Class AnalysisResultSetsWebService

java.lang.Object

ubic.gemma.rest.AnalysisResultSetsWebService

@Service
@Path("/resultSets")
public class AnalysisResultSetsWebService
extends Object

Endpoint for AnalysisResultSet

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject	Similar to PaginatedResponseDataObject, but the data.results is paginated instead of data
static class	AnalysisResultSetsWebService.PvalueDistributionResponseDataObject	Concrete ResponseDataObject type for the pvalueDistribution endpoint so Swagger has a non-generic schema to reference.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	TEXT_TAB_SEPARATED_VALUES_UTF8_Q9

Constructor Summary

Constructors

Constructor	Description
AnalysisResultSetsWebService()

Method Summary

Modifier and Type	Method	Description
ResponseDataObject<Long>	getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet> filter)
jakarta.ws.rs.core.Response	getPvalueDistribution(ExpressionAnalysisResultSetArg analysisResultSet, int bins, String column)	Histogram-binned p-values for a differential-expression result set.
Object	getResultSet(ExpressionAnalysisResultSetArg analysisResultSet, Double threshold, OffsetArg offsetArg, LimitArg limitArg, Boolean includeFactorValuesInContrasts, Boolean includeTaxonInGenes, Boolean excludeResults, jakarta.ws.rs.core.HttpHeaders headers)	Retrieve a AnalysisResultSet given its identifier.
Object	getResultSets(DatasetArrayArg datasets, DatabaseEntryArrayArg databaseEntries, FilterArg<ExpressionAnalysisResultSet> filters, OffsetArg offset, LimitArg limit, SortArg<ExpressionAnalysisResultSet> sort, CursorArg cursorArg)	Retrieve all AnalysisResultSet matching a set of criteria.

Methods inherited from class Object

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

Field Details

TEXT_TAB_SEPARATED_VALUES_UTF8_Q9

public static final String TEXT_TAB_SEPARATED_VALUES_UTF8_Q9

See Also:

• Constant Field Values

Constructor Details

AnalysisResultSetsWebService

public AnalysisResultSetsWebService()

Method Details

getResultSets

@GZIP
@GET
@Produces("application/json")
public Object getResultSets(@QueryParam("datasets")
 DatasetArrayArg datasets,
 @QueryParam("databaseEntries")
 DatabaseEntryArrayArg databaseEntries,
 @QueryParam("filter") @DefaultValue("")
 FilterArg<ExpressionAnalysisResultSet> filters,
 @QueryParam("offset") @DefaultValue("0")
 OffsetArg offset,
 @QueryParam("limit") @DefaultValue("20")
 LimitArg limit,
 @QueryParam("sort") @DefaultValue("+id")
 SortArg<ExpressionAnalysisResultSet> sort,
 @QueryParam("cursor")
 CursorArg cursorArg)

Retrieve all AnalysisResultSet matching a set of criteria.

Parameters:

datasets - filter result sets that belong to any of the provided dataset identifiers, or null to ignore

databaseEntries - filter by associated datasets with given external identifiers, or null to ignore

getNumberOfResultSets

@GET
@Path("/count")
@Produces("application/json")
public ResponseDataObject<Long> getNumberOfResultSets(@QueryParam("filter") @DefaultValue("")
 FilterArg<ExpressionAnalysisResultSet> filter)

getResultSet

@GZIP(mediaTypes="application/json") @GZIP(mediaTypes="text/tab-separated-values; charset=UTF-8",alreadyCompressed=true)
@GET
@Path("/{resultSet}")
@Produces({"application/json","text/tab-separated-values; charset=UTF-8; q=0.9"})
public Object getResultSet(@PathParam("resultSet")
 ExpressionAnalysisResultSetArg analysisResultSet,
 @QueryParam("threshold")
 Double threshold,
 @QueryParam("offset")
 OffsetArg offsetArg,
 @QueryParam("limit")
 LimitArg limitArg,
 @QueryParam("includeFactorValuesInContrasts")
 Boolean includeFactorValuesInContrasts,
 @QueryParam("includeTaxonInGenes")
 Boolean includeTaxonInGenes,
 @QueryParam("excludeResults") @DefaultValue("false")
 Boolean excludeResults,
 @Context
 jakarta.ws.rs.core.HttpHeaders headers)

Retrieve a AnalysisResultSet given its identifier.

getPvalueDistribution

@GET
@Path("/{resultSet}/pvalueDistribution")
@Produces("application/json")
public jakarta.ws.rs.core.Response getPvalueDistribution(@PathParam("resultSet")
 ExpressionAnalysisResultSetArg analysisResultSet,
 @QueryParam("bins") @DefaultValue("20")
 int bins,
 @QueryParam("column") @DefaultValue("raw")
 String column)

Histogram-binned p-values for a differential-expression result set.

Served straight out of the stored PVALUE_DISTRIBUTION row hanging off the result set (ANALYSIS_RESULT_SET.PVALUE_DISTRIBUTION_FK); nothing is aggregated per request. DifferentialExpressionAnalyzerServiceImpl#addPvalueDistribution writes it when the analysis is run: 100 fixed-width bins over [0, 1] of result.getPvalue(), i.e. the RAW p-values. Measured on production 2026-08-31: PVALUE_DISTRIBUTION is 0.1 GB and every one of the 56,616 result sets has a row, whereas the DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT table the previous implementation grouped over is 120.5 GB / ~1,574,396,269 rows.

Because the stored bins are fixed, bins can only merge whole stored bins — it has to divide the stored bin count exactly. Splitting a stored count across two output bins would be inventing data, so a non-divisor is a 400 rather than an approximation.