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

A

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

AttributeResponse - Class in org.molgenis.ontology.sorta.controller

AttributeResponse(String, EntityType, Attribute, Set<String>, Map<String, Set<String>>, UserPermissionEvaluator, DataService) - Constructor for class org.molgenis.ontology.sorta.controller.AttributeResponse

AttributeResponse(String, EntityType, Attribute, UserPermissionEvaluator, DataService) - Constructor for class org.molgenis.ontology.sorta.controller.AttributeResponse

C

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

concatAttributeHref(String, String, Object, String) - Static method in class org.molgenis.ontology.sorta.controller.Href

Create an encoded href for an attribute

concatEntityCollectionHref(String, String, String, List<String>) - Static method in class org.molgenis.ontology.sorta.controller.Href

Create an encoded href for an entity collection

concatEntityHref(String, String, Object) - Static method in class org.molgenis.ontology.sorta.controller.Href

Create an encoded href for an entity

concatEntityHref(Entity) - Static method in class org.molgenis.ontology.sorta.controller.Href

concatMetaAttributeHref(String, String, String) - Static method in class org.molgenis.ontology.sorta.controller.Href

Create an encoded href for an attribute meta

concatMetaEntityHref(String, String) - Static method in class org.molgenis.ontology.sorta.controller.Href

Create an encoded href for an entity meta

concatMetaEntityHrefV2(String, String) - Static method in class org.molgenis.ontology.sorta.controller.Href

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

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

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

DEFAULT_THRESHOLD - Static variable in class org.molgenis.ontology.sorta.controller.SortaController

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

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

download(String, HttpServletResponse) - Method in class org.molgenis.ontology.sorta.controller.SortaController

E

EntityCollectionResponse - Class in org.molgenis.ontology.sorta.controller

EntityCollectionResponse(EntityPager, List<Map<String, Object>>, String, EntityType, UserPermissionEvaluator, DataService) - Constructor for class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

EntityPager - Class in org.molgenis.ontology.sorta.controller

EntityPager(int, int, Long, Iterable<Entity>) - Constructor for class org.molgenis.ontology.sorta.controller.EntityPager

EntityTypeResponse - Class in org.molgenis.ontology.sorta.controller

EntityTypeResponse(EntityType, Set<String>, Map<String, Set<String>>, UserPermissionEvaluator, DataService) - Constructor for class org.molgenis.ontology.sorta.controller.EntityTypeResponse

EntityTypeResponse(EntityType, UserPermissionEvaluator, DataService) - Constructor for class org.molgenis.ontology.sorta.controller.EntityTypeResponse

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>) - Method in class org.molgenis.ontology.sorta.controller.SortaController

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

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

getAttributes() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getAttributes() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

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

getDefaultValue() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

getDescription() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getDescription() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

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

getEnumOptions() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getExpression() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getFieldType() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

getHref() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getHref() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getHref() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getHref() - Method in class org.molgenis.ontology.sorta.controller.Href

getHrefCollection() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getHrefCollection() - Method in class org.molgenis.ontology.sorta.controller.Href

getIdAttribute() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

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

getItems() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getIterable() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

getJobs() - Method in class org.molgenis.ontology.sorta.controller.SortaController

getLabel() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getLabel() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getLabelAttribute() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getLanguageCode() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getLookupAttribute() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getLookupAttributes() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getMappedBy() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getMaxLength() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

getMeta() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getName() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getName() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

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

getNextHref() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getNextStart() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

getNullableExpression() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getNum() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getNum() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

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

getPermissions() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

getPrevHref() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getPrevStart() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

getRange() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getRefEntity() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

getStart() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getStart() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

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

getTotal() - Method in class org.molgenis.ontology.sorta.controller.EntityCollectionResponse

getTotal() - Method in class org.molgenis.ontology.sorta.controller.EntityPager

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

getValidationExpression() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

getVisibleExpression() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

getWritable() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

H

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

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

Href - Class in org.molgenis.ontology.sorta.controller

Href(String, String) - Constructor for class org.molgenis.ontology.sorta.controller.Href

I

ID - Static variable in class org.molgenis.ontology.sorta.controller.SortaController

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

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

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

InformationContentService - Class in org.molgenis.ontology.roc

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

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

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

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

isAbstract() - Method in class org.molgenis.ontology.sorta.controller.EntityTypeResponse

isAggregatable() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

isAuto() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

isLabelAttribute() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

isNillable() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

isReadOnly() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

isUnique() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

isVisible() - Method in class org.molgenis.ontology.sorta.controller.AttributeResponse

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

M

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

MATCH_VIEW_NAME - Static variable in class org.molgenis.ontology.sorta.controller.SortaController

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(String, Model) - Method in class org.molgenis.ontology.sorta.controller.SortaController

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

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

OntologyScriptInitializer - Interface in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl - Class in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl(DataService, ScriptFactory, ScriptParameterFactory, ScriptMetadata) - 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, OntologyTermSynonymMetadata, OntologyTermDynamicAnnotationMetadata, OntologyTermNodePathMetadata, OntologyMetadata) - 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.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.controller - package org.molgenis.ontology.sorta.controller

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(String, String, String, Progress) - 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) - Method in class org.molgenis.ontology.sorta.controller.SortaController

S

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

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

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

SortaConfig - Class in org.molgenis.ontology

SortaConfig(DataService, OntologyTermHitMetaData, OntologyTermSynonymFactory) - Constructor for class org.molgenis.ontology.SortaConfig

SortaController - Class in org.molgenis.ontology.sorta.controller

SortaController(OntologyService, SortaService, UserAccountService, FileStore, UserPermissionEvaluator, DataService, MenuReaderService, IdGenerator, PermissionSystemService, MatchingTaskContentMetaData, SortaJobExecutionMetadata, OntologyTermMetadata, SortaJobExecutionFactory, EntityTypeFactory, AttributeFactory, JobExecutor) - Constructor for class org.molgenis.ontology.sorta.controller.SortaController

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

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

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

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

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

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

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

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

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

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

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

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

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

SortaServiceUtil - Class in org.molgenis.ontology.utils

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

T

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

U

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

upload(String, String, MultipartFile, Model, HttpServletRequest) - Method in class org.molgenis.ontology.sorta.controller.SortaController

URI - Static variable in class org.molgenis.ontology.sorta.controller.SortaController

V

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

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

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