org.hkijena.jipipe.api.nodes

Class JIPipeGraph

java.lang.Object

org.hkijena.jipipe.api.nodes.JIPipeGraph

All Implemented Interfaces:

JIPipeValidatable

public class JIPipeGraph
extends Object
implements JIPipeValidatable

Manages multiple JIPipeGraphNode instances as graph

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	JIPipeGraph.Deserializer Deserializes an JIPipeGraph
static class	JIPipeGraph.GraphChangedEvent Event is triggered when algorithm graph is changed
static class	JIPipeGraph.NodeConnectedEvent Generated when a connection was made in JIPipeGraph
static class	JIPipeGraph.NodeDisconnectedEvent Generated when slots are disconnected
static class	JIPipeGraph.NodeSlotsChangedEvent Triggered when an algorithm's slots change
static class	JIPipeGraph.Serializer Serializes an JIPipeGraph

Constructor Summary

Constructors

Constructor and Description
JIPipeGraph() Creates a new node type graph
JIPipeGraph(JIPipeGraph other) Creates a deep copy of the other algorithm graph.

Method Summary

Modifier and Type	Method and Description
void	attach(Class<?> klass, Object attachment) Attaches an object as the specified type Warning: Attachments are not serialized
void	attach(Object attachment) Attaches the object with its class as key.
void	attachAdditionalMetadata(String key, Object object) Attaches additional metadata (persistent)
boolean	canConnect(JIPipeDataSlot source, JIPipeDataSlot target, boolean user) Slow implementation of connection checking that tests for graph cycles
boolean	canConnectFast(JIPipeDataSlot source, JIPipeDataSlot target, boolean user) Fast implementation of connection checking without copying the graph
boolean	canUserDelete(JIPipeGraphNode algorithm) Returns true if the user can delete the algorithm
boolean	canUserDisconnect(JIPipeDataSlot source, JIPipeDataSlot target) Returns true if the user can disconnect the slots
void	clear() Clears this graph
void	connect(JIPipeDataSlot source, JIPipeDataSlot target) Connects an output slot to an input slot.
void	connect(JIPipeDataSlot source, JIPipeDataSlot target, boolean userCanDisconnect) Connects an output slot to an input slot.
boolean	containsNode(JIPipeDataSlot slot) Returns true if the slot is in this graph
boolean	containsNode(JIPipeGraphNode node) Returns true if this graph contains the algorithm
boolean	containsNode(UUID nodeUUID)
boolean	disconnect(JIPipeDataSlot source, JIPipeDataSlot target, boolean user) Disconnects an input and an output slot
void	disconnectAll(JIPipeDataSlot slot, boolean user) Completely disconnects a slot
void	edgesFromJson(com.fasterxml.jackson.databind.JsonNode jsonNode, JIPipeIssueReport issues)
JIPipeGraph	extract(Collection<JIPipeGraphNode> nodes, boolean withInternal) Copies the selected algorithms into a new graph Connections between the nodes are kept UUIDs are kept
List<LoopGroup>	extractLoopGroups(Set<JIPipeGraphNode> additionalLoopEnds, Set<JIPipeGraphNode> deactivatedNodes) Converts loop structures into equivalent group nodes Please note that nested loops will be put into the group; only order 1 loops will be converted.
JIPipeGraphNode	findNode(String uuidOrAlias) Finds a node by its UUID (as string) or alias ID.
UUID	findNodeUUID(String uuidOrAlias) Finds a node UUID by its UUID (as string) or alias ID.
void	fromJson(com.fasterxml.jackson.databind.JsonNode jsonNode, JIPipeIssueReport issues, JIPipeNotificationInbox notifications) Loads this graph from JSON
String	generateAliasIdFor(JIPipeGraphNode node) Generates an alias ID for a node
Map<String,Object>	getAdditionalMetadata()
<T> T	getAdditionalMetadata(Class<T> klass, String key) Returns additional metadata or null if it does not exist
String	getAliasIdOf(JIPipeGraphNode node) Gets the alias ID of a node A unique alias ID is generated if none is assigned yet
<T> T	getAttachment(Class<T> klass) Returns an attachment or null if it does not exist
Map<Class<?>,Object>	getAttachments()
Set<JIPipeDataSlot>	getAvailableSources(JIPipeDataSlot target, boolean user, boolean fast) Returns all available sources for an input slot.
Set<JIPipeDataSlot>	getAvailableTargets(JIPipeDataSlot source, boolean user, boolean fast) Returns all available target for an output slot Does not check for cycles.
String	getCompartmentDisplayNameOf(JIPipeGraphNode node) Returns a human-readable name of the compartment.
UUID	getCompartmentUUIDOf(JIPipeGraphNode node) Gets the UUID of the compartment
Set<JIPipeGraphNode>	getDeactivatedAlgorithms(boolean cascading) Gets all algorithms and all dependent algorithms that are missing inputs or are deactivated by the user
