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

A

add(MappingProject) - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

add(MappingProject) - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Adds a MappingProject to the MappingProjectRepository

addAttributeMapping(String) - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

Adds a new empty attribute mapping to a target attribute

addEntityMapping(String, String, String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Adds a new EntityMapping to an existing MappingTarget

addMappingProject(String, String, int) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Adds a new mapping project.

addMappingProject(String, String, int) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

addMappingProject(String, String, int) - Method in interface org.molgenis.semanticmapper.service.MappingService

Creates a new MappingProject

addSource(EntityType) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

Adds a new EntityMapping to this target for a certain source.

addTagAttribute(AddTagRequest) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Add a tag for a single attribute

AddTagRequest - Class in org.molgenis.semanticmapper.data.request

AddTagRequest() - Constructor for class org.molgenis.semanticmapper.data.request.AddTagRequest

addTarget(EntityType) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

advancedMappingEditor(String, String, String, String, String, String, Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Returns a view that allows the user to edit mappings involving xrefs / categoricals / strings

ALGORITHM - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

ALGORITHM_STATE - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

AlgorithmEvaluation - Class in org.molgenis.semanticmapper.service.impl

AlgorithmEvaluation(Entity) - Constructor for class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

AlgorithmException - Exception in org.molgenis.semanticmapper.service.impl

Deprecated.

use class that extends from CodedRuntimeException

AlgorithmException(String) - Constructor for exception org.molgenis.semanticmapper.service.impl.AlgorithmException

Deprecated.

AlgorithmGenerator - Interface in org.molgenis.semanticmapper.algorithmgenerator.generator

AlgorithmGeneratorHelper - Class in org.molgenis.semanticmapper.utils

AlgorithmGeneratorService - Interface in org.molgenis.semanticmapper.algorithmgenerator.service

algorithmGeneratorService() - Method in class org.molgenis.semanticmapper.config.MappingConfig

AlgorithmGeneratorServiceImpl - Class in org.molgenis.semanticmapper.algorithmgenerator.service.impl

AlgorithmGeneratorServiceImpl(DataService, UnitResolver, AlgorithmTemplateService) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.service.impl.AlgorithmGeneratorServiceImpl

AlgorithmResult - Class in org.molgenis.semanticmapper.mapping.model

Result of applying algorithm to one source entity row

AlgorithmResult() - Constructor for class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

AlgorithmService - Interface in org.molgenis.semanticmapper.service

algorithmServiceImpl() - Method in class org.molgenis.semanticmapper.config.MappingConfig

AlgorithmServiceImpl - Class in org.molgenis.semanticmapper.service.impl

AlgorithmServiceImpl(SemanticSearchService, AlgorithmGeneratorService, EntityManager, JsMagmaScriptEvaluator) - Constructor for class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

AlgorithmTemplate - Class in org.molgenis.semanticmapper.service.impl

Mapping algorithm template for JavaScript Magma scripts.

AlgorithmTemplate(Script, Map<String, String>) - Constructor for class org.molgenis.semanticmapper.service.impl.AlgorithmTemplate

AlgorithmTemplateService - Interface in org.molgenis.semanticmapper.service.impl

Find suitable algorithm templates for provided attribute matches returned from SemanticSearchService.

algorithmTemplateServiceImpl() - Method in class org.molgenis.semanticmapper.config.MappingConfig

AlgorithmTemplateServiceImpl - Class in org.molgenis.semanticmapper.service.impl

AlgorithmTemplateServiceImpl(DataService) - Constructor for class org.molgenis.semanticmapper.service.impl.AlgorithmTemplateServiceImpl

AmountConvertor - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor

AmountConvertor() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.AmountConvertor

AmountWrapper - Class in org.molgenis.semanticmapper.algorithmgenerator.bean

AmountWrapper() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.bean.AmountWrapper

apply(AttributeMapping, Entity, EntityType, int) - Method in interface org.molgenis.semanticmapper.service.AlgorithmService

Applies an AttributeMapping to a source Entity

apply(AttributeMapping, Entity, EntityType, int) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

applyAlgorithm(Attribute, String, Iterable<Entity>, int) - Method in interface org.molgenis.semanticmapper.service.AlgorithmService

Applies an algorithm to the given attribute of given source entities.

applyAlgorithm(Attribute, String, Iterable<Entity>, int) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

applyCustomRules(Category, Category) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapper

applyCustomRules(Category, Category) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.FrequencyCategoryMapper

applyCustomRules(Category, Category) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.LexicalCategoryMapper

applyMappings(String, String, Boolean, String, String, Progress) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

applyMappings(String, String, Boolean, String, String, Progress) - Method in interface org.molgenis.semanticmapper.service.MappingService

Applies all mappings in a MappingTarget

ATTRIBUTE_MAPPING - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

ATTRIBUTE_MAPPINGS - Static variable in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

