org.molgenis.omx.biobankconnect.ontologyannotator

Class AsyncOntologyAnnotator

java.lang.Object

org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

All Implemented Interfaces:

OntologyAnnotator, org.springframework.beans.factory.InitializingBean

public class AsyncOntologyAnnotator
extends Object
implements OntologyAnnotator, org.springframework.beans.factory.InitializingBean

Constructor Summary

Constructors

Constructor and Description
AsyncOntologyAnnotator()

Method Summary

Methods

Modifier and Type	Method and Description
void	afterPropertiesSet()
void	annotate(Integer dataSetId, List<String> documentTypes)
List<OntologyTerm>	annotateDataItem(String documentType, ObservableFeature feature, String description, org.tartarus.snowball.ext.PorterStemmer stemmer)
ObservableFeature	copyObject(ObservableFeature feature)
float	finishedPercentage()
void	initComplete()
boolean	isComplete()
boolean	isRunning()
void	removeAnnotations(Integer dataSetId)
List<String>	searchAllOntologies()
void	setSearchService(SearchService searchService)
QueryRule[]	toNestedQuery(List<QueryRule> rules)
void	updateIndex(UpdateIndexRequest request)
String	uploadFeatures(File uploadFile, String datasetName)

Methods inherited from class java.lang.Object

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

Constructor Detail

AsyncOntologyAnnotator

public AsyncOntologyAnnotator()

Method Detail

setSearchService

@Autowired
public void setSearchService(SearchService searchService)

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

isRunning

public boolean isRunning()

Specified by:

isRunning in interface OntologyAnnotator

isComplete

public boolean isComplete()

Specified by:

isComplete in interface OntologyAnnotator

initComplete

public void initComplete()

Specified by:

initComplete in interface OntologyAnnotator

uploadFeatures

@Transactional
public String uploadFeatures(File uploadFile,
                                  String datasetName)
                      throws IOException

Specified by:

uploadFeatures in interface OntologyAnnotator

Throws:

IOException

removeAnnotations

@Transactional
public void removeAnnotations(Integer dataSetId)

Specified by:

removeAnnotations in interface OntologyAnnotator

copyObject

public ObservableFeature copyObject(ObservableFeature feature)

annotate

@Transactional
public void annotate(Integer dataSetId,
                          List<String> documentTypes)

Specified by:

annotate in interface OntologyAnnotator

searchAllOntologies

public List<String> searchAllOntologies()

updateIndex

public void updateIndex(UpdateIndexRequest request)

Specified by:

updateIndex in interface OntologyAnnotator

annotateDataItem

public List<OntologyTerm> annotateDataItem(String documentType,
                                  ObservableFeature feature,
                                  String description,
                                  org.tartarus.snowball.ext.PorterStemmer stemmer)

toNestedQuery

public QueryRule[] toNestedQuery(List<QueryRule> rules)

finishedPercentage

public float finishedPercentage()

Specified by:

finishedPercentage in interface OntologyAnnotator