Package adams.flow.transformer

Class BulkSampleDataDbWriter

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, 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.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, SampleDataDatabaseWriter, Serializable, Comparable
    public class BulkSampleDataDbWriter
extends adams.flow.transformer.AbstractDbTransformer
implements SampleDataDatabaseWriter
    Writes sample data to the database and outputs whether the operation was successful.

    Input/output:
    - accepts:
       adams.data.sampledata.SampleData[]
       adams.data.spectrum.Spectrum[]
    - generates:
       java.lang.Boolean


    -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: BulkSampleDataDbWriter
 
    -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
 
    -data-type <S|N|B|U> [-data-type ...] (property: dataTypes)
    The data types to import.
    default:
 
    -skip-fields <boolean> (property: skipFields)
    If enabled, the supplied regular expression is used for identifying fields
    to skip (name + data type, e.g., 'blah[N]').
    default: false
 
    -skip-fields-regexp <adams.core.base.BaseRegExp> (property: skipFieldsRegExp)
    The regular expression for identifying fields to skip (if enabled).
    default: (Parent ID|Sample ID|Sample Type|Format|Insert Timestamp|Instrument|Source).*
    more: https://docs.oracle.com/javase/tutorial/essential/regex/
    https://docs.oracle.com/javase/8/docs/api/java/util/regex/Pattern.html
 
    -batch-size <int> (property: batchSize)
    The batch size to use for the bulk operation.
    default: 1000
    minimum: 1
 
    -auto-commit <boolean> (property: autoCommit)
    If disabled, auto-commit gets turned off for the bulk update, which may
    impact other transactions; use with caution.
    default: true
 
    -new-connection <boolean> (property: newConnection)
    If enabled, a new database connection is opened (and then closed) just for
    this operation; use this when turning off auto-commit.
    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_AutoCommit
      whether to use auto-commit.
      protected int m_BatchSize
      the number of records in a batch.
      protected adams.data.report.DataType[] m_DataTypes
      the types of data to import.
      protected boolean m_NewConnection
      whether to use a new database connection.
      protected SampleDataF m_SampleDataF
      the instance that is currently running a bulk store.
      protected boolean m_SkipFields
      whether to skip fields.
      protected adams.core.base.BaseRegExp m_SkipFieldsRegExp
      the fields to ignore.

      • 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.
      String autoCommitTipText()
      Returns the tip text for this property.
      String batchSizeTipText()
      Returns the tip text for this property.
      String dataTypesTipText()
      Returns the tip text for this property.
      void defineOptions()
      Adds options to the internal list of options.
      Class[] generates()
      Returns the class of objects that it generates.
      boolean getAutoCommit()
      Returns whether to use auto-commit for bulk transactions.
      int getBatchSize()
      Returns the batch size in use.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      adams.data.report.DataType[] getDataTypes()
      Returns the data types to import
      protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
      Returns the default database connection.
      boolean getNewConnection()
      Returns whether to use a new connection for this update.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      boolean getSkipFields()
      Returns whether to skip fields.
      adams.core.base.BaseRegExp getSkipFieldsRegExp()
      Returns the regular expression for identifying fields to skip (if enabled).
      String globalInfo()
      Returns a string describing the object.
      String newConnectionTipText()
      Returns the tip text for this property.
      protected String queryDatabase()
      Performs the actual database query.
      void setAutoCommit​(boolean value)
      Sets whether to use auto-commit for bulk transaction.
      void setBatchSize​(int value)
      Sets the batch size to use.
      void setDataTypes​(adams.data.report.DataType[] value)
      Sets the data types to import.
      void setNewConnection​(boolean value)
      Sets whether to use a new connection for this update.
      void setSkipFields​(boolean value)
      Sets whether to skip fields.
      void setSkipFieldsRegExp​(adams.core.base.BaseRegExp value)
      Sets the regular expression for identifying fields to skip (if enabled).
      String skipFieldsRegExpTipText()
      Returns the tip text for this property.
      String skipFieldsTipText()
      Returns the tip text for this property.
      void stopExecution()
      Stops the execution.
      void wrapUp()
      Cleans up after the execution has finished.

