Module (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.module.Module

All Implemented Interfaces:

ModuleInterface

Direct Known Subclasses:

GenericCommandRunner, GenericMetadataSaver, ProvisionDependenciesBundle, ProvisionFiles, S3CreateFileURLs, S3DeleteFiles, S3ListFiles, S3UploadDirectory, TestModule
```
public abstract class Module
extends Object
implements ModuleInterface
```
Abstract Module class.

Version:

$Id: $Id

Author:

boconnor

Field Summary

Fields
Modifier and Type Field and Description

protected int processingAccession

static String VERSION
Constant VERSION="0.7.0"

Fields
Modifier and Type	Field and Description
`protected int`	`processingAccession`
`static String`	`VERSION` Constant `VERSION="0.7.0"`

Constructor Summary

Constructors
Constructor and Description

Module()

Constructors
Constructor and Description
`Module()`

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`clean_up()` clean_up.
`abstract ReturnValue`	`do_run()` do_run.
`abstract ReturnValue`	`do_test()` do_test.
`abstract ReturnValue`	`do_verify_input()` do_verify_input.
`abstract ReturnValue`	`do_verify_output()` do_verify_output.
`abstract ReturnValue`	`do_verify_parameters()` do_verify_parameters.
`String`	`get_galaxy_xml()` Output Galaxy definition files so you can use this module with Galaxy.
`String`	`get_syntax()` Generates a "help" message for the user of the module.
`String`	`getAlgorithm()` Getter for the field `algorithm`.
`Metadata`	`getMetadata()` Getter for the field `metadata`.
`protected joptsimple.OptionParser`	`getOptionParser()` getOptionParser.
`List<String>`	`getParameters()` Getter for the field `parameters`.
`int`	`getProcessingAccession()` Getter for the field `processingAccession`.
`File`	`getStderrFile()` Getter for the file where the stderr will be redirected.
`File`	`getStdoutFile()` Getter for the file where the stdout will be redirected.
`ReturnValue`	`init()` init.
`void`	`setAlgorithm(String algorithm)` Setter for the field `algorithm`.
`void`	`setMetadata(Metadata metadata)` Setter for the field `metadata`.
`void`	`setParameters(List<String> parameters)` setParameters.
`void`	`setProcessingAccession(int accession)` Setter for the field `processingAccession`.
`void`	`setStderrFile(File stderrFile)` Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
`void`	`setStdoutFile(File stdoutFile)` Setter for the field `stdoutFile`.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - VERSION
```
public static final String VERSION
```
    Constant VERSION="0.7.0"
    
    See Also:
    Constant Field Values
  - processingAccession
```
protected int processingAccession
```
- Constructor Detail
  - Module
```
public Module()
```
- Method Detail
  - getStdoutFile
```
public File getStdoutFile()
```
    Getter for the file where the stdout will be redirected. By default, the stdout will be redirected before the do_run() method and turned off after do_run() method. However, this can be changed via the @StdoutRedirect annotation on the module class
    
    Returns:
    the stdout file object
  - setStdoutFile
```
public void setStdoutFile(File stdoutFile)
```
    Setter for the field stdoutFile.
    
    Parameters:
    stdoutFile - a File object.
  - getStderrFile
```
public File getStderrFile()
```
    Getter for the file where the stderr will be redirected. By default, the stderr will be redirected before the do_run() method and turned off after the do_run(). To change the behavior, use @StderrRedirect annotation.
    
    Returns:
    the stderr file object
  - setStderrFile
```
public void setStderrFile(File stderrFile)
```
    Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
    
    Parameters:
    stderrFile - the stderr file object
  - getMetadata
```
public Metadata getMetadata()
```
    Getter for the field metadata.
    
    Returns:
    a Metadata object.
  - getAlgorithm
```
public String getAlgorithm()
```
    Getter for the field algorithm.
    
    Specified by:
    
    getAlgorithm in interface ModuleInterface
    
    Returns:
    a String object.
  - setAlgorithm
```
public void setAlgorithm(String algorithm)
```
    Setter for the field algorithm.
    
    Parameters:
    algorithm - a String object.
  - setMetadata
```
public void setMetadata(Metadata metadata)
```
    Setter for the field metadata.
    
    Parameters:
    metadata - a Metadata object.
  - getParameters
```
public List<String> getParameters()
```
    Getter for the field parameters.
    
    Returns:
    a List object.
  - setParameters
```
public void setParameters(List<String> parameters)
```
    setParameters.
    This method doesn't just copy the list, it actually parses through the list and looks for values that start with " or ' and then attempts to merge other parameters separated by space until an param ending with " or ' is found. This is to work around a limitation in JOpt. It breaks apart arguments by space regarless if the arg is a quoted string (and hence should be treated as one arg)
    
    Specified by:
    
    setParameters in interface ModuleInterface
    
    Parameters:
    parameters -
  - getOptionParser
```
protected joptsimple.OptionParser getOptionParser()
```
    getOptionParser.
    
    Returns:
    a OptionParser object.
  - get_syntax
```
public String get_syntax()
```
    Generates a "help" message for the user of the module. This will be called by [TODO: what?] to provide information about using the module. It is up to the implementation to defined the format for the returned message. This is not part of the normal life-cycle of a module, but represents an "alternate" life, where the module is called just to provide a self-description. A method used to return the syntax for this module
    
    Specified by:
    
    get_syntax in interface ModuleInterface
    
    Returns:
    Description of how to use this module.
  - get_galaxy_xml
```
public String get_galaxy_xml()
```
    Output Galaxy definition files so you can use this module with Galaxy. See http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
    
    Returns:
    a String object.
  - do_run
```
public abstract ReturnValue do_run()
```
    do_run.
    
    Specified by:
    
    do_run in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - init
```
public ReturnValue init()
```
    init.
    
    Specified by:
    
    init in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - clean_up
```
public ReturnValue clean_up()
```
    clean_up.
    
    Specified by:
    
    clean_up in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - do_test
```
public abstract ReturnValue do_test()
```
    do_test.
    
    Specified by:
    
    do_test in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - do_verify_input
```
public abstract ReturnValue do_verify_input()
```
    do_verify_input.
    
    Specified by:
    
    do_verify_input in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - do_verify_parameters
```
public abstract ReturnValue do_verify_parameters()
```
    do_verify_parameters.
    
    Specified by:
    
    do_verify_parameters in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - do_verify_output
```
public abstract ReturnValue do_verify_output()
```
    do_verify_output.
    
    Specified by:
    
    do_verify_output in interface ModuleInterface
    
    Returns:
    a ReturnValue object.
  - getProcessingAccession
```
public int getProcessingAccession()
```
    Getter for the field processingAccession.
    
    Returns:
    a int.
  - setProcessingAccession
```
public void setProcessingAccession(int accession)
```
    Setter for the field processingAccession.
    
    Parameters:
    accession - a int.

Class Module

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VERSION

processingAccession

Constructor Detail

Module

Method Detail

getStdoutFile

setStdoutFile

getStderrFile

setStderrFile

getMetadata

getAlgorithm

setAlgorithm

setMetadata

getParameters

setParameters

getOptionParser

get_syntax

get_galaxy_xml

do_run

init

clean_up

do_test

do_verify_input

do_verify_parameters

do_verify_output

getProcessingAccession

setProcessingAccession