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)
Long	getEntityId(DatasetArg<?> datasetArg)	Retrieve an ID for a given dataset argument.
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)	Obtain a Filters from a filter argument.
Filters	getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms)
Filters	getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
Set<Long>	getIdsForSearchQuery(QueryArg query, Collection<Throwable> queryWarnings)	Shortcut for extracting the result IDs from getResultsForSearchQuery(QueryArg, Highlighter, Collection).
Set<Long>	getIdsForSearchQuery(QueryArg query, Map<Long,Double> scoreById, Collection<Throwable> queryWarnings)	Shortcut for extracting the result IDs and scores from getResultsForSearchQuery(QueryArg, Highlighter, Collection).
List<ArrayDesignValueObject>	getPlatforms(DatasetArg<?> arg)	Retrieves the Platforms of the Dataset that this argument represents.
QuantitationType	getPreferredQuantitationType(DatasetArg<?> datasetArg)
List<BibliographicReferenceValueObject>	getPublications(DatasetArg<?> datasetArg)
Set<QuantitationTypeValueObject>	getQuantitationTypes(DatasetArg<?> arg)	Retrieve a dataset with quantitation type initialized.
List<SearchResult<ExpressionExperiment>>	getResultsForSearchQuery(QueryArg query, Highlighter highlighter, Collection<Throwable> queryWarnings)	Obtain the search results for a given query and highlighter.
List<BioAssayValueObject>	getSamples(DatasetArg<?> arg)
List<BioAssayValueObject>	getSamples(DatasetArg<?> datasetArg, QuantitationType qt)	Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.
ExpressionExperimentSubSet	getSubSet(DatasetArg<?> datasetArg, Long subSetId)
List<Long>	getSubSetGroupIds(DatasetArg<?> datasetArg, ExpressionExperimentSubSet subset)
List<ExpressionExperimentSubSet>	getSubSets(DatasetArg<?> datasetArg)
List<BioAssayValueObject>	getSubSetSamples(DatasetArg<?> datasetArg, Long subSetId)
Map<ExpressionExperimentSubSet,List<Long>>	getSubSetsGroupIds(DatasetArg<?> datasetArg)
void	populateOutliers(ExpressionExperiment ee, Collection<BioAssayValueObject> bioAssayValueObjects)

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, getSort

Methods inherited from class java.lang.Object

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

Constructor Details

DatasetArgService

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

Method Details

getEntityId

@Nullable
public Long getEntityId(DatasetArg<?> datasetArg)

Retrieve an ID for a given dataset argument.

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

Description copied from interface: EntityArgService

Obtain a Filters from a filter argument.

Specified by:

getFilters in interface EntityArgService<ExpressionExperiment,ExpressionExperimentService>

Overrides:

getFilters in class AbstractEntityArgService<ExpressionExperiment,ExpressionExperimentService>

Throws:

javax.ws.rs.BadRequestException - if the argument is malformed

javax.ws.rs.ServiceUnavailableException

getFilters

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

Throws:

javax.ws.rs.ServiceUnavailableException

getFilters

public Filters getFilters(FilterArg<ExpressionExperiment> filterArg,
 @Nullable
 Collection<OntologyTerm> mentionedTerms,
 @Nullable
 Collection<OntologyTerm> inferredTerms,
 long timeout,
 TimeUnit timeUnit)
                   throws TimeoutException

Throws:

TimeoutException

getResultsForSearchQuery

public List<SearchResult<ExpressionExperiment>> getResultsForSearchQuery(QueryArg query,
 @Nullable
 Highlighter highlighter,
 @Nullable
 Collection<Throwable> queryWarnings)
                                                                  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

queryWarnings - a collection that will receive warnings regarding the full-text query

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,
 @Nullable
 Collection<Throwable> queryWarnings)

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

See Also:

• getResultsForSearchQuery(QueryArg, Highlighter, Collection)

getIdsForSearchQuery

public Set<Long> getIdsForSearchQuery(QueryArg query,
 @Nullable
 Collection<Throwable> queryWarnings)

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

See Also:

• getResultsForSearchQuery(QueryArg, Highlighter, Collection)

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.

getSamples

public List<BioAssayValueObject> getSamples(DatasetArg<?> datasetArg,
 QuantitationType qt)

Obtain a collection of BioAssays that represent the experiments samples for a particular quantitation type.

getAnnotations

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

Returns:

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

getSubSets

public List<ExpressionExperimentSubSet> getSubSets(DatasetArg<?> datasetArg)

getSubSet

public ExpressionExperimentSubSet getSubSet(DatasetArg<?> datasetArg,
 Long subSetId)

getSubSetGroupIds

public List<Long> getSubSetGroupIds(DatasetArg<?> datasetArg,
 ExpressionExperimentSubSet subset)

getSubSetsGroupIds

public Map<ExpressionExperimentSubSet,List<Long>> getSubSetsGroupIds(DatasetArg<?> datasetArg)

getSubSetSamples

public List<BioAssayValueObject> getSubSetSamples(DatasetArg<?> datasetArg,
 Long subSetId)

getPreferredQuantitationType

public QuantitationType getPreferredQuantitationType(DatasetArg<?> datasetArg)

getPublications

public List<BibliographicReferenceValueObject> getPublications(DatasetArg<?> datasetArg)

populateOutliers

public void populateOutliers(ExpressionExperiment ee,
 Collection<BioAssayValueObject> bioAssayValueObjects)