Set<JIPipeGraphNode>	getDeactivatedAlgorithms(Set<JIPipeGraphNode> externallySatisfied) Gets all algorithms and all dependent algorithms that are missing inputs or are deactivated by the user
Set<JIPipeDependency>	getDependencies() Gets all dependencies of all algorithms
Set<Map.Entry<JIPipeDataSlot,JIPipeDataSlot>>	getEdgesBetween(JIPipeGraphNode source, JIPipeGraphNode target) Gets all edges between two algorithm nodes
JIPipeGraphNode	getEquivalentAlgorithm(JIPipeGraphNode foreign) Returns the algorithm that has the same UUID as the foreign algorithm in the foreign graph.
JIPipeDataSlot	getEquivalentSlot(JIPipeDataSlot foreign) Returns the slot with the same name within the algorithm with the same ID.
EventBus	getEventBus() Returns the even bus
org.jgrapht.Graph<JIPipeDataSlot,JIPipeGraphEdge>	getGraph()
Set<JIPipeGraphNode>	getGraphNodes() Returns the set of node instances.
Set<UUID>	getGraphNodeUUIDs() Returns the set of node UUIDs.
Set<JIPipeDataSlot>	getInputIncomingSourceSlots(JIPipeDataSlot target) If exists, returns the output slots that provide data for the input slot Returns and empty list if there are none
JIPipeGraphNode	getNodeByUUID(UUID uuid) Gets a node by its UUID
int	getNodeCount()
Map<UUID,String>	getNodeLegacyCompartmentIDs()
Set<JIPipeGraphNode>	getNodesWithinCompartment(UUID compartmentId) Returns the algorithms within the specified compartment ID.
Set<JIPipeDataSlot>	getOutputOutgoingTargetSlots(JIPipeDataSlot source) Returns the list of input slots that are provided by the source slot Returns an empty set if the target is an input or no slot exists
JIPipeParameterTree	getParameterTree(boolean useAliasIds, Set<UUID> restrictToCompartments) Extracts all parameters as tree.
List<JIPipeGraphNode>	getPredecessorAlgorithms(JIPipeGraphNode target, List<JIPipeGraphNode> traversed) Returns all predecessor algorithms of an algorithm.
JIPipeProject	getProject() Gets the JIPipeProject if this is a project or project compartment graph.
int	getSlotCount()
Set<Map.Entry<JIPipeDataSlot,JIPipeDataSlot>>	getSlotEdges() Returns all edges as set of edges
Set<JIPipeDataSlot>	getSlotNodes()
List<JIPipeDataSlot>	getUnconnectedSlots()
UUID	getUUIDOf(JIPipeGraphNode node) Gets the UUID of a node
Set<UUID>	getVisibleCompartmentUUIDsOf(JIPipeGraphNode node) Gets the compartment UUIDs where the node is also visible inside
boolean	hasAttachmentOfType(Class<?> klass) Returns true if there is an attachment of given type
UUID	insertNode(JIPipeGraphNode node) Inserts a node into the graph.
UUID	insertNode(JIPipeGraphNode node, UUID compartment) Inserts a node into the graph.
UUID	insertNode(UUID uuid, JIPipeGraphNode node, UUID compartment) Inserts an algorithm into the graph
boolean	isEmpty()
Map<UUID,JIPipeGraphNode>	mergeWith(JIPipeGraph otherGraph) Merges another graph into this graph The input is not copied!
void	nodesFromJson(com.fasterxml.jackson.databind.JsonNode jsonNode, JIPipeIssueReport issues, JIPipeNotificationInbox notifications)
void	onAlgorithmSlotsChanged(JIPipeGraph.NodeSlotsChangedEvent event) Should be triggered when an JIPipeGraphNode's slots are changed.
void	onParameterStructureChanged(JIPipeParameterCollection.ParameterStructureChangedEvent event) Should be triggered when an JIPipeGraphNode's parameter structure is changed.
void	rebuildAliasIds(boolean force) Recreates the alias Ids based on their name
void	removeAttachment(Class<?> klass) Removes an attachment Warning: Attachments are not serialized
void	removeCompartment(UUID compartmentUUID) Removes a whole compartment from the graph.
void	removeNode(JIPipeGraphNode node, boolean user) Removes an algorithm.
void	removeNodes(Set<JIPipeGraphNode> nodes, boolean user) Removes multiple nodes at once
void	repairGraph() Repairs the graph by removing old nodes and adding missing ones
void	replaceNode(JIPipeGraphNode target, JIPipeGraphNode replacement) Replaces a node with another.
void	replaceWith(JIPipeGraph other) Replaces all contents with the ones in the other graph Does not apply copying!
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	reportValidity(JIPipeIssueReport report, JIPipeGraphNode targetNode, Set<JIPipeGraphNode> satisfied) Reports the validity for the target node and its dependencies
void	setAdditionalMetadata(Map<String,Object> additionalMetadata)
void	setAttachments(Map<Class<?>,Object> attachments) Sets the attachments map Warning: Attachments are not serialized
void	setCompartment(UUID nodeUUID, UUID compartmentUUID) Sets the compartment of a node
void	setUUIDOf(JIPipeGraphNode node, UUID uuid) Changes the UUID of the node
List<JIPipeGraphNode>	traverse() Traverses the graph in topological order.
List<JIPipeDataSlot>	traverseSlots() Traverses the graph in topological order.

