ProcessingServiceImpl (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

All Implemented Interfaces:

ProcessingService
```
public class ProcessingServiceImpl
extends Object
implements ProcessingService
```
ProcessingServiceImpl class.

Version:

$Id: $Id

Author:

boconnor

Field Summary
- Fields inherited from interface net.sourceforge.seqware.common.business.ProcessingService
  NAME

Constructor Summary

Constructors
Constructor and Description

ProcessingServiceImpl()
Constructor for ProcessingServiceImpl.

Constructors
Constructor and Description
`ProcessingServiceImpl()` Constructor for ProcessingServiceImpl.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(Processing processing, boolean deleteRealFiles)` delete.
`List<Processing>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`Processing`	`findByID(Integer id)` findByID.
`Processing`	`findByIDOnlyWithRunningWR(Integer processingID)` findByIDOnlyWithRunningWR.
`List<Processing>`	`findByOwnerID(Integer registrationId)` findByOwnerID.
`Processing`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`Set<Processing>`	`findFor(Sample sample)` findFor.
`Set<Processing>`	`findFor(Sample sample, WorkflowRun workflowRun)` findFor.
`List<File>`	`getFiles(Integer processingId)` getFiles.
`List<File>`	`getFiles(Integer processingId, String metaType)` getFiles.
`Integer`	`insert(Processing processing)` Inserts a new Processing and returns its sw_accession number.
`Integer`	`insert(Registration registration, Processing processing)` insert.
`void`	`insert(Registration registration, SequencerRun sequencerRun, Processing processing)` insert.
`void`	`insert(SequencerRun sequencerRun, Processing processing)` insert.
`boolean`	`isHasFile(Integer processingId)` isHasFile.
`boolean`	`isHasFile(Integer processingId, String metaType)` isHasFile.
`List<Processing>`	`list()` list.
`void`	`setFileDAO(FileDAO fileDAO)` Sets a private member variable with an instance of an implementation of FileDAO.
`void`	`setProcessingDAO(ProcessingDAO processingDAO)` setProcessingDAO.
`Set<Processing>`	`setWithHasFile(Set<Processing> list)` setWithHasFile.
`Set<Processing>`	`setWithHasFile(Set<Processing> list, String metaType)` setWithHasFile.
`void`	`update(Processing processing)` update.
`void`	`update(Registration registration, Processing processing)` update.
`Processing`	`updateDetached(Processing processing)` updateDetached.
`Processing`	`updateDetached(Registration registration, Processing processing)` updateDetached.

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

- Constructor Detail
  - ProcessingServiceImpl
```
public ProcessingServiceImpl()
```
    Constructor for ProcessingServiceImpl.
- Method Detail
  - setProcessingDAO
```
public void setProcessingDAO(ProcessingDAO processingDAO)
```
    setProcessingDAO.
    Sets a private member variable with an instance of an implementation of ProcessingDAO. This method is called by the Spring framework at run time.
    
    Specified by:
    
    setProcessingDAO in interface ProcessingService
    
    Parameters:
    processingDAO - a ProcessingDAO object.
    See Also:
    ProcessingDAO
  - setFileDAO
```
public void setFileDAO(FileDAO fileDAO)
```
    Sets a private member variable with an instance of an implementation of FileDAO. This method is called by the Spring framework at run time.
    
    Parameters:
    fileDAO - implementation of FileDAO
    See Also:
    FileDAO
  - insert
```
public void insert(SequencerRun sequencerRun,
          Processing processing)
```
    insert.
    Inserts an instance of Processing into the database.
    
    Specified by:
    
    insert in interface ProcessingService
    
    Parameters:
    sequencerRun - a SequencerRun object.
    processing - a Processing object.
  - insert
```
public void insert(Registration registration,
          SequencerRun sequencerRun,
          Processing processing)
```
    insert.
    
    Specified by:
    
    insert in interface ProcessingService
    
    Parameters:
    registration - a Registration object.
    sequencerRun - a SequencerRun object.
    processing - a Processing object.
  - insert
```
public Integer insert(Processing processing)
```
    Inserts a new Processing and returns its sw_accession number.
    
    Specified by:
    
    insert in interface ProcessingService
    
    Parameters:
    processing - Processing to be inserted.
    
    Returns:
    The SeqWare Accession number for the newly inserted Processing.
  - update
```
public void update(Processing processing)
```
    update.
    Updates an instance of Processing in the database.
    
