WorkflowRunService (SeqWare 1.1.2 API)

All Known Implementing Classes:

WorkflowRunServiceImpl
```
public interface WorkflowRunService
```
WorkflowRunService interface.

Version:

$Id: $Id

Author:

boconnor

Field Summary

Fields
Modifier and Type Field and Description

static String NAME
Constant NAME="WorkflowRunService"

Fields
Modifier and Type	Field and Description
`static String`	`NAME` Constant `NAME="WorkflowRunService"`

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`	`setWorkflowRunDAO(WorkflowRunDAO workflowRunDAO)` setWorkflowRunDAO.
`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.

- Field Detail
  - NAME
```
static final String NAME
```
    Constant NAME="WorkflowRunService"
    
    See Also:
    Constant Field Values
- Method Detail
  - setWorkflowRunDAO
```
void setWorkflowRunDAO(WorkflowRunDAO workflowRunDAO)
```
    setWorkflowRunDAO.
    
    Parameters:
    workflowRunDAO - a WorkflowRunDAO object.
  - insert
```
Integer insert(WorkflowRun workflowRun)
```
    Inserts a new WorkflowRun and returns its sw_accession number.
    
    Parameters:
    workflowRun - Workflow run to be inserted.
    
    Returns:
    The SeqWare Accession number for the newly inserted workflow.
  - insert
```
Integer insert(Registration registration,
             WorkflowRun workflowRun)
```
    insert.
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    
    Returns:
    a Integer object.
  - update
```
void update(WorkflowRun workflowRun)
```
    update.
    
    Parameters:
    workflowRun - a WorkflowRun object.
  - delete
```
void delete(WorkflowRun workflowRun,
          boolean deleteRealFiles)
```
    delete.
    
    Parameters:
    workflowRun -
    deleteRealFiles -
  - insert
```
Integer insert(WorkflowRun workflowRun,
             SortedSet<WorkflowRunParam> workflowRunParams,
             Map<String,List<File>> allSelectedFiles)
```
    insert.
    
    Parameters:
    workflowRun - a WorkflowRun object.
    workflowRunParams - a SortedSet object.
    allSelectedFiles - a Map object.
    
    Returns:
    a Integer object.
  - insert
```
Integer insert(Registration registration,
             WorkflowRun workflowRun,
             SortedSet<WorkflowRunParam> workflowRunParams,
             Map<String,List<File>> allSelectedFiles)
```
    insert.
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    workflowRunParams - a SortedSet object.
    allSelectedFiles - a Map object.
    
    Returns:
    a Integer object.
  - update
```
void update(WorkflowRun workflowRun,
          List<Integer> laneIds)
```
    update.
    
    Parameters:
    workflowRun - a WorkflowRun object.
    laneIds - a List object.
  - update
```
void update(Registration registration,
          WorkflowRun workflowRun,
          List<Integer> laneIds)
```
    update.
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
    laneIds - a List object.
  - update
```
void update(Registration registration,
          WorkflowRun workflowRun)
```
    update.
    
    Parameters:
    registration - a Registration object.
    workflowRun - a WorkflowRun object.
  - list
```
List<WorkflowRun> list()
```
    list.
    
    Returns:
    a List object.
  - list
```
List<WorkflowRun> list(Registration registration)
```
    list.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listMyShared
```
List<WorkflowRun> listMyShared(Registration registration)
```
    listMyShared.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listSharedWithMe
```
List<WorkflowRun> listSharedWithMe(Registration registration)
```
    listSharedWithMe.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listSharedWithMeWithSample
```
List<WorkflowRun> listSharedWithMeWithSample(Registration registration)
```
    listSharedWithMeWithSample.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - listRunning
```
List<WorkflowRun> listRunning(Registration registration)
```
    listRunning.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - list
```
List<WorkflowRun> list(Registration registration,
                     Boolean isAsc)
```
    list.
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listMyShared
```
List<WorkflowRun> listMyShared(Registration registration,
                             Boolean isAsc)
```
    listMyShared.
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listSharedWithMe
```
List<WorkflowRun> listSharedWithMe(Registration registration,
                                 Boolean isAsc)
```
    listSharedWithMe.
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - listRunning
```
List<WorkflowRun> listRunning(Registration registration,
                            Boolean isAsc)
```
    listRunning.
    
