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

A

addAttributeTag(EntityMetaData, Tag<AttributeMetaData, OntologyTerm, Ontology>) - Method in class org.molgenis.data.semanticsearch.service.impl.OntologyTagServiceImpl

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

addAttributeTag(EntityMetaData, Tag<AttributeMetaData, LabeledResource, LabeledResource>) - Method in class org.molgenis.data.semanticsearch.service.impl.UntypedTagService

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

addAttributeTag(EntityMetaData, Tag<AttributeMetaData, ObjectType, CodeSystemType>) - Method in interface org.molgenis.data.semanticsearch.service.TagService

Tags an attribute.

addEntityTag(Tag<EntityMetaData, OntologyTerm, Ontology>) - Method in class org.molgenis.data.semanticsearch.service.impl.OntologyTagServiceImpl

addEntityTag(Tag<EntityMetaData, LabeledResource, LabeledResource>) - Method in class org.molgenis.data.semanticsearch.service.impl.UntypedTagService

addEntityTag(Tag<EntityMetaData, ObjectType, CodeSystemType>) - Method in interface org.molgenis.data.semanticsearch.service.TagService

Tags an entity.

B

bestMatchingSynonym(OntologyTerm, Set<String>) - Method in class org.molgenis.data.semanticsearch.service.impl.SemanticSearchServiceImpl

Computes the best matching synonym which is closest to a set of search terms.
Will stem the OntologyTerm 's synonyms and the search terms, and then compute the maximum StringDistance between them.

C

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

Remove illegal characters from the string and stem each single word

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

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

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

convertAttributeEntityToExplainedAttribute(Entity, EntityMetaData, Map<String, String>, List<QueryRule>) - Method in class org.molgenis.data.semanticsearch.service.impl.SemanticSearchServiceImpl

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

create(AttributeMetaData) - Static method in class org.molgenis.data.semanticsearch.explain.bean.ExplainedAttributeMetaData

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

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

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

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

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

Create a disMaxQueryRule with corresponding boosted value

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

Create disMaxJunc query rule based a list of queryTerm.

createLexicalSearchQueryTerms(AttributeMetaData, Set<String>) - Method in class org.molgenis.data.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.data.semanticsearch.string.NGramDistanceAlgorithm

create n-grams tokens of the string.

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

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

D

decisionTreeToFindRelevantAttributes(EntityMetaData, AttributeMetaData, Collection<OntologyTerm>, Set<String>) - Method in class org.molgenis.data.semanticsearch.service.impl.SemanticSearchServiceImpl

decisionTreeToFindRelevantAttributes(EntityMetaData, AttributeMetaData, Collection<OntologyTerm>, Set<String>) - Method in interface org.molgenis.data.semanticsearch.service.SemanticSearchService

A decision tree for getting the relevant attributes 1.

E

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

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

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

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

explain(Query, EntityMetaData, String) - Method in interface org.molgenis.data.semanticsearch.explain.service.ElasticSearchExplainService

Get explanation for a specific document in elasticSearch

explain(Query, EntityMetaData, String) - Method in class org.molgenis.data.semanticsearch.explain.service.ElasticSearchExplainServiceImpl

ExplainedAttributeMetaData - Class in org.molgenis.data.semanticsearch.explain.bean

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

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

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

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

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

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

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

extractMatchedWords(Explanation[]) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

F

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

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

findAttributes(EntityMetaData, Set<String>, Collection<OntologyTerm>) - Method in interface org.molgenis.data.semanticsearch.service.SemanticSearchService

Find all relevant source attributes with an explanation based on ontology terms and search terms

findMatchedWords(Explanation) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

This method is able to recursively collect all the matched words from ElastisSearch Explanation document

findMatchQueries(String, Map<String, String>) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

This method is able to find the queries that are used in the matching.

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

Deduce all the matches that are generated by ElasticSearch

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

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

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

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

findTags(String, List<String>) - Method in interface org.molgenis.data.semanticsearch.service.SemanticSearchService

Finds OntologyTerms that can be used to tag an attribute.

findTags(AttributeMetaData, List<String>) - Method in interface org.molgenis.data.semanticsearch.service.SemanticSearchService

Finds OntologyTerms for an attribute.

