org.molgenis.omx.biobankconnect.ontologymatcher

Class AsyncOntologyMatcher

java.lang.Object

org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

All Implemented Interfaces:

OntologyMatcher, org.springframework.beans.factory.InitializingBean

public class AsyncOntologyMatcher
extends Object
implements OntologyMatcher, org.springframework.beans.factory.InitializingBean

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	AsyncOntologyMatcher.OntologyTermContainer

Field Summary

Fields

Modifier and Type	Field and Description
static String	PROTOCOL_IDENTIFIER
static String	STORE_MAPPING_ALGORITHM_SCRIPT
static String	STORE_MAPPING_CONFIRM_MAPPING
static String	STORE_MAPPING_FEATURE
static String	STORE_MAPPING_MAPPED_FEATURE
static String	STORE_MAPPING_SCORE

Constructor Summary

Constructors

Constructor and Description
AsyncOntologyMatcher()

Method Summary

Methods

Modifier and Type	Method and Description
void	afterPropertiesSet()
boolean	checkExistingMappings(String dataSetIdentifier, DataService dataService)
static String	createMappingDataSetIdentifier(String userName, Integer targetDataSetId, Integer sourceDataSetId)
void	deleteDocumentByIds(String documentType, List<String> documentIds)
SearchResult	generateMapping(String userName, Integer featureId, Integer targetDataSetId, Integer sourceDataSetId) This method is to generate a list of candidate mappings for the chosen feature by using ElasticSearch based on the information from ontology terms
boolean	isRunning()
void	match(String userName, Integer selectedDataSetId, List<Integer> dataSetIdsToMatch, Integer featureId)
Integer	matchPercentage(String currentUserName)
void	setSearchService(SearchService searchService)
Map<String,String>	updateScript(String userName, OntologyMatcherRequest request)

Methods inherited from class java.lang.Object

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

Field Detail

PROTOCOL_IDENTIFIER

public static final String PROTOCOL_IDENTIFIER

See Also:

Constant Field Values

STORE_MAPPING_FEATURE

public static final String STORE_MAPPING_FEATURE

See Also:

Constant Field Values

STORE_MAPPING_MAPPED_FEATURE

public static final String STORE_MAPPING_MAPPED_FEATURE

See Also:

Constant Field Values

STORE_MAPPING_CONFIRM_MAPPING

public static final String STORE_MAPPING_CONFIRM_MAPPING

See Also:

Constant Field Values

STORE_MAPPING_SCORE

public static final String STORE_MAPPING_SCORE

See Also:

Constant Field Values

STORE_MAPPING_ALGORITHM_SCRIPT

public static final String STORE_MAPPING_ALGORITHM_SCRIPT

See Also:

Constant Field Values

Constructor Detail

AsyncOntologyMatcher

public AsyncOntologyMatcher()

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 OntologyMatcher

matchPercentage

public Integer matchPercentage(String currentUserName)

Specified by:

matchPercentage in interface OntologyMatcher

deleteDocumentByIds

public void deleteDocumentByIds(String documentType,
                       List<String> documentIds)

Specified by:

deleteDocumentByIds in interface OntologyMatcher

match

@Transactional
public void match(String userName,
                       Integer selectedDataSetId,
                       List<Integer> dataSetIdsToMatch,
                       Integer featureId)

Specified by:

match in interface OntologyMatcher

generateMapping

@Transactional
public SearchResult generateMapping(String userName,
                                         Integer featureId,
                                         Integer targetDataSetId,
                                         Integer sourceDataSetId)

This method is to generate a list of candidate mappings for the chosen feature by using ElasticSearch based on the information from ontology terms

Specified by:

generateMapping in interface OntologyMatcher

checkExistingMappings

public boolean checkExistingMappings(String dataSetIdentifier,
                            DataService dataService)

Specified by:

checkExistingMappings in interface OntologyMatcher

updateScript

@Transactional
public Map<String,String> updateScript(String userName,
                                            OntologyMatcherRequest request)

Specified by:

updateScript in interface OntologyMatcher

createMappingDataSetIdentifier

public static String createMappingDataSetIdentifier(String userName,
                                    Integer targetDataSetId,
                                    Integer sourceDataSetId)