AttributeMapping - Class in org.molgenis.semanticmapper.mapping.model

AttributeMapping(String, String, Attribute, String, List<Attribute>) - Constructor for class org.molgenis.semanticmapper.mapping.model.AttributeMapping

AttributeMapping(String, String, Attribute, String, List<Attribute>, String) - Constructor for class org.molgenis.semanticmapper.mapping.model.AttributeMapping

AttributeMapping(Attribute) - Constructor for class org.molgenis.semanticmapper.mapping.model.AttributeMapping

Creates a new empty AttributeMapping

AttributeMapping.AlgorithmState - Enum in org.molgenis.semanticmapper.mapping.model

attributeMappingFeedback(String, String, String, String, String, Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

AttributeMappingMetaData - Class in org.molgenis.semanticmapper.meta

AttributeMappingMetaData(MapperPackage) - Constructor for class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

attributeMappingRepository() - Method in class org.molgenis.semanticmapper.config.MappingConfig

AttributeMappingRepository - Interface in org.molgenis.semanticmapper.repository

O/R Mapping between EntityMappingMetaData Entities and EntityMapping s.

AttributeMappingRepositoryImpl - Class in org.molgenis.semanticmapper.repository.impl

AttributeMappingRepositoryImpl(DataService, AttributeMappingMetaData) - Constructor for class org.molgenis.semanticmapper.repository.impl.AttributeMappingRepositoryImpl

autoGenerateAlgorithm(EntityType, EntityType, EntityMapping) - Method in interface org.molgenis.semanticmapper.service.AlgorithmService

Creates an attribute mapping after the semantic search service finds one

autoGenerateAlgorithm(EntityType, EntityType, EntityMapping) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

autoTagAttributes(AutoTagRequest) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Automatically tags all attributes in the current entity using Lucene lexical matching.

AutoTagRequest - Class in org.molgenis.semanticmapper.data.request

AutoTagRequest() - Constructor for class org.molgenis.semanticmapper.data.request.AutoTagRequest

C

Category - Class in org.molgenis.semanticmapper.algorithmgenerator.bean

Category() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

CategoryMapper - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper

CategoryMapper(List<CategoryRule>) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapper

CategoryMapperUtil - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper

CategoryMapping<S,T> - Class in org.molgenis.semanticmapper.mapping.model

CategoryMapping() - Constructor for class org.molgenis.semanticmapper.mapping.model.CategoryMapping

CategoryMatchQuality<T> - Class in org.molgenis.semanticmapper.algorithmgenerator.rules

CategoryMatchQuality() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

CategoryRule - Interface in org.molgenis.semanticmapper.algorithmgenerator.rules

clearAllTags(String) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Clears all tags from every attribute in the current target entity

cloneMappingProject(String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

cloneMappingProject(String, int) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

cloneMappingProject(String) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

cloneMappingProject(String, String) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

cloneMappingProject(String) - Method in interface org.molgenis.semanticmapper.service.MappingService

Clones a MappingProject.

cloneMappingProject(String, String) - Method in interface org.molgenis.semanticmapper.service.MappingService

Clones a MappingProject.

compareTo(CategoryMatchQuality<T>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

compareTo(Quality<Double>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl.NumericQuality

containNegativeAdjectives(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

containsNegativeAdjectives(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

convertDescriptionToAmount(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

convertUnit(Unit<? extends Quantity>, Unit<? extends Quantity>) - Method in class org.molgenis.semanticmapper.utils.MagmaUnitConverter

convertWordToNumber(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

create(Amount<?>) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.bean.AmountWrapper

create(Amount<?>, boolean) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.bean.AmountWrapper

create(String, String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

create(String, String, AmountWrapper) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

create(String, Set<Attribute>, AttributeMapping.AlgorithmState) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.bean.GeneratedAlgorithm

create(boolean, Quality<T>, Category, Category) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

create(double) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl.NumericQuality

create(String, String, String, String) - Static method in class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

create(String, Map<S, T>) - Static method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

create(String, Map<S, T>, T) - Static method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

create(String, Map<S, T>, T, T) - Static method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

create(String) - Static method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

createCategoryMatchQuality(Category, Category) - Method in interface org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryRule

createCategoryMatchQuality(Category, Category) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.InternalAbstractCategoryRule

createEmpty(String) - Static method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

createFailure(Exception, Entity) - Static method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

createIntegratedEntity(String, String, String, String, Boolean) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Creates the integrated entity for a mapping project's target

createSuccess(Object, Entity) - Static method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

D

DailyAmountConvertor - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor

DailyAmountConvertor() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.DailyAmountConvertor

delete(String) - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

delete(String) - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Delete a mapping project.

deleteAttributeMapping(String) - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

deleteMappingProject(String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Removes a mapping project

deleteMappingProject(String) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

deleteMappingProject(String) - Method in interface org.molgenis.semanticmapper.service.MappingService

Deletes a MappingProject

deleteSingleTag(RemoveTagRequest) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Delete a single tag

DEPTH - Static variable in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

E

ENTITY_MAPPING - Static variable in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

ENTITY_MAPPINGS - Static variable in class org.molgenis.semanticmapper.meta.MappingTargetMetaData

EntityMapping - Class in org.molgenis.semanticmapper.mapping.model

EntityMapping(EntityType, EntityType) - Constructor for class org.molgenis.semanticmapper.mapping.model.EntityMapping

Creates a new empty EntityMapping with no AttributeMappings.

