Uses of Class
ubic.gemma.core.search.SearchException

Packages that use SearchException

Package	Description
ubic.gemma.core.association.phenotype
ubic.gemma.core.ontology
ubic.gemma.core.search
ubic.gemma.core.search.lucene
ubic.gemma.core.search.source
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome.gene
ubic.gemma.rest.util.args
ubic.gemma.web.controller
ubic.gemma.web.controller.expression.designElement

Uses of SearchException in ubic.gemma.core.association.phenotype

Methods in ubic.gemma.core.association.phenotype that throw SearchException

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.findExperimentOntologyValue(String givenQueryString, long timeout, TimeUnit timeUnit)	Deprecated. for a given search string look in the database and Ontology for matches
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.findExperimentOntologyValue(String givenQueryString, long timeout, TimeUnit timeUnit)	Deprecated.
List<GeneEvidenceValueObject>	PhenotypeAssociationManagerService.findGenesWithEvidence(String query, Long taxonId)	Deprecated. Does a Gene search (by name or symbol) for a query and return only Genes with evidence
List<GeneEvidenceValueObject>	PhenotypeAssociationManagerServiceImpl.findGenesWithEvidence(String query, Long taxonId)	Deprecated.
Set<CharacteristicValueObject>	PhenotypeAssoOntologyHelper.findPhenotypesInOntology(String searchQuery)	Deprecated. search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
Set<CharacteristicValueObject>	PhenotypeAssoOntologyHelperImpl.findPhenotypesInOntology(String searchQuery)	Deprecated.
Collection<OntologyTerm>	PhenotypeAssoOntologyHelper.findValueUriInOntology(String searchQuery)	Deprecated. search the disease, hp and mp ontology for OntologyTerm
Collection<OntologyTerm>	PhenotypeAssoOntologyHelperImpl.findValueUriInOntology(String searchQuery)	Deprecated.
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.searchInDatabaseForPhenotype(String searchQuery, int maxResults, long timeout, TimeUnit timeUnit)	Deprecated. For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.searchInDatabaseForPhenotype(String searchQuery, int maxResults, long timeout, TimeUnit timeUnit)	Deprecated.
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerService.searchOntologyForPhenotypes(String searchQuery, Long geneId)	Deprecated. Giving a phenotype searchQuery, returns a selection choice to the user
Collection<CharacteristicValueObject>	PhenotypeAssociationManagerServiceImpl.searchOntologyForPhenotypes(String searchQuery, Long geneId)	Deprecated.

Uses of SearchException in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology that throw SearchException

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	OntologyService.findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Deprecated.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findExperimentsCharacteristicTags(String searchQuery, int maxResults, boolean useNeuroCartaOntology, long timeout, TimeUnit timeUnit)	Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
Collection<OntologySearchResult<OntologyTerm>>	OntologyService.findTerms(String query, int maxResults, long timeout, TimeUnit timeUnit)	Given a search string will look through the loaded ontologies for terms that match the search term.
Collection<OntologySearchResult<OntologyTerm>>	OntologyServiceImpl.findTerms(String search, int maxResults, long timeout, TimeUnit timeUnit)
Collection<CharacteristicValueObject>	OntologyService.findTermsInexact(String givenQueryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)	Given a search string will first look through the characteristic database for any entries that have a match.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findTermsInexact(String queryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)

Uses of SearchException in ubic.gemma.core.search

Subclasses of SearchException in ubic.gemma.core.search

Modifier and Type	Class	Description
class	BaseCodeOntologySearchException	Exception that wraps a baseCode OntologySearchException.
class	ParseSearchException	An exception that indicate that the search query could not be parsed.
class	SearchTimeoutException	Indicate that the search failed due to a TimeoutException.

Methods in ubic.gemma.core.search that throw SearchException

Modifier and Type	Method	Description
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon)	finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)	finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon)
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)
Collection<GeneSetValueObject>	GeneSetSearch.findByPhenotypeName(String phenotypeQuery, Taxon taxon)
Collection<GeneSetValueObject>	GeneSetSearchImpl.findByPhenotypeName(String phenotypeQuery, Taxon taxon)
Collection<GeneSet>	GeneSetSearch.findGeneSetsByName(String query, Long taxonId)	Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
Collection<GeneSet>	GeneSetSearchImpl.findGeneSetsByName(String query, Long taxonId)
SearchService.SearchResultMap	SearchService.search(SearchSettings settings)	The results are sorted in order of decreasing score, organized by class.
SearchService.SearchResultMap	SearchServiceImpl.search(SearchSettings settings)
default Collection<SearchResult<ArrayDesign>>	SearchSource.searchArrayDesign(SearchSettings settings)
default Collection<SearchResult<BibliographicReference>>	SearchSource.searchBibliographicReference(SearchSettings settings)
default Collection<SearchResult<BioSequence>>	SearchSource.searchBioSequence(SearchSettings settings)
default Collection<SearchResult<?>>	SearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
default Collection<SearchResult<BlacklistedEntity>>	SearchSource.searchBlacklistedEntities(SearchSettings settings)
default Collection<SearchResult<CompositeSequence>>	SearchSource.searchCompositeSequence(SearchSettings settings)
default Collection<SearchResult<?>>	SearchSource.searchCompositeSequenceAndGene(SearchSettings settings)	Deprecated. use SearchSource.searchCompositeSequence(SearchSettings) instead
default Collection<SearchResult<ExpressionExperimentSet>>	SearchSource.searchExperimentSet(SearchSettings settings)
default Collection<SearchResult<ExpressionExperiment>>	SearchSource.searchExpressionExperiment(SearchSettings settings)
default Collection<SearchResult<Gene>>	SearchSource.searchGene(SearchSettings settings)
default Collection<SearchResult<GeneSet>>	SearchSource.searchGeneSet(SearchSettings settings)

