Processing (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.security.PermissionsAware
- - net.sourceforge.seqware.common.model.Processing

All Implemented Interfaces:: Serializable, Comparable<Processing>, Annotatable<ProcessingAttribute>, FirstTierModel, ParentAccessionModel

public class Processing
extends PermissionsAware
implements Serializable, Comparable<Processing>, ParentAccessionModel, Annotatable<ProcessingAttribute>, FirstTierModel

See Also:: Serialized Form

Constructor Summary

Constructors
Constructor and Description

Processing()
Constructor for Processing.

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

Method Summary

Methods
Modifier and Type	Method and Description
`static ReturnValue`	`clone(Processing newP)` clone.
`static Processing`	`cloneToHibernate(Processing newP)` cloneToHibernate.
`int`	`compareTo(Processing that)`
`boolean`	`equals(Object other)`
`String`	`getAlgorithm()` Getter for the field `algorithm`.
`Set<ProcessingAttribute>`	`getAnnotations()` Get the annotations for this model
`Set<Processing>`	`getChildren()` Getter for the field `children`.
`Date`	`getCreateTimestamp()` Getter for the field `createTimestamp`.
`String`	`getDescription()` Getter for the field `description`.
`Integer`	`getExitStatus()` Getter for the field `exitStatus`.
`Set<Experiment>`	`getExperiments()` Getter for the field `experiments`.
`String`	`getFilePath()` Getter for the field `filePath`.
`Set<File>`	`getFiles()` Getter for the field `files`.
`Boolean`	`getIsHasFile()` Getter for the field `isHasFile`.
`Boolean`	`getIsSelected()` Getter for the field `isSelected`.
`Set<IUS>`	`getIUS()` getIUS.
`String`	`getJsonEscapeAlgorithm()` getJsonEscapeAlgorithm.
`String`	`getJsonEscapeDescription()` getJsonEscapeDescription.
`Set<Lane>`	`getLanes()` Getter for the field `lanes`.
`Registration`	`getOwner()` Getter for the field `owner`.
`String`	`getParameters()` Getter for the field `parameters`.
`Set<Processing>`	`getParents()` Getter for the field `parents`.
`Integer`	`getProcessExitStatus()` Getter for the field `processExitStatus`.
`Set<ProcessingAttribute>`	`getProcessingAttributes()` Getter for the field `processingAttributes`.
`Integer`	`getProcessingId()` Getter for the field `processingId`.
`Date`	`getRunStartTimestamp()` Getter for the field `runStartTimestamp`.
`Date`	`getRunStopTimestamp()` Getter for the field `runStopTimestamp`.
`Set<Sample>`	`getSamples()` Getter for the field `samples`.
`Set<SequencerRun>`	`getSequencerRuns()` Getter for the field `sequencerRuns`.
`static long`	`getSerialVersionUID()` Getter for the field `serialVersionUID`.
`ProcessingStatus`	`getStatus()`
`String`	`getStderr()` Getter for the field `stderr`.
`String`	`getStdout()` Getter for the field `stdout`.
`Set<Study>`	`getStudies()` Getter for the field `studies`.
`Integer`	`getSwAccession()` Getter for the field `swAccession`.
`Date`	`getUpdateTimestamp()` Getter for the field `updateTimestamp`.
`String`	`getUrl()` Getter for the field `url`.
`String`	`getUrlLabel()` Getter for the field `urlLabel`.
`String`	`getVersion()` Getter for the field `version`.
`WorkflowRun`	`getWorkflowRun()` Getter for the field `workflowRun`.
`WorkflowRun`	`getWorkflowRunByAncestorWorkflowRunId()` Getter for the field `workflowRunByAncestorWorkflowRunId`.
`Integer`	`getWorkflowRunId()` Getter for the field `workflowRunId`.
`boolean`	`givesPermissionInternal(Registration registration, Set<Integer> considered)` Short-circuit permission checking by providing a set of entities that have already been checked
`int`	`hashCode()`
`boolean`	`isTaskGroup()` isTaskGroup.
`void`	`resetCompletedChildren()` resetCompletedChildren.
`void`	`resetRunningChildren()` resetRunningChildren.
`void`	`setAlgorithm(String algorithm)` Setter for the field `algorithm`.
`void`	`setChildren(Set<Processing> children)` Setter for the field `children`.
`void`	`setCreateTimestamp(Date createTimestamp)` Setter for the field `createTimestamp`.
`void`	`setDescription(String description)` Setter for the field `description`.
`void`	`setExitStatus(Integer exitStatus)` Setter for the field `exitStatus`.
`void`	`setExperiments(Set<Experiment> experiments)` Setter for the field `experiments`.
`void`	`setFilePath(String filePath)` Setter for the field `filePath`.
`void`	`setFiles(Set<File> files)` Setter for the field `files`.
`void`	`setIsHasFile(Boolean isHasFile)` Setter for the field `isHasFile`.
`void`	`setIsSelected(Boolean isSelected)` Setter for the field `isSelected`.
`void`	`setIUS(Set<IUS> ius)` setIUS.
`void`	`setLanes(Set<Lane> lanes)` Setter for the field `lanes`.
`void`	`setOwner(Registration owner)` Setter for the field `owner`.
`void`	`setParameters(String parameters)` Setter for the field `parameters`.
`void`	`setParents(Set<Processing> parents)` Setter for the field `parents`.
`void`	`setProcessExitStatus(Integer processExitStatus)` Setter for the field `processExitStatus`.
`void`	`setProcessingAttributes(Set<ProcessingAttribute> processingAttributes)` Setter for the field `processingAttributes`.
`void`	`setProcessingId(Integer processingId)` Setter for the field `processingId`.
`void`	`setRunStartTimestamp(Date runStartTimestamp)` Setter for the field `runStartTimestamp`.
`void`	`setRunStopTimestamp(Date runStopTimestamp)` Setter for the field `runStopTimestamp`.
`void`	`setSamples(Set<Sample> samples)` Setter for the field `samples`.
`void`	`setSequencerRuns(Set<SequencerRun> sequencerRuns)` Setter for the field `sequencerRuns`.
`void`	`setStatus(ProcessingStatus status)`
`void`	`setStderr(String stderr)` Setter for the field `stderr`.
`void`	`setStdout(String stdout)` Setter for the field `stdout`.
`void`	`setStudies(Set<Study> studies)` Setter for the field `studies`.
`void`	`setSwAccession(Integer swAccession)` Setter for the field `swAccession`.
`void`	`setTaskGroup(boolean taskGroup)` Setter for the field `taskGroup`.
`void`	`setUpdateTimestamp(Date updateTimestamp)` Setter for the field `updateTimestamp`.
`void`	`setUrl(String url)` Setter for the field `url`.
`void`	`setUrlLabel(String urlLabel)` Setter for the field `urlLabel`.
`void`	`setVersion(String version)` Setter for the field `version`.
`void`	`setWorkflowRun(WorkflowRun workflowRun)` Setter for the field `workflowRun`.
`void`	`setWorkflowRunByAncestorWorkflowRunId(WorkflowRun workflowRunByAncestorWorkflowRunId)` Setter for the field `workflowRunByAncestorWorkflowRunId`.
`void`	`setWorkflowRunId(Integer workflowRunId)` Setter for the field `workflowRunId`.
`String`	`toString()`