EntityMapping(String, EntityType, EntityType, List<AttributeMapping>) - Constructor for class org.molgenis.semanticmapper.mapping.model.EntityMapping

EntityMappingMetaData - Class in org.molgenis.semanticmapper.meta

EntityMappingMetaData(MapperPackage, AttributeMappingMetaData) - Constructor for class org.molgenis.semanticmapper.meta.EntityMappingMetaData

entityMappingRepository() - Method in class org.molgenis.semanticmapper.config.MappingConfig

EntityMappingRepository - Interface in org.molgenis.semanticmapper.repository

O/R Mapping between EntityMappingMetaData Entities and EntityMapping s.

EntityMappingRepositoryImpl - Class in org.molgenis.semanticmapper.repository.impl

O/R mapping between EntityMapping Entity and EntityMapping POJO

EntityMappingRepositoryImpl(AttributeMappingRepository) - Constructor for class org.molgenis.semanticmapper.repository.impl.EntityMappingRepositoryImpl

equals(Object) - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

equals(Object) - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

equals(Object) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

equals(Object) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

equals(Object) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmTemplate

errorMessage(String) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

extractNumbers(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

extractSourceAttributesFromAlgorithm(String, EntityType) - Static method in class org.molgenis.semanticmapper.utils.AlgorithmGeneratorHelper

F

find(Hits<ExplainedAttribute>) - Method in interface org.molgenis.semanticmapper.service.impl.AlgorithmTemplateService

find(Hits<ExplainedAttribute>) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmTemplateServiceImpl

findBestCategoryMatch(Category, List<Category>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapper

findBestCategoryMatch(Category, List<Category>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.FrequencyCategoryMapper

findBestCategoryMatch(Category, List<Category>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.LexicalCategoryMapper

findDurationUnit(String) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

FirstAttributeMappingInfo - Class in org.molgenis.semanticmapper.controller

FirstAttributeMappingInfo() - Constructor for class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

FrequencyCategoryMapper - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper

FrequencyCategoryMapper(List<CategoryRule>) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.FrequencyCategoryMapper

G

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in interface org.molgenis.semanticmapper.algorithmgenerator.generator.AlgorithmGenerator

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.NumericAlgorithmGenerator

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToManyCategoryAlgorithmGenerator

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToOneCategoryAlgorithmGenerator

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in interface org.molgenis.semanticmapper.algorithmgenerator.service.AlgorithmGeneratorService

generate(Attribute, Hits<ExplainedAttribute>, EntityType, EntityType) - Method in interface org.molgenis.semanticmapper.algorithmgenerator.service.AlgorithmGeneratorService

generate(Attribute, List<Attribute>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.algorithmgenerator.service.impl.AlgorithmGeneratorServiceImpl

generate(Attribute, Hits<ExplainedAttribute>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.algorithmgenerator.service.impl.AlgorithmGeneratorServiceImpl

generateAlgorithm(Attribute, EntityType, List<Attribute>, EntityType) - Method in interface org.molgenis.semanticmapper.service.AlgorithmService

Generates the algorithm based on the given targetAttribute and sourceAttribute

generateAlgorithm(Attribute, EntityType, List<Attribute>, EntityType) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

GenerateAlgorithmRequest - Class in org.molgenis.semanticmapper.data.request

GenerateAlgorithmRequest() - Constructor for class org.molgenis.semanticmapper.data.request.GenerateAlgorithmRequest

GeneratedAlgorithm - Class in org.molgenis.semanticmapper.algorithmgenerator.bean

GeneratedAlgorithm() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.bean.GeneratedAlgorithm

generateWeightedMap(Attribute) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToManyCategoryAlgorithmGenerator

getAlgorithm() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.GeneratedAlgorithm

getAlgorithm() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getAlgorithm() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getAlgorithm() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

getAlgorithmState() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.GeneratedAlgorithm

getAlgorithmState() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getAllMappingProjects() - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

getAllMappingProjects() - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Get a list of all MappingProject

getAllMappingProjects() - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

getAllMappingProjects() - Method in interface org.molgenis.semanticmapper.service.MappingService

Retrieves all MappingProjects.

getAllOntologyTerms(GetOntologyTermRequest) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Returns ontology terms based on a search term and a selected ontology

getAmount() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.AmountWrapper

getAmount(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.AmountConvertor

getAmountWrapper() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

getAttributeMapping(String) - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getAttributeMappings() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getAttributeMappings(List<Entity>, EntityType, EntityType) - Method in interface org.molgenis.semanticmapper.repository.AttributeMappingRepository