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

Constructor Detail

JIPipeGraph

public JIPipeGraph()

Creates a new node type graph

JIPipeGraph

public JIPipeGraph(JIPipeGraph other)

Creates a deep copy of the other algorithm graph. UUIDs are copied. Will not copy the additional metadata

Parameters:

other - The original graph

Method Detail

generateAliasIdFor

public String generateAliasIdFor(JIPipeGraphNode node)

Generates an alias ID for a node

Parameters:

node - the node

Returns:

a unique alias ID for the node

getAliasIdOf

public String getAliasIdOf(JIPipeGraphNode node)

Gets the alias ID of a node A unique alias ID is generated if none is assigned yet

Parameters:

node - the node

Returns:

the alias ID or null if the node is not contained within this graph.

getUUIDOf

public UUID getUUIDOf(JIPipeGraphNode node)

Gets the UUID of a node

Parameters:

node - the node

Returns:

the UUID or null if the node is not contained within this graph.

getNodeByUUID

public JIPipeGraphNode getNodeByUUID(UUID uuid)

Gets a node by its UUID

Parameters:

uuid - the UUID

Returns:

the node assigned to this UUID

setUUIDOf

public void setUUIDOf(JIPipeGraphNode node,
                      UUID uuid)

Changes the UUID of the node

Parameters:

node - the node

uuid - the uuid

getCompartmentUUIDOf

public UUID getCompartmentUUIDOf(JIPipeGraphNode node)

Gets the UUID of the compartment

Parameters:

node - the node

Returns:

the UUID of the compartment

getVisibleCompartmentUUIDsOf

public Set<UUID> getVisibleCompartmentUUIDsOf(JIPipeGraphNode node)

Gets the compartment UUIDs where the node is also visible inside

Parameters:

node - the node

Returns:

set of compartment UUIDs (writeable)

findNodeUUID

public UUID findNodeUUID(String uuidOrAlias)

Finds a node UUID by its UUID (as string) or alias ID. Prefers UUID.