Uses of SearchException in ubic.gemma.core.search.lucene

Subclasses of SearchException in ubic.gemma.core.search.lucene

Modifier and Type	Class	Description
class	LuceneParseSearchException

Methods in ubic.gemma.core.search.lucene that throw SearchException

Modifier and Type	Method	Description
static Set<String>	LuceneQueryUtils.extractTerms(SearchSettings settings)	Extract terms, regardless of their logical organization.
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings)
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings, boolean allowWildcards)	Extract a DNF (Disjunctive Normal Form) from the terms of a query.
static org.apache.lucene.search.Query	LuceneQueryUtils.parseSafely(String query, org.apache.lucene.queryParser.QueryParser queryParser, Consumer<? super org.apache.lucene.queryParser.ParseException> report)	Safely parse the given search query into a Lucene query, falling back on a query with special characters escaped if necessary.
static org.apache.lucene.search.Query	LuceneQueryUtils.parseSafely(SearchSettings settings, org.apache.lucene.queryParser.QueryParser queryParser)	Safely parse the given search settings into a Lucene query, falling back on a query with special characters escaped if necessary.
static String	LuceneQueryUtils.prepareDatabaseQuery(String query, boolean allowWildcards)
static String	LuceneQueryUtils.prepareDatabaseQuery(SearchSettings settings)	Escape the query for a database match.
static String	LuceneQueryUtils.prepareDatabaseQuery(SearchSettings settings, boolean allowWildcards)	Obtain a query suitable for a database match.
static URI	LuceneQueryUtils.prepareTermUriQuery(String s)
static URI	LuceneQueryUtils.prepareTermUriQuery(SearchSettings settings)

Uses of SearchException in ubic.gemma.core.search.source

Subclasses of SearchException in ubic.gemma.core.search.source

Modifier and Type	Class	Description
class	HibernateSearchException

Methods in ubic.gemma.core.search.source that throw SearchException

Modifier and Type	Method	Description
Collection<SearchResult<ArrayDesign>>	CompositeSearchSource.searchArrayDesign(SearchSettings settings)
Collection<SearchResult<ArrayDesign>>	DatabaseSearchSource.searchArrayDesign(SearchSettings settings)	A general search for array designs.
Collection<SearchResult<ArrayDesign>>	HibernateSearchSource.searchArrayDesign(SearchSettings settings)
Collection<SearchResult<BibliographicReference>>	CompositeSearchSource.searchBibliographicReference(SearchSettings settings)
Collection<SearchResult<BibliographicReference>>	HibernateSearchSource.searchBibliographicReference(SearchSettings settings)
Collection<SearchResult<BioSequence>>	CompositeSearchSource.searchBioSequence(SearchSettings settings)
Collection<SearchResult<BioSequence>>	DatabaseSearchSource.searchBioSequence(SearchSettings settings)	A database search for biosequences.
Collection<SearchResult<BioSequence>>	HibernateSearchSource.searchBioSequence(SearchSettings settings)
Collection<SearchResult<?>>	CompositeSearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated.
Collection<SearchResult<?>>	DatabaseSearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)
Collection<SearchResult<BlacklistedEntity>>	CompositeSearchSource.searchBlacklistedEntities(SearchSettings settings)
Collection<SearchResult<BlacklistedEntity>>	DatabaseSearchSource.searchBlacklistedEntities(SearchSettings settings)
Collection<SearchResult<CompositeSequence>>	CompositeSearchSource.searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<CompositeSequence>>	DatabaseSearchSource.searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<CompositeSequence>>	HibernateSearchSource.searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<?>>	CompositeSearchSource.searchCompositeSequenceAndGene(SearchSettings settings)	Deprecated.
Collection<SearchResult<?>>	DatabaseSearchSource.searchCompositeSequenceAndGene(SearchSettings settings)	Search the DB for composite sequences and the genes that are matched to them.
Collection<SearchResult<ExpressionExperimentSet>>	CompositeSearchSource.searchExperimentSet(SearchSettings settings)
Collection<SearchResult<ExpressionExperimentSet>>	DatabaseSearchSource.searchExperimentSet(SearchSettings settings)
Collection<SearchResult<ExpressionExperimentSet>>	HibernateSearchSource.searchExperimentSet(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	CompositeSearchSource.searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	DatabaseSearchSource.searchExpressionExperiment(SearchSettings settings)	Does search on exact string by: id, name and short name.
Collection<SearchResult<ExpressionExperiment>>	HibernateSearchSource.searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	OntologySearchSource.searchExpressionExperiment(SearchSettings settings)	Search via characteristics i.e.
Collection<SearchResult<Gene>>	CompositeSearchSource.searchGene(SearchSettings settings)
Collection<SearchResult<Gene>>	DatabaseSearchSource.searchGene(SearchSettings settings)	Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence tables
Collection<SearchResult<Gene>>	GeneOntologySearchSource.searchGene(SearchSettings settings)
Collection<SearchResult<Gene>>	HibernateSearchSource.searchGene(SearchSettings settings)
Collection<SearchResult<GeneSet>>	CompositeSearchSource.searchGeneSet(SearchSettings settings)
Collection<SearchResult<GeneSet>>	DatabaseSearchSource.searchGeneSet(SearchSettings settings)
Collection<SearchResult<GeneSet>>	HibernateSearchSource.searchGeneSet(SearchSettings settings)