Creates a list of fully reconstructed AttributeMappings.

getAttributeMappings(List<Entity>, EntityType, EntityType) - Method in class org.molgenis.semanticmapper.repository.impl.AttributeMappingRepositoryImpl

getAttributeName() - Method in class org.molgenis.semanticmapper.data.request.AddTagRequest

getAttributeName() - Method in class org.molgenis.semanticmapper.data.request.RemoveTagRequest

getCode() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

getCompatibleEntityTypes(EntityType) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

Public for testability

getCompatibleEntityTypes(EntityType) - Method in interface org.molgenis.semanticmapper.service.MappingService

Retrieves a Stream of existing compatible EntityTypes that are valid as a mapping target.

getDefaultValue() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

getDepth() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getDepth() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

getEntity() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

getEntityMappings() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getEntityTypeId() - Method in class org.molgenis.semanticmapper.data.request.AddTagRequest

getEntityTypeId() - Method in class org.molgenis.semanticmapper.data.request.AutoTagRequest

getEntityTypeId() - Method in class org.molgenis.semanticmapper.data.request.RemoveTagRequest

getErrorMessage() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

getException() - Method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

getFirstAttributeMappingInfo(String, String, List<AttributeMapping.AlgorithmState>, Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Find the firstattributeMapping skip the the algorithmStates that are given in the AttributeMapping to an EntityMapping.

getIdentifier() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getIdentifier() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getIdentifier() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

getIdentifier() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getLabel() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.Category

getLabel() - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

getLabel() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getMap() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

getMappingForSource(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getMappingProject(String) - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

getMappingProject(String) - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Get a MappingProject object based on the project identifier

getMappingProject(String) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

getMappingProject(String) - Method in interface org.molgenis.semanticmapper.service.MappingService

Retrieves a MappingProject from the repository.

getMappingProjectId() - Method in class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

getMappingProjectId() - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

getMappingProjects(Query<Entity>) - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

getMappingProjects(Query<Entity>) - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Get a list of MappingProject based on a query

getMappingTarget(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

getMappingTargets() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

getMatchedTermFromTheRulelabelContainsWords(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.InternalAbstractCategoryRule

getMissingTargetAttributeNames() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getMissingTargetAttributeNames() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getMoreSpecificUnit(Unit<?>) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

getMostGeneralUnit(List<Unit<?>>) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

getName() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getName() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

getName() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getNullValue() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

getNum() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getOffset() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getOntologyIds() - Method in class org.molgenis.semanticmapper.data.request.AutoTagRequest

getOntologyIds() - Method in class org.molgenis.semanticmapper.data.request.GetOntologyTermRequest

getOntologyTermIRI() - Method in class org.molgenis.semanticmapper.data.request.RemoveTagRequest

getOntologyTermIRIs() - Method in class org.molgenis.semanticmapper.data.request.AddTagRequest

GetOntologyTermRequest - Class in org.molgenis.semanticmapper.data.request

GetOntologyTermRequest() - Constructor for class org.molgenis.semanticmapper.data.request.GetOntologyTermRequest

getPackageId() - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

getQuality() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

getQualityIndicator() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl.NumericQuality

getQualityIndicator() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.Quality

getRelationIRI() - Method in class org.molgenis.semanticmapper.data.request.AddTagRequest

getRelationIRI() - Method in class org.molgenis.semanticmapper.data.request.RemoveTagRequest

getSearchTerm() - Method in class org.molgenis.semanticmapper.data.request.GetOntologyTermRequest

getSemanticSearchAttributeMapping(Map<String, String>) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

This controller will first of all check if the user-defined search terms exist.

getSource() - Method in class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

getSourceAttributeName() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

getSourceAttributeNames(String) - Method in interface org.molgenis.semanticmapper.service.AlgorithmService

Retrieves the names of the source attributes in an algorithm

getSourceAttributeNames(String) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmServiceImpl

getSourceAttributes() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.GeneratedAlgorithm

getSourceAttributes() - Method in class org.molgenis.semanticmapper.data.request.GenerateAlgorithmRequest

getSourceAttributes() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getSourceCategory() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

getSourceEntity() - Method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

getSourceEntityName() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getSourceEntityType() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getSourceEntityTypeId() - Method in class org.molgenis.semanticmapper.data.request.GenerateAlgorithmRequest

getSuggestedAlgorithm(GenerateAlgorithmRequest) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

getTarget() - Method in class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

getTarget() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

getTargetAttribute() - Method in class org.molgenis.semanticmapper.controller.FirstAttributeMappingInfo

getTargetAttribute() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getTargetAttributeName() - Method in class org.molgenis.semanticmapper.data.request.GenerateAlgorithmRequest

getTargetAttributeName() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getTargetAttributeName() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

getTargetCategory() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

getTargetEntityName() - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

getTargetEntityType() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

getTargetEntityTypeId() - Method in class org.molgenis.semanticmapper.data.request.GenerateAlgorithmRequest

getTargetEntityTypeId() - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

getValue() - Method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

getValue() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

groupCategoryValues(Attribute) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToManyCategoryAlgorithmGenerator

