@sjcrh/proteinpaint-types 2.113.0 → 2.115.0

package/src/routes/{gdc.topMutatedGenes.ts → termdb.topMutatedGenes.ts}

@@ -1,6 +1,8 @@
 import type { RoutePayload } from './routeApi.js'
 
-export type GdcTopMutatedGeneRequest = {
+export type topMutatedGeneRequest = {
+	genome: string
+	dslabel: string
 	/** to restrict to CGC genes */
 	geneFilter?: 'CGC'
 	/** max number of genes to return */
@@ -9,7 +11,7 @@ export type GdcTopMutatedGeneRequest = {
 	filter0?: object
 }
 
-export type GdcGene = {
+export type MutatedGene = {
 	/** gene symbol */
 	gene: string
 	/** optional attributes on number of mutated cases per dt */
@@ -22,16 +24,16 @@ export type GdcGene = {
 	}[]
 }
 
-export type GdcTopMutatedGeneResponse = {
-	genes: GdcGene[]
+export type topMutatedGeneResponse = {
+	genes: MutatedGene[]
 }
 
-export const gdcTopMutatedGenePayload: RoutePayload = {
+export const topMutatedGenePayload: RoutePayload = {
 	request: {
-		typeId: 'GdcTopMutatedGeneRequest'
+		typeId: 'topMutatedGeneRequest'
 	},
 	response: {
-		typeId: 'GdcTopMutatedGeneResponse'
+		typeId: 'topMutatedGeneResponse'
 	}
 	//examples: []
 }

package/src/routes/wsisamples.ts

@@ -0,0 +1,25 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type WSISamplesRequest = {
+	genome: string
+	dslabel: string
+}
+
+export type WSISamplesResponse = {
+	samples: Array<WSISample>
+	error?: string
+}
+
+export type WSISample = {
+	sampleId: string
+	wsimages: Array<string>
+}
+
+export const wsiSamplesPayload: RoutePayload = {
+	request: {
+		typeId: 'WSISamplesRequest'
+	},
+	response: {
+		typeId: 'WSISamplesResponse'
+	}
+}

package/src/terms/geneVariant.ts

@@ -1,5 +1,13 @@
-import { MinBaseQ, BaseTerm, EnabledTermGroupSetting, BaseTW, GroupSettingQ, ValuesQ } from '../index.ts'
-import { TermSettingInstance } from '../termsetting.ts'
+import type {
+	MinBaseQ,
+	BaseTerm,
+	EnabledTermGroupSetting,
+	BaseTW,
+	GroupSettingQ,
+	ValuesQ,
+	TermValues
+} from '../index.ts'
+import type { TermSettingInstance } from '../termsetting.ts'
 
 export type GeneVariantBaseQ = MinBaseQ & {
 	cnvGainCutoff?: number
@@ -49,3 +57,16 @@ export type GeneVariantTermSettingInstance = TermSettingInstance & {
 	category2samplecount: any
 	groupSettingInstance?: any
 }
+
+export type DtTerm = {
+	id: string
+	name: string
+	parent_id: any
+	isleaf: boolean
+	type: string
+	dt: number
+	origin?: string
+	values?: TermValues
+	min?: number
+	max?: number
+}

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'
+	type: 'integer' | 'float' | 'geneExpression' | 'metaboliteIntensity' | 'date'
 	bins: PresetNumericBins
 	values?: TermValues
 	unit?: string
@@ -50,7 +50,7 @@ export type NumericTerm = BaseTerm & {
 
 export type NumericDictTerm = BaseTerm & {
 	id?: string
-	type: 'integer' | 'float'
+	type: 'integer' | 'float' | 'date'
 	bins: PresetNumericBins
 	values?: TermValues
 	unit?: string

package/src/terms/term.ts

@@ -1,10 +1,10 @@
-import { Filter } from '../filter.js'
-import { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
-import { ConditionTerm } from './condition.js'
-import { NumericTerm } from './numeric.js'
-import { GeneVariantTerm } from './geneVariant.js'
-import { SampleLstTerm } from './samplelst.js'
-import { SnpsTerm } from './snps.js'
+import type { Filter } from '../filter.js'
+import type { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
+import type { ConditionTerm } from './condition.js'
+import type { NumericTerm } from './numeric.js'
+import type { GeneVariantTerm } from './geneVariant.js'
+import type { SampleLstTerm } from './samplelst.js'
+import type { SnpsTerm } from './snps.js'
 
 /**
  * @param id      term.id for dictionary terms, undefined for non-dictionary terms
@@ -56,6 +56,8 @@ export type BaseQ = {
 		| 'custom-groupset'
 		/** Applies to samplelst terms */
 		| 'custom-samplelst'
+		/** Applies to geneVariant term */
+		| 'filter'
 }
 
 export type ValuesQ = CategoricalBaseQ & {
@@ -72,7 +74,11 @@ export type CustomGroupSettingQ = CategoricalBaseQ & {
 	customset: BaseGroupSet
 }
 
-export type GroupSettingQ = ValuesQ | PredefinedGroupSettingQ | CustomGroupSettingQ
+export type FilterQ = BaseQ & {
+	type: 'filter'
+}
+
+export type GroupSettingQ = ValuesQ | FilterQ | PredefinedGroupSettingQ | CustomGroupSettingQ
 
 /*** types supporting termwrapper term ***/
 
@@ -99,6 +105,7 @@ export type BaseTerm = {
 	included_types?: string[]
 	isleaf?: boolean
 	values?: TermValues
+	filter?: any
 }
 
 export type Term = BaseTerm &
@@ -115,7 +122,8 @@ export type ValuesGroup = {
 export type FilterGroup = {
 	name: string
 	type: 'filter'
-	filter: Filter
+	filter: any
+	uncomputable?: boolean // if true, do not include this group in computations
 }
 
 export type GroupEntry = ValuesGroup | FilterGroup
@@ -128,6 +136,7 @@ type Groupset = {
 	name: string
 	is_grade?: boolean
 	is_subcondition?: boolean
+	id?: string // to identify groupset, used by geneVariant term
 } & BaseGroupSet
 
 export type EnabledTermGroupSetting = {

package/dist/gdc.topMutatedGenes.js

@@ -1,11 +0,0 @@
-import {
-  gdcTopMutatedGenePayload,
-  validGdcTopMutatedGeneRequest,
-  validGdcTopMutatedGeneResponse
-} from "./chunk-Q5F2XI6A.js";
-import "./chunk-CNSSF43V.js";
-export {
-  gdcTopMutatedGenePayload,
-  validGdcTopMutatedGeneRequest,
-  validGdcTopMutatedGeneResponse
-};