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

        doExecute, initialize, setUpDatabaseConnection

      • 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, 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, toCommandLine, variableChanged

      • 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_DataTypes

        protected adams.data.report.DataType[] m_DataTypes
        the types of data to import.

      • m_SkipFields

        protected boolean m_SkipFields
        whether to skip fields.

      • m_SkipFieldsRegExp

        protected adams.core.base.BaseRegExp m_SkipFieldsRegExp
        the fields to ignore.

      • m_BatchSize

        protected int m_BatchSize
        the number of records in a batch.

      • m_AutoCommit

        protected boolean m_AutoCommit
        whether to use auto-commit.

      • m_NewConnection

        protected boolean m_NewConnection
        whether to use a new database connection.

      • m_SampleDataF

        protected transient SampleDataF m_SampleDataF
        the instance that is currently running a bulk store.

    • Constructor Detail

      • BulkSampleDataDbWriter

        public BulkSampleDataDbWriter()

    • 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.core.AbstractActor

      • setDataTypes

        public void setDataTypes​(adams.data.report.DataType[] value)
        Sets the data types to import.
        Parameters:
        value - the data types

      • getDataTypes

        public adams.data.report.DataType[] getDataTypes()
        Returns the data types to import
        Returns:
        the data types

      • dataTypesTipText

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

      • setSkipFields

        public void setSkipFields​(boolean value)
        Sets whether to skip fields.
        Parameters:
        value - true if to skip fields

      • getSkipFields

        public boolean getSkipFields()
        Returns whether to skip fields.
        Returns:
        true if to skip fields

      • skipFieldsTipText

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

      • setSkipFieldsRegExp

        public void setSkipFieldsRegExp​(adams.core.base.BaseRegExp value)
        Sets the regular expression for identifying fields to skip (if enabled).
        Parameters:
        value - the expression

      • getSkipFieldsRegExp

        public adams.core.base.BaseRegExp getSkipFieldsRegExp()
        Returns the regular expression for identifying fields to skip (if enabled).
        Returns:
        the expression

      • skipFieldsRegExpTipText

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

      • setBatchSize

        public void setBatchSize​(int value)
        Sets the batch size to use.
        Parameters:
        value - the size

      • getBatchSize

        public int getBatchSize()
        Returns the batch size in use.
        Returns:
        the size

      • batchSizeTipText

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

      • setAutoCommit

        public void setAutoCommit​(boolean value)
        Sets whether to use auto-commit for bulk transaction. May impact other transactions, therefore use with caution!
        Parameters:
        value - true if to use auto-commit

      • getAutoCommit

        public boolean getAutoCommit()
        Returns whether to use auto-commit for bulk transactions. May impact other transactions, therefore use with caution!
        Returns:
        true if to use auto-commit

      • autoCommitTipText

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

      • setNewConnection

        public void setNewConnection​(boolean value)
        Sets whether to use a new connection for this update. Use when autoCommit is off.
        Parameters:
        value - true if to use new connection

      • getNewConnection

        public boolean getNewConnection()
        Returns whether to use a new connection for this update. Use when autoCommit is off.
        Returns:
        true if to use new connection

      • newConnectionTipText

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

      • 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

      • getDefaultDatabaseConnection

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

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Returns:
        the report class

      • 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

      • queryDatabase

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

      • stopExecution

        public void stopExecution()
        Stops the execution. No message set.
        Specified by:
        stopExecution in interface adams.flow.core.Actor
        Specified by:
        stopExecution in interface adams.core.Stoppable
        Overrides:
        stopExecution in class adams.flow.core.AbstractActor

      • wrapUp

        public void wrapUp()
        Cleans up after the execution has finished. Graphical output is left untouched.
        Specified by:
        wrapUp in interface adams.flow.core.Actor
        Overrides:
        wrapUp in class adams.flow.transformer.AbstractDbTransformer