Package ubic.gemma.core.search.source

Class DatabaseSearchSource

java.lang.Object

ubic.gemma.core.search.source.DatabaseSearchSource

All Implemented Interfaces:

org.springframework.core.Ordered, SearchSource

@Component
public class DatabaseSearchSource
extends Object
implements SearchSource, org.springframework.core.Ordered

Search source for direct database results.

Author:

klc, paul, keshav, poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final double	MATCH_BY_ACCESSION_SCORE
static final double	MATCH_BY_ID_SCORE	Score when a result is matched exactly by numerical ID.
static final double	MATCH_BY_NAME_SCORE
static final double	MATCH_BY_SHORT_NAME_SCORE
static final String	NCBI_GENE_ID_URI_PREFIX

Fields inherited from interface org.springframework.core.Ordered

HIGHEST_PRECEDENCE, LOWEST_PRECEDENCE

Constructor Summary

Constructors

Constructor	Description
DatabaseSearchSource()

Method Summary

Modifier and Type	Method	Description
boolean	accepts(SearchSettings settings)	Indicate if this source accepts the given search settings.
int	getOrder()
Collection<SearchResult<ArrayDesign>>	searchArrayDesign(SearchSettings settings, SearchContext context)	A general search for array designs.
Collection<SearchResult<BioSequence>>	searchBioSequence(SearchSettings settings, SearchContext context)	A database search for biosequences.
Collection<SearchResult<?>>	searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)	Search for biosequence and, unfortunately genes.
Collection<SearchResult<BlacklistedEntity>>	searchBlacklistedEntities(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<?>>	searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Search the DB for composite sequences and the genes that are matched to them.
Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings, SearchContext context)	Does search on exact string by: id, name and short name.
Collection<SearchResult<Gene>>	searchGene(SearchSettings settings, SearchContext context)	Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence tables
Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings, SearchContext context)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.search.SearchSource

searchBibliographicReference

Field Details

NCBI_GENE_ID_URI_PREFIX

public static final String NCBI_GENE_ID_URI_PREFIX

See Also:

• Constant Field Values

MATCH_BY_ID_SCORE

public static final double MATCH_BY_ID_SCORE

Score when a result is matched exactly by numerical ID.

See Also:

• Constant Field Values

MATCH_BY_SHORT_NAME_SCORE

public static final double MATCH_BY_SHORT_NAME_SCORE

See Also:

• Constant Field Values

MATCH_BY_ACCESSION_SCORE

public static final double MATCH_BY_ACCESSION_SCORE

See Also:

• Constant Field Values

MATCH_BY_NAME_SCORE

public static final double MATCH_BY_NAME_SCORE

See Also:

• Constant Field Values

Constructor Details

DatabaseSearchSource

public DatabaseSearchSource()

Method Details

getOrder

public int getOrder()

Specified by:

getOrder in interface org.springframework.core.Ordered

accepts

public boolean accepts(SearchSettings settings)

Description copied from interface: SearchSource

Indicate if this source accepts the given search settings.

Specified by:

accepts in interface SearchSource

searchArrayDesign

public Collection<SearchResult<ArrayDesign>> searchArrayDesign(SearchSettings settings,
 SearchContext context)
                                                        throws SearchException

A general search for array designs.

This search does both an database search and a compass search. This is also contains an underlying CompositeSequence search, returning the ArrayDesign collection for the given composite sequence search string (the returned collection of array designs does not contain duplicates).

Searches the DB for array designs which have composite sequences whose names match the given search string. Because of the underlying database search, this is acl aware. That is, returned array designs are filtered based on access control list (ACL) permissions.

Specified by:

searchArrayDesign in interface SearchSource

Throws:

SearchException

searchExperimentSet

public Collection<SearchResult<ExpressionExperimentSet>> searchExperimentSet(SearchSettings settings,
 SearchContext context)
                                                                      throws SearchException

Specified by:

searchExperimentSet in interface SearchSource

Throws:

SearchException

searchBioSequence

public Collection<SearchResult<BioSequence>> searchBioSequence(SearchSettings settings,
 SearchContext context)
                                                        throws SearchException

A database search for biosequences. Biosequence names are already indexed by compass...

Specified by:

searchBioSequence in interface SearchSource

Throws:

SearchException

searchBioSequenceAndGene

public Collection<SearchResult<?>> searchBioSequenceAndGene(SearchSettings settings,
 SearchContext context,
 @Nullable
 Collection<SearchResult<Gene>> previousGeneSearchResults)
                                                     throws SearchException

Description copied from interface: SearchSource

Search for biosequence and, unfortunately genes.

I wanted to remove this, but there's some logic with indirect gene hit penalty that we might want to keep around.

Specified by:

searchBioSequenceAndGene in interface SearchSource

Returns:

a mixture of BioSequence and Gene matching the search settings.

Throws:

SearchException

searchCompositeSequence

public Collection<SearchResult<CompositeSequence>> searchCompositeSequence(SearchSettings settings,
 SearchContext context)
                                                                    throws SearchException

Specified by:

searchCompositeSequence in interface SearchSource

Throws:

SearchException

searchCompositeSequenceAndGene

public Collection<SearchResult<?>> searchCompositeSequenceAndGene(SearchSettings settings,
 SearchContext context)
                                                           throws SearchException

Search the DB for composite sequences and the genes that are matched to them.

Specified by:

searchCompositeSequenceAndGene in interface SearchSource

Returns:

a mixture of Gene and CompositeSequence matching the search settings

Throws:

SearchException

searchExpressionExperiment

public Collection<SearchResult<ExpressionExperiment>> searchExpressionExperiment(SearchSettings settings,
 SearchContext context)
                                                                          throws SearchException

Does search on exact string by: id, name and short name. This only returns results if these fields match exactly, but it's fast.

Specified by:

searchExpressionExperiment in interface SearchSource

Returns:

Collection

Throws:

SearchException

searchGene

public Collection<SearchResult<Gene>> searchGene(SearchSettings settings,
 SearchContext context)
                                          throws SearchException

Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence tables

Specified by:

searchGene in interface SearchSource

Throws:

SearchException

searchGeneSet

public Collection<SearchResult<GeneSet>> searchGeneSet(SearchSettings settings,
 SearchContext context)
                                                throws SearchException

Specified by:

searchGeneSet in interface SearchSource

Throws:

SearchException

searchBlacklistedEntities

public Collection<SearchResult<BlacklistedEntity>> searchBlacklistedEntities(SearchSettings settings,
 SearchContext context)
                                                                      throws SearchException

Specified by:

searchBlacklistedEntities in interface SearchSource

Throws:

SearchException