Parameters:

uuidOrAlias - the UUID string or alias ID

Returns:

the node or null if it could not be found

findNode

public JIPipeGraphNode findNode(String uuidOrAlias)

Finds a node by its UUID (as string) or alias ID. Prefers UUID.

Parameters:

uuidOrAlias - the UUID string or alias ID

Returns:

the node or null if it could not be found

getAdditionalMetadata

public Map<String,Object> getAdditionalMetadata()

setAdditionalMetadata

public void setAdditionalMetadata(Map<String,Object> additionalMetadata)

insertNode

public UUID insertNode(UUID uuid,
                       JIPipeGraphNode node,
                       UUID compartment)

Inserts an algorithm into the graph

Parameters:

uuid - The unique ID

node - The node

compartment - The compartment where the algorithm will be placed. Can be null.

Returns:

the ID of the inserted node

insertNode

public UUID insertNode(JIPipeGraphNode node)

Inserts a node into the graph. Its compartment is null.

Parameters:

node - The node

Returns:

the ID of the inserted node

insertNode

public UUID insertNode(JIPipeGraphNode node,
                       UUID compartment)

Inserts a node into the graph.

Parameters:

node - The node

compartment - The compartment where the algorithm will be placed

Returns:

the ID of the inserted node

getAttachment

public <T> T getAttachment(Class<T> klass)

Returns an attachment or null if it does not exist

Type Parameters:

T - the attachment class

Parameters:

klass - the attachment class

Returns:

the attachment or null

getAdditionalMetadata

public <T> T getAdditionalMetadata(Class<T> klass,
                                   String key)

Returns additional metadata or null if it does not exist

Type Parameters:

T - returned metadata class

Parameters:

klass - returned metadata class

key - metadata key

Returns:

the object or null

attachAdditionalMetadata

public void attachAdditionalMetadata(String key,
                                     Object object)

Attaches additional metadata (persistent)

Parameters:

key - the key

object - JSON-serializable object

attach

public void attach(Class<?> klass,
                   Object attachment)

Attaches an object as the specified type Warning: Attachments are not serialized

Parameters:

klass - the type the attachment is attached as

attachment - the attachment

attach

public void attach(Object attachment)

Attaches the object with its class as key. Warning: Attachments are not serialized

Parameters:

attachment - the attachment

removeAttachment

public void removeAttachment(Class<?> klass)

Removes an attachment Warning: Attachments are not serialized

Parameters:

klass - the class

hasAttachmentOfType

public boolean hasAttachmentOfType(Class<?> klass)

Returns true if there is an attachment of given type

Parameters:

klass - the attachment class

Returns:

if there is an attachment

canUserDelete

public boolean canUserDelete(JIPipeGraphNode algorithm)

Returns true if the user can delete the algorithm

Parameters:

algorithm - The algorithm

Returns:

True if the user can delete the algorithm

canUserDisconnect

public boolean canUserDisconnect(JIPipeDataSlot source,
                                 JIPipeDataSlot target)

Returns true if the user can disconnect the slots

Parameters:

source - Source slot

target - Target slot

Returns:

True if the user can disconnect those slots. Returns false if the connection does not exist.

setCompartment

public void setCompartment(UUID nodeUUID,
                           UUID compartmentUUID)

Sets the compartment of a node

Parameters:

nodeUUID - the node

compartmentUUID - the compartment

removeCompartment

public void removeCompartment(UUID compartmentUUID)

Removes a whole compartment from the graph. Will fail silently if the ID does not exist

Parameters:

compartmentUUID - The compartment ID

removeNode

public void removeNode(JIPipeGraphNode node,
                       boolean user)

Removes an algorithm. The algorithm should exist within the graph.

