Package adams.flow.transformer

Class MergeSampleDataFromMap

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.ClassCrossReference, adams.core.CleanUpHandler, adams.core.CrossReference, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.LenientModeSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.ShallowCopySupporter<adams.flow.core.Actor>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.core.VariablesInspectionHandler, adams.event.VariableChangeListener, adams.flow.control.StorageUser, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class MergeSampleDataFromMap
extends adams.flow.transformer.AbstractTransformer
implements adams.flow.control.StorageUser, adams.core.ClassCrossReference, adams.core.LenientModeSupporter
    Merges the passing through spectrum/sample data objects with the referenced map of sample data objects in storage (the map uses the sample ID as key).

    See also:
    adams.data.conversion.SampleDataArrayToMap

    Input/output:
    - accepts:
       adams.data.spectrum.Spectrum
       adams.data.sampledata.SampleData
    - generates:
       adams.data.spectrum.Spectrum
       adams.data.sampledata.SampleData


    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -name <java.lang.String> (property: name)
    The name of the actor.
    default: MergeSampleDataFromMap
 
    -annotation <adams.core.base.BaseAnnotation> (property: annotations)
    The annotations to attach to this actor.
    default:
 
    -skip <boolean> (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded
    as it is.
    default: false
 
    -stop-flow-on-error <boolean> (property: stopFlowOnError)
    If set to true, the flow execution at this level gets stopped in case this
    actor encounters an error; the error gets propagated; useful for critical
    actors.
    default: false
 
    -silent <boolean> (property: silent)
    If enabled, then no errors are output in the console; Note: the enclosing
    actor handler must have this enabled as well.
    default: false
 
    -storage-name <adams.flow.control.StorageName> (property: storageName)
    The name of the stored map containing the sample ID <-> sample data object
    mapping.
    default: storage
 
    -merge <REPLACE|MERGE_CURRENT_WITH_OTHER|MERGE_OTHER_WITH_CURRENT> (property: merge)
    Determines how to perform the merge.
    default: MERGE_CURRENT_WITH_OTHER
 
    -lenient <boolean> (property: lenient)
    If enabled, missing IDs in the map won't cause an error.
    default: false
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected boolean m_Lenient
      whether to be lenient.
      protected adams.flow.transformer.MergeReport.MergeType m_Merge
      the merge type.
      protected adams.flow.control.StorageName m_StorageName
      the name of the stored value.

      • Fields inherited from class adams.flow.transformer.AbstractTransformer

        BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

      • Fields inherited from class adams.flow.core.AbstractActor

        m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

      • Fields inherited from interface adams.flow.core.Actor

        FILE_EXTENSION, FILE_EXTENSION_GZ

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Class[] accepts()
      Returns the class that the consumer accepts.
      void defineOptions()
      Adds options to the internal list of options.
      protected String doExecute()
      Executes the flow item.
      Class[] generates()
      Returns the class of objects that it generates.
      Class[] getClassCrossReferences()
      Returns the cross-referenced classes.
      boolean getLenient()
      Returns whether to use lenient mode (missing IDs in map won't cause error).
      adams.flow.transformer.MergeReport.MergeType getMerge()
      Returns the merge type.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      adams.flow.control.StorageName getStorageName()
      Returns the name of the stored map with the sample data objects.
      String globalInfo()
      Returns a string describing the object.
      boolean isUsingStorage()
      Returns whether storage items are being used.
      String lenientTipText()
      Returns the tip text for this property.
      String mergeTipText()
      Returns the tip text for this property.
      void setLenient​(boolean value)
      Sets whether to use lenient mode (missing IDs in map won't cause error).
      void setMerge​(adams.flow.transformer.MergeReport.MergeType value)
      Sets the merge type.
      void setStorageName​(adams.flow.control.StorageName value)
      Sets the name of the stored map with the sample data objects.
      String storageNameTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.flow.transformer.AbstractTransformer

        backupState, currentInput, execute, hasInput, hasPendingOutput, input, output, postExecute, restoreState, wrapUp

      • Methods inherited from class adams.flow.core.AbstractActor

        annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, preExecute, pruneBackup, pruneBackup, reset, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, silentTipText, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

      • Methods inherited from class adams.core.logging.LoggingObject

        getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

      • Methods inherited from interface adams.flow.core.Actor

        cleanUp, compareTo, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, sizeOf, stopExecution, stopExecution, toCommandLine, variableChanged

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel, setLoggingLevel

      • Methods inherited from interface adams.core.logging.LoggingSupporter

        getLogger, isLoggingEnabled

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Field Detail

      • m_StorageName

        protected adams.flow.control.StorageName m_StorageName
        the name of the stored value.

      • m_Merge

        protected adams.flow.transformer.MergeReport.MergeType m_Merge
        the merge type.

      • m_Lenient

        protected boolean m_Lenient
        whether to be lenient.

    • Constructor Detail

      • MergeSampleDataFromMap

        public MergeSampleDataFromMap()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • getClassCrossReferences

        public Class[] getClassCrossReferences()
        Returns the cross-referenced classes.
        Specified by:
        getClassCrossReferences in interface adams.core.ClassCrossReference
        Returns:
        the classes

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.flow.core.AbstractActor

      • setStorageName

        public void setStorageName​(adams.flow.control.StorageName value)
        Sets the name of the stored map with the sample data objects.
        Parameters:
        value - the name

      • getStorageName

        public adams.flow.control.StorageName getStorageName()
        Returns the name of the stored map with the sample data objects.
        Returns:
        the name

      • storageNameTipText

        public String storageNameTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setMerge

        public void setMerge​(adams.flow.transformer.MergeReport.MergeType value)
        Sets the merge type.
        Parameters:
        value - the merge

      • getMerge

        public adams.flow.transformer.MergeReport.MergeType getMerge()
        Returns the merge type.
        Returns:
        the merge

      • mergeTipText

        public String mergeTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setLenient

        public void setLenient​(boolean value)
        Sets whether to use lenient mode (missing IDs in map won't cause error).
        Specified by:
        setLenient in interface adams.core.LenientModeSupporter
        Parameters:
        value - true if to turn on lenient mode

      • getLenient

        public boolean getLenient()
        Returns whether to use lenient mode (missing IDs in map won't cause error).
        Specified by:
        getLenient in interface adams.core.LenientModeSupporter
        Returns:
        true if lenient mode on

      • lenientTipText

        public String lenientTipText()
        Returns the tip text for this property.
        Specified by:
        lenientTipText in interface adams.core.LenientModeSupporter
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Returns:
        the Class of objects that can be processed

      • generates

        public Class[] generates()
        Returns the class of objects that it generates.
        Specified by:
        generates in interface adams.flow.core.OutputProducer
        Returns:
        the Class of the generated tokens

      • isUsingStorage

        public boolean isUsingStorage()
        Returns whether storage items are being used.
        Specified by:
        isUsingStorage in interface adams.flow.control.StorageUser
        Returns:
        true if storage items are used

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the actor, which will be displayed in the GUI.
        Specified by:
        getQuickInfo in interface adams.flow.core.Actor
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class adams.flow.core.AbstractActor
        Returns:
        null if no info available, otherwise short string

      • doExecute

        protected String doExecute()
        Executes the flow item.
        Specified by:
        doExecute in class adams.flow.core.AbstractActor
        Returns:
        null if everything is fine, otherwise error message