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

A

ALLOWED_IDENTIFIER - Static variable in class org.molgenis.ontology.sorta.repo.SortaCsvRepository

C

call(Progress) - Method in class org.molgenis.ontology.sorta.job.SortaJobImpl

COMBINED_SCORE - Static variable in class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

count() - Method in class org.molgenis.ontology.sorta.repo.SortaCsvRepository

countMatchResult(String) - Method in class org.molgenis.ontology.controller.SortaServiceController

create(SortaJobExecution) - Method in class org.molgenis.ontology.sorta.job.SortaJobFactory

createStemmedWordSet(String) - Method in class org.molgenis.ontology.roc.InformationContentService

D

DEFAULT_MATCHING_IDENTIFIER - Static variable in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

DEFAULT_MATCHING_NAME_FIELD - Static variable in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

DEFAULT_MATCHING_SYNONYM_PREFIX_FIELD - Static variable in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

DEFAULT_SEPARATOR - Static variable in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

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

DELETE_URL - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

deleteResult(String, Model) - Method in class org.molgenis.ontology.controller.SortaServiceController

download(HttpServletRequest, HttpServletResponse) - Method in class org.molgenis.ontology.controller.SortaServiceAnonymousController

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

E

equals(Object) - Method in class org.molgenis.ontology.roc.OntologyWord

equals(Object) - Method in class org.molgenis.ontology.sorta.bean.OntologyTermHitEntity

F

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

findOntologyTermEntities(String, Entity) - Method in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

findOntologyTermEntities(String, Entity) - Method in interface org.molgenis.ontology.sorta.service.SortaService

Find a list of relevant ontologyterm typed entities using lexical matching (elasticsearch + ngram) in generic type based on given ontologyIri and a set of query inputs (name, synonym, ontology database id, e.g.

G

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

getAllOntologyEntities() - Method in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

getAllOntologyEntities() - Method in interface org.molgenis.ontology.sorta.service.SortaService

Get all ontology entities in generic type

getCapabilities() - Method in class org.molgenis.ontology.sorta.repo.SortaCsvRepository

getDeleteUrl() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

getEntityAsMap(Iterable<? extends Entity>) - Static method in class org.molgenis.ontology.utils.SortaServiceUtil

getEntityAsMap(Entity) - Static method in class org.molgenis.ontology.utils.SortaServiceUtil

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

getEntityType() - Method in class org.molgenis.ontology.sorta.repo.SortaCsvRepository

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

getInputData() - Method in class org.molgenis.ontology.sorta.request.SortaServiceResponse

getJobs(Model) - Method in class org.molgenis.ontology.controller.SortaServiceController

getMessage() - Method in class org.molgenis.ontology.sorta.request.SortaServiceResponse

getName() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

getOntologyEntity(String) - Method in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

getOntologyEntity(String) - Method in interface org.molgenis.ontology.sorta.service.SortaService

Get a specified ontology entity in generic type based on the given ontologyIri

getOntologyIri() - Method in class org.molgenis.ontology.roc.OntologyWord

getOntologyIri() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

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

getOntologyTermEntity(String, String) - Method in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

getOntologyTermEntity(String, String) - Method in interface org.molgenis.ontology.sorta.service.SortaService

Get a specified ontologyterm in generic type based on the given ontologyIri and ontologyTermIri

getOntologyTerms() - Method in class org.molgenis.ontology.sorta.request.SortaServiceResponse

getResultEntityName() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

getSortaJobExecutionId() - Method in class org.molgenis.ontology.sorta.request.SortaServiceRequest

getSourceEntityName() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

getThreshold() - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

getTotalHitCount() - Method in class org.molgenis.ontology.sorta.request.SortaServiceResponse

getWord() - Method in class org.molgenis.ontology.roc.OntologyWord

H

hashCode() - Method in class org.molgenis.ontology.roc.OntologyWord

hashCode() - Method in class org.molgenis.ontology.sorta.bean.OntologyTermHitEntity