Parameters:

node - The node to be removed

user - if a user triggered the operation. If true, will not remove internal nodes

canConnect

public boolean canConnect(JIPipeDataSlot source,
                          JIPipeDataSlot target,
                          boolean user)

Slow implementation of connection checking that tests for graph cycles

Parameters:

source - Source slot. Must be an output.

target - Target slot. Must be an input.

user - If true, the user is generating the connection

Returns:

True if the connection could be possible

canConnectFast

public boolean canConnectFast(JIPipeDataSlot source,
                              JIPipeDataSlot target,
                              boolean user)

Fast implementation of connection checking without copying the graph

Parameters:

source - Source slot. Must be an output.

target - Target slot. Must be an input.

user - If triggered by a user

Returns:

True if the connection could be possible. Please check again with canConnect()

connect

public void connect(JIPipeDataSlot source,
                    JIPipeDataSlot target)

Connects an output slot to an input slot. Allows users to disconnect this connection

Parameters:

source - An output slot

target - An input slot

connect

public void connect(JIPipeDataSlot source,
                    JIPipeDataSlot target,
                    boolean userCanDisconnect)

Connects an output slot to an input slot.

Parameters:

source - An output slot.

target - An input slot.

userCanDisconnect - If true, users are allowed to disconnect this connection again

getParameterTree

public JIPipeParameterTree getParameterTree(boolean useAliasIds,
                                            Set<UUID> restrictToCompartments)

Extracts all parameters as tree.

Parameters:

useAliasIds - if enabled, paths will use alias Ids instead of UUIDs

restrictToCompartments - if not null or empty, restrict to specific compartments

Returns:

the tree

repairGraph

public void repairGraph()

Repairs the graph by removing old nodes and adding missing ones

getInputIncomingSourceSlots

public Set<JIPipeDataSlot> getInputIncomingSourceSlots(JIPipeDataSlot target)

If exists, returns the output slots that provide data for the input slot Returns and empty list if there are none

Parameters:

target - The input slot

Returns:

The output slot that generates data for the input. Null if no source exists.

getOutputOutgoingTargetSlots

public Set<JIPipeDataSlot> getOutputOutgoingTargetSlots(JIPipeDataSlot source)

Returns the list of input slots that are provided by the source slot Returns an empty set if the target is an input or no slot exists

Parameters:

source - An output slot

Returns:

All slots that receive data from the output slot

getAvailableSources

public Set<JIPipeDataSlot> getAvailableSources(JIPipeDataSlot target,
                                               boolean user,
                                               boolean fast)

Returns all available sources for an input slot. This function does not check for cycles.

Parameters:

target - An input slot

user - If true, only connections that can be created by a user are shown

fast - If true, use canConnectFast instead of canConnect

Returns:

Set of potential sources

disconnectAll

public void disconnectAll(JIPipeDataSlot slot,
                          boolean user)

Completely disconnects a slot

Parameters:

slot - An input or output slot

user - If true, indicates that is disconnect was issued by a user

disconnect

public boolean disconnect(JIPipeDataSlot source,
                          JIPipeDataSlot target,
                          boolean user)

Disconnects an input and an output slot

Parameters:

source - An output slot

target - An input slot

user - Indicates if the command was issued by a user

Returns:

True if the disconnect was successful, otherwise false

getAvailableTargets

public Set<JIPipeDataSlot> getAvailableTargets(JIPipeDataSlot source,
                                               boolean user,
                                               boolean fast)

Returns all available target for an output slot Does not check for cycles.

Parameters:

source - An output slot

user - Indicates that a user issues the connection

fast - If true, use canConnectFast instead of canConnect

Returns:

A list of all available input slots

onAlgorithmSlotsChanged

public void onAlgorithmSlotsChanged(JIPipeGraph.NodeSlotsChangedEvent event)

Should be triggered when an JIPipeGraphNode's slots are changed. Triggers a graph repair

Parameters:

event - The generated event

onParameterStructureChanged

public void onParameterStructureChanged(JIPipeParameterCollection.ParameterStructureChangedEvent event)

Should be triggered when an JIPipeGraphNode's parameter structure is changed. This event is re-triggered into getEventBus()

Parameters:

event - Generated event

getDependencies

public Set<JIPipeDependency> getDependencies()

Gets all dependencies of all algorithms

Returns:

Set of dependencies

getEventBus

public EventBus getEventBus()

Returns the even bus

Returns:

Event bus instance

getGraphNodeUUIDs

public Set<UUID> getGraphNodeUUIDs()

Returns the set of node UUIDs. This is an immutable set. Not safe for modification.

