biolockj.module

Interface ScriptModule

All Superinterfaces:

BioModule

All Known Subinterfaces:

ClassifierModule, JavaModule, ParserModule, SeqModule

All Known Implementing Classes:

AddMetadataToPathwayTables, AddMetadataToTaxaTables, AwkFastaConverter, BuildQiimeMapping, BuildTaxaTables, ClassifierModuleImpl, CompileOtuCounts, Demultiplexer, Gunzipper, Humann2Classifier, Humann2CountModule, Humann2Parser, JavaModuleImpl, JsonReport, KneadData, Kraken2Classifier, Kraken2Parser, KrakenClassifier, KrakenParser, LogTransformTaxaTables, MergeQiimeOtuTables, Metaphlan2Classifier, Metaphlan2Parser, Multiplexer, NormalizeTaxaTables, OtuCountModule, ParserModuleImpl, PearMergeReads, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, QiimeParser, R_CalculateStats, R_Module, R_PlotEffectSize, R_PlotMds, R_PlotOtus, R_PlotPvalHistograms, RarefyOtuCounts, RarefySeqs, RdpClassifier, RdpParser, RegisterNumReads, RemoveLowOtuCounts, RemoveLowPathwayCounts, RemoveScarceOtuCounts, RemoveScarcePathwayCounts, ScriptModuleImpl, SeqFileValidator, SeqModuleImpl, TaxaCountModule, TrimPrimers

public interface ScriptModule
extends BioModule

Classes that implement this interface are

Field Summary

Fields

Modifier and Type	Field and Description
static String	SCRIPT_BATCH_SIZE Config Integer property: "script.batchSize" Set number of samples to process per script (if parallel processing)
static String	SCRIPT_DEFAULT_HEADER Config List property: "script.defaultHeader" Store default script header for MAIN script and locally run WORKER scripts.
static String	SCRIPT_NUM_THREADS Config Integer property: "script.numThreads" Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.
static String	SCRIPT_PERMISSIONS Config String property: "script.permissions" Used as chmod permission parameter (ex: 774)
static String	SCRIPT_TIMEOUT Config Integer property: "script.timeout" Sets # of minutes before worker scripts times out.

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Method returns a nested list of bash script lines to classify samples containing forward reads only.
List<List<String>>	buildScriptForPairedReads(List<File> files) Method returns a nested list of bash script lines to classify samples containing paired reads. The inner list contains the bash script lines required to classify 1 sample.
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() Method returns MAIN module script that calls each of the worker scripts.
File	getScriptDir() ScriptModules that generate scripts to complete their task, create script files in this directory. The main script must begin with prefix and there must only be one main script. The main script executes, or submits to the job queue, each of the other scripts in this directory. The # subscripts generated by the ScriptModule depends upon "script.batchSize".
List<String>	getScriptErrors() Return a list of the error messages saved the failure scripts in the module script directory.
Integer	getTimeout() ScriptModule that run scripts can opt to set a timeout (such as used by the R script).
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getSummary, getTempDir, init, isValidInputModule

Field Detail

SCRIPT_BATCH_SIZE

static final String SCRIPT_BATCH_SIZE

Config Integer property: "script.batchSize"
Set number of samples to process per script (if parallel processing)

See Also:

Constant Field Values

SCRIPT_DEFAULT_HEADER

static final String SCRIPT_DEFAULT_HEADER

Config List property: "script.defaultHeader"
Store default script header for MAIN script and locally run WORKER scripts.

See Also:

Constant Field Values

SCRIPT_NUM_THREADS

static final String SCRIPT_NUM_THREADS

Config Integer property: "script.numThreads"
Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter.

See Also:

Constant Field Values

SCRIPT_PERMISSIONS

static final String SCRIPT_PERMISSIONS

Config String property: "script.permissions"
Used as chmod permission parameter (ex: 774)

See Also:

Constant Field Values

SCRIPT_TIMEOUT

static final String SCRIPT_TIMEOUT

Config Integer property: "script.timeout"
Sets # of minutes before worker scripts times out.

See Also:

Constant Field Values

Method Detail

buildScript

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

Method returns a nested list of bash script lines to classify samples containing forward reads only. The inner list contains the bash script lines required to classify 1 sample.

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

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

Method returns a nested list of bash script lines to classify samples containing paired reads.
The inner list contains the bash script lines required to classify 1 sample.

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

getJobParams

String[] getJobParams()
               throws Exception

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.

Returns:

Runtime.exec(String) parameters

Throws:

Exception - if unable to build the job parameters

getMainScript

File getMainScript()
            throws Exception

Method returns MAIN module script that calls each of the worker scripts.

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getScriptDir

File getScriptDir()

ScriptModules that generate scripts to complete their task, create script files in this directory.
The main script must begin with prefix and there must only be one main script.
The main script executes, or submits to the job queue, each of the other scripts in this directory.
The # subscripts generated by the ScriptModule depends upon "script.batchSize".

Returns:

File directory containing all ScriptModule scripts

getScriptErrors

List<String> getScriptErrors()
                      throws Exception

Return a list of the error messages saved the failure scripts in the module script directory.

Returns:

List of error messages or empty list

Throws:

Exception - if runtime errors occur

getTimeout

Integer getTimeout()
            throws ConfigFormatException

ScriptModule that run scripts can opt to set a timeout (such as used by the R script).

Returns:

Number of minutes before script is cancelled due to timeout

Throws:

ConfigFormatException - if the "script.timeout" value is invalid

getWorkerScriptFunctions

List<String> getWorkerScriptFunctions()
                               throws Exception

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

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur