public class IteratingRScriptAlgorithm extends JIPipeIteratingAlgorithm
JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer
JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener
SLOT_PARAMETERS
Constructor and Description |
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IteratingRScriptAlgorithm(IteratingRScriptAlgorithm other) |
IteratingRScriptAlgorithm(JIPipeNodeInfo info) |
Modifier and Type | Method and Description |
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JIPipeTextAnnotationMergeMode |
getAnnotationMergeStrategy() |
void |
getExternalEnvironments(List<JIPipeEnvironment> target)
Gathers all known external environments
|
OptionalREnvironment |
getOverrideEnvironment() |
RScriptParameter |
getScript() |
JIPipeDynamicParameterCollection |
getVariables() |
boolean |
isCleanUpAfterwards() |
protected void |
onDeserialized(com.fasterxml.jackson.databind.JsonNode node,
JIPipeValidationReport issues,
JIPipeNotificationInbox notifications)
Override this method to add operations to be run after deserialization from JSON
|
void |
reportValidity(JIPipeValidationReportContext reportContext,
JIPipeValidationReport report)
Generates a validity report
|
protected void |
runIteration(JIPipeSingleIterationStep iterationStep,
JIPipeIterationContext iterationContext,
JIPipeGraphNodeRunContext runContext,
JIPipeProgressInfo progressInfo)
Runs code on one data row
|
void |
setAnnotationMergeStrategy(JIPipeTextAnnotationMergeMode annotationMergeStrategy) |
void |
setBaseDirectory(Path baseDirectory)
Sets the current work directory of this algorithm.
|
void |
setCleanUpAfterwards(boolean cleanUpAfterwards) |
void |
setOverrideEnvironment(OptionalREnvironment overrideEnvironment) |
void |
setScript(RScriptParameter script) |
createUIInputSlotIconDescriptionMenuItems, generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isParameterUIVisible, isParameterUIVisible, runParameterSet, runPassThrough, supportsParallelization
getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, onParameterChanged, run
canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped
archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDependencies, getDisplayName, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getLocations, getLocationWithin, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setLocations, setLocationWithin, setLocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots
getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
generateDataBatchesDryRun
installUIOverrideParameterEditor, installUIParameterOptions
emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, setParameter
generateValidityReport
onParameterUIChanged
onParameterStructureChanged
public IteratingRScriptAlgorithm(JIPipeNodeInfo info)
public IteratingRScriptAlgorithm(IteratingRScriptAlgorithm other)
public void getExternalEnvironments(List<JIPipeEnvironment> target)
JIPipeGraphNode
getExternalEnvironments
in class JIPipeGraphNode
target
- the list where the external environments will be gatheredpublic boolean isCleanUpAfterwards()
public void setCleanUpAfterwards(boolean cleanUpAfterwards)
public void reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report)
JIPipeValidatable
reportValidity
in interface JIPipeValidatable
reportValidity
in class JIPipeAlgorithm
reportContext
- the report contextreport
- the report to be added topublic OptionalREnvironment getOverrideEnvironment()
public void setOverrideEnvironment(OptionalREnvironment overrideEnvironment)
protected void onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeValidationReport issues, JIPipeNotificationInbox notifications)
JIPipeGraphNode
onDeserialized
in class JIPipeAlgorithm
node
- the JSON node where the data was loadedissues
- issues during deserialization. if you want to notify the user about potential issues that can be acted upon, use the notification inboxnotifications
- additional notifications for the user. these can be acted uponprotected void runIteration(JIPipeSingleIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo)
JIPipeIteratingAlgorithm
runIteration
in class JIPipeIteratingAlgorithm
iterationStep
- The data interfaceiterationContext
- The iteration contextrunContext
- the run contextprogressInfo
- the progress info from the runpublic void setBaseDirectory(Path baseDirectory)
JIPipeGraphNode
JIPipeGraphNode.BaseDirectoryChangedEvent
that can be received by JIPipeDataSlot
instances to adapt to the work directory.setBaseDirectory
in class JIPipeGraphNode
baseDirectory
- The work directory. Can be nullpublic JIPipeDynamicParameterCollection getVariables()
public RScriptParameter getScript()
public void setScript(RScriptParameter script)
public JIPipeTextAnnotationMergeMode getAnnotationMergeStrategy()
public void setAnnotationMergeStrategy(JIPipeTextAnnotationMergeMode annotationMergeStrategy)
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