Returns:

the UUIDs

getGraphNodes

public Set<JIPipeGraphNode> getGraphNodes()

Returns the set of node instances. This is an immutable set. Not safe for modification.

Returns:

the node instances

containsNode

public boolean containsNode(JIPipeGraphNode node)

Returns true if this graph contains the algorithm

Parameters:

node - The algorithm instance

Returns:

True if the algorithm is part of this graph

getSlotEdges

public Set<Map.Entry<JIPipeDataSlot,JIPipeDataSlot>> getSlotEdges()

Returns all edges as set of edges

Returns:

Set of entries where the key is an output slot and the value is an input slot

fromJson

public void fromJson(com.fasterxml.jackson.databind.JsonNode jsonNode,
                     JIPipeIssueReport issues,
                     JIPipeNotificationInbox notifications)

Loads this graph from JSON

Parameters:

jsonNode - JSON data

issues - issues reported during deserializing

notifications - notifications for the user

edgesFromJson

public void edgesFromJson(com.fasterxml.jackson.databind.JsonNode jsonNode,
                          JIPipeIssueReport issues)

nodesFromJson

public void nodesFromJson(com.fasterxml.jackson.databind.JsonNode jsonNode,
                          JIPipeIssueReport issues,
                          JIPipeNotificationInbox notifications)

mergeWith

public Map<UUID,JIPipeGraphNode> mergeWith(JIPipeGraph otherGraph)

Merges another graph into this graph The input is not copied!

Parameters:

otherGraph - The other graph

Returns:

A map from ID in source graph to algorithm in target graph

extract

public JIPipeGraph extract(Collection<JIPipeGraphNode> nodes,
                           boolean withInternal)

Copies the selected algorithms into a new graph Connections between the nodes are kept UUIDs are kept

Parameters:

nodes - the nodes

withInternal - also copy internal algorithms

Returns:

graph that only contains the selected algorithms, UUIDs are the same between the original and copies

getNodeCount

public int getNodeCount()

Returns:

The number of all algorithms

getSlotCount

public int getSlotCount()

Returns:

The number of all algorithm slots in this graph

traverseSlots

public List<JIPipeDataSlot> traverseSlots()

Traverses the graph in topological order. The order guarantees that input is always available

Returns:

Sorted list of data slots

getPredecessorAlgorithms

public List<JIPipeGraphNode> getPredecessorAlgorithms(JIPipeGraphNode target,
                                                      List<JIPipeGraphNode> traversed)

Returns all predecessor algorithms of an algorithm. The predecessors are ordered according to the list of traversed algorithms (topological order)

Parameters:

target - the target algorithm

traversed - list of algorithms to sort by (usually this is in topological order)

Returns:

predecessors in topological order

getDeactivatedAlgorithms

public Set<JIPipeGraphNode> getDeactivatedAlgorithms(boolean cascading)

Gets all algorithms and all dependent algorithms that are missing inputs or are deactivated by the user

Parameters:

cascading - if predecessors are also checked.

