org.oncoblocks.centromere.core.dataimport.pipeline

Class ImportJobRunner

java.lang.Object

org.oncoblocks.centromere.core.dataimport.pipeline.ImportJobRunner

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class ImportJobRunner
extends Object
implements org.springframework.context.ApplicationContextAware

Configures and runs a data import job, as defined by a ImportJob object.

Author:

woemler

Constructor Summary

Constructors

Constructor and Description
ImportJobRunner()
ImportJobRunner(org.springframework.context.ApplicationContext applicationContext)

Method Summary

Modifier and Type	Method and Description
protected void	configurationCheck() Checks that all necessary configurations have taken place place before the import job runs.
protected void	configureDataSetManager()
protected void	configureDataTypeManager() Creates and populates a DataTypeManager to handle mapping data types to RecordProcessor beans.
org.springframework.context.ApplicationContext	getApplicationContext()
protected Object	getDataSetId(DataSetMetadata dataSet, InputFile inputFile) Returns a data set identifier based upon its DataSetMetadata reference.
DataSetManager	getDataSetManager()
DataTypeManager	getDataTypeManager()
ImportJob	getImportJob()
static org.slf4j.Logger	getLogger()
protected RecordProcessor	getProcessorInstanceByDataType(String name) Returns reference to existing RecordProcessor bean, given an associated data type.
protected void	jobSetup() Runs the required configuration before the import job executes.
protected ImportOptions	mergeImportOptions(ImportOptions fileOptions, ImportOptions jobOptions) Merges the data set-level ImportOptions with the file-level options.
protected void	processDataSet(DataSetMetadata dataSet, InputFile inputFile) Processes the current data set record.
void	runImport() Executes the import pipeline and processes all of the files in the ImportJob.
void	setApplicationContext(org.springframework.context.ApplicationContext applicationContext)
void	setImportJob(ImportJob importJob)
protected void	validateImportJob() Checks that the submitted ImportJob object contains all the required components.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImportJobRunner

public ImportJobRunner()

ImportJobRunner

public ImportJobRunner(org.springframework.context.ApplicationContext applicationContext)

Method Detail

runImport

public void runImport()
               throws DataImportException

Executes the import pipeline and processes all of the files in the ImportJob.

Throws:

DataImportException

mergeImportOptions

protected ImportOptions mergeImportOptions(ImportOptions fileOptions,
                                           ImportOptions jobOptions)

Merges the data set-level ImportOptions with the file-level options. File-level options are given precendence over data set-level options, in case a file requires special handling.

Parameters:

fileOptions -

jobOptions -

Returns:

jobSetup

protected void jobSetup()

Runs the required configuration before the import job executes.

processDataSet

protected void processDataSet(DataSetMetadata dataSet,
                              InputFile inputFile)
                       throws DataImportException

Processes the current data set record. Should be overridden to handle record creation or manipulation.

Parameters:

dataSet -

Throws:

DataImportException

getDataSetId

protected Object getDataSetId(DataSetMetadata dataSet,
                              InputFile inputFile)

Returns a data set identifier based upon its DataSetMetadata reference. This method should be overridden along with processDataSet(DataSetMetadata, InputFile), to handle implementation-specific data sets.

Parameters:

dataSet -

Returns:

configurationCheck

protected void configurationCheck()
                           throws DataImportException

Checks that all necessary configurations have taken place place before the import job runs.

Throws:

DataImportException

validateImportJob

protected void validateImportJob()
                          throws DataImportException

Checks that the submitted ImportJob object contains all the required components.

Throws:

DataImportException

configureDataTypeManager

protected void configureDataTypeManager()

Creates and populates a DataTypeManager to handle mapping data types to RecordProcessor beans.

configureDataSetManager

protected void configureDataSetManager()

getProcessorInstanceByDataType

protected RecordProcessor getProcessorInstanceByDataType(String name)
                                                  throws DataImportException

Returns reference to existing RecordProcessor bean, given an associated data type. Throws an exception of the data type is not registered in the configuration, or if the bean has not already been created.

Parameters:

name -

Returns:

Throws:

DataImportException

getImportJob

public ImportJob getImportJob()

getApplicationContext

public org.springframework.context.ApplicationContext getApplicationContext()

getDataTypeManager

public DataTypeManager getDataTypeManager()

getDataSetManager

public DataSetManager getDataSetManager()

getLogger

public static org.slf4j.Logger getLogger()

setImportJob

public void setImportJob(ImportJob importJob)
                  throws DataImportException

Throws:

DataImportException

setApplicationContext

public void setApplicationContext(org.springframework.context.ApplicationContext applicationContext)

Specified by:

setApplicationContext in interface org.springframework.context.ApplicationContextAware