Uses of SearchException in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description that throw SearchException

Modifier and Type	Method	Description
List<BibliographicReferenceValueObject>	BibliographicReferenceService.search(String query)
List<BibliographicReferenceValueObject>	BibliographicReferenceService.search(SearchSettingsValueObject settings)
List<BibliographicReferenceValueObject>	BibliographicReferenceServiceImpl.search(String query)
List<BibliographicReferenceValueObject>	BibliographicReferenceServiceImpl.search(SearchSettingsValueObject settings)

Uses of SearchException in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that throw SearchException

Modifier and Type	Method	Description
Collection<Long>	ExpressionExperimentService.filter(String searchString)	returns ids of search results.
Collection<Long>	ExpressionExperimentServiceImpl.filter(String searchString)	returns ids of search results
List<SearchResultDisplayObject>	ExpressionExperimentSearchService.searchExperimentsAndExperimentGroups(String query, Long taxonId)	does not include session bound sets
List<SearchResultDisplayObject>	ExpressionExperimentSearchServiceImpl.searchExperimentsAndExperimentGroups(String query, Long taxonId)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(String query)
Collection<Long>	ExpressionExperimentSearchService.searchExpressionExperiments(String query, Long taxonId)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(List<String> value)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(String query)
Collection<Long>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(String query, Long taxonId)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(List<String> query)

Uses of SearchException in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene that throw SearchException

Modifier and Type	Method	Description
Collection<GeneSetValueObject>	GeneSetService.findGeneSetsByName(String query, Long taxonId)
Collection<GeneSetValueObject>	GeneSetServiceImpl.findGeneSetsByName(String query, Long taxonId)
Collection<Gene>	GeneSearchService.getGOGroupGenes(String goQuery, Taxon taxon)
Collection<Gene>	GeneSearchServiceImpl.getGOGroupGenes(String goQuery, Taxon taxon)
Collection<GeneValueObject>	GeneService.searchGenes(String query, Long taxonId)
Collection<GeneValueObject>	GeneServiceImpl.searchGenes(String query, Long taxonId)	Search for genes (by name or symbol)
Collection<SearchResultDisplayObject>	GeneSearchService.searchGenesAndGeneGroups(String query, Long taxonId)
Collection<SearchResultDisplayObject>	GeneSearchServiceImpl.searchGenesAndGeneGroups(String query, Long taxonId)
Collection<GeneValueObject>	GeneSearchService.searchMultipleGenes(String query, Long taxonId)	Search for multiple genes at once.
Collection<GeneValueObject>	GeneSearchServiceImpl.searchMultipleGenes(String query, Long taxonId)
Map<String,GeneValueObject>	GeneSearchService.searchMultipleGenesGetMap(Collection<String> query, Long taxonId)	Search for multiple genes at once.
Map<String,GeneValueObject>	GeneSearchServiceImpl.searchMultipleGenesGetMap(Collection<String> query, Long taxonId)

Uses of SearchException in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that throw SearchException

Modifier and Type	Method	Description
List<GeneEvidenceValueObject>	GeneArgService.getGeneEvidence(GeneArg<?> arg, Taxon taxon)	Deprecated.

Uses of SearchException in ubic.gemma.web.controller

Methods in ubic.gemma.web.controller that throw SearchException

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	PhenotypeController.findExperimentOntologyValue(String givenQueryString, String categoryUri, Long taxonId)
Collection<CharacteristicValueObject>	PhenotypeController.searchOntologyForPhenotypes(String query, Long geneId)	Returns all phenotypes satisfied the given search criteria.

Uses of SearchException in ubic.gemma.web.controller.expression.designElement

Methods in ubic.gemma.web.controller.expression.designElement that throw SearchException

Modifier and Type	Method	Description
Collection<CompositeSequenceMapValueObject>	CompositeSequenceController.search(String searchString, String arrayDesignId)