@sjcrh/proteinpaint-types 2.183.0 → 2.184.0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-R7BQWUIF.js";
+} from "./chunk-LOFBLGRE.js";
 import "./chunk-YNHC5SXO.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -2,7 +2,7 @@ import {
   validViolinBoxRequest,
   validViolinBoxResponse,
   violinBoxPayload
-} from "./chunk-NF6RKK5E.js";
+} from "./chunk-WNUWRPXG.js";
 import {
   tilePayload,
   validTileRequest,
@@ -42,7 +42,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-URG6BNUU.js";
+} from "./chunk-UWK6LBTQ.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -107,7 +107,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-YDJG6VT4.js";
+} from "./chunk-Y6FNAG22.js";
 import {
   diffMethPayload,
   validDiffMethRequest,
@@ -157,7 +157,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-2UNWSR7Y.js";
+} from "./chunk-INIT6CVR.js";
 import {
   validChatRequest,
   validChatResponse
@@ -169,7 +169,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-JYTPHVO2.js";
+} from "./chunk-M7WMC7GC.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -261,7 +261,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-R7BQWUIF.js";
+} from "./chunk-LOFBLGRE.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -319,7 +319,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-7ZYM6FC6.js";
+} from "./chunk-TI565XIR.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-2UNWSR7Y.js";
+} from "./chunk-INIT6CVR.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-JYTPHVO2.js";
+} from "./chunk-M7WMC7GC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-YDJG6VT4.js";
+} from "./chunk-Y6FNAG22.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-URG6BNUU.js";
+} from "./chunk-UWK6LBTQ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.violinBox.js

@@ -2,7 +2,7 @@ import {
   validViolinBoxRequest,
   validViolinBoxResponse,
   violinBoxPayload
-} from "./chunk-NF6RKK5E.js";
+} from "./chunk-WNUWRPXG.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinBoxRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.183.0",
+  "version": "2.184.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -120,7 +120,7 @@ type SnvindelByRange = {
 	/** allow to apply special configurations to certain INFO fields of the bcf file */
 	infoFields?: InfoFieldEntry[]
 	/** getter function to retrieve data. dynamically added or ds-supplied */
-	get?: (f: any) => void
+	get?: (f: any, f2?: any) => void
 }
 
 type URLEntry = {
@@ -714,7 +714,6 @@ type ProteomeFilter = {
 }
 
 type ProteomeCohortConfig = {
-	cohortName: string
 	controlFilter: ProteomeFilter[]
 	caseFilter: ProteomeFilter[]
 }
@@ -722,7 +721,9 @@ type ProteomeCohortConfig = {
 type ProteomeAssayConfig = {
 	columnIdx: number
 	columnValue: string | number
-	cohorts: ProteomeCohortConfig[]
+	cohorts: {
+		[cohortName: string]: ProteomeCohortConfig
+	}
 	/** optional PTM type for PTM assay type */
 	PTMType?: string
 	/** optional specific mclass override for PTM assay type */
@@ -732,6 +733,7 @@ type ProteomeAssayConfig = {
 export type ProteomeAbundanceQuery = {
 	/** database file path */
 	dbfile?: string
+	overlayTerm?: BaseTerm
 	/** document structure */
 	assays: {
 		[assayName: string]: ProteomeAssayConfig

package/src/terms/termCollection.ts

@@ -123,13 +123,13 @@ export type TermCollectionTWQual = BaseTW & {
 // TODO: may add different termCollection TW types here
 export type TermCollectionTW = TermCollectionTWCont | TermCollectionTWQual
 
-export type RawTermCollectionTWCont = {
+export type RawTermCollectionTWCont = BaseTW & {
 	type?: 'TermCollectionTWCont'
 	term: RawNumericTermCollection
 	q?: TermCollectionQCont
 }
 
-export type RawTermCollectionTWQual = {
+export type RawTermCollectionTWQual = BaseTW & {
 	type?: 'TermCollectionTWQual'
 	term: RawCategoricalTermCollection
 	q?: TermCollectionQQual

package/src/terms/tw.ts

@@ -1,10 +1,10 @@
 import type { SnpsQ, SnpsTW } from './snps.ts'
-import type { ConditionQ, ConditionTW } from './condition.ts'
+import type { ConditionQ, ConditionTW, RawConditionTW } from './condition.ts'
 import type { SampleLstQ } from './samplelst.ts'
-import type { NumTW, NumericQ } from './numeric.ts'
-import type { GvTW, GvQ } from './geneVariant.ts'
-import type { QualTW, QualQ } from './qualitative.ts'
-import type { TermCollectionTW, TermCollectionQ } from './termCollection.ts'
+import type { NumTW, NumericQ, RawNumTW } from './numeric.ts'
+import type { GvTW, GvQ, RawGvTW } from './geneVariant.ts'
+import type { QualTW, QualQ, RawQualTW } from './qualitative.ts'
+import type { TermCollectionTW, TermCollectionQ, RawTermCollectionTW } from './termCollection.ts'
 
 export type BaseTW = {
 	id?: string
@@ -19,6 +19,7 @@ export type BaseTW = {
 	sortSamples?: any
 	minNumSamples?: number
 	valueFilter?: any
+	values?: { [key: string]: any }
 }
 
 export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW | TermCollectionTW
@@ -30,27 +31,33 @@ export type TwLst = TermWrapper[]
 
 //export type Q = BaseQ | CategoricalQ | ConditionQ | NumericQ | SampleLstQ | SnpsQ
 
-export type RawTW =
-	//{ id: string } | RawCatTW
-	//
-	// BELOW TYPE IS NOT TESTED, only being used to compare tsc type checking behavior
-	// between non-union versus type-unions, which way is easier to code against
-	{
-		id?: string
-		term?: {
-			type: 'categorical' | 'condition'
-			[key: string | number]: any
-		}
-		q?: {
-			//predefined_groupset_idx?: number
-			//customset?: any
-			[key: string]: any
-			//type?: string //'custom-groupset' |
-			//customset?: any
-		}
-		isAtomic?: true
-		$id?: string
-	}
+export type RawDictTW = BaseTW & {
+	id: string
+	term?: undefined
+	q?: any
+}
+
+export type RawTW = RawDictTW | RawQualTW | RawNumTW | RawGvTW | RawConditionTW | RawTermCollectionTW
+//{ id: string } | RawCatTW
+//
+// BELOW TYPE IS NOT TESTED, only being used to compare tsc type checking behavior
+// between non-union versus type-unions, which way is easier to code against
+// {
+// 	id?: string
+// 	term?: {
+// 		type: 'categorical' | 'condition'
+// 		[key: string | number]: any
+// 	}
+// 	q?: {
+// 		//predefined_groupset_idx?: number
+// 		//customset?: any
+// 		[key: string]: any
+// 		//type?: string //'custom-groupset' |
+// 		//customset?: any
+// 	}
+// 	isAtomic?: true
+// 	$id?: string
+// }
 
 export interface TwHandler {
 	render?: (opts?: any) => void