@sjcrh/proteinpaint-types 2.140.1-2 → 2.140.1

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-34LXTZYA.js";
+} from "./chunk-IDP5KXE6.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-2QKCLUH3.js";
+} from "./chunk-BWLSDIHM.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -12,17 +12,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-5BKOSJEU.js";
+} from "./chunk-WKT3H4P4.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-P3Z422N2.js";
+} from "./chunk-ECF6WSOD.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-Y6Z6XAFN.js";
+} from "./chunk-PPFFVFUI.js";
 import {
   tilePayload,
   validTileRequest,
@@ -82,7 +82,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NHELOLDH.js";
+} from "./chunk-EWON4FG5.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -97,7 +97,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-KDHGWAOS.js";
+} from "./chunk-2WLN6PMW.js";
 import {
   FilterTermValuesPayload,
   validFilterTermValuesRequest,
@@ -107,12 +107,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-G5BYLEJC.js";
+} from "./chunk-AADDTYUL.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-4S36DRJ4.js";
+} from "./chunk-ZA3FDGAD.js";
 import {
   ProfileFormScoresPayload,
   validProfileFormScoresRequest,
@@ -152,12 +152,12 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-F2ZZ5J3F.js";
+} from "./chunk-XXHHUIEV.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZHCVV36H.js";
+} from "./chunk-FZJ3E7JA.js";
 import {
   GRIN2Payload,
   validGRIN2Request,
@@ -245,7 +245,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-HJ7XFSJK.js";
+} from "./chunk-KS74VVON.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -267,7 +267,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-34LXTZYA.js";
+} from "./chunk-IDP5KXE6.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

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

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZHCVV36H.js";
+} from "./chunk-FZJ3E7JA.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NHELOLDH.js";
+} from "./chunk-EWON4FG5.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-KDHGWAOS.js";
+} from "./chunk-2WLN6PMW.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

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

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-4S36DRJ4.js";
+} from "./chunk-ZA3FDGAD.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

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

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-5BKOSJEU.js";
+} from "./chunk-WKT3H4P4.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-P3Z422N2.js";
+} from "./chunk-ECF6WSOD.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.140.1-2",
+  "version": "2.140.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -721,6 +721,8 @@ export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
 export type GeneExpressionQueryGdc = {
 	src: 'gdcapi'
 	geneExpression2bins?: { [index: string]: any }
+	/** gene expression unit (e.g. 'FPKM') */
+	unit?: string
 }
 
 export type GeneExpressionQueryNative = {
@@ -736,6 +738,8 @@ export type GeneExpressionQueryNative = {
 	get?: (param: any) => void
 	/** This dictionary is used to store/cache the default bins calculated for a geneExpression term when initialized in the fillTermWrapper */
 	geneExpression2bins?: { [index: string]: any }
+	/** gene expression unit (e.g. 'FPKM') */
+	unit?: string
 }
 
 export type GeneExpressionQuery = GeneExpressionQueryGdc | GeneExpressionQueryNative
@@ -749,10 +753,14 @@ export type SingleCellGeneExpressionNative = {
 	get?: (q: any) => any
 	/** cached gene exp bins */
 	sample2gene2expressionBins?: { [sample: string]: { [gene: string]: any } }
+	/** gene expression unit (e.g. 'FPKM') */
+	unit?: string
 }
 
 export type SingleCellGeneExpressionGdc = {
 	src: 'gdcapi'
+	/** gene expression unit (e.g. 'FPKM') */
+	unit?: string
 }
 
 export type SingleCellSamples = {
@@ -1498,17 +1506,17 @@ keep this setting here for reason of:
 	}
 	*/
 	q?: any
-	termMatch2geneSet?: any
 	mclass?: Mclass
 	lollipop?: any
 	hasAncestry?: boolean
+	/** set to true for genome-level geneset db */
+	isGeneSetTermdb?: boolean
 
 	//GDC
 	termid2totalsize2?: GdcApi
 	/** Do not use a union here. */
 	dictionary?: GdcApi & AiApi
 	allowCaseDetails?: AllowCaseDetails
-	isGeneSetTermdb?: boolean
 	/** Searches the genedb alias list to return the genecode ID */
 	getGeneAlias?: (q: any, tw: any) => { gencodeId: any }
 	convertSampleId?: GdcApi

package/src/routes/termdb.cluster.ts

@@ -2,9 +2,9 @@ import type { RoutePayload } from './routeApi.js'
 import type { ErrorResponse } from './errorResponse.ts'
 import type { Filter } from '../filter.ts'
 import type { Term } from '../terms/term.ts'
-import type { GeneExpressionTerm } from '../terms/geneExpression.ts'
-import type { MetaboliteIntensityTerm } from '../terms/metaboliteIntensity.ts'
-import type { NumericDictTerm } from '../terms/numeric.ts'
+import type { GeneExpressionTW } from '../terms/geneExpression.ts'
+import type { MetaboliteIntensityTW } from '../terms/metaboliteIntensity.ts'
+import type { NumericTW } from '../terms/numeric.ts'
 