H

handleRuntimeException(RuntimeException) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

hasError() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

hashCode() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

hashCode() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

hashCode() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

hashCode() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

hashCode() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmTemplate

hasMappingFor(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

hasSelfReferences() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

hasValue() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

I

ID - Static variable in class org.molgenis.semanticmapper.controller.MappingServiceController

ID - Static variable in class org.molgenis.semanticmapper.controller.TagWizardController

IDENTIFIER - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

IDENTIFIER - Static variable in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

IDENTIFIER - Static variable in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

IDENTIFIER - Static variable in class org.molgenis.semanticmapper.meta.MappingTargetMetaData

init() - Method in class org.molgenis.semanticmapper.job.MappingJobExecutionMetadata

init() - Method in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

init() - Method in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

init() - Method in class org.molgenis.semanticmapper.meta.MapperPackage

init() - Method in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

init() - Method in class org.molgenis.semanticmapper.meta.MappingTargetMetaData

InternalAbstractCategoryRule - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.impl

InternalAbstractCategoryRule(Set<String>) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.InternalAbstractCategoryRule

isAddSourceAttribute() - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

isAmountRanged(Amount<?>) - Static method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapperUtil

isDefaultValueUndefined() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

isDetermined() - Method in class org.molgenis.semanticmapper.algorithmgenerator.bean.AmountWrapper

isNewEntity(String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Checks if an entityTypeID already exists.

isNullValueUndefined() - Method in class org.molgenis.semanticmapper.mapping.model.CategoryMapping

isRuleApplied() - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.CategoryMatchQuality

isSuccess() - Method in class org.molgenis.semanticmapper.mapping.model.AlgorithmResult

isSuitable(Attribute, List<Attribute>) - Method in interface org.molgenis.semanticmapper.algorithmgenerator.generator.AlgorithmGenerator

isSuitable(Attribute, List<Attribute>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.NumericAlgorithmGenerator

isSuitable(Attribute, List<Attribute>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToManyCategoryAlgorithmGenerator

isSuitable(Attribute, List<Attribute>) - Method in class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToOneCategoryAlgorithmGenerator

L

LexicalCategoryMapper - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper

LexicalCategoryMapper(List<CategoryRule>) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.LexicalCategoryMapper

M

MagmaUnitConverter - Class in org.molgenis.semanticmapper.utils

MagmaUnitConverter() - Constructor for class org.molgenis.semanticmapper.utils.MagmaUnitConverter

MapperPackage - Class in org.molgenis.semanticmapper.meta

MapperPackage(PackageMetadata, RootSystemPackage) - Constructor for class org.molgenis.semanticmapper.meta.MapperPackage

MAPPING_BATCH_SIZE - Static variable in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

MAPPING_JOB_EXECUTION - Static variable in class org.molgenis.semanticmapper.job.MappingJobExecutionMetadata

MAPPING_PROJECT - Static variable in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

MAPPING_TARGET - Static variable in class org.molgenis.semanticmapper.meta.MappingTargetMetaData

MAPPING_TARGETS - Static variable in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

MappingConfig - Class in org.molgenis.semanticmapper.config

MappingConfig(PermissionSystemService, DataService, SystemPackageRegistry, OntologyTagService, SemanticSearchService, OntologyService, IdGenerator, OntologyTermRepository, AttributeMappingMetaData, AttributeFactory, MappingProjectMetaData, EntityManager, JsMagmaScriptEvaluator) - Constructor for class org.molgenis.semanticmapper.config.MappingConfig

MappingJobConfig - Class in org.molgenis.semanticmapper.job

MappingJobConfig(MappingService, ScheduledJobTypeFactory, MappingJobExecutionMetadata) - Constructor for class org.molgenis.semanticmapper.job.MappingJobConfig

MappingJobExecution - Class in org.molgenis.semanticmapper.job

MappingJobExecution(Entity) - Constructor for class org.molgenis.semanticmapper.job.MappingJobExecution

MappingJobExecution(EntityType) - Constructor for class org.molgenis.semanticmapper.job.MappingJobExecution

MappingJobExecution(String, EntityType) - Constructor for class org.molgenis.semanticmapper.job.MappingJobExecution

MappingJobExecutionFactory - Class in org.molgenis.semanticmapper.job

MappingJobExecutionMetadata - Class in org.molgenis.semanticmapper.job

mappingJobFactory() - Method in class org.molgenis.semanticmapper.job.MappingJobConfig

The MappingJob Factory bean.

mappingJobType() - Method in class org.molgenis.semanticmapper.job.MappingJobConfig

MappingProject - Class in org.molgenis.semanticmapper.mapping.model

MappingProject(String, int) - Constructor for class org.molgenis.semanticmapper.mapping.model.MappingProject

Creates a new empty mapping project.

