Workflow (SeqWare 1.1.2 API)

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

All Implemented Interfaces:

Serializable, Comparable<Workflow>, Annotatable<WorkflowAttribute>, FirstTierModel
```
public class Workflow
extends PermissionsAware
implements Serializable, Comparable<Workflow>, Annotatable<WorkflowAttribute>, FirstTierModel
```
Workflow class.

Version:

$Id: $Id

Author:

boconnor

See Also:
Serialized Form

Constructor Summary

Constructors
Constructor and Description

Workflow()
Constructor for Workflow.

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

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(Workflow that)`
`boolean`	`equals(Object other)`
`Set<WorkflowAttribute>`	`getAnnotations()` Get the annotations for this model
`String`	`getBaseIniFile()` Getter for the field `baseIniFile`.
`String`	`getCommand()` Getter for the field `command`.
`Date`	`getCreateTimestamp()` Getter for the field `createTimestamp`.
`String`	`getCwd()` Getter for the field `cwd`.
`String`	`getDescription()` Getter for the field `description`.
`String`	`getFullName()` getFullName.
`String`	`getHost()` Deprecated.
`String`	`getInputAlgorithm()` Getter for the field `inputAlgorithm`.
`String`	`getJsonEscapeDescription()` getJsonEscapeDescription.
`String`	`getJsonEscapeFullName()` getJsonEscapeFullName.
`String`	`getJsonEscapeName()` getJsonEscapeName.
`String`	`getName()` Getter for the field `name`.
`Registration`	`getOwner()` Getter for the field `owner`.
`String`	`getPermanentBundleLocation()` Getter for the field `permanentBundleLocation`.
`boolean`	`getPrivate()` getPrivate.
`boolean`	`getPublic()` getPublic.
`String`	`getSeqwareVersion()` Getter for the field `seqwareVersion`.
`Integer`	`getSwAccession()` Getter for the field `swAccession`.
`String`	`getTemplate()` Getter for the field `template`.
`Date`	`getUpdateTimestamp()` Getter for the field `updateTimestamp`.
`String`	`getUsername()` Getter for the field `username`.
`String`	`getVersion()` Getter for the field `version`.
`SortedSet<WorkflowParam>`	`getVisibleWorkflowParams()` getVisibleWorkflowParams.
`SortedSet<WorkflowParam>`	`getVisibleWorkflowParamsWithDifferentValue()` getVisibleWorkflowParamsWithDifferentValue.
`Set<WorkflowAttribute>`	`getWorkflowAttributes()` Getter for the field `workflowAttributes`.
`String`	`getWorkflowClass()`
`String`	`getWorkflowEngine()`
`Integer`	`getWorkflowId()` Getter for the field `workflowId`.
`SortedSet<WorkflowParam>`	`getWorkflowParams()` Getter for the field `workflowParams`.
`SortedSet<WorkflowParam>`	`getWorkflowParamsWithDifferentFileMetaType()` getWorkflowParamsWithDifferentFileMetaType.
`SortedSet<WorkflowRun>`	`getWorkflowRuns()` Getter for the field `workflowRuns`.
`String`	`getWorkflowType()`
`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`	`isLaunch()` isLaunch.
`boolean`	`isPrivate()` isPrivate.
`boolean`	`isPublic()` isPublic.
`void`	`setBaseIniFile(String baseIniFile)` Setter for the field `baseIniFile`.
`void`	`setCommand(String command)` Setter for the field `command`.
`void`	`setCreateTimestamp(Date createTimestamp)` Setter for the field `createTimestamp`.
`void`	`setCwd(String cwd)` Setter for the field `cwd`.
`void`	`setDescription(String description)` Setter for the field `description`.
`void`	`setHost(String host)` Deprecated.
`void`	`setInputAlgorithm(String inputAlgorithm)` Setter for the field `inputAlgorithm`.
`void`	`setName(String name)` Setter for the field `name`.
`void`	`setOwner(Registration owner)` Setter for the field `owner`.
`void`	`setPermanentBundleLocation(String permanentBundleLocation)` Setter for the field `permanentBundleLocation`.
`void`	`setPrivate(boolean isPrivate)` setPrivate.
`void`	`setPublic(boolean isPublic)` setPublic.
`void`	`setSeqwareVersion(String seqwareVersion)` Setter for the field `seqwareVersion`.
`void`	`setSwAccession(Integer swAccession)` Setter for the field `swAccession`.
`void`	`setTemplate(String template)` Setter for the field `template`.
`void`	`setUpdateTimestamp(Date updateTimestamp)` Setter for the field `updateTimestamp`.
`void`	`setUsername(String username)` Setter for the field `username`.
`void`	`setVersion(String version)` Setter for the field `version`.
`void`	`setWorkflowAttributes(Set<WorkflowAttribute> workflowAttributes)` Setter for the field `workflowAttributes`.
`void`	`setWorkflowClass(String workflowClass)`
`void`	`setWorkflowEngine(String workflowEngine)`
`void`	`setWorkflowId(Integer workflowId)` Setter for the field `workflowId`.
`void`	`setWorkflowParams(SortedSet<WorkflowParam> workflowParams)` Setter for the field `workflowParams`.
`void`	`setWorkflowRuns(SortedSet<WorkflowRun> workflowRuns)` Setter for the field `workflowRuns`.
`void`	`setWorkflowType(String workflowType)`
`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
  - Workflow
```
public Workflow()
```
    Constructor for Workflow.
- Method Detail
  - compareTo
```
public int compareTo(Workflow that)
```
    Specified by:
    