Methods inherited from class net.sourceforge.seqware.common.security.PermissionsAware
givesPermission, givesPermission

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

- Constructor Detail
  - Processing
```
public Processing()
```
    Constructor for Processing.
- Method Detail
  - compareTo
```
public int compareTo(Processing that)
```
    Specified by:
    
    compareTo in interface Comparable<Processing>
    
    Parameters:
    that -
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - equals
```
public boolean equals(Object other)
```
    Overrides:
    
    equals in class Object
    
    Parameters:
    other -
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - getExitStatus
```
public Integer getExitStatus()
```
    Getter for the field exitStatus.
    
    Returns:
    a Integer object.
  - setExitStatus
```
public void setExitStatus(Integer exitStatus)
```
    Setter for the field exitStatus.
    
    Parameters:
    exitStatus - a Integer object.
  - getProcessExitStatus
```
public Integer getProcessExitStatus()
```
    Getter for the field processExitStatus.
    
    Returns:
    a Integer object.
  - setProcessExitStatus
```
public void setProcessExitStatus(Integer processExitStatus)
```
    Setter for the field processExitStatus.
    
    Parameters:
    processExitStatus - a Integer object.
  - getParents
```
public Set<Processing> getParents()
```
    Getter for the field parents.
    
    Returns:
    a Set object.
  - setParents
```
public void setParents(Set<Processing> parents)
```
    Setter for the field parents.
    
