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

A

addAttributeTag(String, String, String, List<String>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

addAttributeTag(String, String, String, List<String>) - Method in interface org.molgenis.semanticsearch.service.OntologyTagService

addAttributeTag(EntityType, SemanticTag<Attribute, O, C>) - Method in interface org.molgenis.semanticsearch.service.TagService

Tags an attribute.

addAttributeTag(EntityType, SemanticTag<Attribute, LabeledResource, LabeledResource>) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

addAttributeTag(EntityType, SemanticTag<Attribute, OntologyTerm, Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

addEntityTag(SemanticTag<EntityType, O, C>) - Method in interface org.molgenis.semanticsearch.service.TagService

Tags an entity.

addEntityTag(SemanticTag<EntityType, LabeledResource, LabeledResource>) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

addEntityTag(SemanticTag<EntityType, OntologyTerm, Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

AttributeSearchResults - Class in org.molgenis.semanticsearch.explain.bean

AttributeSearchResults() - Constructor for class org.molgenis.semanticsearch.explain.bean.AttributeSearchResults

C

cleanStemPhrase(String) - Static method in class org.molgenis.semanticsearch.string.Stemmer

Remove illegal characters from the string and stem each single word

collectExpandedQueryMap(Set<String>, Collection<OntologyTerm>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

collectOntologyTermQueryMap(Map<String, String>, OntologyTerm) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

compareTo(Hit<T>) - Method in class org.molgenis.semanticsearch.semantic.Hit

convertAttributeToExplainedAttribute(Attribute, Map<String, String>, Query<Entity>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

A helper function to explain each of the matched attributes returned by the explain-API

create(String, String, String, double) - Static method in class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

create(List<Hit<T>>) - Static method in class org.molgenis.semanticsearch.semantic.Hits

create(Attribute) - Static method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

create(Attribute, Iterable<ExplainedQueryString>, boolean) - Static method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

create(Attribute, Set<ExplainedQueryString>, boolean) - Static method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttribute

create(Attribute, Hits<ExplainedAttribute>) - Static method in class org.molgenis.semanticsearch.explain.bean.AttributeSearchResults

create(EntityType, List<AttributeSearchResults>) - Static method in class org.molgenis.semanticsearch.explain.bean.EntityTypeSearchResults

create(OntologyTerm, Relation) - Static method in class org.molgenis.semanticsearch.semantic.OntologyTag

create(Hit<T>...) - Static method in class org.molgenis.semanticsearch.semantic.Hits

create(T, float) - Static method in class org.molgenis.semanticsearch.semantic.Hit

createBoostedDisMaxQueryRuleForTerms(List<String>, Double) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

Create a disMaxQueryRule with corresponding boosted value

createDisMaxQueryRuleForAttribute(Set<String>, Collection<OntologyTerm>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

Create a disMaxJunc query rule based on the given search terms as well as the information from given ontology terms

createDisMaxQueryRuleForTerms(List<String>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

Create disMaxJunc query rule based a list of queryTerm.

createLexicalSearchQueryTerms(Attribute, Set<String>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

A helper function to create a list of queryTerms based on the information from the targetAttribute as well as user defined searchTerms.

createNGrams(String, boolean) - Static method in class org.molgenis.semanticsearch.string.NGramDistanceAlgorithm

create n-grams tokens of the string.

createShouldQueryRule(String) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

Create a boolean should query for composite tags containing multiple ontology terms

E

ElasticSearchExplainService - Interface in org.molgenis.semanticsearch.explain.service

ElasticSearchExplainServiceImpl - Class in org.molgenis.semanticsearch.explain.service

ElasticSearchExplainServiceImpl(ElasticsearchService, ExplainServiceHelper) - Constructor for class org.molgenis.semanticsearch.explain.service.ElasticSearchExplainServiceImpl

EntityTypeSearchResults - Class in org.molgenis.semanticsearch.explain.bean

EntityTypeSearchResults() - Constructor for class org.molgenis.semanticsearch.explain.bean.EntityTypeSearchResults

escapeCharsExcludingCaretChar(String) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

explain(Query<Entity>, EntityType, Object) - Method in interface org.molgenis.semanticsearch.explain.service.ElasticSearchExplainService

