S3UploadDirectory (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.module.Module
- - net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

All Implemented Interfaces:

ModuleInterface
```
public class S3UploadDirectory
extends Module
```
Purpose: This module uses the Amazon API to recursively upload a directory to an S3 bucket.

Author:

boconnor

Field Summary

Fields
Modifier and Type Field and Description

protected joptsimple.OptionSet options
- Fields inherited from class net.sourceforge.seqware.pipeline.module.Module
  processingAccession, VERSION

Fields
Modifier and Type	Field and Description
`protected joptsimple.OptionSet`	`options`

Constructor Summary

Constructors
Constructor and Description

S3UploadDirectory()

Constructors
Constructor and Description
`S3UploadDirectory()`

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`do_run()` do_run.
`ReturnValue`	`do_test()` Things to check: * FIXME
`ReturnValue`	`do_verify_input()` do_verify_input.
`ReturnValue`	`do_verify_output()` do_verify_output.
`ReturnValue`	`do_verify_parameters()` do_verify_parameters.
`String`	`get_syntax()` Generates a "help" message for the user of the module.
`protected joptsimple.OptionParser`	`getOptionParser()` getOptionParser.
`protected ReturnValue`	`recursivelyUploadDir(String inputDir, String outputBucket, String outputPrefix, com.amazonaws.services.s3.transfer.TransferManager tx)`

Methods inherited from class net.sourceforge.seqware.pipeline.module.Module
clean_up, get_galaxy_xml, getAlgorithm, getMetadata, getParameters, getProcessingAccession, getStderrFile, getStdoutFile, init, setAlgorithm, setMetadata, setParameters, setProcessingAccession, setStderrFile, setStdoutFile

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

- Field Detail
  - options
```
protected joptsimple.OptionSet options
```
- Constructor Detail
  - S3UploadDirectory
```
public S3UploadDirectory()
```
- Method Detail
  - getOptionParser
```
protected joptsimple.OptionParser getOptionParser()
```
    Description copied from class: Module
    
    getOptionParser.
    
    Overrides:
    
    getOptionParser in class Module
    
    Returns:
    a OptionParser object.
  - get_syntax
```
public String get_syntax()
```
    Description copied from class: Module
    
    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
    
    Overrides:
    
    get_syntax in class Module
    
    Returns:
    Description of how to use this module.
  - do_test
```
public ReturnValue do_test()
```
    Things to check: * FIXME
    
    Specified by:
    
    do_test in interface ModuleInterface
    
    Specified by:
    
    do_test in class Module
    
    Returns:
  - do_verify_parameters
```
public ReturnValue do_verify_parameters()
```
    Description copied from class: Module
    
    do_verify_parameters.
    
    Specified by:
    
    do_verify_parameters in interface ModuleInterface
    
    Specified by:
    
    do_verify_parameters in class Module
    
    Returns:
    a ReturnValue object.
  - do_verify_input
```
public ReturnValue do_verify_input()
```
    Description copied from class: Module
    
    do_verify_input.
    
    Specified by:
    
    do_verify_input in interface ModuleInterface
    
    Specified by:
    
    do_verify_input in class Module
    
    Returns:
    a ReturnValue object.
  - do_run
```
public ReturnValue do_run()
```
    Description copied from class: Module
    
    do_run.
    
    Specified by:
    
    do_run in interface ModuleInterface
    
    Specified by:
    
    do_run in class Module
    
    Returns:
    a ReturnValue object.
  - recursivelyUploadDir
```
protected ReturnValue recursivelyUploadDir(String inputDir,
                               String outputBucket,
                               String outputPrefix,
                               com.amazonaws.services.s3.transfer.TransferManager tx)
```
  - do_verify_output
```
public ReturnValue do_verify_output()
```
    Description copied from class: Module
    
    do_verify_output.
    
    Specified by:
    
    do_verify_output in interface ModuleInterface
    
    Specified by:
    
    do_verify_output in class Module
    
    Returns:
    a ReturnValue object.

Class S3UploadDirectory

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.module.Module

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.module.Module

Methods inherited from class java.lang.Object

Field Detail

options

Constructor Detail

S3UploadDirectory

Method Detail

getOptionParser

get_syntax

do_test

do_verify_parameters

do_verify_input

do_run

recursivelyUploadDir

do_verify_output