    compareTo in interface Comparable<Workflow>
    
    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
  - getCwd
```
public String getCwd()
```
    Getter for the field cwd.
    
    Returns:
    a String object.
  - setCwd
```
public void setCwd(String cwd)
```
    Setter for the field cwd.
    
    Parameters:
    cwd - a String object.
  - getCommand
```
public String getCommand()
```
    Getter for the field command.
    
    Returns:
    a String object.
  - setCommand
```
public void setCommand(String command)
```
    Setter for the field command.
    
    Parameters:
    command - a String object.
  - getTemplate
```
public String getTemplate()
```
    Getter for the field template.
    
    Returns:
    a String object.
  - setTemplate
```
public void setTemplate(String template)
```
    Setter for the field template.
    
    Parameters:
    template - a String object.
  - getWorkflowId
```
public Integer getWorkflowId()
```
    Getter for the field workflowId.
    
    Returns:
    a Integer object.
  - setWorkflowId
```
public void setWorkflowId(Integer workflowId)
```
    Setter for the field workflowId.
    
    Parameters:
    workflowId - a Integer object.
  - 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.
  - getName
```
public String getName()
```
    Getter for the field name.
    
    Returns:
    a String object.
  - getJsonEscapeName
```
public String getJsonEscapeName()
```
    getJsonEscapeName.
    
    Returns:
    a String object.
  - setName
```
public void setName(String name)
```
    Setter for the field name.
    
    Parameters:
    name - a String object.
  - 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.
  - getInputAlgorithm
```
public String getInputAlgorithm()
```
    Getter for the field inputAlgorithm.
    
    Returns:
    a String object.
  - setInputAlgorithm
```
public void setInputAlgorithm(String inputAlgorithm)
```
    Setter for the field inputAlgorithm.
    
    Parameters:
    inputAlgorithm - 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.
  - getSeqwareVersion
```
public String getSeqwareVersion()
```
    Getter for the field seqwareVersion.
    
    Returns:
    a String object.
  - setSeqwareVersion
```
public void setSeqwareVersion(String seqwareVersion)
```
    Setter for the field seqwareVersion.
    
    Parameters:
    seqwareVersion - a String object.
  - getBaseIniFile
```
public String getBaseIniFile()
```
    Getter for the field baseIniFile.
    
    Returns:
    a String object.
  - setBaseIniFile
```
public void setBaseIniFile(String baseIniFile)
```
    Setter for the field baseIniFile.
    
    Parameters:
    baseIniFile - a String object.
  - getHost
```
public String getHost()
```
    Deprecated.
    
    Getter for the field host.
    
    Returns:
    a String object.
  - setHost
```
public void setHost(String host)
```
    Deprecated.
    
    Setter for the field host.
    
    Parameters:
    host - a String object.
  - getUsername
```
public String getUsername()
```
    Getter for the field username.
    
    Returns:
    a String object.
  - setUsername
```
public void setUsername(String username)
```
    Setter for the field username.
    
    Parameters:
    username - a String 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.
  - isPrivate
```
public boolean isPrivate()
```
    isPrivate.
    
    Returns:
    a boolean.
  - getPrivate
```
public boolean getPrivate()
```
    getPrivate.
    
    Returns:
    a boolean.
  - setPrivate
```
public void setPrivate(boolean isPrivate)
```
    setPrivate.
    
    Parameters:
    isPrivate - a boolean.
  - isPublic
```
public boolean isPublic()
```
    isPublic.
    
    Returns:
    a boolean.
  - getPublic
```
public boolean getPublic()
```
    getPublic.
    
    Returns:
    a boolean.
  - setPublic
```
public void setPublic(boolean isPublic)
```
    setPublic.
    
    Parameters:
    isPublic - a boolean.
  - 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.
  - getWorkflowRuns
```
public SortedSet<WorkflowRun> getWorkflowRuns()
```
    Getter for the field workflowRuns.
    