I

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

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

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

ID - Static variable in class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

IDENTIFIER - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

InformationContentService - Class in org.molgenis.ontology.roc

InformationContentService(DataService) - Constructor for class org.molgenis.ontology.roc.InformationContentService

informationContentService() - Method in class org.molgenis.ontology.SortaConfiguration

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

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

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

init() - Method in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

init() - Method in class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

init() - Method in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

initialize() - Method in interface org.molgenis.ontology.initializer.OntologyScriptInitializer

initialize() - Method in class org.molgenis.ontology.initializer.OntologyScriptInitializerImpl

INPUT_TERM - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

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

iterator() - Method in class org.molgenis.ontology.sorta.repo.SortaCsvRepository

M

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

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

MATCH_VIEW_NAME - Static variable in class org.molgenis.ontology.controller.SortaServiceController

MATCHED_TERM - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

MATCHING_TASK_CONTENT - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

MatchingTaskContentMetaData - Class in org.molgenis.ontology.sorta.meta

matchResult(HttpServletRequest) - Method in class org.molgenis.ontology.controller.SortaServiceAnonymousController

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

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

N

NAME - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

O

ONTOLOGY_IRI - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

ONTOLOGY_TERM_HIT - Static variable in class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

OntologyManagerController - Class in org.molgenis.ontology.controller

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

OntologyScriptInitializer - Interface in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl - Class in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl(DataService, ScriptFactory, ScriptParameterFactory) - Constructor for class org.molgenis.ontology.initializer.OntologyScriptInitializerImpl

OntologyTermHitEntity - Class in org.molgenis.ontology.sorta.bean

OntologyTermHitEntity(Entity, EntityType) - Constructor for class org.molgenis.ontology.sorta.bean.OntologyTermHitEntity

OntologyTermHitMetaData - Class in org.molgenis.ontology.sorta.meta

OntologyTermHitMetaData(OntologyPackage) - Constructor for class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

OntologyWord - Class in org.molgenis.ontology.roc

OntologyWord(String, String) - Constructor for class org.molgenis.ontology.roc.OntologyWord

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

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

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

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

org.molgenis.ontology.sorta.bean - package org.molgenis.ontology.sorta.bean

org.molgenis.ontology.sorta.job - package org.molgenis.ontology.sorta.job

org.molgenis.ontology.sorta.meta - package org.molgenis.ontology.sorta.meta

org.molgenis.ontology.sorta.repo - package org.molgenis.ontology.sorta.repo

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

org.molgenis.ontology.sorta.service - package org.molgenis.ontology.sorta.service

org.molgenis.ontology.sorta.service.impl - package org.molgenis.ontology.sorta.service.impl

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

P

process() - Method in class org.molgenis.ontology.sorta.job.SortaJobProcessor

R

redistributedNGramScore(String, String) - Method in class org.molgenis.ontology.roc.InformationContentService

RESULT_ENTITY - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

retrieveSortaJobResults(SortaServiceRequest, HttpServletRequest) - Method in class org.molgenis.ontology.controller.SortaServiceController

S

SCORE - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

SCORE - Static variable in class org.molgenis.ontology.sorta.meta.OntologyTermHitMetaData

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

setDeleteUrl(String) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

setName(String) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

setOntologyIri(String) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

setResultEntityName(String) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

setSourceEntityName(String) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

setThreshold(double) - Method in class org.molgenis.ontology.sorta.job.SortaJobExecution

SIGNIFICANT_VALUE - Static variable in class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

SIMPLE_NAME - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

SIMPLE_NAME - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

SORTA_JOB_EXECUTION - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

SORTA_MATCH_JOB_TYPE - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

SortaConfiguration - Class in org.molgenis.ontology

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

SortaCsvRepository - Class in org.molgenis.ontology.sorta.repo

SortaCsvRepository(File, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.ontology.sorta.repo.SortaCsvRepository

