WorkflowRunServiceImpl (SeqWare 1.1.2 API)

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

All Implemented Interfaces:

WorkflowRunService
```
public class WorkflowRunServiceImpl
extends Object
implements WorkflowRunService
```
WorkflowRunServiceImpl class.

Version:

$Id: $Id

Author:

boconnor

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

Constructor Summary

Constructors
Constructor and Description

WorkflowRunServiceImpl()
Constructor for WorkflowRunServiceImpl.

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(WorkflowRun workflowRun, boolean deleteRealFiles)` delete.
`List<WorkflowRun>`	`findByCriteria(String criteria)` findByCriteria.
`List<WorkflowRun>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`WorkflowRun`	`findByID(Integer wfrID)` findByID.
`WorkflowRun`	`findByIDWithIUS(Integer wfrID)` findByIDWithIUS.
`WorkflowRun`	`findByIDWithIUSAndRunningWR(Integer wfrID)` findByIDWithIUSAndRunningWR.
`WorkflowRun`	`findByName(String name)` findByName.
`List<WorkflowRun>`	`findByOwnerID(Integer registrationID)` findByOwnerID.
`WorkflowRun`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`List<File>`	`findFiles(Integer swAccession)` findFiles.
`Set<WorkflowRun>`	`findRunsForIUS(IUS ius)` findRunsForIUS.
`Set<WorkflowRun>`	`findRunsForSample(Sample sample)` Find all the workflow runs for the specific sample.
`List<File>`	`getFiles(Integer wfrId)` getFiles.
`Processing`	`getRootProcessing(Integer wfrId)` getRootProcessing.
`Integer`	`insert(Registration registration, WorkflowRun workflowRun)` insert.
`Integer`	`insert(Registration registration, WorkflowRun workflowRun, SortedSet<WorkflowRunParam> workflowRunParams, Map<String,List<File>> allSelectedFiles)` insert.
`Integer`	`insert(WorkflowRun workflowRun)` Inserts a new WorkflowRun and returns its sw_accession number.
`Integer`	`insert(WorkflowRun workflowRun, SortedSet<WorkflowRunParam> workflowRunParams, Map<String,List<File>> allSelectedFiles)` insert.
`List<WorkflowRun>`	`list()` list.
`List<WorkflowRun>`	`list(Registration registration)` list.
`List<WorkflowRun>`	`list(Registration registration, Boolean isAsc)` list.
`List<WorkflowRun>`	`listMyShared(Registration registration)` listMyShared.
`List<WorkflowRun>`	`listMyShared(Registration registration, Boolean isAsc)` listMyShared.
`List<Workflow>`	`listRelatedWorkflows(Registration registration)` listRelatedWorkflows.
`List<WorkflowRun>`	`listRunning(Registration registration)` listRunning.
`List<WorkflowRun>`	`listRunning(Registration registration, Boolean isAsc)` listRunning.
`List<WorkflowRun>`	`listSharedWithMe(Registration registration)` listSharedWithMe.
`List<WorkflowRun>`	`listSharedWithMe(Registration registration, Boolean isAsc)` listSharedWithMe.
`List<WorkflowRun>`	`listSharedWithMeWithSample(Registration registration)` listSharedWithMeWithSample.
`List<WorkflowRun>`	`listWithHasFile(List<WorkflowRun> list)` listWithHasFile.
`void`	`setFileDAO(FileDAO fileDAO)` Sets a private member variable with an instance of an implementation of FileDAO.
`void`	`setProcessingDAO(ProcessingDAO processingDAO)` Setter for the field `processingDAO`.
`void`	`setWorkflowRunDAO(WorkflowRunDAO workflowRunDAO)` setWorkflowRunDAO.
`void`	`setWorkflowRunParamDAO(WorkflowRunParamDAO workflowRunParamDAO)` Setter for the field `workflowRunParamDAO`.
`void`	`update(Registration registration, WorkflowRun workflowRun)` update.
`void`	`update(Registration registration, WorkflowRun workflowRun, List<Integer> laneIds)` update.
`void`	`update(WorkflowRun workflowRun)` update.
`void`	`update(WorkflowRun workflowRun, List<Integer> laneIds)` update.
`WorkflowRun`	`updateDetached(WorkflowRun workflowRun)` updateDetached.

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

- Constructor Detail
  - WorkflowRunServiceImpl
```
public WorkflowRunServiceImpl()
```
    Constructor for WorkflowRunServiceImpl.
- Method Detail
  - setWorkflowRunDAO
```
public void setWorkflowRunDAO(WorkflowRunDAO workflowRunDAO)
```
    setWorkflowRunDAO.
    Sets a private member variable with an instance of an implementation of WorkflowRunDAO. This method is called by the Spring framework at run time.
    
