@sjcrh/proteinpaint-types 2.138.3-5 → 2.139.0

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/routes/termdb.percentile.ts

@@ -1,5 +1,6 @@
 import type { RoutePayload } from './routeApi.js'
 import type { Filter } from '../filter.ts'
+import type { Term } from '../terms/term.ts'
 
 export type PercentileRequest = {
 	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
@@ -9,8 +10,9 @@ export type PercentileRequest = {
 	embedder: string
 	getpercentile: number[]
 	/** term id string */
-	tid: string
-	filter: Filter
+	term: Term
+	filter?: Filter
+	filter0?: any
 }
 
 export type PercentileResponse = {
@@ -32,7 +34,7 @@ export const percentilePayload: RoutePayload = {
 					dslabel: 'TermdbTest',
 					embedder: 'localhost',
 					getpercentile: [50],
-					tid: 'agedx',
+					term: { id: 'agedx' },
 					filter: {
 						type: 'tvslst',
 						in: true,

package/src/terms/geneExpression.ts

@@ -10,7 +10,10 @@ GeneExpressionTermSettingInstance
 
 */
 
-export type GeneExpressionQ = NumericQ & { dt?: number }
+export type GeneExpressionQ = NumericQ & {
+	dt?: number
+	preferredBins?: string
+}
 
 export type GeneExpressionTW = TermWrapper & {
 	q: GeneExpressionQ

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
+}

package/src/vocab.ts

@@ -19,7 +19,7 @@ export type VocabApi = {
 	findTerm: (f: string, activeCohort: number, usecase: UseCase, x: string) => { lst: Term[] }
 	getCategories: (term: Term, filter?: Filter, body?: any) => any
 	getCustomTermQLst: (f: Term) => any
-	getPercentile: (term_id: string | number, percentile_lst: number[], filter?: Filter) => any
+	getPercentile: (term: Term, percentile_lst: number[], termfilter?) => any
 	getterm: (f: any) => Term
 	getTerms: (f: any) => any
 	getTermdbConfig: () => any