SortaCsvRepository(String, String, File, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.ontology.sorta.repo.SortaCsvRepository

SortaJobExecution - Class in org.molgenis.ontology.sorta.job

SortaJobExecution(Entity) - Constructor for class org.molgenis.ontology.sorta.job.SortaJobExecution

SortaJobExecution(EntityType) - Constructor for class org.molgenis.ontology.sorta.job.SortaJobExecution

SortaJobExecution(String, EntityType) - Constructor for class org.molgenis.ontology.sorta.job.SortaJobExecution

SortaJobExecutionFactory - Class in org.molgenis.ontology.sorta.job

SortaJobExecutionMetaData - Class in org.molgenis.ontology.sorta.meta

SortaJobFactory - Class in org.molgenis.ontology.sorta.job

SortaJobFactory() - Constructor for class org.molgenis.ontology.sorta.job.SortaJobFactory

SortaJobImpl - Class in org.molgenis.ontology.sorta.job

SortaJobImpl(SortaJobProcessor, Authentication, Progress, TransactionTemplate) - Constructor for class org.molgenis.ontology.sorta.job.SortaJobImpl

SortaJobProcessor - Class in org.molgenis.ontology.sorta.job

SortaJobProcessor(String, String, String, Progress, DataService, SortaService, IdGenerator, MenuReaderService) - Constructor for class org.molgenis.ontology.sorta.job.SortaJobProcessor

SortaService - Interface in org.molgenis.ontology.sorta.service

sortaService() - Method in class org.molgenis.ontology.SortaConfiguration

SortaServiceAnonymousController - Class in org.molgenis.ontology.controller

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

SortaServiceController - Class in org.molgenis.ontology.controller

SortaServiceController(OntologyService, SortaService, SortaJobFactory, ExecutorService, UserAccountService, FileStore, PermissionService, DataService, LanguageService, MenuReaderService, IdGenerator, PermissionSystemService, MatchingTaskContentMetaData, SortaJobExecutionMetaData, OntologyTermMetaData, SortaJobExecutionFactory, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.ontology.controller.SortaServiceController

SortaServiceImpl - Class in org.molgenis.ontology.sorta.service.impl

SortaServiceImpl(DataService, InformationContentService, OntologyTermHitMetaData, OntologyTermSynonymFactory) - Constructor for class org.molgenis.ontology.sorta.service.impl.SortaServiceImpl

SortaServiceRequest - Class in org.molgenis.ontology.sorta.request

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

SortaServiceResponse - Class in org.molgenis.ontology.sorta.request

This function is used to parse the results from OntologyService

SortaServiceResponse(String) - Constructor for class org.molgenis.ontology.sorta.request.SortaServiceResponse

SortaServiceResponse(Entity, Iterable<? extends Entity>) - Constructor for class org.molgenis.ontology.sorta.request.SortaServiceResponse

SortaServiceResponse(Map<String, Object>, List<Map<String, Object>>) - Constructor for class org.molgenis.ontology.sorta.request.SortaServiceResponse

SortaServiceUtil - Class in org.molgenis.ontology.utils

SortaServiceUtil() - Constructor for class org.molgenis.ontology.utils.SortaServiceUtil

SOURCE_ENTITY - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

T

termFrequencyService() - Method in class org.molgenis.ontology.SortaConfiguration

THRESHOLD - Static variable in class org.molgenis.ontology.sorta.meta.SortaJobExecutionMetaData

U

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

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

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

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

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

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

V

VALIDATED - Static variable in class org.molgenis.ontology.sorta.meta.MatchingTaskContentMetaData

validateValueType(String, Object) - Method in class org.molgenis.ontology.sorta.bean.OntologyTermHitEntity

VIEW_NAME - Static variable in class org.molgenis.ontology.controller.SortaServiceAnonymousController

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

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