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.

Restored for HS-7 search restoration Step 3. The DAO-level surface here is unchanged from the pre-strip implementation; the only rename was gemma.gsec.util.SecurityUtil → SecurityUtil.

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_NCBI_ID_SCORE
static final double	MATCH_BY_SHORT_NAME_SCORE

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)
Collection<SearchResult<BioSequence>>	searchBioSequence(SearchSettings settings, SearchContext context)
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 for composite sequences and, unfortunately, genes.
Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<Gene>>	searchGene(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings, SearchContext context)

Methods inherited from class Object

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

Methods inherited from interface SearchSource

searchBibliographicReference

Field Details

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_NCBI_ID_SCORE

public static final double MATCH_BY_NCBI_ID_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

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

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

Description copied from interface: SearchSource

Search for composite sequences and, unfortunately, genes.

FIXME: this should solely return CompositeSequence.

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

Specified by:

searchExpressionExperiment in interface SearchSource

Throws:

SearchException

searchGene

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

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