Package ubic.gemma.rest.util.args

Class DatasetArgService

java.lang.Object

ubic.gemma.rest.util.args.AbstractEntityArgService<ExpressionExperiment,ExpressionExperimentService>

ubic.gemma.rest.util.args.DatasetArgService

All Implemented Interfaces:

EntityArgService<ExpressionExperiment,ExpressionExperimentService>

@Service
public class DatasetArgService
extends AbstractEntityArgService<ExpressionExperiment,ExpressionExperimentService>

Field Summary

Fields inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

service

Constructor Summary

Constructors

Constructor	Description
DatasetArgService(ExpressionExperimentService service, SearchService searchService, ArrayDesignService adService, BioAssayService baService, OutlierDetectionService outlierDetectionService)

Method Summary

Modifier and Type	Method	Description
Set<AnnotationValueObject>	getAnnotations(DatasetArg<?> arg)
List<String>	getExcludedUris(StringArrayArg excludedUrisArg, boolean excludeFreeText, boolean excludeUncategorizedTerms)	Obtain a list of exclude URIs from an argument containing excluded URIs.
Filters	getFilters(FilterArg<ExpressionExperiment> filterArg)
Filters	getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerm)
Set<Long>	getIdsForSearchQuery(QueryArg query)	Shortcut for extracting the result IDs from getResultsForSearchQuery(QueryArg, Highlighter).
Set<Long>	getIdsForSearchQuery(QueryArg query, Map<Long,Double> scoreById)	Shortcut for extracting the result IDs and scores from getResultsForSearchQuery(QueryArg, Highlighter).
List<ArrayDesignValueObject>	getPlatforms(DatasetArg<?> arg)	Retrieves the Platforms of the Dataset that this argument represents.
Set<QuantitationTypeValueObject>	getQuantitationTypes(DatasetArg<?> arg)	Retrieve a dataset with quantitation type initialized.
List<SearchResult<ExpressionExperiment>>	getResultsForSearchQuery(QueryArg query, Highlighter highlighter)	Obtain the search results for a given query and highlighter.
List<BioAssayValueObject>	getSamples(DatasetArg<?> arg)
Sort	getSort(SortArg<ExpressionExperiment> sortArg)

Methods inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

checkEntity, entityArgValueOf, getArgsByPropertyName, getElementClass, getEntities, getEntities, getEntity, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getFilters, getFilters

Methods inherited from class java.lang.Object

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

Constructor Detail

DatasetArgService

@Autowired
public DatasetArgService(ExpressionExperimentService service,
                         SearchService searchService,
                         ArrayDesignService adService,
                         BioAssayService baService,
                         OutlierDetectionService outlierDetectionService)

Method Detail

getExcludedUris

@Nullable
public List<String> getExcludedUris(@Nullable
                                    StringArrayArg excludedUrisArg,
                                    boolean excludeFreeText,
                                    boolean excludeUncategorizedTerms)

Obtain a list of exclude URIs from an argument containing excluded URIs.

Parameters:

excludedUrisArg - argument containing excluded URIs or null if unspecified

excludeFreeText - if true, null will be included in the returned list which will result in the exclusion of free-text categories or terms

Returns:

null if excludedUrisArg is null and excludeFreeText is false, otherwise a list of excluded URIs

getFilters

public Filters getFilters(FilterArg<ExpressionExperiment> filterArg)
                   throws javax.ws.rs.BadRequestException,
                          javax.ws.rs.ServiceUnavailableException

Specified by:

getFilters in interface EntityArgService<ExpressionExperiment,ExpressionExperimentService>

Overrides:

getFilters in class AbstractEntityArgService<ExpressionExperiment,ExpressionExperimentService>

Throws:

javax.ws.rs.BadRequestException

javax.ws.rs.ServiceUnavailableException

getSort

public Sort getSort(SortArg<ExpressionExperiment> sortArg)
             throws javax.ws.rs.BadRequestException

Specified by:

getSort in interface EntityArgService<ExpressionExperiment,ExpressionExperimentService>

Overrides:

getSort in class AbstractEntityArgService<ExpressionExperiment,ExpressionExperimentService>

Throws:

javax.ws.rs.BadRequestException

getFilters

public Filters getFilters(FilterArg<ExpressionExperiment> filterArg,
                          @Nullable
                          Collection<OntologyTerm> mentionedTerm)
                   throws javax.ws.rs.ServiceUnavailableException

Throws:

javax.ws.rs.ServiceUnavailableException

getResultsForSearchQuery

public List<SearchResult<ExpressionExperiment>> getResultsForSearchQuery(QueryArg query,
                                                                         @Nullable
                                                                         Highlighter highlighter)
                                                                  throws javax.ws.rs.BadRequestException,
                                                                         javax.ws.rs.ServiceUnavailableException,
                                                                         javax.ws.rs.InternalServerErrorException

Obtain the search results for a given query and highlighter.

Parameters:

highlighter - a highlighter to use for the query or null to ignore

Throws:

javax.ws.rs.BadRequestException - if the query is empty

javax.ws.rs.ServiceUnavailableException - if the search times out

javax.ws.rs.InternalServerErrorException - for any other search-related exceptions

getIdsForSearchQuery

public Set<Long> getIdsForSearchQuery(QueryArg query,
                                      Map<Long,Double> scoreById)

Shortcut for extracting the result IDs and scores from getResultsForSearchQuery(QueryArg, Highlighter).

See Also:

getResultsForSearchQuery(QueryArg, Highlighter)

getIdsForSearchQuery

public Set<Long> getIdsForSearchQuery(QueryArg query)

Shortcut for extracting the result IDs from getResultsForSearchQuery(QueryArg, Highlighter).

See Also:

getResultsForSearchQuery(QueryArg, Highlighter)

getQuantitationTypes

public Set<QuantitationTypeValueObject> getQuantitationTypes(DatasetArg<?> arg)

Retrieve a dataset with quantitation type initialized.

getPlatforms

public List<ArrayDesignValueObject> getPlatforms(DatasetArg<?> arg)

Retrieves the Platforms of the Dataset that this argument represents.

Returns:

a collection of Platforms that the dataset represented by this argument is in.

getSamples

public List<BioAssayValueObject> getSamples(DatasetArg<?> arg)

Returns:

a collection of BioAssays that represent the experiments samples.

getAnnotations

public Set<AnnotationValueObject> getAnnotations(DatasetArg<?> arg)

Returns:

a collection of Annotations value objects that represent the experiments annotations.