Class DatasetVisualizationWebService

java.lang.Object

ubic.gemma.rest.DatasetVisualizationWebService

@Service
@Path("/datasets")
public class DatasetVisualizationWebService
extends Object

Dataset visualization endpoints. Carved out of DatasetsWebService (already 4000+ LOC) for the client-side heatmap rewrite. Sits alongside /datasets/{id}/svd and /datasets/{id}/data/processed; ships raw matrix + meta with NO server-side ordering decisions, NO colour assignment, NO legend assembly.

Locked decisions for the session-2 scaffold:

• Single-EE endpoint (client batches if needed; mirrors /svd).
• Continuous factors carry their per-sample measurements on the factors[] entry, keyed by bioAssayId.
• JSON number[][] encoding by default; ?encoding=base64f32 opt-in for large matrices.
• Diffex requests set rows[].pvalue and rows[].validated; non-diffex requests leave both null.

Author:

claude

Constructor Summary

Constructors

Constructor	Description
DatasetVisualizationWebService()

Method Summary

Modifier and Type	Method	Description
ResponseDataObject<HeatmapDataValueObject>	getDatasetHeatmapData(DatasetArg<?> datasetArg, String genesCsv, String probesCsv, Long resultSetId, Double threshold, Integer pcaComponent, Integer pcaCount, Integer sampleSize, String encoding, Long subSetId, QuantitationTypeArg<?> quantitationTypeArg, boolean maskOutliers)	Resolve raw matrix + metadata for a client-rendered heatmap.

Methods inherited from class Object

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

Constructor Details

DatasetVisualizationWebService

public DatasetVisualizationWebService()

Method Details

getDatasetHeatmapData

@GET
@GZIP
@Path("/{dataset}/heatmap-data")
@Produces("application/json")
public ResponseDataObject<HeatmapDataValueObject> getDatasetHeatmapData(@PathParam("dataset")
 DatasetArg<?> datasetArg,
 @QueryParam("genes") @Nullable
 String genesCsv,
 @QueryParam("probes") @Nullable
 String probesCsv,
 @QueryParam("resultSet") @Nullable
 Long resultSetId,
 @QueryParam("threshold") @Nullable
 Double threshold,
 @QueryParam("pcaComponent") @Nullable
 Integer pcaComponent,
 @QueryParam("pcaCount") @Nullable
 Integer pcaCount,
 @QueryParam("sampleSize") @Nullable
 Integer sampleSize,
 @QueryParam("encoding") @DefaultValue("json")
 String encoding,
 @QueryParam("subSet") @Nullable
 Long subSetId,
 @QueryParam("quantitationType") @Nullable
 QuantitationTypeArg<?> quantitationTypeArg,
 @QueryParam("maskOutliers") @DefaultValue("true")
 boolean maskOutliers)

Resolve raw matrix + metadata for a client-rendered heatmap. See class-level Javadoc.

Parameters:

datasetArg - dataset id or short name; ACL-gated by the standard mechanism.

genesCsv - CSV of gene IDs (mutually exclusive with the other selection modes; takes precedence over them).

probesCsv - CSV of probe (composite sequence) IDs.

resultSetId - differential analysis result-set id; the endpoint returns top hits below threshold.

threshold - p-value threshold for diffex mode. Default 0.01.

pcaComponent - PCA component (1-based); the endpoint returns the top-loaded probes for that component.

pcaCount - how many top-loaded probes per PCA component. Default 20.

sampleSize - fallback random sample size when no other selection mode is given. Default 20, max 200.

encoding - "json" (default) or "base64f32".

subSetId - optional ExpressionExperimentSubSet id; when present, the response is restricted to the subset's sample columns.

quantitationTypeArg - optional quantitation-type selector (id or name). When omitted the processed QT is used (current behaviour). A non-processed QT is served from its raw vectors and supports the genes / probes selection modes and the random-sample fallback (sampleSize); resultSet / pcaComponent are rejected.

maskOutliers - when true (default) values for assays flagged as outliers are masked to NaN; when false their stored expression values are returned instead. Always effective for a non-processed quantitationType (raw vectors). For the processed QT it returns whatever is on disk: processed data is currently masked at creation time, so the flag is usually a no-op there today.