MappingProject(String, String, int, List<MappingTarget>) - Constructor for class org.molgenis.semanticmapper.mapping.model.MappingProject

Creates a new instance of MappingProject.

MappingProjectMetaData - Class in org.molgenis.semanticmapper.meta

MappingProjectMetaData(MapperPackage, MappingTargetMetaData) - Constructor for class org.molgenis.semanticmapper.meta.MappingProjectMetaData

mappingProjectRepository() - Method in class org.molgenis.semanticmapper.config.MappingConfig

MappingProjectRepository - Interface in org.molgenis.semanticmapper.repository

MappingProjectRepositoryImpl - Class in org.molgenis.semanticmapper.repository.impl

MappingProjectRepositoryImpl(DataService, MappingTargetRepository, IdGenerator, MappingProjectMetaData) - Constructor for class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

mappingService() - Method in class org.molgenis.semanticmapper.config.MappingConfig

MappingService - Interface in org.molgenis.semanticmapper.service

MappingServiceController - Class in org.molgenis.semanticmapper.controller

MappingServiceController(AlgorithmService, MappingService, DataService, OntologyTagService, SemanticSearchService, MenuReaderService, MappingJobExecutionFactory, UserAccountService, JobExecutor, JobsController) - Constructor for class org.molgenis.semanticmapper.controller.MappingServiceController

MappingServiceImpl - Class in org.molgenis.semanticmapper.service.impl

MappingServiceImpl(DataService, AlgorithmService, MappingProjectRepository, PermissionSystemService, AttributeFactory, EntityManager) - Constructor for class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

MappingServiceRequest - Class in org.molgenis.semanticmapper.data.request

MappingServiceRequest(String, String, String, String, int) - Constructor for class org.molgenis.semanticmapper.data.request.MappingServiceRequest

MappingTarget - Class in org.molgenis.semanticmapper.mapping.model

MappingTarget(EntityType) - Constructor for class org.molgenis.semanticmapper.mapping.model.MappingTarget

Creates a new empty MappingTarget

MappingTarget(String, EntityType, Collection<EntityMapping>) - Constructor for class org.molgenis.semanticmapper.mapping.model.MappingTarget

Creates a new instance of MappingTarget.

MappingTargetMetaData - Class in org.molgenis.semanticmapper.meta

MappingTargetMetaData(MapperPackage, EntityMappingMetaData) - Constructor for class org.molgenis.semanticmapper.meta.MappingTargetMetaData

mappingTargetRepository() - Method in class org.molgenis.semanticmapper.config.MappingConfig

MappingTargetRepository - Interface in org.molgenis.semanticmapper.repository

MappingTargetRepositoryImpl - Class in org.molgenis.semanticmapper.repository.impl

MappingTargetRepositoryImpl(EntityMappingRepository) - Constructor for class org.molgenis.semanticmapper.repository.impl.MappingTargetRepositoryImpl

matchCriteria(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.AmountConvertor

matchCriteria(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.DailyAmountConvertor

matchCriteria(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.NumberAmountConvertor

matchCriteria(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.SeveralTimesConvertor

MissingCategoryRule - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.impl

MissingCategoryRule() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.MissingCategoryRule

N

NAME - Static variable in class org.molgenis.semanticmapper.meta.MappingProjectMetaData

NegativeCategoryRule - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.impl

NegativeCategoryRule() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.NegativeCategoryRule

NumberAmountConvertor - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor

NumberAmountConvertor() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.NumberAmountConvertor

numberToSuperscript(String) - Static method in class org.molgenis.semanticmapper.utils.UnitHelper

NumericAlgorithmGenerator - Class in org.molgenis.semanticmapper.algorithmgenerator.generator

NumericAlgorithmGenerator(UnitResolver) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.generator.NumericAlgorithmGenerator

NumericQuality - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl

NumericQuality() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl.NumericQuality

O

OneToManyCategoryAlgorithmGenerator - Class in org.molgenis.semanticmapper.algorithmgenerator.generator

OneToManyCategoryAlgorithmGenerator(DataService) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToManyCategoryAlgorithmGenerator

OneToOneCategoryAlgorithmGenerator - Class in org.molgenis.semanticmapper.algorithmgenerator.generator

