@sjcrh/proteinpaint-types 2.81.5 → 2.83.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.81.5",
+  "version": "2.83.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -915,6 +915,11 @@ type MatrixSettings = {
 	cnvUnit?: 'log2ratio' | 'segmedian'
 }
 
+type NumericDictTermClusterSettings = {
+	/** default hiercluster group name */
+	termGroupName?: string
+}
+
 type Matrix = {
 	/** alternative name, e.g. the plot is called "oncomatrix" in gdc; by default it's called "matrix" */
 	appName?: string
@@ -927,6 +932,15 @@ type Matrix = {
 	legendValueFilter?: any
 }
 
+type NumericDictTermCluster = {
+	/** alternative name, e.g. the plot is called "drug sensitivity" in ALL-pharmacotyping; by default it's called "Numeric Dictionary Term cluster" */
+	appName?: string
+	/** default settings for numericDictTermCluster plot */
+	settings?: NumericDictTermClusterSettings
+	/** list of numeric term ids that will be excluded from the numeric dictionary term cluster, add to usecase.detail to exclude terms*/
+	exclude?: string[]
+}
+
 type Survival = {
 	/** default settings for survival plot */
 	settings?: SurvivalSettings
@@ -1031,6 +1045,7 @@ keep this setting here for reason of:
 
 	scatterplots?: Scatterplots
 	matrix?: Matrix
+	numericDictTermCluster?: NumericDictTermCluster
 	survival?: Survival
 	logscaleBase2?: boolean
 	plotConfigByCohort?: PlotConfigByCohort
@@ -1509,9 +1524,30 @@ export type Mds = BaseMds & {
 	}
 }
 
+type PreInitStatus = {
+	status: string
+	message?: string
+	[props: string]: any
+}
+
+export type PreInit = {
+	getStatus: () => Promise<PreInitStatus>
+	retryDelay?: number
+	retryMax?: number
+	errorCallback?: (response: PreInitStatus) => void
+	test?: {
+		numCalls: number
+		minor: number
+		mayEditResponse: (response: any) => any
+	}
+}
+
 export type Mds3 = BaseMds & {
 	label?: Title
 	isMds3: boolean
+	loadWithoutBlocking?: boolean
+	preInit?: PreInit
+	initErrorCallback?: (a: any) => void
 	viewModes?: ViewMode[]
 	dsinfo?: KeyVal[]
 	queries?: Mds3Queries
@@ -1522,7 +1558,7 @@ export type Mds3 = BaseMds & {
 	ssm2canonicalisoform?: GdcApi
 	variant2samples?: Variant2Samples
 	// !!! TODO: improve these type definitions below !!!
-	getHostHeaders?: (q: any) => any
+	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any
 	customTwQByType?: {
 		[termType: string]: {

package/src/routes/termdb.cluster.ts

@@ -3,6 +3,7 @@ import { Filter } from '../filter.ts'
 import { Term } from '../terms/term.ts'
 import { GeneExpressionTerm } from '../terms/geneExpression.ts'
 import { MetaboliteIntensityTerm } from '../terms/metaboliteIntensity.ts'
+import { NumericDictTerm } from '../terms/numeric.ts'
 
 export type Gene = {
 	/** gene symbol, required */
@@ -42,7 +43,17 @@ export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
 	terms: MetaboliteIntensityTerm[]
 }
 
-export type TermdbClusterRequest = TermdbClusterRequestGeneExpression | TermdbClusterRequestMetabolite
+export type TermdbClusterRequestNumericDictTerm = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'numericDictTerm'
+	/** List of terms */
+	terms: NumericDictTerm[]
+}
+
+export type TermdbClusterRequest =
+	| TermdbClusterRequestGeneExpression
+	| TermdbClusterRequestMetabolite
+	| TermdbClusterRequestNumericDictTerm
 
 export type Hclust = {
 	merge: { n1: number; n2: number }[]

package/src/routes/termdb.singlecellData.ts

@@ -18,8 +18,10 @@ export type Cell = {
 export type Plot = {
 	/** name of the plot */
 	name: string
-	/** List of cells */
-	cells: Cell[]
+	/** List of cells with gene expression */
+	expCells?: Cell[]
+	/** List of cells with no gene expression, if no gene provided all cells will be here */
+	noExpCells?: Cell[]
 	/** Column name to color by, e.g Cell type, CNV, Fusion */
 	colorBy: string
 	colorColumns: string[]

package/src/terms/numeric.ts

@@ -50,6 +50,14 @@ export type NumericTerm = BaseTerm & {
 	valueConversion?: ValueConversion*/
 }
 
+export type NumericDictTerm = BaseTerm & {
+	id?: string
+	type: 'integer' | 'float'
+	bins: PresetNumericBins
+	values?: TermValues
+	unit?: string
+}
+
 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