    Parameters:
    registration - a Registration object.
    isAsc - a Boolean object.
    
    Returns:
    a List object.
  - findByName
```
WorkflowRun findByName(String name)
```
    findByName.
    
    Parameters:
    name - a String object.
    
    Returns:
    a WorkflowRun object.
  - findByID
```
WorkflowRun findByID(Integer wfrID)
```
    findByID.
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findByIDWithIUS
```
WorkflowRun findByIDWithIUS(Integer wfrID)
```
    findByIDWithIUS.
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findByIDWithIUSAndRunningWR
```
WorkflowRun findByIDWithIUSAndRunningWR(Integer wfrID)
```
    findByIDWithIUSAndRunningWR.
    
    Parameters:
    wfrID - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findBySWAccession
```
WorkflowRun findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a WorkflowRun object.
  - findByOwnerID
```
List<WorkflowRun> findByOwnerID(Integer registrationID)
```
    findByOwnerID.
    
    Parameters:
    registrationID - a Integer object.
    
    Returns:
    a List object.
  - getRootProcessing
```
Processing getRootProcessing(Integer wfrId)
```
    getRootProcessing.
    
    Parameters:
    wfrId - a Integer object.
    
    Returns:
    a Processing object.
  - getFiles
```
List<File> getFiles(Integer wfrId)
```
    getFiles.
    
    Parameters:
    wfrId - a Integer object.
    
    Returns:
    a List object.
  - listWithHasFile
```
List<WorkflowRun> listWithHasFile(List<WorkflowRun> list)
```
    listWithHasFile.
    
    Parameters:
    list - a List object.
    
    Returns:
    a List object.
  - updateDetached
```
WorkflowRun updateDetached(WorkflowRun workflowRun)
```
    updateDetached.
    
    Parameters:
    workflowRun - a WorkflowRun object.
    
    Returns:
    a WorkflowRun object.
  - findByCriteria
```
List<WorkflowRun> findByCriteria(String criteria,
                               boolean isCaseSens)
```
    findByCriteria.
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - findByCriteria
```
List<WorkflowRun> findByCriteria(String criteria)
```
    findByCriteria.
    
    Parameters:
    criteria - a String object.
    
    Returns:
    a List object.
  - listRelatedWorkflows
```
List<Workflow> listRelatedWorkflows(Registration registration)
```
    listRelatedWorkflows.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - findRunsForIUS
```
Set<WorkflowRun> findRunsForIUS(IUS ius)
```
    findRunsForIUS.
    
    Parameters:
    ius - a IUS object.
    
    Returns:
    a Set object.
  - findRunsForSample
```
Set<WorkflowRun> findRunsForSample(Sample sample)
```
    Find all the workflow runs for the specific sample. This function doesn't look into the nested samples.
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Set object.
  - findFiles
```
List<File> findFiles(Integer swAccession)
```
    findFiles.
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a List object.

Interface WorkflowRunService

Field Summary

Method Summary

Field Detail

NAME

Method Detail

setWorkflowRunDAO

insert

insert

update

delete

insert

insert

update

update

update

list

list

listMyShared

listSharedWithMe

listSharedWithMeWithSample

listRunning

list

listMyShared

listSharedWithMe

listRunning

findByName

findByID

findByIDWithIUS

findByIDWithIUSAndRunningWR

findBySWAccession

findByOwnerID

getRootProcessing

getFiles

listWithHasFile

updateDetached

findByCriteria

findByCriteria

listRelatedWorkflows

findRunsForIUS

findRunsForSample

findFiles