@sjcrh/proteinpaint-types 2.137.2 → 2.138.0

package/dist/termdb.categories.js

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

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-657TS66W.js";
+} from "./chunk-LTGT4NK4.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-IE3MSHTB.js";
+} from "./chunk-I2BMMKPN.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

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

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-6LRQCE3E.js";
+} from "./chunk-6HAS5WRS.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.singleSampleMutation.js

@@ -2,7 +2,7 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-YW6G7WTF.js";
+} from "./chunk-GGZUN2GE.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbSingleSampleMutationPayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-7YFANJ2A.js";
+} from "./chunk-CC3OBRKE.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-SUL2XLYM.js";
+} from "./chunk-2YASZMH3.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-6H6TQ3MA.js";
+} from "./chunk-7FTOFTNK.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-YGOZU46P.js";
+} from "./chunk-S2M5SN7Q.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.137.2",
+  "version": "2.138.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1363,9 +1363,15 @@ if missing, name is value of m[url.namekey], as used in url itself (e.g. snp rsi
 }
 
 /*** type of ds.cohort.termdb{} ***/
-type Termdb = {
+export type Termdb = {
 	/** Terms */
 	termIds?: TermIds
+	/**
+	 * The required minimum number of samples with data as queried with getData() or other code,
+	 * in order to minimize the ease of extracting identifiable information from aggregate data
+	 * in server response
+	 */
+	minSampleSizeForFilterCharts?: number
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: (clientAuthResult: any) => boolean
 	converSampleIds?: boolean
@@ -1517,15 +1523,13 @@ keep this setting here for reason of:
 		/** colors for a category multivalues */
 		[index: string]: { [index: string]: string }
 	}
-	/** terms are shown in the dictionary based on term and user role.
-	 */
-	isTermVisible?: (clientAuthResult: any, id: string) => boolean
-	/** when ds supports chart types e.g. summarizeMutationDiagnosis, this setting is required to supply a dict term to populate the chart ui
-	 */
 	defaultTw4correlationPlot?: {
 		/** key is string as disease/survial etc, value is tw */
 		[index: string]: Tw
 	}
+	//terms  are shown in the dictionary based on term and user role.
+	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
+	getAdditionalFilter?: (clientAuthResult: any, term: any) => Filter | undefined
 }
 
 type SampleType = {
@@ -1548,7 +1552,7 @@ type Tw = {
 	/** short hand for using either id (dict term) or term{} */
 	id?: string
 	term?: object
-	q: object
+	q: unknown
 	/** quick fix for generating URL links in mds3 tk sample table! adhoc design. may move to tw.term.baseURL and not specific to mds3 tk
 	 */
 	baseURL?: string

package/src/routes/termdb.categories.ts

@@ -14,6 +14,11 @@ export type CategoriesRequest = {
 	currentGeneNames?: string[]
 	/** optional property added by mds3 tk, to limit to cases mutated in this region */
 	rglst?: any
+	__protected__?: {
+		sessionId?: string
+		clientAuthResults?: any
+		ignoredTermIds?: any
+	}
 }
 
 interface Entries {

package/src/routes/termdb.descrstats.ts

@@ -17,6 +17,7 @@ export type DescrStatsRequest = {
 	filter?: Filter
 	/** optional gdc filter */
 	filter0?: any
+	__protected__?: any //reuse definition from termdb.matrix.ts!!!
 }
 
 interface entries {

package/src/routes/termdb.singleSampleMutation.ts

@@ -14,7 +14,7 @@ type ValidResponse = {
 	mlst: object[]
 	/** total number of items for each dt, useful to indicate snvindel limited to 10k for a hypermutator */
 	dt2total?: { dt: number; total: number }[]
-	/** alternative data by dt
+	/** this declares alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
 	key: dt value
 	value: array of objects, each is a distinct set of data points for this dt
 		on ui, selecting an object will allow to show this data in disco plot
@@ -26,6 +26,8 @@ type ValidResponse = {
 			nameHtml?: string
 			/** name in text */
 			name?: string
+			/** one set of data must have this flag set to true to indicate its data is already present in ValidResponse.mlst */
+			inuse?: boolean
 			/** required list of events from this data */
 			mlst: object[]
 		}[]

package/src/terms/geneVariant.ts

@@ -20,7 +20,7 @@ export type GvCustomGsQ = GvBaseQ & { type: 'custom-groupset'; customset: BaseGr
 export type GvQ = GvValuesQ | GvPredefinedGsQ | GvCustomGsQ
 
 // term types
-export type GvGene = {
+type Gene = {
 	kind: 'gene'
 	gene: string
 	// chr,start,stop should exist together as a separate type called
@@ -31,14 +31,22 @@ export type GvGene = {
 	stop?: number
 }
 
-export type GvCoord = {
+type Coord = {
 	kind: 'coord'
 	chr: string
 	start: number
 	stop: number
 }
 
-type GvBaseTerm = BaseTerm & { type: 'geneVariant' } & (GvGene | GvCoord)
+type GvGeneTerm = BaseTerm & (Gene | Coord)
+
+// including (Gene | Coord) for backwards compatibility
+// with older geneVariant term structure
+type GvBaseTerm = BaseTerm &
+	(Gene | Coord) & {
+		type: 'geneVariant'
+		genes: GvGeneTerm[]
+	}
 
 export type RawGvTerm = GvBaseTerm & {
 	groupsetting?: TermGroupSetting