JIPipeProject (jipipe 1.76.1-SNAPSHOT API)

java.lang.Object
- org.hkijena.jipipe.api.JIPipeProject

All Implemented Interfaces:

JIPipeValidatable
```
public class JIPipeProject
extends Object
implements JIPipeValidatable
```
A JIPipe project. It contains all information to setup and run an analysis

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`JIPipeProject.CompartmentAddedEvent` Triggered when a sample is added to an `JIPipeProject`
`static class`	`JIPipeProject.CompartmentRemovedEvent` Triggered when a sample is removed from an `JIPipeProject`
`static class`	`JIPipeProject.Deserializer` Deserializes a project
`static class`	`JIPipeProject.Serializer` Serializes a project

Field Summary

Fields
Modifier and Type Field and Description

static int CURRENT_PROJECT_FORMAT_VERSION
The current version of the project format.

Fields
Modifier and Type	Field and Description
`static int`	`CURRENT_PROJECT_FORMAT_VERSION` The current version of the project format.

Constructor Summary

Constructors
Constructor and Description

JIPipeProject()
A JIPipe project

Constructors
Constructor and Description
`JIPipeProject()` A JIPipe project

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`JIPipeProjectCompartment`	`addCompartment(JIPipeProjectCompartment compartment, UUID uuid)` Adds an existing compartment instance
`JIPipeProjectCompartment`	`addCompartment(String name)` Adds a new project compartment
`void`	`connectCompartments(JIPipeProjectCompartment source, JIPipeProjectCompartment target)` Connects two compartments
`JIPipeProjectCompartment`	`findCompartment(String uuidOrAlias)` Finds a compartment by UUID or alias
`void`	`fixCompartmentOutputs()` Repairs restored compartment outputs
`void`	`fromJson(com.fasterxml.jackson.databind.JsonNode jsonNode, JIPipeIssueReport report, JIPipeNotificationInbox notifications)` Loads the project from JSON
`Map<String,Object>`	`getAdditionalMetadata()`
`JIPipeProjectCache`	`getCache()`
`JIPipeGraph`	`getCompartmentGraph()`
`BiMap<UUID,JIPipeProjectCompartment>`	`getCompartments()`
`Set<JIPipeGraphNode>`	`getDeactivatedAlgorithms()` Returns a list of all nodes that cannot be executed or are deactivated by the user.
`EventBus`	`getEventBus()`
`JIPipeGraph`	`getGraph()`
`Set<JIPipeDataSlot>`	`getHeavyIntermediateAlgorithmOutputSlots()` Returns a list of all nodes that generate heavy data (`JIPipeHeavyData`) and are intermediate (see getIntermediateAlgorithms()).
`JIPipeProjectHistoryJournal`	`getHistoryJournal()`
`Set<JIPipeGraphNode>`	`getIntermediateAlgorithms()` Returns all nodes that have at least one connected algorithm that uses its generated data.
`JIPipeProjectMetadata`	`getMetadata()`
`List<JIPipeNodeExample>`	`getNodeExamples(String nodeTypeId)` Gets all examples for a node type ID.
`JIPipeProjectInfoParameters`	`getPipelineParameters()` Returns the global parameters for this pipeline
`Set<JIPipeDependency>`	`getSimplifiedMinimalDependencies()`
`Path`	`getWorkDirectory()` Gets the folder where the project is currently working in
`static Set<JIPipeDependency>`	`loadDependenciesFromJson(com.fasterxml.jackson.databind.JsonNode node)` Deserializes the set of project dependencies from JSON.
`static JIPipeProjectMetadata`	`loadMetadataFromJson(com.fasterxml.jackson.databind.JsonNode node)` Deserializes the project metadata from JSON
`static JIPipeProject`	`loadProject(Path fileName, JIPipeIssueReport report)` Loads a project from a file
`static JIPipeProject`	`loadProject(Path fileName, JIPipeIssueReport report, JIPipeNotificationInbox notifications)` Loads a project from a file
`void`	`onCompartmentGraphChanged(JIPipeGraph.GraphChangedEvent event)` Triggered when the compartment graph is changed
`void`	`rebuildAliasIds(boolean force)` Re-assigns graph node Ids based on their name
`void`	`rebuildCompartmentsFromGraph()` Rebuilds the compartment list from the current state of the compartment graph
`void`	`removeCompartment(JIPipeProjectCompartment compartment)` Removes a compartment
`void`	`reportValidity(JIPipeIssueReport report)` Generates a validity report
`void`	`reportValidity(JIPipeIssueReport report, JIPipeGraphNode targetNode)` Reports the validity for the target node and its dependencies
`void`	`saveProject(OutputStream outputStream)` Saves the project
`void`	`saveProject(Path fileName)` Saves the project
`void`	`saveProject(Writer writer)` Saves the project
`void`	`setAdditionalMetadata(Map<String,Object> additionalMetadata)`
`void`	`setWorkDirectory(Path workDirectory)` Sets the folder where the project is currently working in.
`void`	`toJson(com.fasterxml.jackson.core.JsonGenerator generator)` Writes the project to JSON

