Package adams.flow.source

Class OrphanedSampleDataIdSupplier

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.ArrayProvider, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, 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.db.DatabaseConnectionUser, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ArrayProvider, adams.flow.core.ErrorHandler, adams.flow.core.OutputProducer, Serializable, Comparable
    public class OrphanedSampleDataIdSupplier
extends adams.flow.source.AbstractDbArrayProvider
    Retrieves sample IDs of sample data that have no spectra associated.

    Input/output:
    - generates:
       java.lang.String


    -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: OrphanedSampleDataIdSupplier
 
    -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
 
    -output-array <boolean> (property: outputArray)
    If enabled, outputs the sample IDs as array rather than one by one.
    default: false
 
    -conditions <adams.db.OrphanedSampleDataConditions> (property: conditions)
    The conditions for retrieving the orphaned sample IDs.
    default: adams.db.OrphanedSampleDataConditions
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected OrphanedSampleDataConditions m_Conditions
      the conditions for retrieving the orphaned IDs.

      • Fields inherited from class adams.flow.source.AbstractDbArrayProvider

        m_DatabaseConnection

      • Fields inherited from class adams.flow.source.AbstractArrayProvider

        m_Index, m_OutputArray, m_Queue

      • 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
      String conditionsTipText()
      Returns the tip text for this property.
      void defineOptions()
      Adds options to the internal list of options.
      OrphanedSampleDataConditions getConditions()
      Returns whether to output the items as array or as single strings.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      protected OrphanedSampleDataConditions getDefaultConditions()
      Returns the conditions container to use for retrieving the spectra.
      protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
      Returns the default database connection.
      protected Class getItemClass()
      Returns the based class of the items.
      String globalInfo()
      Returns a string describing the object.
      String outputArrayTipText()
      Returns the tip text for this property.
      protected String queryDatabase()
      Performs the actual database query.
      void setConditions​(OrphanedSampleDataConditions value)
      Sets whether to output the items as array or as single strings.

      • Methods inherited from class adams.flow.source.AbstractDbArrayProvider

        doExecute, initialize, setUpDatabaseConnection, wrapUp

      • Methods inherited from class adams.flow.source.AbstractArrayProvider

        generates, getOutputArray, hasPendingOutput, output, preExecute, reset, setOutputArray

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

        annotationsTipText, backupState, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, execute, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getQuickInfo, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, postExecute, pruneBackup, pruneBackup, restoreState, 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, execute, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getQuickInfo, 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

    • Constructor Detail

      • OrphanedSampleDataIdSupplier

        public OrphanedSampleDataIdSupplier()

    • 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

      • getItemClass

        protected Class getItemClass()
        Returns the based class of the items.
        Specified by:
        getItemClass in class adams.flow.source.AbstractArrayProvider
        Returns:
        the class

      • outputArrayTipText

        public String outputArrayTipText()
        Returns the tip text for this property.
        Specified by:
        outputArrayTipText in interface adams.core.ArrayProvider
        Specified by:
        outputArrayTipText in interface adams.flow.core.ArrayProvider
        Specified by:
        outputArrayTipText in class adams.flow.source.AbstractArrayProvider
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • 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.source.AbstractArrayProvider

      • getDefaultConditions

        protected OrphanedSampleDataConditions getDefaultConditions()
        Returns the conditions container to use for retrieving the spectra.
        Returns:
        the conditions

      • setConditions

        public void setConditions​(OrphanedSampleDataConditions value)
        Sets whether to output the items as array or as single strings.
        Parameters:
        value - the conditions

      • getConditions

        public OrphanedSampleDataConditions getConditions()
        Returns whether to output the items as array or as single strings.
        Returns:
        the conditions

      • conditionsTipText

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

      • getDefaultDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
        Returns the default database connection.
        Specified by:
        getDefaultDatabaseConnection in class adams.flow.source.AbstractDbArrayProvider
        Returns:
        the default database connection

      • getDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
        Determines the database connection in the flow.
        Specified by:
        getDatabaseConnection in class adams.flow.source.AbstractDbArrayProvider
        Returns:
        the database connection to use

      • queryDatabase

        protected String queryDatabase()
        Performs the actual database query.
        Specified by:
        queryDatabase in class adams.flow.source.AbstractDbArrayProvider
        Returns:
        null if everything is fine, otherwise error message