    Specified by:
    
    setWorkflowRunDAO in interface WorkflowRunService
    
    Parameters:
    workflowRunDAO - a WorkflowRunDAO object.
    See Also:
    WorkflowRunDAO
  - setProcessingDAO
```
public void setProcessingDAO(ProcessingDAO processingDAO)
```
    Setter for the field processingDAO.
    
    Parameters:
    processingDAO - a ProcessingDAO object.
  - setWorkflowRunParamDAO
```
public void setWorkflowRunParamDAO(WorkflowRunParamDAO workflowRunParamDAO)
```
    Setter for the field workflowRunParamDAO.
    
    Parameters:
    workflowRunParamDAO - a WorkflowRunParamDAO object.
  - 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 Integer insert(WorkflowRun workflowRun)
```
    Inserts a new WorkflowRun and returns its sw_accession number.
    
    Specified by:
    
    insert in interface WorkflowRunService
    
    Parameters:
    workflowRun - Workflow run to be inserted.
    
    Returns:
    The SeqWare Accession number for the newly inserted workflow.
  - insert
```
public Integer insert(WorkflowRun workflowRun,
             SortedSet<WorkflowRunParam> workflowRunParams,
             Map<String,List<File>> allSelectedFiles)
```
    insert.
    
    Specified by:
    
    insert in interface WorkflowRunService
    
    Parameters:
    workflowRun - a WorkflowRun object.
    workflowRunParams - a SortedSet object.
    allSelectedFiles - a Map object.
    
    Returns:
    a Integer object.
  - insert
```
public Integer insert(Registration registration,
             WorkflowRun workflowRun,
             SortedSet<WorkflowRunParam> workflowRunParams,
             Map<String,List<File>> allSelectedFiles)
```
    insert.
    
    Specified by:
    
    insert in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    workflowRunParams - a SortedSet object.
    allSelectedFiles - a Map object.
    
    Returns:
    a Integer object.
  - update
```
public void update(WorkflowRun workflowRun)
```
    update.
    
    Specified by:
    
    update in interface WorkflowRunService
    
    Parameters:
    workflowRun - a WorkflowRun object.
  - update
```
public void update(WorkflowRun workflowRun,
          List<Integer> laneIds)
```
    update.
    
    Specified by:
    
    update in interface WorkflowRunService
    
    Parameters:
    workflowRun - a WorkflowRun object.
    laneIds - a List object.
  - delete
```
public void delete(WorkflowRun workflowRun,
          boolean deleteRealFiles)
```
    delete.
    
    Specified by:
    
    delete in interface WorkflowRunService
    
    Parameters:
    workflowRun -
    deleteRealFiles -
  - getRootProcessing
```
public Processing getRootProcessing(Integer wfrId)
```
    getRootProcessing.
    
    Specified by:
    
    getRootProcessing in interface WorkflowRunService
    
    Parameters:
    wfrId - a Integer object.
    
    Returns:
    a Processing object.
  - getFiles
```
public List<File> getFiles(Integer wfrId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface WorkflowRunService
    
    Parameters:
    wfrId - a Integer object.
    
    Returns:
    a List object.
  - listWithHasFile
```
public List<WorkflowRun> listWithHasFile(List<WorkflowRun> list)
```
    listWithHasFile.
    
    Specified by:
    
    listWithHasFile in interface WorkflowRunService
    
    Parameters:
    list - a List object.
    
    Returns:
    a List object.
  - list
```
public List<WorkflowRun> list()
```
    list.
    
    Specified by:
    
    list in interface WorkflowRunService
    
    Returns:
    a List object.
  - list
```
public List<WorkflowRun> list(Registration registration)
```
    list.
    
    Specified by:
    
    list in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listMyShared
```
public List<WorkflowRun> listMyShared(Registration registration)
```
    listMyShared.
    
    Specified by:
    
    listMyShared in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listSharedWithMe
```
public List<WorkflowRun> listSharedWithMe(Registration registration)
```
    listSharedWithMe.
    
    Specified by:
    
    listSharedWithMe in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listRunning
```
public List<WorkflowRun> listRunning(Registration registration)
```
    listRunning.
    
    Specified by:
    
    listRunning in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - list
```
public List<WorkflowRun> list(Registration registration,
                     Boolean isAsc)
```
    list.
    
    Specified by:
    
    list in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listMyShared
```
public List<WorkflowRun> listMyShared(Registration registration,
                             Boolean isAsc)
```
    listMyShared.
    