    Parameters:
    parents - a Set object.
  - getChildren
```
public Set<Processing> getChildren()
```
    Getter for the field children.
    
    Returns:
    a Set object.
  - setChildren
```
public void setChildren(Set<Processing> children)
```
    Setter for the field children.
    
    Parameters:
    children - a Set object.
  - isTaskGroup
```
public boolean isTaskGroup()
```
    isTaskGroup.
    
    Returns:
    a boolean.
  - setTaskGroup
```
public void setTaskGroup(boolean taskGroup)
```
    Setter for the field taskGroup.
    
    Parameters:
    taskGroup - a boolean.
  - getSwAccession
```
public Integer getSwAccession()
```
    Getter for the field swAccession.
    
    Specified by:
    
    getSwAccession in interface FirstTierModel
    
    Returns:
    a Integer object.
  - setSwAccession
```
public void setSwAccession(Integer swAccession)
```
    Setter for the field swAccession.
    
    Parameters:
    swAccession - a Integer object.
  - getCreateTimestamp
```
public Date getCreateTimestamp()
```
    Getter for the field createTimestamp.
    
    Returns:
    a Date object.
  - setCreateTimestamp
```
public void setCreateTimestamp(Date createTimestamp)
```
    Setter for the field createTimestamp.
    
    Parameters:
    createTimestamp - a Date object.
  - getUpdateTimestamp
```
public Date getUpdateTimestamp()
```
    Getter for the field updateTimestamp.
    
    Returns:
    a Date object.
  - setUpdateTimestamp
```
public void setUpdateTimestamp(Date updateTimestamp)
```
    Setter for the field updateTimestamp.
    
    Parameters:
    updateTimestamp - a Date object.
  - getSerialVersionUID
```
public static long getSerialVersionUID()
```
    Getter for the field serialVersionUID.
    
    Returns:
    a long.
  - getAlgorithm
```
public String getAlgorithm()
```
    Getter for the field algorithm.
    
    Returns:
    a String object.
  - getJsonEscapeAlgorithm
```
public String getJsonEscapeAlgorithm()
```
    getJsonEscapeAlgorithm.
    
    Returns:
    a String object.
  - setAlgorithm
```
public void setAlgorithm(String algorithm)
```
    Setter for the field algorithm.
    
    Parameters:
    algorithm - a String object.
  - getFilePath
```
public String getFilePath()
```
    Getter for the field filePath.
    
    Returns:
    a String object.
  - setFilePath
```
public void setFilePath(String filePath)
```
    Setter for the field filePath.
    
    Parameters:
    filePath - a String object.
  - getProcessingId
```
public Integer getProcessingId()
```
    Getter for the field processingId.
    
    Returns:
    a Integer object.
  - setProcessingId
```
public void setProcessingId(Integer processingId)
```
    Setter for the field processingId.
    
    Parameters:
    processingId - a Integer object.
  - getStatus
```
public ProcessingStatus getStatus()
```
  - setStatus
```
public void setStatus(ProcessingStatus status)
```
  - getJsonEscapeDescription
```
public String getJsonEscapeDescription()
```
    getJsonEscapeDescription.
    
    Returns:
    a String object.
  - getDescription
```
public String getDescription()
```
    Getter for the field description.
    
    Returns:
    a String object.
  - setDescription
```
public void setDescription(String description)
```
    Setter for the field description.
    
    Parameters:
    description - a String object.
  - getUrl
```
public String getUrl()
```
    Getter for the field url.
    
    Returns:
    a String object.
  - setUrl
```
public void setUrl(String url)
```
    Setter for the field url.
    
    Parameters:
    url - a String object.
  - getLanes
```
public Set<Lane> getLanes()
```
    Getter for the field lanes.
    
    Returns:
    a Set object.
  - setLanes
```
public void setLanes(Set<Lane> lanes)
```
    Setter for the field lanes.
    
    Parameters:
    lanes - a Set object.
  - getUrlLabel
```
public String getUrlLabel()
```
    Getter for the field urlLabel.
    
    Returns:
    a String object.
  - setUrlLabel
```
public void setUrlLabel(String urlLabel)
```
    Setter for the field urlLabel.
    
    Parameters:
    urlLabel - a String object.
  - getVersion
```
public String getVersion()
```
    Getter for the field version.
    