Get explanation for a specific document in elasticSearch

explain(Query<Entity>, EntityType, Object) - Method in class org.molgenis.semanticsearch.explain.service.ElasticSearchExplainServiceImpl

ExplainedAttribute - Class in org.molgenis.semanticsearch.explain.bean

ExplainedAttribute() - Constructor for class org.molgenis.semanticsearch.explain.bean.ExplainedAttribute

ExplainedAttributeDto - Class in org.molgenis.semanticsearch.explain.bean

ExplainedAttributeDto() - Constructor for class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

ExplainedQueryString - Class in org.molgenis.semanticsearch.explain.bean

ExplainedQueryString() - Constructor for class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

explainServiceHelper() - Method in class org.molgenis.semanticsearch.config.SemanticSearchConfig

ExplainServiceHelper - Class in org.molgenis.semanticsearch.explain.service

ExplainServiceHelper() - Constructor for class org.molgenis.semanticsearch.explain.service.ExplainServiceHelper

ExplainServiceHelper.Options - Enum in org.molgenis.semanticsearch.explain.service

F

findAttributes(EntityType, Set<String>, Collection<OntologyTerm>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

public for testability

findAttributes(EntityType, EntityType) - Method in interface org.molgenis.semanticsearch.service.SemanticSearchService

Find attributes in a source entity type that match attributes in a target entity type.

findAttributes(EntityType, EntityType, Set<String>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

findAttributes(EntityType, EntityType, Set<String>) - Method in interface org.molgenis.semanticsearch.service.SemanticSearchService

Find attributes in a source entity type that match attributes in a target entity type.

findAttributes(EntityType, EntityType, Attribute) - Method in interface org.molgenis.semanticsearch.service.SemanticSearchService

Find attributes in a entity type that match the given target attribute in the target entity type.

findAttributes(EntityType, EntityType, Attribute, Set<String>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

findAttributes(EntityType, EntityType, Attribute, Set<String>) - Method in interface org.molgenis.semanticsearch.service.SemanticSearchService

Find attributes in an entity type that match the given target attribute in the target entity type.

findOntologyTerms(Attribute, Collection<Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

findOntologyTerms(Attribute, Collection<Ontology>) - Method in interface org.molgenis.semanticsearch.service.SemanticSearchService

Finds ontology terms in the given ontologies that can be used to tag an attribute.

findQueriesFromExplanation(Map<String, String>, Explanation) - Method in interface org.molgenis.semanticsearch.explain.service.ElasticSearchExplainService

Deduce all the matches that are generated by ElasticSearch

findQueriesFromExplanation(Map<String, String>, Explanation) - Method in class org.molgenis.semanticsearch.explain.service.ElasticSearchExplainServiceImpl

findTags(String, List<String>) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

G

getAttribute() - Method in class org.molgenis.semanticsearch.explain.bean.AttributeSearchResults

getAttribute() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttribute

getAttribute() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

getAttributeIdentifiers(EntityType) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

A helper function that gets identifiers of all the attributes from one EntityType

getAttributeSearchResults() - Method in class org.molgenis.semanticsearch.explain.bean.EntityTypeSearchResults

getEntityType() - Method in class org.molgenis.semanticsearch.explain.bean.EntityTypeSearchResults

getExplainedQueryStrings() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttribute

getExplainedQueryStrings() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

getHits() - Method in class org.molgenis.semanticsearch.explain.bean.AttributeSearchResults

getHits() - Method in class org.molgenis.semanticsearch.semantic.Hits

getItem() - Method in interface org.molgenis.semanticsearch.semantic.SearchResult

getMatchedWords() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

getOntologyTerm() - Method in class org.molgenis.semanticsearch.semantic.OntologyTag

getOtLabelAndSynonyms(OntologyTerm) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