Returns:

list of algorithms

getDeactivatedAlgorithms

public Set<JIPipeGraphNode> getDeactivatedAlgorithms(Set<JIPipeGraphNode> externallySatisfied)

Gets all algorithms and all dependent algorithms that are missing inputs or are deactivated by the user

Parameters:

externallySatisfied - list of algorithms that have their input set externally

Returns:

list of algorithms

traverse

public List<JIPipeGraphNode> traverse()

Traverses the graph in topological order. The order guarantees that input is always available

Returns:

Sorted list of algorithms

getSlotNodes

public Set<JIPipeDataSlot> getSlotNodes()

Returns:

All data slots

containsNode

public boolean containsNode(JIPipeDataSlot slot)

Returns true if the slot is in this graph

Parameters:

slot - A slot

Returns:

True if this graph contains the slot

getProject

public JIPipeProject getProject()

Gets the JIPipeProject if this is a project or project compartment graph. Otherwise will return null

Returns:

the project or null if no project was attached to this graph

getCompartmentDisplayNameOf

public String getCompartmentDisplayNameOf(JIPipeGraphNode node)

Returns a human-readable name of the compartment.

Parameters:

node - the node

Returns:

the compartment name, human-readable

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

getAttachments

public Map<Class<?>,Object> getAttachments()

setAttachments

public void setAttachments(Map<Class<?>,Object> attachments)

Sets the attachments map Warning: Attachments are not serialized

Parameters:

attachments - attachments

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

reportValidity

public void reportValidity(JIPipeIssueReport report,
                           JIPipeGraphNode targetNode,
                           Set<JIPipeGraphNode> satisfied)

Reports the validity for the target node and its dependencies

Parameters:

report - the report

targetNode - the target node

satisfied - all algorithms that are considered to have a satisfied input

getGraph

public org.jgrapht.Graph<JIPipeDataSlot,JIPipeGraphEdge> getGraph()

Returns:

The underlying graph

clear

public void clear()

Clears this graph

replaceNode

public void replaceNode(JIPipeGraphNode target,
                        JIPipeGraphNode replacement)

Replaces a node with another.

Parameters:

target - the target node

replacement - the replacement node

getEquivalentAlgorithm

public JIPipeGraphNode getEquivalentAlgorithm(JIPipeGraphNode foreign)

Returns the algorithm that has the same UUID as the foreign algorithm in the foreign graph.

Parameters:

foreign - An algorithm

Returns:

Equivalent algorithm within this graph

getEquivalentSlot

public JIPipeDataSlot getEquivalentSlot(JIPipeDataSlot foreign)

Returns the slot with the same name within the algorithm with the same ID.

Parameters:

foreign - A data slot

Returns:

slot with the same name within the algorithm with the same ID

getUnconnectedSlots

public List<JIPipeDataSlot> getUnconnectedSlots()

Returns:

All unconnected slots

getNodesWithinCompartment

public Set<JIPipeGraphNode> getNodesWithinCompartment(UUID compartmentId)

Returns the algorithms within the specified compartment ID.

Parameters:

compartmentId - The compartment ID

Returns:

Algorithms that have the specified compartment ID. Empty set if the compartment does not exist.

removeNodes

public void removeNodes(Set<JIPipeGraphNode> nodes,
                        boolean user)

Removes multiple nodes at once

Parameters:

nodes - list of nodes

user - if the operation is done by a user

replaceWith

public void replaceWith(JIPipeGraph other)

Replaces all contents with the ones in the other graph Does not apply copying!

Parameters:

other - the other graph

getEdgesBetween

public Set<Map.Entry<JIPipeDataSlot,JIPipeDataSlot>> getEdgesBetween(JIPipeGraphNode source,
                                                                     JIPipeGraphNode target)

Gets all edges between two algorithm nodes

Parameters:

source - the source

target - the target

Returns:

all edges

getNodeLegacyCompartmentIDs

public Map<UUID,String> getNodeLegacyCompartmentIDs()

rebuildAliasIds

public void rebuildAliasIds(boolean force)

Recreates the alias Ids based on their name

Parameters:

force - force rebuilding

isEmpty

public boolean isEmpty()

extractLoopGroups

public List<LoopGroup> extractLoopGroups(Set<JIPipeGraphNode> additionalLoopEnds,
                                         Set<JIPipeGraphNode> deactivatedNodes)

Converts loop structures into equivalent group nodes Please note that nested loops will be put into the group; only order 1 loops will be converted.

Parameters:

additionalLoopEnds - nodes that are marked as loop ends

containsNode

public boolean containsNode(UUID nodeUUID)