    Returns:
    a String object.
  - setVersion
```
public void setVersion(String version)
```
    Setter for the field version.
    
    Parameters:
    version - a String object.
  - getFiles
```
public Set<File> getFiles()
```
    Getter for the field files.
    
    Returns:
    a Set object.
  - setFiles
```
public void setFiles(Set<File> files)
```
    Setter for the field files.
    
    Parameters:
    files - a Set object.
  - getWorkflowRunId
```
public Integer getWorkflowRunId()
```
    Getter for the field workflowRunId.
    
    Returns:
    a Integer object.
  - setWorkflowRunId
```
public void setWorkflowRunId(Integer workflowRunId)
```
    Setter for the field workflowRunId.
    
    Parameters:
    workflowRunId - a Integer object.
  - getOwner
```
public Registration getOwner()
```
    Getter for the field owner.
    
    Returns:
    a Registration object.
  - setOwner
```
public void setOwner(Registration owner)
```
    Setter for the field owner.
    
    Parameters:
    owner - a Registration object.
  - getWorkflowRun
```
public WorkflowRun getWorkflowRun()
```
    Getter for the field workflowRun.
    
    Returns:
    a WorkflowRun object.
  - setWorkflowRun
```
public void setWorkflowRun(WorkflowRun workflowRun)
```
    Setter for the field workflowRun.
    
    Parameters:
    workflowRun - a WorkflowRun object.
  - getIsSelected
```
public Boolean getIsSelected()
```
    Getter for the field isSelected.
    
    Returns:
    a Boolean object.
  - setIsSelected
```
public void setIsSelected(Boolean isSelected)
```
    Setter for the field isSelected.
    
    Parameters:
    isSelected - a Boolean object.
  - getIsHasFile
```
public Boolean getIsHasFile()
```
    Getter for the field isHasFile.
    
    Returns:
    a Boolean object.
  - setIsHasFile
```
public void setIsHasFile(Boolean isHasFile)
```
    Setter for the field isHasFile.
    
    Parameters:
    isHasFile - a Boolean object.
  - getIUS
```
public Set<IUS> getIUS()
```
    getIUS.
    
    Returns:
    a Set object.
  - setIUS
```
public void setIUS(Set<IUS> ius)
```
    setIUS.
    
    Parameters:
    ius - a Set object.
  - getStudies
```
public Set<Study> getStudies()
```
    Getter for the field studies.
    
    Returns:
    a Set object.
  - setStudies
```
public void setStudies(Set<Study> studies)
```
    Setter for the field studies.
    
    Parameters:
    studies - a Set object.
  - getSamples
```
public Set<Sample> getSamples()
```
    Getter for the field samples.
    
    Returns:
    a Set object.
  - setSamples
```
public void setSamples(Set<Sample> samples)
```
    Setter for the field samples.
    
    Parameters:
    samples - a Set object.
  - getSequencerRuns
```
public Set<SequencerRun> getSequencerRuns()
```
    Getter for the field sequencerRuns.
    
    Returns:
    a Set object.
  - setSequencerRuns
```
public void setSequencerRuns(Set<SequencerRun> sequencerRuns)
```
    Setter for the field sequencerRuns.
    
    Parameters:
    sequencerRuns - a Set object.
  - getExperiments
```
public Set<Experiment> getExperiments()
```
    Getter for the field experiments.
    
    Returns:
    a Set object.
  - setExperiments
```
public void setExperiments(Set<Experiment> experiments)
```
    Setter for the field experiments.
    
    Parameters:
    experiments - a Set object.
  - getRunStartTimestamp
```
public Date getRunStartTimestamp()
```
    Getter for the field runStartTimestamp.
    
    Returns:
    a Date object.
  - setRunStartTimestamp
```
public void setRunStartTimestamp(Date runStartTimestamp)
```
    Setter for the field runStartTimestamp.
    
    Parameters:
    runStartTimestamp - a Date object.
  - getRunStopTimestamp
```
public Date getRunStopTimestamp()
```
    Getter for the field runStopTimestamp.
    
    Returns:
    a Date object.
  - setRunStopTimestamp
```
public void setRunStopTimestamp(Date runStopTimestamp)
```
    Setter for the field runStopTimestamp.
    
    Parameters:
    runStopTimestamp - a Date object.
  - getParameters
```
public String getParameters()
```
    Getter for the field parameters.
    