    Specified by:
    
    listMyShared in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listSharedWithMe
```
public List<WorkflowRun> listSharedWithMe(Registration registration,
                                 Boolean isAsc)
```
    listSharedWithMe.
    
    Specified by:
    
    listSharedWithMe in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listRunning
```
public List<WorkflowRun> listRunning(Registration registration,
                            Boolean isAsc)
```
    listRunning.
    
    Specified by:
    
    listRunning in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listRelatedWorkflows
```
public List<Workflow> listRelatedWorkflows(Registration registration)
```
    listRelatedWorkflows.
    
    Specified by:
    
    listRelatedWorkflows in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - findByName
```
public WorkflowRun findByName(String name)
```
    findByName.
    
    Specified by:
    
    findByName in interface WorkflowRunService
    
    Parameters:
    name - a String object.
    
    Returns:
    a WorkflowRun object.
  - findByID
```
public WorkflowRun findByID(Integer wfrID)
```
    findByID.
    
    Specified by:
    
    findByID in interface WorkflowRunService
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findBySWAccession
```
public WorkflowRun findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface WorkflowRunService
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findByOwnerID
```
public List<WorkflowRun> findByOwnerID(Integer registrationID)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface WorkflowRunService
    
    Parameters:
    registrationID - a Integer object.
    
    Returns:
    a List object.
  - findByIDWithIUS
```
public WorkflowRun findByIDWithIUS(Integer wfrID)
```
    findByIDWithIUS.
    
    Specified by:
    
    findByIDWithIUS in interface WorkflowRunService
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findByIDWithIUSAndRunningWR
```
public WorkflowRun findByIDWithIUSAndRunningWR(Integer wfrID)
```
    findByIDWithIUSAndRunningWR.
    
    Specified by:
    
    findByIDWithIUSAndRunningWR in interface WorkflowRunService
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - listSharedWithMeWithSample
```
public List<WorkflowRun> listSharedWithMeWithSample(Registration registration)
```
    listSharedWithMeWithSample.
    
    Specified by:
    
    listSharedWithMeWithSample in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<WorkflowRun> findByCriteria(String criteria,
                               boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface WorkflowRunService
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<WorkflowRun> findByCriteria(String criteria)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface WorkflowRunService
    
    Parameters:
    criteria - a String object.
    
    Returns:
    a List object.
  - updateDetached
```
public WorkflowRun updateDetached(WorkflowRun workflowRun)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface WorkflowRunService
    
    Parameters:
    workflowRun - a WorkflowRun object.
    
    Returns:
    a WorkflowRun object.
  - findRunsForIUS
```
public Set<WorkflowRun> findRunsForIUS(IUS ius)
```
    findRunsForIUS.
    
    Specified by:
    
    findRunsForIUS in interface WorkflowRunService
    
    Parameters:
    ius - a IUS object.
    
    Returns:
    a Set object.
  - findFiles
```
public List<File> findFiles(Integer swAccession)
```
    findFiles.
    
    Specified by:
    
    findFiles in interface WorkflowRunService
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a List object.
  - findRunsForSample
```
public Set<WorkflowRun> findRunsForSample(Sample sample)
```
    Find all the workflow runs for the specific sample. This function doesn't look into the nested samples.
    
    Specified by:
    
    findRunsForSample in interface WorkflowRunService
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Set object.
  - update
```
public void update(Registration registration,
          WorkflowRun workflowRun)
```
    update.
    
    Specified by:
    
    update in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
  - insert
```
public Integer insert(Registration registration,
             WorkflowRun workflowRun)
```
    insert.
    
    Specified by:
    
    insert in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    
    Returns:
    a Integer object.
  - update
```
public void update(Registration registration,
          WorkflowRun workflowRun,
          List<Integer> laneIds)
```
    update.
    
    Specified by:
    
    update in interface WorkflowRunService
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    laneIds - a List object.

Class WorkflowRunServiceImpl

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

WorkflowRunServiceImpl

Method Detail

setWorkflowRunDAO

setProcessingDAO

setWorkflowRunParamDAO

setFileDAO

insert

insert

insert

update

update

delete

getRootProcessing

getFiles

listWithHasFile

list

list

listMyShared

listSharedWithMe

listRunning

list

listMyShared

listSharedWithMe

listRunning

listRelatedWorkflows

findByName

findByID

findBySWAccession

findByOwnerID

findByIDWithIUS

findByIDWithIUSAndRunningWR

listSharedWithMeWithSample

findByCriteria

findByCriteria

updateDetached

findRunsForIUS

findFiles

findRunsForSample

update

insert

update