A helper function to collect synonyms as well as label of ontologyterm

getQueryString() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

getRelationIRI() - Method in class org.molgenis.semanticsearch.semantic.OntologyTag

getRelevance() - Method in interface org.molgenis.semanticsearch.semantic.SearchResult

getResult() - Method in class org.molgenis.semanticsearch.semantic.Hit

getScore() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

getScore() - Method in class org.molgenis.semanticsearch.semantic.Hit

getScoreInt() - Method in class org.molgenis.semanticsearch.semantic.Hit

getTagEntity(String, String, Relation, String) - Method in class org.molgenis.semanticsearch.repository.TagRepository

Fetches a tag from the repository.

getTagEntity(SemanticTag<?, LabeledResource, LabeledResource>) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

getTagEntity(SemanticTag<?, OntologyTerm, Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

getTagName() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedQueryString

getTagsForAttribute(EntityType, Attribute) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

getTagsForAttribute(EntityType, Attribute) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

getTagsForAttribute(EntityType, Attribute) - Method in interface org.molgenis.semanticsearch.service.TagService

Retrieves all tags for an attribute, and groups them by relation

getTagsForEntity(EntityType) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

getTagsForEntity(EntityType) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

getTagsForEntity(EntityType) - Method in interface org.molgenis.semanticsearch.service.TagService

Retrieves all tags for an entity.

getTagsForPackage(Package) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

getTagsForPackage(Package) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

getTagsForPackage(Package) - Method in interface org.molgenis.semanticsearch.service.TagService

Retrieves all tags for a package

H

hasHits() - Method in class org.molgenis.semanticsearch.semantic.Hits

Hit<T> - Class in org.molgenis.semanticsearch.semantic

Hit() - Constructor for class org.molgenis.semanticsearch.semantic.Hit

Hits<T> - Class in org.molgenis.semanticsearch.semantic

Hits() - Constructor for class org.molgenis.semanticsearch.semantic.Hits

I

isHighQuality() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttribute

isHighQuality() - Method in class org.molgenis.semanticsearch.explain.bean.ExplainedAttributeDto

iterator() - Method in class org.molgenis.semanticsearch.semantic.Hits

M

MAX_NUM_TAGS - Static variable in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

MAX_OF - org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

elasticsearch description that is max of:

N

NGramDistanceAlgorithm - Class in org.molgenis.semanticsearch.string

This class has implemented n-gram distance algorithm so a similarity score could be calculated between two sequences.

O

OntologyTag - Class in org.molgenis.semanticsearch.semantic

OntologyTag() - Constructor for class org.molgenis.semanticsearch.semantic.OntologyTag

ontologyTagService() - Method in class org.molgenis.semanticsearch.config.SemanticSearchConfig

OntologyTagService - Interface in org.molgenis.semanticsearch.service

OntologyTagServiceImpl - Class in org.molgenis.semanticsearch.service.impl

Service to tag metadata with ontology terms.

OntologyTagServiceImpl(DataService, OntologyService, TagRepository, IdGenerator, TagMetadata) - Constructor for class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

org.molgenis.semanticsearch.config - package org.molgenis.semanticsearch.config

org.molgenis.semanticsearch.explain.bean - package org.molgenis.semanticsearch.explain.bean

org.molgenis.semanticsearch.explain.service - package org.molgenis.semanticsearch.explain.service

org.molgenis.semanticsearch.repository - package org.molgenis.semanticsearch.repository

org.molgenis.semanticsearch.semantic - package org.molgenis.semanticsearch.semantic

org.molgenis.semanticsearch.service - package org.molgenis.semanticsearch.service

org.molgenis.semanticsearch.service.impl - package org.molgenis.semanticsearch.service.impl

org.molgenis.semanticsearch.string - package org.molgenis.semanticsearch.string

P

parseBoostQueryString(String, double) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

parseOntologyTermQueries(OntologyTerm) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

Create a list of string queries based on the information collected from current ontologyterm including label, synonyms and child ontologyterms

processQueryString(String) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

PRODUCT_OF - org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

elasticsearch description that is product of:

R

removeAllTagsFromEntity(String) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

removeAllTagsFromEntity(String) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

removeAllTagsFromEntity(String) - Method in interface org.molgenis.semanticsearch.service.TagService

Removes all tags for a given entity

removeAttributeTag(String, String, String, String) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

removeAttributeTag(String, String, String, String) - Method in interface org.molgenis.semanticsearch.service.OntologyTagService

removeAttributeTag(EntityType, SemanticTag<Attribute, O, C>) - Method in interface org.molgenis.semanticsearch.service.TagService