    Returns:
    a String object.
  - setParameters
```
public void setParameters(String parameters)
```
    Setter for the field parameters.
    
    Parameters:
    parameters - a String object.
  - getStdout
```
public String getStdout()
```
    Getter for the field stdout.
    
    Returns:
    a String object.
  - setStdout
```
public void setStdout(String stdout)
```
    Setter for the field stdout.
    
    Parameters:
    stdout - a String object.
  - getStderr
```
public String getStderr()
```
    Getter for the field stderr.
    
    Returns:
    a String object.
  - setStderr
```
public void setStderr(String stderr)
```
    Setter for the field stderr.
    
    Parameters:
    stderr - a String object.
  - getWorkflowRunByAncestorWorkflowRunId
```
public WorkflowRun getWorkflowRunByAncestorWorkflowRunId()
```
    Getter for the field workflowRunByAncestorWorkflowRunId.
    
    Returns:
    a WorkflowRun object.
  - setWorkflowRunByAncestorWorkflowRunId
```
public void setWorkflowRunByAncestorWorkflowRunId(WorkflowRun workflowRunByAncestorWorkflowRunId)
```
    Setter for the field workflowRunByAncestorWorkflowRunId.
    
    Parameters:
    workflowRunByAncestorWorkflowRunId - a WorkflowRun object.
  - getProcessingAttributes
```
public Set<ProcessingAttribute> getProcessingAttributes()
```
    Getter for the field processingAttributes.
    
    Returns:
    a Set object.
  - setProcessingAttributes
```
public void setProcessingAttributes(Set<ProcessingAttribute> processingAttributes)
```
    Setter for the field processingAttributes.
    
    Parameters:
    processingAttributes - a Set object.
  - resetCompletedChildren
```
public void resetCompletedChildren()
```
    resetCompletedChildren.
  - resetRunningChildren
```
public void resetRunningChildren()
```
    resetRunningChildren.
  - clone
```
public static ReturnValue clone(Processing newP)
                         throws org.restlet.resource.ResourceException,
                                SQLException
```
    clone.
    
    Parameters:
    newP - a Processing object.
    
    Returns:
    a ReturnValue object.
    
    Throws:
    
    org.restlet.resource.ResourceException - if any.
    
    SQLException - if any.
  - cloneToHibernate
```
public static Processing cloneToHibernate(Processing newP)
```
    cloneToHibernate.
    
    Parameters:
    newP - a Processing object.
    
    Returns:
    a Processing object.
  - givesPermissionInternal
```
public boolean givesPermissionInternal(Registration registration,
                              Set<Integer> considered)
```
    Short-circuit permission checking by providing a set of entities that have already been checked
    
    Specified by:
    
    givesPermissionInternal in class PermissionsAware
    
    Returns:
  - getAnnotations
```
public Set<ProcessingAttribute> getAnnotations()
```
    Description copied from interface: Annotatable
    
    Get the annotations for this model
    
    Specified by:
    
    getAnnotations in interface Annotatable<ProcessingAttribute>
    
    Returns:

Class Processing

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.common.security.PermissionsAware

Methods inherited from class java.lang.Object

Constructor Detail

Processing

Method Detail

compareTo

toString

equals

hashCode

getExitStatus

setExitStatus

getProcessExitStatus

setProcessExitStatus

getParents

setParents

getChildren

setChildren

isTaskGroup

setTaskGroup

getSwAccession

setSwAccession

getCreateTimestamp

setCreateTimestamp

getUpdateTimestamp

setUpdateTimestamp

getSerialVersionUID

getAlgorithm

getJsonEscapeAlgorithm

setAlgorithm

getFilePath

setFilePath

getProcessingId

setProcessingId

getStatus

setStatus

getJsonEscapeDescription

getDescription

setDescription

getUrl

setUrl

getLanes

setLanes

getUrlLabel

setUrlLabel

getVersion

setVersion

getFiles

setFiles

getWorkflowRunId

setWorkflowRunId

getOwner

setOwner

getWorkflowRun

setWorkflowRun

getIsSelected

setIsSelected

getIsHasFile

setIsHasFile

getIUS

setIUS

getStudies

setStudies

getSamples

setSamples

getSequencerRuns

setSequencerRuns

getExperiments

setExperiments

getRunStartTimestamp

setRunStartTimestamp

getRunStopTimestamp

setRunStopTimestamp

getParameters

setParameters

getStdout

setStdout

getStderr