DeciderInterface (SeqWare 1.1.2 API)

All Known Implementing Classes:

BasicDecider
```
public interface DeciderInterface
```
DeciderInterface interface.
Since:
20120408
This interface defines the required behavior of a SeqWare Pipeline decider. Essentially it assumes a life-cycle made up of several phases for a decider, 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_summary()
6. do_run()
7. do_verify_output()
8. 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.

The lifecyle is very similar to the module or plugin lifecycle but with a different emphasis. Modules are designed to call an external tool from within workflows whereas plugins are intended to extend the core functionality of SeqWare Pipeline tool itself and have nothing to with calling external tools. The decider is most similar to the plugin but has some extra metadata that helps a user quickly write the decider logic.

Methods that are not implemented can return ReturnValue.NOTIMPLEMENTED (-1). The DeciderRunner will skip over these steps, and only fail on error if a method returns > 0.
Version:

$Id: $Id

Author:

briandoconnor@gmail.com

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 plugin.
`ReturnValue`	`do_summary()` Just returns a summary of what would be run.
`ReturnValue`	`do_test()` Perform any active system testing here.
`String`	`get_description()` Generates a short description of the plugin, preferably one line.
`String`	`get_syntax()` Generates a "help" message for the user of the plugin.
`ReturnValue`	`init()` Plugin initialization code goes here.
`ReturnValue`	`parse_parameters()` Parameter validation code goes here.
`void`	`setConfig(Map<String,String> config)` Let's you set the config this object should use.
`void`	`setMetadata(Metadata metadata)` Lets you set the metadata object
`void`	`setParams(List<String> params)` Lets you set a List of params so the plugin can deal with parameters

- Method Detail
  - setConfig
```
void setConfig(Map<String,String> config)
```
    Let's you set the config this object should use.
    
    Parameters:
    config - A map that includes the key/values from the SeqWare settings file.
  - setParams
```
void setParams(List<String> params)
```
    Lets you set a List of params so the plugin can deal with parameters
    
    Parameters:
    params - The parameters specifically passed in to the plugin.
  - setMetadata
```
void setMetadata(Metadata metadata)
```
    Lets you set the metadata object
    
    Parameters:
    metadata - a Metadata object.
  - get_syntax
```
String get_syntax()
```
    Generates a "help" message for the user of the plugin. This will be called by the PluginRunner to provide information about using the plugin. It is up to the implementation to defined the format for the returned message. This is triggered if no options are provided to the PluginRunner.
    
    Returns:
    Description of the command line parameters for this plugin.
  - get_description
```
String get_description()
```
    Generates a short description of the plugin, preferably one line.
    
    Returns:
    Description of the plugin.
  - parse_parameters
```
ReturnValue parse_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 happens here where the existence and content of input data files will be checked.
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - init
```
ReturnValue init()
```
    Plugin initialization code goes here. This is the first phase of the plugin 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(). The SEQWARE_SETTINGS file contents is passed in here.
    
    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 available, 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_summary
```
ReturnValue do_summary()
```
    Just returns a summary of what would be run.
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - do_run
```
ReturnValue do_run()
```
    Performs the main tasks for the plugin. This is where you actually execute your task and where the bulk of your implementation will go.
    
    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 close db connections, etc.
    
    Returns:
    Success or failure info from this phase, along with any console output.

Interface DeciderInterface

Method Summary

Method Detail

setConfig

setParams

setMetadata

get_syntax

get_description

parse_parameters

init

do_test

do_summary

do_run

clean_up