Package org.openforis.collect.io.metadata.species

Class SpeciesImportTask

java.lang.Object

org.openforis.concurrency.Worker

org.openforis.concurrency.Task

org.openforis.collect.io.metadata.ReferenceDataImportTask<ParsingError>

org.openforis.collect.io.metadata.species.SpeciesImportTask

@Component
@Scope("prototype")
public class SpeciesImportTask
extends ReferenceDataImportTask<ParsingError>

Nested Class Summary

Nested classes/interfaces inherited from class org.openforis.concurrency.Worker

org.openforis.concurrency.Worker.Status

Constructor Summary

Constructors

Constructor	Description
SpeciesImportTask()

Method Summary

Modifier and Type	Method	Description
protected void	checkDuplicates(SpeciesLine line, String code, Integer taxonId)
protected void	checkDuplicateScientificName(SpeciesLine line, Taxon parent, String normalizedScientificName)
protected Taxon	createTaxon(SpeciesLine line, Taxon.TaxonRank rank, Taxon parent)
protected Taxon	createTaxon(SpeciesLine line, Taxon.TaxonRank rank, Taxon parent, String normalizedScientificName)
protected Taxon	createTaxonFamily(SpeciesLine line)
protected Taxon	createTaxonGenus(SpeciesLine line)
protected Taxon	createTaxonSpecies(SpeciesLine line)
protected void	execute()
protected void	initializeInternalVariables()
protected void	parseTaxonCSVLines(File file)
protected void	persistTaxa()
protected boolean	processLine(SpeciesLine line, Taxon.TaxonRank rank)
protected void	processLines()
protected void	processVernacularNames(SpeciesLine line, Taxon taxon)
void	setCsvFileOptions(CSVFileOptions csvFileOptions)
void	setFile(File file)
void	setOverwriteAll(boolean overwriteAll)
void	setSpeciesManager(SpeciesManager speciesManager)
void	setSurvey(CollectSurvey survey)
void	setSurveyManager(SurveyManager surveyManager)
void	setTaxonomyId(int taxonomyId)
protected void	throwDuplicateRowParsingException(SpeciesLine line, SpeciesFileColumn column, TaxonTree.Node foundNode)
protected void	validateInput()

Methods inherited from class org.openforis.collect.io.metadata.ReferenceDataImportTask

addParsingError, addParsingError, addProcessedRow, getErrors, getProcessedRows, getRowsInError, getSkippedRows, hasErrors, isRowInError, isRowProcessed

Methods inherited from class org.openforis.concurrency.Task

beforeExecuteInternal, countTotalItems, getProcessedItems, getProgressPercent, getRemainingItems, getSkippedItems, getTotalItems, incrementProcessedItems, incrementSkippedItems, setProcessedItems, setTotalItems

Methods inherited from class org.openforis.concurrency.Worker

abort, addStatusChangeListener, afterExecute, afterExecuteInternal, beforeExecute, changeStatus, createInternalVariables, destroy, getDuration, getEndTime, getErrorMessage, getErrorMessageArgs, getId, getLastException, getName, getResult, getStartTime, getStatus, getWeight, initialize, isAborted, isCompleted, isEnded, isFailed, isPending, isRunning, logDebug, logError, logInfo, logWarning, notifyAllStatusChangeListeners, onAborted, onCompleted, onEnd, onFailed, prepareResult, release, removeStatusChangeListener, run, setErrorMessage, setErrorMessageArgs, setLastException, setResult, setWeight, waitFor

Methods inherited from class java.lang.Object

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

Constructor Details

SpeciesImportTask

public SpeciesImportTask()

Method Details

initializeInternalVariables

protected void initializeInternalVariables()
                                    throws Throwable

Overrides:

initializeInternalVariables in class org.openforis.concurrency.Worker

Throws:

Throwable

validateInput

protected void validateInput()
                      throws Throwable

Overrides:

validateInput in class org.openforis.concurrency.Worker

Throws:

Throwable

execute

protected void execute()
                throws Throwable

Specified by:

execute in class org.openforis.concurrency.Worker

Throws:

Throwable

parseTaxonCSVLines

protected void parseTaxonCSVLines(File file)

processLines

protected void processLines()

processLine

protected boolean processLine(SpeciesLine line,
 Taxon.TaxonRank rank)
                       throws ParsingException

Throws:

ParsingException

processVernacularNames

protected void processVernacularNames(SpeciesLine line,
 Taxon taxon)

persistTaxa

protected void persistTaxa()
                    throws SurveyStoreException

Throws:

SurveyStoreException

createTaxonFamily

protected Taxon createTaxonFamily(SpeciesLine line)
                           throws ParsingException

Throws:

ParsingException

createTaxonGenus

protected Taxon createTaxonGenus(SpeciesLine line)
                          throws ParsingException

Throws:

ParsingException

createTaxonSpecies

protected Taxon createTaxonSpecies(SpeciesLine line)
                            throws ParsingException

Throws:

ParsingException

createTaxon

protected Taxon createTaxon(SpeciesLine line,
 Taxon.TaxonRank rank,
 Taxon parent)
                     throws ParsingException

Throws:

ParsingException

createTaxon

protected Taxon createTaxon(SpeciesLine line,
 Taxon.TaxonRank rank,
 Taxon parent,
 String normalizedScientificName)
                     throws ParsingException

Throws:

ParsingException

checkDuplicates

protected void checkDuplicates(SpeciesLine line,
 String code,
 Integer taxonId)
                        throws ParsingException

Throws:

ParsingException

checkDuplicateScientificName

protected void checkDuplicateScientificName(SpeciesLine line,
 Taxon parent,
 String normalizedScientificName)
                                     throws ParsingException

Throws:

ParsingException

throwDuplicateRowParsingException

protected void throwDuplicateRowParsingException(SpeciesLine line,
 SpeciesFileColumn column,
 TaxonTree.Node foundNode)
                                          throws ParsingException

Throws:

ParsingException

setSpeciesManager

public void setSpeciesManager(SpeciesManager speciesManager)

setSurveyManager

public void setSurveyManager(SurveyManager surveyManager)

setSurvey

public void setSurvey(CollectSurvey survey)

setTaxonomyId

public void setTaxonomyId(int taxonomyId)

setFile

public void setFile(File file)

setCsvFileOptions

public void setCsvFileOptions(CSVFileOptions csvFileOptions)

setOverwriteAll

public void setOverwriteAll(boolean overwriteAll)