@sjcrh/proteinpaint-types 2.129.6 → 2.131.0

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-6C4DMGK3.js";
+} from "./chunk-J7ODYX6N.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.129.6",
+  "version": "2.131.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -549,8 +549,16 @@ configs for types of cnv data
 important: presence of filtering properties indiate the type of cnv quantification
 and will trigger rendering of ui controls
 */
-type CnvSegment = {
-	/** ds supplied ordynamically added getter */
+type CnvSegmentQuery = {
+	/** ds supplied or dynamically added getter
+	todo properly type input/output
+	returns:
+		{
+			cnvs:[]
+				{ chr, start, stop, value?, class, samples[], occurrence=1, ssm_id }
+			cnvMsg:string
+		}
+	*/
 	get?: (q: any) => any
 	/** either file or get is required. file is bgzipped with columns:
 	1. chr
@@ -633,7 +641,7 @@ type CnvSegment = {
 no longer used!!
 file content is a probe-by-sample matrix, values are signals
 for a given region, the median signal from probes in the region is used to make a gain/loss call for each sample
-this is alternative to CnvSegment
+this is alternative to CnvSegmentQuery
 
 type Probe2Cnv = {
                 file: string
@@ -901,7 +909,7 @@ type Mds3Queries = {
 	gbRestrictMode?: 'protein' | 'genomic'
 	snvindel?: SnvIndelQuery
 	svfusion?: SvFusion
-	cnv?: CnvSegment
+	cnv?: CnvSegmentQuery
 	trackLst?: TrackLst
 	ld?: LdQuery
 	defaultCoord?: string

package/src/routes/termdb.singleSampleMutation.ts

@@ -6,8 +6,8 @@ export type TermdbSingleSampleMutationRequest = {
 	genome: string
 	/** Dataset label */
 	dslabel: string
-	/** sample id */
-	sample: string
+	/** sample id, allow string or number; for native ds, sample name in number will be cast into string */
+	sample: string | number
 }
 type ValidResponse = {
 	/** List of mutation data points from this sample TODO change to type of M elements */

package/src/termdb.matrix.ts

@@ -17,6 +17,12 @@ type SampleEntry = {
 	}
 }
 
+type CategoryEntry = {
+	key: string
+	label: string
+	samplecount: number
+}
+
 export type ValidGetDataResponse = {
 	samples: {
 		[index: string | number]: SampleEntry
@@ -33,6 +39,9 @@ export type ValidGetDataResponse = {
 				bins?: any
 				/** CTE.events. These info are not available in term object and is computed during run time. */
 				events?: any
+				/** Categories of term. Only computed for categorical terms that
+				have an empty term.values{}. */
+				categories?: CategoryEntry[]
 			}
 		>
 		/** metadata about samples (e.g. print names). avoid duplicating such in sample data elements (e.g. mutations)

package/src/terms/term.ts

@@ -105,6 +105,9 @@ export type BaseTerm = {
 	included_types?: string[]
 	isleaf?: boolean
 	values?: TermValues
+	/** Do not build .values{} when building termdb. Used for 
+	making categorical term with empty .values{} in TermdbTest */
+	skipValuesBuild?: boolean
 }
 
 export type Term = BaseTerm & (NumericTerm | CategoricalTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm)