@sjcrh/proteinpaint-types 2.138.3-5 → 2.138.3-7

package/dist/index.js

@@ -12,7 +12,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-CC3OBRKE.js";
+} from "./chunk-2QKCLUH3.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -22,17 +22,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2YASZMH3.js";
+} from "./chunk-5BKOSJEU.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-7FTOFTNK.js";
+} from "./chunk-P3Z422N2.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-O3NHQOWL.js";
+} from "./chunk-Y6Z6XAFN.js";
 import {
   tilePayload,
   validTileRequest,
@@ -87,12 +87,12 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-HCBXL376.js";
+} from "./chunk-ZHCVV36H.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-LTGT4NK4.js";
+} from "./chunk-NHELOLDH.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -107,7 +107,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-I2BMMKPN.js";
+} from "./chunk-KDHGWAOS.js";
 import {
   FilterTermValuesPayload,
   validFilterTermValuesRequest,
@@ -117,12 +117,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-DD2RLZHC.js";
+} from "./chunk-G5BYLEJC.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-6HAS5WRS.js";
+} from "./chunk-R3DIKDES.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
@@ -162,7 +162,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-IY6W7HXW.js";
+} from "./chunk-F2ZZ5J3F.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
@@ -255,7 +255,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-JKBVXIRQ.js";
+} from "./chunk-HJ7XFSJK.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -277,7 +277,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-QG776KAI.js";
+} from "./chunk-34LXTZYA.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-IY6W7HXW.js";
+} from "./chunk-F2ZZ5J3F.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-HCBXL376.js";
+} from "./chunk-ZHCVV36H.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-LTGT4NK4.js";
+} from "./chunk-NHELOLDH.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-I2BMMKPN.js";
+} from "./chunk-KDHGWAOS.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-DD2RLZHC.js";
+} from "./chunk-G5BYLEJC.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-6HAS5WRS.js";
+} from "./chunk-R3DIKDES.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-CC3OBRKE.js";
+} from "./chunk-2QKCLUH3.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2YASZMH3.js";
+} from "./chunk-5BKOSJEU.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-7FTOFTNK.js";
+} from "./chunk-P3Z422N2.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-O3NHQOWL.js";
+} from "./chunk-Y6Z6XAFN.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.138.3-5",
+  "version": "2.138.3-7",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -973,6 +973,14 @@ type Mds3Queries = {
 	singleSampleMutation?: SingleSampleMutationQuery
 	NIdata?: NIdataQuery
 	geneExpression?: GeneExpressionQuery
+	/** single-sample gsea precomputed scores for rnaseq samples, for genesets from geneset db
+	requires genome to be equipped with geneset db
+	*/
+	ssGSEA?: {
+		/** path to h5 file, matrix of NES scores. rows are msigdb geneset ids, columns are rnaseq samples */
+		file: string
+		// in case a genome may have more than 1 geneset dbs, here may specify name of db that this result is based on */
+	}
 	rnaseqGeneCount?: RnaseqGeneCount
 	/** Used to create the top mutated genes UI in the gene
 	 * set edit ui and data requests. */
@@ -981,7 +989,7 @@ type Mds3Queries = {
 	 * set edit ui. Also used for data requests */
 	topVariablyExpressedGenes?: TopVariablyExpressedGenesQuery
 	metaboliteIntensity?: {
-		src: 'native' | 'gdc'
+		src: 'native'
 		file: string
 	}
 	singleCell?: SingleCellQuery

package/src/index.ts

@@ -71,6 +71,7 @@ export * from './terms/singleCellGeneExpression.ts'
 export * from './terms/snp.ts'
 export * from './terms/snps.ts'
 export * from './terms/samplelst.ts'
+export * from './terms/ssGSEA.ts'
 export * from './terms/q.ts'
 export * from './terms/term.ts'
 export * from './terms/tw.ts'

package/src/terms/numeric.ts

@@ -34,7 +34,7 @@ export type NumericTerm = BaseTerm & {
 	id?: string
 	// these concrete term.type values make it clear that only these are numeric,
 	// "categorical", "condition", and other term.types are not included in this union
-	type: 'integer' | 'float' | 'geneExpression' | 'metaboliteIntensity' | 'date'
+	type: 'integer' | 'float' | 'geneExpression' | 'metaboliteIntensity' | 'date' | 'ssGSEA'
 	bins: PresetNumericBins
 	values?: TermValues
 	unit?: string

package/src/terms/ssGSEA.ts

@@ -0,0 +1,26 @@
+import type { TermWrapper } from './tw.ts'
+import type { NumericTerm, NumericQ } from './numeric.ts'
+import type { TermSettingInstance } from '../termsetting.ts'
+
+/*
+duplicated from geneExpression.ts
+*/
+
+export type SsGSEAQ = NumericQ & { dt?: number }
+
+export type SsGSEATW = TermWrapper & {
+	q: SsGSEAQ
+	term: SsGSEATerm
+}
+
+export type SsGSEATerm = NumericTerm & {
+	/** term.id: geneset db term id for native term, and cache file name for custom term */
+	/** term.name: geneset db term name for native term, and user-defined name for custom term */
+	/** custom term has list of gene names used for computing score */
+	genes?: string[]
+}
+
+export type SsGSEATermSettingInstance = TermSettingInstance & {
+	q: SsGSEAQ
+	term: SsGSEATerm
+}