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

Methods inherited from interface org.hkijena.jipipe.api.JIPipeValidatable
generateValidityReport

- Field Detail
  - CURRENT_PROJECT_FORMAT_VERSION
```
public static final int CURRENT_PROJECT_FORMAT_VERSION
```
    The current version of the project format. This is here for any future addition.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - JIPipeProject
```
public JIPipeProject()
```
    A JIPipe project
- Method Detail
  - loadProject
```
public static JIPipeProject loadProject(Path fileName,
                                        JIPipeIssueReport report)
                                 throws IOException
```
    Loads a project from a file
    
    Parameters:
    
    fileName - JSON file
    
    report - issue report
    
    Returns:
    
    Loaded project
    
    Throws:
    
    IOException - Triggered by ObjectMapper
  - loadProject
```
public static JIPipeProject loadProject(Path fileName,
                                        JIPipeIssueReport report,
                                        JIPipeNotificationInbox notifications)
                                 throws IOException
```
    Loads a project from a file
    
    Parameters:
    
    fileName - JSON file
    
    report - issue report
    
    notifications - notifications for the user
    
    Returns:
    
    Loaded project
    
    Throws:
    
    IOException - Triggered by ObjectMapper
  - loadDependenciesFromJson
```
public static Set<JIPipeDependency> loadDependenciesFromJson(com.fasterxml.jackson.databind.JsonNode node)
```
    Deserializes the set of project dependencies from JSON. Does not require the dependencies to be actually registered.
    
    Parameters:
    
    node - JSON node
    
    Returns:
    
    The dependencies as JIPipeMutableDependency
  - loadMetadataFromJson
```
public static JIPipeProjectMetadata loadMetadataFromJson(com.fasterxml.jackson.databind.JsonNode node)
```
    Deserializes the project metadata from JSON
    
    Parameters:
    
    node - JSON node
    
    Returns:
    
    the metadata
  - findCompartment
```
public JIPipeProjectCompartment findCompartment(String uuidOrAlias)
```
    Finds a compartment by UUID or alias
    
    Parameters:
    
    uuidOrAlias - UUID or alias
    
    Returns:
    
    the compartment or null if it could not be found
  - getEventBus
```
public EventBus getEventBus()
```
    Returns:
    
    The event bus
  - getGraph
```
public JIPipeGraph getGraph()
```
    Returns:
    
    The algorithm graph
  - saveProject
```
public void saveProject(Path fileName)
                 throws IOException
```
    Saves the project
    
    Parameters:
    
    fileName - Target file
    
    Throws:
    
    IOException - Triggered by ObjectMapper
  - saveProject
```
public void saveProject(Writer writer)
                 throws IOException
```
    Saves the project
    
    Parameters:
    
    writer - Target writer
    
    Throws:
    
    IOException - Triggered by ObjectMapper
  - saveProject
```
public void saveProject(OutputStream outputStream)
                 throws IOException
```
    Saves the project
    
    Parameters:
    
    outputStream - Target writer
    
    Throws:
    
    IOException - Triggered by ObjectMapper
  - getCache
```
public JIPipeProjectCache getCache()
```
  - getCompartments
```
public BiMap<UUID,JIPipeProjectCompartment> getCompartments()
```
    Returns:
    
    The current project compartments
  - addCompartment
```
public JIPipeProjectCompartment addCompartment(String name)
```
    Adds a new project compartment
    
    Parameters:
    
    name - Compartment name
    
    Returns:
    
    The compartment
  - addCompartment
```
public JIPipeProjectCompartment addCompartment(JIPipeProjectCompartment compartment,
                                               UUID uuid)
```
    Adds an existing compartment instance
    
    Parameters:
    
    compartment - Compartment
    
    uuid - the UUID of the compartment
    
    Returns:
    
    The compartment
  - connectCompartments
```
public void connectCompartments(JIPipeProjectCompartment source,
                                JIPipeProjectCompartment target)
```
    Connects two compartments
    
    Parameters:
    
    source - Source compartment
    
    target - Target compartment
  - onCompartmentGraphChanged
```
public void onCompartmentGraphChanged(JIPipeGraph.GraphChangedEvent event)
```
    Triggered when the compartment graph is changed
    
    Parameters:
    
    event - Generated event
  - reportValidity
```
public void reportValidity(JIPipeIssueReport report)
```
    Description copied from interface: JIPipeValidatable
    
    Generates a validity report
    
    Specified by:
    
    reportValidity in interface JIPipeValidatable
    
    Parameters:
    
    report - the report to be added to
  - reportValidity
```
public void reportValidity(JIPipeIssueReport report,
                           JIPipeGraphNode targetNode)
```
    Reports the validity for the target node and its dependencies
    