    Specified by:
    
    update in interface ProcessingService
    
    Parameters:
    processing - a Processing object.
  - delete
```
public void delete(Processing processing,
          boolean deleteRealFiles)
```
    delete.
    
    Specified by:
    
    delete in interface ProcessingService
    
    Parameters:
    processing -
    deleteRealFiles -
  - getFiles
```
public List<File> getFiles(Integer processingId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface ProcessingService
    
    Parameters:
    processingId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer processingId)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface ProcessingService
    
    Parameters:
    processingId - a Integer object.
    
    Returns:
    a boolean.
  - setWithHasFile
```
public Set<Processing> setWithHasFile(Set<Processing> list)
```
    setWithHasFile.
    
    Specified by:
    
    setWithHasFile in interface ProcessingService
    
    Parameters:
    list - a Set object.
    
    Returns:
    a Set object.
  - getFiles
```
public List<File> getFiles(Integer processingId,
                  String metaType)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface ProcessingService
    
    Parameters:
    processingId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer processingId,
                String metaType)
```
    isHasFile.
    
    Parameters:
    processingId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - setWithHasFile
```
public Set<Processing> setWithHasFile(Set<Processing> list,
                             String metaType)
```
    setWithHasFile.
    
    Specified by:
    
    setWithHasFile in interface ProcessingService
    
    Parameters:
    list - a Set object.
    metaType - a String object.
    
    Returns:
    a Set object.
  - findByID
```
public Processing findByID(Integer id)
```
    findByID.
    
    Specified by:
    
    findByID in interface ProcessingService
    
    Parameters:
    id -
    
    Returns:
    a Processing object.
  - findByIDOnlyWithRunningWR
```
public Processing findByIDOnlyWithRunningWR(Integer processingID)
```
    findByIDOnlyWithRunningWR.
    
    Specified by:
    
    findByIDOnlyWithRunningWR in interface ProcessingService
    
    Parameters:
    processingID - a Integer object.
    
    Returns:
    a Processing object.
  - findBySWAccession
```
public Processing findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface ProcessingService
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Processing object.
  - findByOwnerID
```
public List<Processing> findByOwnerID(Integer registrationId)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface ProcessingService
    
    Parameters:
    registrationId - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Processing> findByCriteria(String criteria,
                              boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface ProcessingService
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - updateDetached
```
public Processing updateDetached(Processing processing)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface ProcessingService
    
    Parameters:
    processing - a Processing object.
    
    Returns:
    a Processing object.
  - list
```
public List<Processing> list()
```
    list.
    
    Specified by:
    
    list in interface ProcessingService
    
    Returns:
    a List object.
  - update
```
public void update(Registration registration,
          Processing processing)
```
    update.
    
    Specified by:
    
    update in interface ProcessingService
    
    Parameters:
    registration - a Registration object.
    processing - a Processing object.
  - insert
```
public Integer insert(Registration registration,
             Processing processing)
```
    insert.
    
    Specified by:
    
    insert in interface ProcessingService
    
    Parameters:
    registration - a Registration object.
    processing - a Processing object.
    
    Returns:
    a Integer object.
  - updateDetached
```
public Processing updateDetached(Registration registration,
                        Processing processing)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface ProcessingService
    
    Parameters:
    registration - a Registration object.
    processing - a Processing object.
    
    Returns:
    a Processing object.
  - findFor
```
public Set<Processing> findFor(Sample sample,
                      WorkflowRun workflowRun)
```
    findFor.
    Returns the Set of the Processings belongs to the specific Sample, WorkflowRun.
    
    Specified by:
    
    findFor in interface ProcessingService
    
    Parameters:
    sample - a Sample object.
    workflowRun - a WorkflowRun object.
    
    Returns:
    a Set object.
  - findFor
```
public Set<Processing> findFor(Sample sample)
```
    findFor.
    
    Specified by:
    
    findFor in interface ProcessingService
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Set object.

Class ProcessingServiceImpl

Field Summary

Fields inherited from interface net.sourceforge.seqware.common.business.ProcessingService

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ProcessingServiceImpl

Method Detail

setProcessingDAO

setFileDAO

insert

insert

insert

update

delete

getFiles

isHasFile

setWithHasFile

getFiles

isHasFile

setWithHasFile

findByID

findByIDOnlyWithRunningWR

findBySWAccession

findByOwnerID

findByCriteria

updateDetached

list

update

insert

updateDetached

findFor

findFor