 export type Gene = {
 	/** gene symbol, required */
@@ -34,7 +34,7 @@ export type TermdbClusterRequestGeneExpression = TermdbClusterRequestBase & {
 	/** Data type */
 	dataType: 'geneExpression'
 	/** List of terms */
-	terms: GeneExpressionTerm[]
+	terms: GeneExpressionTW[]
 	/** perform z-score transformation on values */
 	zScoreTransformation?: string
 }
@@ -43,7 +43,7 @@ export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
 	/** Data type */
 	dataType: 'metaboliteIntensity'
 	/** List of terms */
-	terms: MetaboliteIntensityTerm[]
+	terms: MetaboliteIntensityTW[]
 	/** perform z-score transformation on values */
 	zScoreTransformation?: string
 }
@@ -52,7 +52,7 @@ export type TermdbClusterRequestNumericDictTerm = TermdbClusterRequestBase & {
 	/** Data type */
 	dataType: 'numericDictTerm'
 	/** List of terms */
-	terms: NumericDictTerm[]
+	terms: NumericTW[]
 	/** perform z-score transformation on values */
 	zScoreTransformation?: string
 }

package/src/terms/geneExpression.ts

@@ -1,28 +1,18 @@
-import type { TermWrapper } from './updated-types.ts'
-import type { NumericTerm, NumericQ } from './numeric.ts'
+import type { BaseTW, PresetNumericBins, NumericBaseTerm, NumericQ } from '../index.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 /*
 --------EXPORTED--------
-GeneExpressionQ
+GeneExpressionTerm
 GeneExpressionTermWrapper
 GeneExpressionTermSettingInstance
-
 */
 
-export type GeneExpressionQ = NumericQ & {
-	dt?: number
-	preferredBins?: string
-}
-
-export type GeneExpressionTW = TermWrapper & {
-	q: GeneExpressionQ
-	term: GeneExpressionTerm
-	type: 'NumTWRegularBin' | 'NumTWCustomBin' | 'NumTWCont' | 'NumTWSpline'
-}
-
-export type GeneExpressionTerm = NumericTerm & {
+export type GeneExpressionTerm = NumericBaseTerm & {
 	gene: string
+	name: string
+	type: 'geneExpression'
+	bins?: PresetNumericBins
 	// temporarily allowing chr/start/stop to support
 	// legacy fpkm files
 	chr?: string
@@ -30,7 +20,13 @@ export type GeneExpressionTerm = NumericTerm & {
 	stop?: number
 }
 
+export type GeneExpressionTW = BaseTW & {
+	q: NumericQ
+	term: GeneExpressionTerm
+	type: string
+}
+
 export type GeneExpressionTermSettingInstance = TermSettingInstance & {
-	q: GeneExpressionQ
+	q: NumericQ
 	term: GeneExpressionTerm
 }

package/src/terms/numeric.ts

@@ -1,4 +1,4 @@
-import type { MinBaseQ, BaseTW, TermValues, BaseTerm } from '../index.ts'
+import type { MinBaseQ, BaseTW, TermValues, BaseTerm, GeneExpressionTerm } from '../index.ts'
 
 export type RawRegularBin = Partial<RegularNumericBinConfig> & { preferredBins?: string }
 
@@ -30,32 +30,21 @@ export type RawNumTWSpline = BaseTW & {
 
 export type RawNumTW = RawNumTWCustomBin | RawNumTWRegularBin | RawNumTWCont | RawNumTWSpline
 
-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' | 'ssGSEA'
-	bins: PresetNumericBins
-	values?: TermValues
-	unit?: string
+export type NumericBaseTerm = BaseTerm & {
 	/** tailored color scale for this term, so that when the term is used for color gradient in scatter, this set of colors will be used by default */
 	continuousColorScale?: { minColor: string; maxColor: string }
-	/*densityNotAvailable?: boolean //Not used?
-	logScale?: string | number
-	max?: number
-	min?: number
-	skip0forPercentile?: boolean
-	valueConversion?: ValueConversion*/
+	unit?: string
 }
 
-export type NumericDictTerm = BaseTerm & {
+export type NumericDictTerm = NumericBaseTerm & {
 	id?: string
 	type: 'integer' | 'float' | 'date'
 	bins: PresetNumericBins
 	values?: TermValues
-	unit?: string
 }
 
+export type NumericTerm = NumericDictTerm | GeneExpressionTerm
+
 export type StartUnboundedBin = {
 	// where possible, assign a concrete value (true) when it is known in advance,
 	// in which case, do not use an abstract type (boolean) to startunbounded
@@ -157,7 +146,7 @@ export type BinaryNumericQ = MinBaseQ & {
 }
 
 export type ContinuousNumericQ = MinBaseQ & {
-	mode: 'continuous'
+	mode?: 'continuous'
 	// TODO: do not use a boolean, convert to a `transform: 'zscore' | ...` option
 	convert2ZScore?: boolean
 	//scale?: string

package/src/terms/singleCellGeneExpression.ts

@@ -1,7 +1,6 @@
 import type { TermWrapper } from './tw.ts'
-import type { GeneExpressionQ } from './geneExpression.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
-import type { NumericTerm } from './numeric.ts'
+import type { NumericTerm, NumericQ } from './numeric.ts'
 
 /*
 --------EXPORTED--------
@@ -12,7 +11,7 @@ GeneExpressionTermSettingInstance
 */
 
 export type SingleCellGeneExpressionTW = TermWrapper & {
-	q: GeneExpressionQ
+	q: NumericQ
 	term: SingleCellGeneExpressionTerm
 }
 
@@ -22,6 +21,6 @@ export type SingleCellGeneExpressionTerm = NumericTerm & {
 }
 
 export type SingleCellGeneExpressionTermSettingInstance = TermSettingInstance & {
-	q: GeneExpressionQ
+	q: NumericQ
 	term: SingleCellGeneExpressionTerm
 }