    Parameters:
    
    report - the report
    
    targetNode - the target node
  - getCompartmentGraph
```
public JIPipeGraph getCompartmentGraph()
```
    Returns:
    
    The compartment graph. Contains only JIPipeProjectCompartment nodes.
  - removeCompartment
```
public void removeCompartment(JIPipeProjectCompartment compartment)
```
    Removes a compartment
    
    Parameters:
    
    compartment - The compartment
  - getMetadata
```
public JIPipeProjectMetadata getMetadata()
```
    Returns:
    
    Project metadata
  - getWorkDirectory
```
public Path getWorkDirectory()
```
    Gets the folder where the project is currently working in
    
    Returns:
    
    the folder where the project is currently working in
  - setWorkDirectory
```
public void setWorkDirectory(Path workDirectory)
```
    Sets the folder where the project is currently working in. This information is passed to the algorithms to adapt to the work directory if needed (usually ony Filesystem nodes are affected)
    
    Parameters:
    
    workDirectory - Project work directory
  - getSimplifiedMinimalDependencies
```
public Set<JIPipeDependency> getSimplifiedMinimalDependencies()
```
    Returns:
    
    All project dependencies
  - rebuildAliasIds
```
public void rebuildAliasIds(boolean force)
```
    Re-assigns graph node Ids based on their name
    
    Parameters:
    
    force - force updating
  - getAdditionalMetadata
```
public Map<String,Object> getAdditionalMetadata()
```
  - setAdditionalMetadata
```
public void setAdditionalMetadata(Map<String,Object> additionalMetadata)
```
  - toJson
```
public void toJson(com.fasterxml.jackson.core.JsonGenerator generator)
            throws IOException
```
    Writes the project to JSON
    
    Parameters:
    
    generator - the JSON generator
    
    Throws:
    
    IOException - thrown by JsonGenerator
  - fromJson
```
public void fromJson(com.fasterxml.jackson.databind.JsonNode jsonNode,
                     JIPipeIssueReport report,
                     JIPipeNotificationInbox notifications)
              throws IOException
```
    Loads the project from JSON
    
    Parameters:
    
    jsonNode - the node
    
    notifications - notifications for the user
    
    Throws:
    
    IOException
  - rebuildCompartmentsFromGraph
```
public void rebuildCompartmentsFromGraph()
```
    Rebuilds the compartment list from the current state of the compartment graph
  - getDeactivatedAlgorithms
```
public Set<JIPipeGraphNode> getDeactivatedAlgorithms()
```
    Returns a list of all nodes that cannot be executed or are deactivated by the user. This method works on transitive deactivation (e.g. a dependency is deactivated).
    
    Returns:
    
    list of deactivated nodes
  - getIntermediateAlgorithms
```
public Set<JIPipeGraphNode> getIntermediateAlgorithms()
```
    Returns all nodes that have at least one connected algorithm that uses its generated data.
    
    Returns:
    
    Intermediate nodes
  - getHeavyIntermediateAlgorithmOutputSlots
```
public Set<JIPipeDataSlot> getHeavyIntermediateAlgorithmOutputSlots()
```
    Returns a list of all nodes that generate heavy data (JIPipeHeavyData) and are intermediate (see getIntermediateAlgorithms()). Skips all nodes that do not save outputs.
    
    Returns:
    
    intermediate nodes with heavy data
  - getPipelineParameters
```
public JIPipeProjectInfoParameters getPipelineParameters()
```
    Returns the global parameters for this pipeline
    
    Returns:
    
    global parameters
  - fixCompartmentOutputs
```
public void fixCompartmentOutputs()
```
    Repairs restored compartment outputs
  - getHistoryJournal
```
public JIPipeProjectHistoryJournal getHistoryJournal()
```
  - getNodeExamples
```
public List<JIPipeNodeExample> getNodeExamples(String nodeTypeId)
```
    Gets all examples for a node type ID. Includes project templates
    
    Parameters:
    
    nodeTypeId - the ID
    
    Returns:
    
    the examples

Class JIPipeProject

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.hkijena.jipipe.api.JIPipeValidatable

Field Detail

CURRENT_PROJECT_FORMAT_VERSION

Constructor Detail

JIPipeProject

Method Detail

loadProject

loadProject

loadDependenciesFromJson

loadMetadataFromJson

findCompartment

getEventBus

getGraph

saveProject

saveProject

saveProject

getCache

getCompartments

addCompartment

addCompartment

connectCompartments

onCompartmentGraphChanged

reportValidity

reportValidity

getCompartmentGraph

removeCompartment

getMetadata

getWorkDirectory

setWorkDirectory

getSimplifiedMinimalDependencies

rebuildAliasIds

getAdditionalMetadata

setAdditionalMetadata

toJson

fromJson

rebuildCompartmentsFromGraph

getDeactivatedAlgorithms

getIntermediateAlgorithms

getHeavyIntermediateAlgorithmOutputSlots

getPipelineParameters

fixCompartmentOutputs

getHistoryJournal

getNodeExamples