OneToOneCategoryAlgorithmGenerator(DataService) - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.generator.OneToOneCategoryAlgorithmGenerator

org.molgenis.semanticmapper.algorithmgenerator.bean - package org.molgenis.semanticmapper.algorithmgenerator.bean

org.molgenis.semanticmapper.algorithmgenerator.categorymapper - package org.molgenis.semanticmapper.algorithmgenerator.categorymapper

org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor - package org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor

org.molgenis.semanticmapper.algorithmgenerator.generator - package org.molgenis.semanticmapper.algorithmgenerator.generator

org.molgenis.semanticmapper.algorithmgenerator.rules - package org.molgenis.semanticmapper.algorithmgenerator.rules

org.molgenis.semanticmapper.algorithmgenerator.rules.impl - package org.molgenis.semanticmapper.algorithmgenerator.rules.impl

org.molgenis.semanticmapper.algorithmgenerator.rules.quality - package org.molgenis.semanticmapper.algorithmgenerator.rules.quality

org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl - package org.molgenis.semanticmapper.algorithmgenerator.rules.quality.impl

org.molgenis.semanticmapper.algorithmgenerator.service - package org.molgenis.semanticmapper.algorithmgenerator.service

org.molgenis.semanticmapper.algorithmgenerator.service.impl - package org.molgenis.semanticmapper.algorithmgenerator.service.impl

org.molgenis.semanticmapper.config - package org.molgenis.semanticmapper.config

org.molgenis.semanticmapper.controller - package org.molgenis.semanticmapper.controller

org.molgenis.semanticmapper.data.request - package org.molgenis.semanticmapper.data.request

org.molgenis.semanticmapper.job - package org.molgenis.semanticmapper.job

org.molgenis.semanticmapper.mapping.model - package org.molgenis.semanticmapper.mapping.model

org.molgenis.semanticmapper.meta - package org.molgenis.semanticmapper.meta

Metadata for the mapping storage

org.molgenis.semanticmapper.repository - package org.molgenis.semanticmapper.repository

org.molgenis.semanticmapper.repository.impl - package org.molgenis.semanticmapper.repository.impl

org.molgenis.semanticmapper.service - package org.molgenis.semanticmapper.service

org.molgenis.semanticmapper.service.impl - package org.molgenis.semanticmapper.service.impl

org.molgenis.semanticmapper.utils - package org.molgenis.semanticmapper.utils

P

PACKAGE_MAPPER - Static variable in class org.molgenis.semanticmapper.meta.MapperPackage

PositiveCategoryRule - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.impl

PositiveCategoryRule() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.PositiveCategoryRule

Q

Quality<T> - Class in org.molgenis.semanticmapper.algorithmgenerator.rules.quality

Quality() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.rules.quality.Quality

R

removeAttributeMapping(String, String, String, String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Removes a attribute mapping

removeEntityMapping(String, String, String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Removes entity mapping

removeIdentifiers() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

removeIdentifiers() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

removeIdentifiers() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

removeIllegalChars(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.InternalAbstractCategoryRule

removeSource(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

RemoveTagRequest - Class in org.molgenis.semanticmapper.data.request

RemoveTagRequest() - Constructor for class org.molgenis.semanticmapper.data.request.RemoveTagRequest

render() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmTemplate

resolveUnit(Attribute, EntityType) - Method in class org.molgenis.semanticmapper.service.impl.UnitResolverImpl

resolveUnit(Attribute, EntityType) - Method in interface org.molgenis.semanticmapper.service.UnitResolver

Determine attribute unit based on meta data

retrieveAttributesFromAlgorithm(String, EntityType) - Method in interface org.molgenis.semanticmapper.repository.AttributeMappingRepository

Translates an algorithm to a list of Attribute based on the algorithm, and the EntityType of the source entity

retrieveAttributesFromAlgorithm(String, EntityType) - Method in class org.molgenis.semanticmapper.repository.impl.AttributeMappingRepositoryImpl

rules - Variable in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.CategoryMapper

S

saveAttributeMapping(String, String, String, String, String, AttributeMapping.AlgorithmState) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Adds a new AttributeMapping to an EntityMapping.

saveCategoryMapping(String, String, String, String, String) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

scheduleMappingJob(String, String, String, String, Boolean) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Schedules a MappingJobExecution.

setAddSourceAttribute(Boolean) - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

setAlgorithm(String) - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

setAlgorithmState(AttributeMapping.AlgorithmState) - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

setDepth(int) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

setErrorMessage(String) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

setIdentifier(String) - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

setIdentifier(String) - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

setIdentifier(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

setIdentifier(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

setLabel(String) - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

setMappingProjectId(String) - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

setName(String) - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

setNum(Long) - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

setOffset(Long) - Method in class org.molgenis.semanticmapper.data.request.MappingServiceRequest

setPackageId(String) - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

setTargetEntityTypeId(String) - Method in class org.molgenis.semanticmapper.job.MappingJobExecution

setValue(Object) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

SeveralTimesConvertor - Class in org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor

The several times converter is able to convert any frequency related categories, in which 'several times' have occurred, to a quantifiable amount.