    Returns:
    a SortedSet object.
  - setWorkflowRuns
```
public void setWorkflowRuns(SortedSet<WorkflowRun> workflowRuns)
```
    Setter for the field workflowRuns.
    
    Parameters:
    workflowRuns - a SortedSet object.
  - getWorkflowParams
```
public SortedSet<WorkflowParam> getWorkflowParams()
```
    Getter for the field workflowParams.
    
    Returns:
    a SortedSet object.
  - getVisibleWorkflowParams
```
public SortedSet<WorkflowParam> getVisibleWorkflowParams()
```
    getVisibleWorkflowParams.
    
    Returns:
    a SortedSet object.
  - getVisibleWorkflowParamsWithDifferentValue
```
public SortedSet<WorkflowParam> getVisibleWorkflowParamsWithDifferentValue()
```
    getVisibleWorkflowParamsWithDifferentValue.
    
    Returns:
    a SortedSet object.
  - getWorkflowParamsWithDifferentFileMetaType
```
public SortedSet<WorkflowParam> getWorkflowParamsWithDifferentFileMetaType()
```
    getWorkflowParamsWithDifferentFileMetaType.
    
    Returns:
    a SortedSet object.
  - isLaunch
```
public boolean isLaunch()
```
    isLaunch.
    
    Returns:
    a boolean.
  - setWorkflowParams
```
public void setWorkflowParams(SortedSet<WorkflowParam> workflowParams)
```
    Setter for the field workflowParams.
    
    Parameters:
    workflowParams - a SortedSet object.
  - getFullName
```
public String getFullName()
```
    getFullName.
    
    Returns:
    a String object.
  - getJsonEscapeFullName
```
public String getJsonEscapeFullName()
```
    getJsonEscapeFullName.
    
    Returns:
    a String object.
  - getPermanentBundleLocation
```
public String getPermanentBundleLocation()
```
    Getter for the field permanentBundleLocation.
    
    Returns:
    a String object.
  - getWorkflowClass
```
public String getWorkflowClass()
```
  - setWorkflowClass
```
public void setWorkflowClass(String workflowClass)
```
  - getWorkflowType
```
public String getWorkflowType()
```
  - setWorkflowType
```
public void setWorkflowType(String workflowType)
```
  - getWorkflowEngine
```
public String getWorkflowEngine()
```
  - setWorkflowEngine
```
public void setWorkflowEngine(String workflowEngine)
```
  - setPermanentBundleLocation
```
public void setPermanentBundleLocation(String permanentBundleLocation)
```
    Setter for the field permanentBundleLocation.
    
    Parameters:
    permanentBundleLocation - a String 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:
  - getWorkflowAttributes
```
public Set<WorkflowAttribute> getWorkflowAttributes()
```
    Getter for the field workflowAttributes.
    
    Returns:
    a Set object.
  - setWorkflowAttributes
```
public void setWorkflowAttributes(Set<WorkflowAttribute> workflowAttributes)
```
    Setter for the field workflowAttributes.
    
    Parameters:
    workflowAttributes - a Set object.
  - getAnnotations
```
public Set<WorkflowAttribute> getAnnotations()
```
    Description copied from interface: Annotatable
    
    Get the annotations for this model
    
    Specified by:
    
    getAnnotations in interface Annotatable<WorkflowAttribute>
    
    Returns:

Class Workflow

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

Workflow

Method Detail

compareTo

toString

equals

hashCode

getCwd

setCwd

getCommand

setCommand

getTemplate

setTemplate

getWorkflowId

setWorkflowId

getSwAccession

setSwAccession

getName

getJsonEscapeName

setName

getJsonEscapeDescription

getDescription

setDescription

getInputAlgorithm

setInputAlgorithm

getVersion

setVersion

getSeqwareVersion

setSeqwareVersion

getBaseIniFile

setBaseIniFile

getHost

setHost

getUsername

setUsername

getCreateTimestamp

setCreateTimestamp

getUpdateTimestamp

setUpdateTimestamp

isPrivate

getPrivate

setPrivate

isPublic

getPublic

setPublic

getOwner

setOwner

getWorkflowRuns

setWorkflowRuns

getWorkflowParams

getVisibleWorkflowParams

getVisibleWorkflowParamsWithDifferentValue

getWorkflowParamsWithDifferentFileMetaType

isLaunch

setWorkflowParams

getFullName

getJsonEscapeFullName

getPermanentBundleLocation

getWorkflowClass

setWorkflowClass

getWorkflowType

setWorkflowType

getWorkflowEngine

setWorkflowEngine

setPermanentBundleLocation

givesPermissionInternal

getWorkflowAttributes

setWorkflowAttributes

getAnnotations