ModuleInterface (SeqWare 1.1.2 API)

All Known Implementing Classes:

GenericCommandRunner, GenericMetadataSaver, Module, ProvisionDependenciesBundle, ProvisionFiles, S3CreateFileURLs, S3DeleteFiles, S3ListFiles, S3UploadDirectory, TestModule
```
public interface ModuleInterface
```
This interface defines the required behavior of a SeqWare module. Essentially it assumes a life-cycle made up of several phases for a module, specifying a function for each of these phase that an implementation overrides to provide the code executed during that phase. The phases are:
1. init()
2. do_verify_parameters()
3. do_verify_input()
4. do_test()
5. do_run()
6. do_verify_output()
7. clean_up()
Information about the the success or failure of each step is packaged into a ReturnValue object, including anything sent to STDOUT and STDERR.
Version:

$Id: $Id

Author:

boconnor

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`clean_up()` Perform post-task clean-up here.
`ReturnValue`	`do_run()` Performs the main tasks for the module.
`ReturnValue`	`do_test()` Perform any active system testing here.
`ReturnValue`	`do_verify_input()` Input data validation code goes here.
`ReturnValue`	`do_verify_output()` Perform post-task tests here.
`ReturnValue`	`do_verify_parameters()` Parameter validation code goes here.
`String`	`get_syntax()` Generates a "help" message for the user of the module.
`String`	`getAlgorithm()` getAlgorithm.
`ReturnValue`	`init()` Module initialization code goes here.
`void`	`setParameters(List<String> params)` setParameters.

- Method Detail
  - setParameters
```
void setParameters(List<String> params)
```
    setParameters.
    
    Parameters:
    params - a List object.
  - getAlgorithm
```
String getAlgorithm()
```
    getAlgorithm.
    
    Returns:
    a String object.
  - get_syntax
```
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.
    
    Returns:
    Description of how to use this module.
  - init
```
ReturnValue init()
```
    Module initialization code goes here. This is the first phase of the module lifecycle run. Might do things here like set up database access, create temp files, define defaults, etc. Preprocessing can be done here, although normally processing should be done by/during do_run().
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_verify_parameters
```
ReturnValue do_verify_parameters()
```
    Parameter validation code goes here. Use to make sure all required parameters are available, that parameters are known, that they have reasonable values, etc. Validation involving multiple options is best deferred to the next step where the existence and content of input data files will be checked, do_verify_input().
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_verify_input
```
ReturnValue do_verify_input()
```
    Input data validation code goes here. Use to make sure that input file exist that needed output directories exist and can be written to, or can be created, etc. Modules should fail up front when possible to avoid wasting large amounts of processing time. This is also the place to validate combinations of parameters (individual parameters and their values are validated in the previous step, do_verify_parameters().
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_test
```
ReturnValue do_test()
```
    Perform any active system testing here. Use to make sure a DB is only, [TODO: Huh?], that a command line tools can be run, etc. You can even write functional tests that run the program you're wrapping on a small known good and then verify the output.
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_run
```
ReturnValue do_run()
```
    Performs the main tasks for the module. This is where you actually execute your task, run the external program, etc.
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_verify_output
```
ReturnValue do_verify_output()
```
    Perform post-task tests here. Use to check that expected directories exist, that files were not empty unexpectedly, etc. In practice, this check should be light-weight. If the output appears to be fine, then assume it is. Let the next module's input checking do any deep verification. Otherwise, everything gets checked twice and that can waste a lot of time. If it is a quick check, go ahead and do it. Note: Long/hard to do QC checks might deserve their own module!
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - clean_up
```
ReturnValue clean_up()
```
    Perform post-task clean-up here. Use to remove temporary files and directories, flush buffers and db connections, etc.
    
    Returns:
    Success or failure info from this phase, along with any console output.

Interface ModuleInterface

Method Summary

Method Detail

setParameters

getAlgorithm

get_syntax

init

do_verify_parameters

do_verify_input

do_test

do_run

do_verify_output

clean_up