SeveralTimesConvertor() - Constructor for class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.SeveralTimesConvertor

SIMPLE_NAME - Static variable in class org.molgenis.semanticmapper.meta.MapperPackage

SOURCE_ATTRIBUTES - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

SOURCE_ENTITY_TYPE - Static variable in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

split(String) - Method in class org.molgenis.semanticmapper.algorithmgenerator.rules.impl.InternalAbstractCategoryRule

STANDARD_PER_WEEK_UNIT - Static variable in class org.molgenis.semanticmapper.algorithmgenerator.categorymapper.convertor.AmountConvertor

superscriptToNumber(String) - Static method in class org.molgenis.semanticmapper.utils.UnitHelper

T

TagWizardController - Class in org.molgenis.semanticmapper.controller

TagWizardController() - Constructor for class org.molgenis.semanticmapper.controller.TagWizardController

TARGET - Static variable in class org.molgenis.semanticmapper.meta.MappingTargetMetaData

TARGET_ATTRIBUTE - Static variable in class org.molgenis.semanticmapper.meta.AttributeMappingMetaData

TARGET_ENTITY_TYPE - Static variable in class org.molgenis.semanticmapper.meta.EntityMappingMetaData

testScript(MappingServiceRequest) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Tests an algoritm by computing it for all entities in the source repository.

toEntityMappings(List<Entity>) - Method in interface org.molgenis.semanticmapper.repository.EntityMappingRepository

Creates a list of fully reconstructed EntityMappings.

toEntityMappings(List<Entity>) - Method in class org.molgenis.semanticmapper.repository.impl.EntityMappingRepositoryImpl

toMappingTargets(List<Entity>) - Method in class org.molgenis.semanticmapper.repository.impl.MappingTargetRepositoryImpl

toMappingTargets(List<Entity>) - Method in interface org.molgenis.semanticmapper.repository.MappingTargetRepository

Creates a list of fully reconstructed MappingTargets.

toString() - Method in enum org.molgenis.semanticmapper.mapping.model.AttributeMapping.AlgorithmState

toString() - Method in class org.molgenis.semanticmapper.mapping.model.AttributeMapping

toString() - Method in class org.molgenis.semanticmapper.mapping.model.EntityMapping

toString() - Method in class org.molgenis.semanticmapper.mapping.model.MappingProject

toString() - Method in class org.molgenis.semanticmapper.mapping.model.MappingTarget

toString() - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmTemplate

U

UnitHelper - Class in org.molgenis.semanticmapper.utils

unitResolver() - Method in class org.molgenis.semanticmapper.config.MappingConfig

UnitResolver - Interface in org.molgenis.semanticmapper.service

UnitResolverImpl - Class in org.molgenis.semanticmapper.service.impl

UnitResolverImpl(OntologyService) - Constructor for class org.molgenis.semanticmapper.service.impl.UnitResolverImpl

update(MappingProject) - Method in class org.molgenis.semanticmapper.repository.impl.MappingProjectRepositoryImpl

update(MappingProject) - Method in interface org.molgenis.semanticmapper.repository.MappingProjectRepository

Update an existing MappingProject

updateMappingProject(MappingProject) - Method in class org.molgenis.semanticmapper.service.impl.MappingServiceImpl

updateMappingProject(MappingProject) - Method in interface org.molgenis.semanticmapper.service.MappingService

Updates a MappingProject in the repository.

upsert(Collection<AttributeMapping>) - Method in interface org.molgenis.semanticmapper.repository.AttributeMappingRepository

Inserts or updates a Collection of AttributeMapping.

upsert(Collection<EntityMapping>) - Method in interface org.molgenis.semanticmapper.repository.EntityMappingRepository

Inserts or updates a list of EntityMappings and their AttributeMappings.

upsert(Collection<AttributeMapping>) - Method in class org.molgenis.semanticmapper.repository.impl.AttributeMappingRepositoryImpl

upsert(Collection<EntityMapping>) - Method in class org.molgenis.semanticmapper.repository.impl.EntityMappingRepositoryImpl

upsert(Collection<MappingTarget>) - Method in class org.molgenis.semanticmapper.repository.impl.MappingTargetRepositoryImpl

upsert(Collection<MappingTarget>) - Method in interface org.molgenis.semanticmapper.repository.MappingTargetRepository

Inserts or updates a list of MappingTargets and their EntityMappings and AttributeMapping s.

URI - Static variable in class org.molgenis.semanticmapper.controller.MappingServiceController

URI - Static variable in class org.molgenis.semanticmapper.controller.TagWizardController

V

validateAttributeMapping(MappingServiceRequest) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

value(Object) - Method in class org.molgenis.semanticmapper.service.impl.AlgorithmEvaluation

valueOf(String) - Static method in enum org.molgenis.semanticmapper.mapping.model.AttributeMapping.AlgorithmState

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.semanticmapper.mapping.model.AttributeMapping.AlgorithmState

Returns an array containing the constants of this enum type, in the order they are declared.

viewAttributeMapping(String, String, String, String, Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Displays an AttributeMapping

viewMappingProject(String, Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Displays a mapping project.

viewMappingProjects(Model) - Method in class org.molgenis.semanticmapper.controller.MappingServiceController

Initializes the model with all mapping projects and all entities to the model.

viewTagWizard(String, Model) - Method in class org.molgenis.semanticmapper.controller.TagWizardController

Displays on tag wizard button press

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