GenericMetadataSaver (SeqWare 1.1.2 API)

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

All Implemented Interfaces:

ModuleInterface

Deprecated.
Deprecating this in favour of Metadata(plugin) and the new CLI
```
public class GenericMetadataSaver
extends Module
```
This is a very simple module is used to save both a processing event and 0 or more files to the metadb. It does absolutely no computation at all, it just saves metadata. You might want to use this if your module or call to genericCommandRunner results in a bunch of files being created, each of which need to be associated with different parent objects in the database. You might also use this to combine the outputs of several different steps into a single processing event so the UI in the Portal is simplified. Here's an example of how you might call the program: ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver -- --gms-output-file test:test:/tmp/foo.txt --gms-algorithm foobarAlgorithm You could, of course, supply metadata db information so the status is written to the database and also a parent accession along with an accession output file to be read in by a subsequent step. Please use JavaDoc to document each method (the user interface documents will be autogenerated using these comments). See http://en.wikipedia.org/wiki/Javadoc for more information.

Version:

$Id: $Id

Author:

briandoconnor@gmail.com

Field Summary
- Fields inherited from class net.sourceforge.seqware.pipeline.module.Module
  processingAccession, VERSION

Constructor Summary

Constructors
Constructor and Description

GenericMetadataSaver()
Deprecated.

Constructors
Constructor and Description
`GenericMetadataSaver()` Deprecated.

Method Summary

Methods
Modifier and Type	Method and Description
`ReturnValue`	`clean_up()` Deprecated. clean_up.
`ReturnValue`	`do_run()` Deprecated. do_run.
`ReturnValue`	`do_test()` Deprecated. do_test.
`ReturnValue`	`do_verify_input()` Deprecated. do_verify_input.
`ReturnValue`	`do_verify_output()` Deprecated. do_verify_output.
`ReturnValue`	`do_verify_parameters()` Deprecated. do_verify_parameters.
`String`	`get_syntax()` Deprecated. Generates a "help" message for the user of the module.
`protected joptsimple.OptionParser`	`getOptionParser()` Deprecated. getOptionParser is an internal method to parse command line args.
`ReturnValue`	`init()` Deprecated. init.

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

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

- Constructor Detail
  - GenericMetadataSaver
```
public GenericMetadataSaver()
```
    Deprecated.
- Method Detail
  - getOptionParser
```
protected joptsimple.OptionParser getOptionParser()
```
    Deprecated.
    
    getOptionParser is an internal method to parse command line args.
    
    Overrides:
    
    getOptionParser in class Module
    
    Returns:
    OptionParser this is used to get command line options
  - get_syntax
```
public String get_syntax()
```
    Deprecated.
    
    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 A method used to return the syntax for this module
    
    Specified by:
    
    get_syntax in interface ModuleInterface
    
    Overrides:
    
    get_syntax in class Module
    
    Returns:
  - init
```
public ReturnValue init()
```
    Deprecated.
    
    init.
    The init method is where you put any code needed to setup your module. Here I set some basic information in the ReturnValue object which will eventually populate the "processing" table in seqware_meta_db. I also create a temporary directory using the FileTools object. init is optional
    
    Specified by:
    
    init in interface ModuleInterface
    
    Overrides:
    
    init in class Module
    
    Returns:
  - do_verify_parameters
```
public ReturnValue do_verify_parameters()
```
    Deprecated.
    
    do_verify_parameters.
    Verifies that the parameters make sense
    
    Specified by:
    
    do_verify_parameters in interface ModuleInterface
    
    Specified by:
    
    do_verify_parameters in class Module
    
    Returns:
  - do_verify_input
```
public ReturnValue do_verify_input()
```
    Deprecated.
    
    do_verify_input.
    The do_verify_input method ensures that the input is reasonable and valid for this tool. For this generic command runner we really can't tell if the
    
    Specified by:
    
    do_verify_input in interface ModuleInterface
    
    Specified by:
    
    do_verify_input in class Module
    
    Returns:
  - do_test
```
public ReturnValue do_test()
```
    Deprecated.
    
    do_test.
    This is really an optional method but a very good idea. You would test the programs your calling here by running them on a "known good" test dataset and then compare the new answer with the previous known good answer. Other forms of testing could be encapsulated here as well.
    
    Specified by:
    
    do_test in interface ModuleInterface
    
    Specified by:
    
    do_test in class Module
    
    Returns:
  - do_run
```
public ReturnValue do_run()
```
    Deprecated.
    
    do_run.
    This is the core of a module. It just saves metadata back to the DB using the standardized ReturnValue object as a wrapper.
    
    Specified by:
    
    do_run in interface ModuleInterface
    
    Specified by:
    
    do_run in class Module
    
    Returns:
  - do_verify_output
```
public ReturnValue do_verify_output()
```
    Deprecated.
    
    do_verify_output.
    A method to check to make sure the output was created correctly
    
    Specified by:
    
    do_verify_output in interface ModuleInterface
    
    Specified by:
    
    do_verify_output in class Module
    
    Returns:
  - clean_up
```
public ReturnValue clean_up()
```
    Deprecated.
    
    clean_up.
    A cleanup method, make sure you cleanup files that are outside the current working directory since Pegasus won't clean those for you. clean_up is optional
    
    Specified by:
    
    clean_up in interface ModuleInterface
    
    Overrides:
    
    clean_up in class Module
    
    Returns:

Class GenericMetadataSaver

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

Constructor Detail

GenericMetadataSaver

Method Detail

getOptionParser

get_syntax

init

do_verify_parameters

do_verify_input

do_test

do_run

do_verify_output

clean_up