metaphlan2, or humann2 }

getDbCache

protected File getDbCache()

DB directory path getter

Returns:

DB directory

setDbCache

protected void setDbCache(File db)

Set DB cache directory path on 1st access

Parameters:

db - Database file

validateModuleOrder

protected void validateModuleOrder()
                            throws Exception

Validate that no biolockj.module.seq modules run after this classifier unless a new classifier branch is started.

Throws:

Exception - if modules are out of order