A C D E G H I L M N O P R S T U V

A

AdaptedCsvRepository - Class in org.molgenis.ontology.matching

AdaptedCsvRepository(String, CsvRepository) - Constructor for class org.molgenis.ontology.matching.AdaptedCsvRepository

addEntityMeta(EntityMetaData) - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

ALLOWED_IDENTIFIER - Static variable in class org.molgenis.ontology.matching.AdaptedCsvRepository

C

canImport(File, RepositoryCollection) - Method in class org.molgenis.ontology.importer.OntologyImportService

close() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

CODE_SYSTEM - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

D

DATA_CREATED - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

deleteResult(String) - Method in class org.molgenis.ontology.controller.OntologyServiceController

doImport(RepositoryCollection, DatabaseAction) - Method in class org.molgenis.ontology.importer.OntologyImportService

download(String, HttpServletResponse, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

E

ENTITY_NAME - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.model.OntologyMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermSynonymMetaData

G

getAllOntologies() - Method in class org.molgenis.ontology.controller.OntologyManagerController

getCapabilities() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getCurrentJob(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getEntityMetaData() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getEntityName() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getEntityNames() - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

getEntityPager() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getFilterQuery() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getMustChangeEntityName() - Method in class org.molgenis.ontology.importer.OntologyImportService

getName() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getName() - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

getNodePath() - Method in class org.molgenis.ontology.utils.OWLClassContainer

getOntologyIri() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getOntologyTermSynonyms(Map<String, Object>) - Method in class org.molgenis.ontology.controller.OntologyServiceController

getOrder() - Method in class org.molgenis.ontology.importer.OntologyImportService

getOwlClass() - Method in class org.molgenis.ontology.utils.OWLClassContainer

getPackageInstance() - Static method in class org.molgenis.ontology.model.OntologyPackage

getPercentage(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getRepository(String) - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

getSearchResult() - Method in class org.molgenis.ontology.response.OntologyServiceBatchResponse

getSupportedDatabaseActions() - Method in class org.molgenis.ontology.importer.OntologyImportService

getSupportedFileExtensions() - Method in class org.molgenis.ontology.importer.OntologyImportService

getTerm() - Method in class org.molgenis.ontology.response.OntologyServiceBatchResponse

getThreshold(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getUserClickMode(String) - Method in class org.molgenis.ontology.matching.UploadProgress

H

hasRepository(String) - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

I

ID - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

ID - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

ID - Static variable in class org.molgenis.ontology.model.OntologyMetaData

ID - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

ID - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ID - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

ID - Static variable in class org.molgenis.ontology.model.OntologyTermSynonymMetaData

ID - Static variable in class org.molgenis.ontology.tree.OntologyTreeController

IDENTIFIER - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

IDENTIFIER - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

incrementProgress(String) - Method in class org.molgenis.ontology.matching.UploadProgress

init(Model) - Method in class org.molgenis.ontology.controller.OntologyManagerController

init(Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

init(Model) - Method in class org.molgenis.ontology.tree.OntologyTreeController

INPUT_TERM - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

INSTANCE - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

INSTANCE - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

INSTANCE - Static variable in class org.molgenis.ontology.model.OntologyMetaData

INSTANCE - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

INSTANCE - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

INSTANCE - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

INSTANCE - Static variable in class org.molgenis.ontology.model.OntologyTermSynonymMetaData

INVALID_TOTAL_NUMBER - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

isMatched() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

isRoot() - Method in class org.molgenis.ontology.utils.OWLClassContainer

isUserExists(String) - Method in class org.molgenis.ontology.matching.UploadProgress

iterator() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

iterator() - Method in class org.molgenis.ontology.repository.OntologyRepositoryCollection

L

LABEL - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

M

match(String, String, String, Model, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

MATCHED_TERM - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

MatchingTaskContentEntityMetaData - Class in org.molgenis.ontology.matching

matchingTaskContentEntityMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

MatchingTaskEntityMetaData - Class in org.molgenis.ontology.matching

matchingTaskEntityMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

matchResult(String, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchResult(OntologyServiceRequest, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchResult(Map<String, Object>, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchTask(Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

MOLGENIS_USER - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

N

NAME - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

O

onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.ontology.importer.OntologyImporterServiceRegistrator

ONTOLOGY - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_IRI - Static variable in class org.molgenis.ontology.model.OntologyMetaData

ONTOLOGY_MANAGER_PLUGIN - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

ONTOLOGY_NAME - Static variable in class org.molgenis.ontology.model.OntologyMetaData

ONTOLOGY_TERM_DYNAMIC_ANNOTATION - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_TERM_IRI - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_TERM_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_TERM_NODE_PATH - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_TERM_NODE_PATH - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

ONTOLOGY_TERM_SYNONYM - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

ONTOLOGY_TERM_SYNONYM - Static variable in class org.molgenis.ontology.model.OntologyTermSynonymMetaData

OntologyConfiguration - Class in org.molgenis.ontology

OntologyConfiguration() - Constructor for class org.molgenis.ontology.OntologyConfiguration

OntologyDataConfig - Class in org.molgenis.ontology

OntologyDataConfig() - Constructor for class org.molgenis.ontology.OntologyDataConfig

OntologyImporterServiceRegistrator - Class in org.molgenis.ontology.importer

OntologyImporterServiceRegistrator(OntologyImportService, ImportServiceFactory) - Constructor for class org.molgenis.ontology.importer.OntologyImporterServiceRegistrator

OntologyImportService - Class in org.molgenis.ontology.importer

OntologyImportService(FileRepositoryCollectionFactory, DataService, SearchService, PermissionSystemService) - Constructor for class org.molgenis.ontology.importer.OntologyImportService

OntologyManagerController - Class in org.molgenis.ontology.controller

OntologyManagerController() - Constructor for class org.molgenis.ontology.controller.OntologyManagerController

OntologyMetaData - Class in org.molgenis.ontology.model

ontologyMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyPackage - Class in org.molgenis.ontology.model

OntologyPackage() - Constructor for class org.molgenis.ontology.model.OntologyPackage

OntologyRepositoryCollection - Class in org.molgenis.ontology.repository

RepositoryCollection for the import of an owl file.