G

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

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

getAttributeMetaData() - Method in class org.molgenis.data.semanticsearch.explain.bean.ExplainedAttributeMetaData

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

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

getMatchedWord(String) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

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

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

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

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

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

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

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

getRelevantSubItems() - Method in interface org.molgenis.data.semanticsearch.semantic.ItemizedSearchResult

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

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

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

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

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

Fetches a tag from the repository.

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

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

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

getTagsForAttribute(EntityMetaData, AttributeMetaData) - Method in class org.molgenis.data.semanticsearch.service.impl.OntologyTagServiceImpl

getTagsForAttribute(EntityMetaData, AttributeMetaData) - Method in class org.molgenis.data.semanticsearch.service.impl.UntypedTagService

getTagsForAttribute(EntityMetaData, AttributeMetaData) - Method in interface org.molgenis.data.semanticsearch.service.TagService

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

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

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

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

Retrieves all tags for an entity.

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

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

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

Retrieves all tags for a package

H

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

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

I

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

ItemizedSearchResult<ItemType> - Interface in org.molgenis.data.semanticsearch.semantic

M

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

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

META_DATA - Static variable in class org.molgenis.data.semanticsearch.repository.TagRepository

N

NGramDistanceAlgorithm - Class in org.molgenis.data.semanticsearch.string

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

NGramDistanceAlgorithm() - Constructor for class org.molgenis.data.semanticsearch.string.NGramDistanceAlgorithm

O

OntologyTag - Class in org.molgenis.data.semanticsearch.semantic

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

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

OntologyTagService - Interface in org.molgenis.data.semanticsearch.service

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

Service to tag metadata with ontology terms.

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

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

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

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

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

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

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

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

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

P

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

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

R

reachLastLevel(Explanation) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

REGEXR_PATTERN - Static variable in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

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

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

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

Removes all tags for a given entity

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

removeAttributeTag(EntityMetaData, Tag<AttributeMetaData, OntologyTerm, Ontology>) - Method in class org.molgenis.data.semanticsearch.service.impl.OntologyTagServiceImpl

removeAttributeTag(EntityMetaData, Tag<AttributeMetaData, LabeledResource, LabeledResource>) - Method in class org.molgenis.data.semanticsearch.service.impl.UntypedTagService

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

removeAttributeTag(EntityMetaData, Tag<AttributeMetaData, ObjectType, CodeSystemType>) - Method in interface org.molgenis.data.semanticsearch.service.TagService

Removes attribute tag

removeBoostFromQuery(String) - Method in class org.molgenis.data.semanticsearch.explain.service.ExplainServiceHelper

removeEntityTag(Tag<EntityMetaData, OntologyTerm, Ontology>) - Method in class org.molgenis.data.semanticsearch.service.impl.OntologyTagServiceImpl

removeEntityTag(Tag<EntityMetaData, LabeledResource, LabeledResource>) - Method in class org.molgenis.data.semanticsearch.service.impl.UntypedTagService

removeEntityTag(Tag<EntityMetaData, ObjectType, CodeSystemType>) - Method in interface org.molgenis.data.semanticsearch.service.TagService

Removes an entity tag.

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

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

S

SearchResult<ItemType> - Interface in org.molgenis.data.semanticsearch.semantic

SemanticSearchConfig - Class in org.molgenis.data.semanticsearch.config

SemanticSearchConfig() - Constructor for class org.molgenis.data.semanticsearch.config.SemanticSearchConfig

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

SemanticSearchService - Interface in org.molgenis.data.semanticsearch.service

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

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

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

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

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

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

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

Stemmer - Class in org.molgenis.data.semanticsearch.string

Stemmer() - Constructor for class org.molgenis.data.semanticsearch.string.Stemmer

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

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

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

T

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

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

TagRepository - Class in org.molgenis.data.semanticsearch.repository

Helper class around the TagMetaData repository.

TagRepository(Repository, IdGenerator) - Constructor for class org.molgenis.data.semanticsearch.repository.TagRepository

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

TagService<ObjectType,CodeSystemType> - Interface in org.molgenis.data.semanticsearch.service

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

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

U

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

Service to tag metadata with simple String terms.

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

V

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

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

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

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

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