WorkflowScheduler (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.plugin.Plugin
- - io.seqware.pipeline.plugins.WorkflowScheduler

All Implemented Interfaces:

PluginInterface
```
public class WorkflowScheduler
extends Plugin
```
The Workflow Scheduler is only responsible for scheduling workflows. This is a fork of the WorkflowLauncher intended to de-tangle the functions of launching, scheduling, waiting, etc. Typically, after scheduling a workflow, you would use WorkflowLauncher in order to launch scheduled workflows on a host with connectivity to HDFS and Oozie. WorkflowScheduler itself only needs access to the web service in order to schedule.

Author:

dyuen

Field Summary

Fields
Modifier and Type Field and Description

static String INPUT_FILES

static String OVERRIDE_INI_DESC
- Fields inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin
  config, metadata, options, params, parser

Fields
Modifier and Type	Field and Description
`static String`	`INPUT_FILES`
`static String`	`OVERRIDE_INI_DESC`

Constructor Summary

Constructors
Constructor and Description

WorkflowScheduler()

Constructors
Constructor and Description
`WorkflowScheduler()`

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`clean_up()` Perform post-task clean-up here.
`static joptsimple.ArgumentAcceptingOptionSpec<String>`	`createIniFileSpec(joptsimple.OptionParser parser)`
`static joptsimple.OptionSpecBuilder`	`createMetadataWriteBackOffSpec(joptsimple.OptionParser parser)`
`static joptsimple.ArgumentAcceptingOptionSpec<String>`	`createParentAccessionSpec(joptsimple.OptionParser parser)`
`static joptsimple.ArgumentAcceptingOptionSpec<String>`	`createWorkflowEngineSpec(joptsimple.OptionParser parser)`
`ReturnValue`	`do_run()` Performs the main tasks for the plugin.
`ReturnValue`	`do_test()` Perform any active system testing here.
`String`	`get_description()` Generates a short description of the plugin, preferably one line.
`ReturnValue`	`init()` Plugin initialization code goes here.
`static ReturnValue`	`validateEngineString(String engine)`

Methods inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin
get_syntax, parse_parameters, print, println, setConfig, setMetadata, setParams

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

- Field Detail
  - INPUT_FILES
```
public static final String INPUT_FILES
```
    See Also:
    Constant Field Values
  - OVERRIDE_INI_DESC
```
public static final String OVERRIDE_INI_DESC
```
    See Also:
    Constant Field Values
- Constructor Detail
  - WorkflowScheduler
```
public WorkflowScheduler()
```
- Method Detail
  - createParentAccessionSpec
```
public static final joptsimple.ArgumentAcceptingOptionSpec<String> createParentAccessionSpec(joptsimple.OptionParser parser)
```
  - createMetadataWriteBackOffSpec
```
public static final joptsimple.OptionSpecBuilder createMetadataWriteBackOffSpec(joptsimple.OptionParser parser)
```
  - createWorkflowEngineSpec
```
public static final joptsimple.ArgumentAcceptingOptionSpec<String> createWorkflowEngineSpec(joptsimple.OptionParser parser)
```
  - createIniFileSpec
```
public static final joptsimple.ArgumentAcceptingOptionSpec<String> createIniFileSpec(joptsimple.OptionParser parser)
```
  - init
```
public ReturnValue init()
```
    Description copied from interface: PluginInterface
    
    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.
  - validateEngineString
```
public static ReturnValue validateEngineString(String engine)
```
  - do_test
```
public ReturnValue do_test()
```
    Description copied from interface: PluginInterface
    
    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.
  - clean_up
```
public ReturnValue clean_up()
```
    Description copied from interface: PluginInterface
    
    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.
  - get_description
```
public String get_description()
```
    Description copied from class: Plugin
    
    Generates a short description of the plugin, preferably one line.
    
    Specified by:
    
    get_description in interface PluginInterface
    
    Overrides:
    
    get_description in class Plugin
    
    Returns:
    Description of the plugin.
  - do_run
```
public ReturnValue do_run()
```
    Description copied from interface: PluginInterface
    
    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.

Class WorkflowScheduler

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.plugin.Plugin

Methods inherited from class java.lang.Object

Field Detail

INPUT_FILES

OVERRIDE_INI_DESC

Constructor Detail

WorkflowScheduler

Method Detail

createParentAccessionSpec

createMetadataWriteBackOffSpec

createWorkflowEngineSpec

createIniFileSpec

init

validateEngineString

do_test

clean_up

get_description

do_run