OntologyRepositoryCollection(File) - Constructor for class org.molgenis.ontology.repository.OntologyRepositoryCollection

Creates a new OntologyRepositoryCollection for an ontology file

OntologyServiceBatchResponse - Class in org.molgenis.ontology.response

OntologyServiceBatchResponse(String, SearchResult) - Constructor for class org.molgenis.ontology.response.OntologyServiceBatchResponse

OntologyServiceController - Class in org.molgenis.ontology.controller

OntologyServiceController() - Constructor for class org.molgenis.ontology.controller.OntologyServiceController

OntologyServiceRequest - Class in org.molgenis.ontology.request

OntologyServiceRequest(String, String, String, boolean, EntityPager) - Constructor for class org.molgenis.ontology.request.OntologyServiceRequest

OntologyTermDynamicAnnotationMetaData - Class in org.molgenis.ontology.model

ontologyTermDynamicAnnotationMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTermMetaData - Class in org.molgenis.ontology.model

ontologyTermMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTermNodePathMetaData - Class in org.molgenis.ontology.model

ontologyTermNodePathMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTermSynonymMetaData - Class in org.molgenis.ontology.model

ontologyTermSynonymMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTreeController - Class in org.molgenis.ontology.tree

OntologyTreeController() - Constructor for class org.molgenis.ontology.tree.OntologyTreeController

org.molgenis.ontology - package org.molgenis.ontology

org.molgenis.ontology.controller - package org.molgenis.ontology.controller

org.molgenis.ontology.importer - package org.molgenis.ontology.importer

org.molgenis.ontology.matching - package org.molgenis.ontology.matching

org.molgenis.ontology.model - package org.molgenis.ontology.model

org.molgenis.ontology.repository - package org.molgenis.ontology.repository

org.molgenis.ontology.request - package org.molgenis.ontology.request

org.molgenis.ontology.response - package org.molgenis.ontology.response

org.molgenis.ontology.tree - package org.molgenis.ontology.tree

org.molgenis.ontology.utils - package org.molgenis.ontology.utils

OWLClassContainer - Class in org.molgenis.ontology.utils

OWLClassContainer(OWLClass, String, boolean) - Constructor for class org.molgenis.ontology.utils.OWLClassContainer

P

PACKAGE_NAME - Static variable in class org.molgenis.ontology.model.OntologyPackage

process(SecurityContext, MolgenisUser, String, String, File, RepositoryCollection) - Method in class org.molgenis.ontology.matching.ProcessInputTermService

ProcessInputTermService - Class in org.molgenis.ontology.matching

ProcessInputTermService(EmxImportService, DataService, UploadProgress, OntologyService) - Constructor for class org.molgenis.ontology.matching.ProcessInputTermService

processInputTermService() - Method in class org.molgenis.ontology.OntologyConfiguration

R

REF_ENTITY - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

registerOntologyRepositorySource() - Method in class org.molgenis.ontology.OntologyDataConfig

Registers the OntologyRepositorySource factory so it can be used by DataService.createFileRepositorySource(File file);

registerUser(String, String, Integer) - Method in class org.molgenis.ontology.matching.UploadProgress

registerUser(String, String) - Method in class org.molgenis.ontology.matching.UploadProgress

removeUser(String) - Method in class org.molgenis.ontology.matching.UploadProgress

resetUserThreshold(String, Integer) - Method in class org.molgenis.ontology.matching.UploadProgress

ROOT - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

S

SCORE - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

search(Map<String, Object>, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

setUserClickMode(String, Boolean) - Method in class org.molgenis.ontology.matching.UploadProgress

SIMPLE_NAME - Static variable in class org.molgenis.ontology.model.OntologyMetaData

SIMPLE_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

SIMPLE_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermMetaData

SIMPLE_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermNodePathMetaData

SIMPLE_NAME - Static variable in class org.molgenis.ontology.model.OntologyTermSynonymMetaData

T

THRESHOLD - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

U

updateThreshold(String, String, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

upload(String, String, Part, Model, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

UploadProgress - Class in org.molgenis.ontology.matching

UploadProgress() - Constructor for class org.molgenis.ontology.matching.UploadProgress

uploadProgress() - Method in class org.molgenis.ontology.OntologyConfiguration

URI - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

URI - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

URI - Static variable in class org.molgenis.ontology.tree.OntologyTreeController

V

VALIDATED - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

validateImport(File, RepositoryCollection) - Method in class org.molgenis.ontology.importer.OntologyImportService

VALUE - Static variable in class org.molgenis.ontology.model.OntologyTermDynamicAnnotationMetaData

A C D E G H I L M N O P R S T U V