Removes attribute tag

removeAttributeTag(EntityType, SemanticTag<Attribute, LabeledResource, LabeledResource>) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

removeAttributeTag(EntityType, SemanticTag<Attribute, OntologyTerm, Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

removeEntityTag(SemanticTag<EntityType, O, C>) - Method in interface org.molgenis.semanticsearch.service.TagService

Removes an entity tag.

removeEntityTag(SemanticTag<EntityType, LabeledResource, LabeledResource>) - Method in class org.molgenis.semanticsearch.service.impl.UntypedTagService

removeEntityTag(SemanticTag<EntityType, OntologyTerm, Ontology>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

removeStopWords(String) - Method in class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

replaceIllegalCharacter(String) - Static method in class org.molgenis.semanticsearch.string.Stemmer

S

SearchResult<I> - Interface in org.molgenis.semanticsearch.semantic

SemanticSearchConfig - Class in org.molgenis.semanticsearch.config

SemanticSearchConfig(DataService, OntologyService, IdGenerator, TermFrequencyService, TagMetadata, TagFactory, ElasticsearchService) - Constructor for class org.molgenis.semanticsearch.config.SemanticSearchConfig

semanticSearchService() - Method in class org.molgenis.semanticsearch.config.SemanticSearchConfig

SemanticSearchService - Interface in org.molgenis.semanticsearch.service

semanticSearchServiceHelper() - Method in class org.molgenis.semanticsearch.config.SemanticSearchConfig

SemanticSearchServiceHelper - Class in org.molgenis.semanticsearch.service.impl

SemanticSearchServiceHelper(DataService, OntologyService, TermFrequencyService) - Constructor for class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceHelper

SemanticSearchServiceImpl - Class in org.molgenis.semanticsearch.service.impl

SemanticSearchServiceImpl(DataService, OntologyService, SemanticSearchServiceHelper, ElasticSearchExplainService, OntologyTagService) - Constructor for class org.molgenis.semanticsearch.service.impl.SemanticSearchServiceImpl

stem(String) - Static method in class org.molgenis.semanticsearch.string.Stemmer

stemAndJoin(Set<String>) - Static method in class org.molgenis.semanticsearch.string.Stemmer

Stemmer - Class in org.molgenis.semanticsearch.string

STOPWORDSLIST - Static variable in class org.molgenis.semanticsearch.string.NGramDistanceAlgorithm

stringMatching(String, String) - Static method in class org.molgenis.semanticsearch.string.NGramDistanceAlgorithm

stringMatching(String, String, boolean) - Static method in class org.molgenis.semanticsearch.string.NGramDistanceAlgorithm

SUM_OF - org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

elasticsearch description that is sum of:

T

tagAttributesInEntity(String, Map<Attribute, OntologyTerm>) - Method in class org.molgenis.semanticsearch.service.impl.OntologyTagServiceImpl

tagAttributesInEntity(String, Map<Attribute, OntologyTerm>) - Method in interface org.molgenis.semanticsearch.service.OntologyTagService

TagRepository - Class in org.molgenis.semanticsearch.repository

Helper class around the TagMetadata repository.

TagRepository(DataService, IdGenerator, TagFactory) - Constructor for class org.molgenis.semanticsearch.repository.TagRepository

tagService() - Method in class org.molgenis.semanticsearch.config.SemanticSearchConfig

TagService<O,C> - Interface in org.molgenis.semanticsearch.service

Service that administrates tags on attributes, entities and packages of a particular code system.

toString() - Method in enum org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

U

UntypedTagService - Class in org.molgenis.semanticsearch.service.impl

Service to tag metadata with simple String terms.

UntypedTagService(DataService, TagRepository) - Constructor for class org.molgenis.semanticsearch.service.impl.UntypedTagService

V

valueOf(String) - Static method in enum org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

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

values() - Static method in enum org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

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

W

WEIGHT - org.molgenis.semanticsearch.explain.service.ExplainServiceHelper.Options

elasticsearch description that starts with weight:

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