Package adams.flow.transformer

Class SpectrumDbReader

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, 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.db.DatabaseConnectionUser, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, adams.flow.transformer.DataContainerDbReader<Spectrum>, SpectrumDatabaseReader, Serializable, Comparable
    public class SpectrumDbReader
extends adams.flow.transformer.AbstractDataContainerDbReader<Spectrum>
implements SpectrumDatabaseReader
    Loads a spectrum from the database and passes it on.

    Input/output:
    - accepts:
       java.lang.Integer
       java.lang.String
    - generates:
       knir.data.spectrum.Spectrum


    Valid options are: 

    -D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to
    the console (0 = off).
    default: 0
    minimum: 0
 
    -name <java.lang.String> (property: name)
    The name of the actor.
    default: SpectrumDbReader
 
    -annotation <adams.core.base.BaseText> (property: annotations)
    The annotations to attach to this actor.
    default:
 
    -skip (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded
    as it is.
 
    -raw (property: raw)
    If set to true, then the raw data is returned instead of being filtered
    through the global data container filter.
 
    -store (property: useStoreTable)
    If set to true, then the data will get read from the store table, otherwise
    the active one.
 
    -format <java.lang.String> (property: format)
    The format of spectrum to retrieve from the database (if sample IDs arrive
    at the input port).
    default: NIR
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected String m_Format
      what type of spectrum to retrieve from the database.

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

        m_Lenient, m_PostProcessor, m_Raw

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

        m_DatabaseConnection

      • 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.
      String formatTipText()
      Returns the tip text for this property.
      Class[] generates()
      Returns the class of objects that it generates.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      adams.db.DataProvider<Spectrum> getDataProvider()
      Returns the data provider to use for storing the container in the database.
      protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
      Returns the default database connection.
      String getFormat()
      Returns the format of spectrum to retrieve from the database.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      String globalInfo()
      Returns a string describing the object.
      protected String queryDatabase()
      Executes the flow item.
      void setFormat​(String value)
      Sets the format of spectrum to retrieve from the database.

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

        getLenient, getPostProcessor, getRaw, lenientTipText, postProcessorTipText, rawTipText, setLenient, setPostProcessor, setRaw

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

        doExecute, initialize, setUpDatabaseConnection, wrapUp

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

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

      • 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, 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, execute, 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, wrapUp

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

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

        currentInput, hasInput, input

      • 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.flow.core.OutputProducer

        hasPendingOutput, output

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Field Detail

      • m_Format

        protected String m_Format
        what type of spectrum to retrieve from the database.

    • Constructor Detail

      • SpectrumDbReader

        public SpectrumDbReader()

    • 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

      • 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.transformer.AbstractDataContainerDbReader<Spectrum>

      • 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

      • setFormat

        public void setFormat​(String value)
        Sets the format of spectrum to retrieve from the database.
        Parameters:
        value - the format

      • getFormat

        public String getFormat()
        Returns the format of spectrum to retrieve from the database.
        Returns:
        the format

      • formatTipText

        public String formatTipText()
        Returns the tip text for this property.
        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
        Overrides:
        accepts in class adams.flow.transformer.AbstractDataContainerDbReader<Spectrum>
        Returns:
        java.lang.Integer.class, java.lang.String.class

      • generates

        public Class[] generates()
        Returns the class of objects that it generates.
        Specified by:
        generates in interface adams.flow.core.OutputProducer
        Specified by:
        generates in class adams.flow.transformer.AbstractDataContainerDbReader<Spectrum>
        Returns:
        the data to retrieve from the database

      • getDataProvider

        public adams.db.DataProvider<Spectrum> getDataProvider()
        Returns the data provider to use for storing the container in the database.
        Specified by:
        getDataProvider in interface adams.flow.transformer.DataContainerDbReader<Spectrum>
        Returns:
        the data provider

      • getDefaultDatabaseConnection

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

      • getDatabaseConnection

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

      • queryDatabase

        protected String queryDatabase()
        Executes the flow item.
        Overrides:
        queryDatabase in class adams.flow.transformer.AbstractDataContainerDbReader<Spectrum>
        Returns:
        null if everything is fine, otherwise error message