@sjcrh/proteinpaint-types 2.82.0 → 2.84.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.82.0",
+  "version": "2.84.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",
@@ -21,9 +21,11 @@
   "devDependencies": {
     "ts-node": "^10.9.2",
     "ts-patch": "^3.2.1",
-    "typescript": "^5.6.2",
     "typia": "^4.1.14"
   },
+  "peerDependencies": {
+    "typescript": "^5.6.3"
+  },
   "files": [
     "src"
   ]

package/src/dataset.ts

@@ -545,7 +545,7 @@ export type SingleCellDataGdc = {
 	src: 'gdcapi'
 	sameLegend: boolean
 	get?: (q: any) => any
-	refName: string
+	refName?: string
 	plots: GDCSingleCellPlot[]
 	width?: number
 	height?: number
@@ -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
@@ -1520,6 +1535,11 @@ export type PreInit = {
 	retryDelay?: number
 	retryMax?: number
 	errorCallback?: (response: PreInitStatus) => void
+	test?: {
+		numCalls: number
+		minor: number
+		mayEditResponse: (response: any) => any
+	}
 }
 
 export type Mds3 = BaseMds & {

package/src/routes/brainImaging.ts

@@ -1,3 +1,5 @@
+import { CategoricalTW } from '../terms/categorical.ts'
+
 export type GetBrainImagingRequest = {
 	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
 	genome: string
@@ -5,17 +7,36 @@ export type GetBrainImagingRequest = {
 	dslabel: string
 	/** a user-defined brain template label in dataset file, such as Ref1, Ref2 */
 	refKey: string
-	/** when true will only return all the samples that have NIdata */
-	samplesOnly?: boolean
 	/** the slice index of sagittal, coronal and axial planes*/
 	l?: string
 	f?: string
 	t?: string
 	/** the sample names selected by the users to plot on brain template */
-	selectedSampleFileNames?: string[]
+	selectedSampleFileNames: string[]
+	/* the term to divide the samples into groups */
+	divideByTW?: CategoricalTW
+	/* the term to color the samples based on their category */
+	overlayTW?: CategoricalTW
 }
 
+export type GetBrainImagingSamplesRequest = {
+	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
+	genome: string
+	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
+	dslabel: string
+	/** a user-defined brain template label in dataset file, such as Ref1, Ref2 */
+	refKey: string
+}
+
+export type GetBrainImagingSamplesResponse = {
+	samples: BrainSample[]
+}
+
+export type BrainSample = { [key: string]: string }
+
 export type GetBrainImagingResponse = {
 	/** the brain imaging plot */
 	brainImage: string
 }
+
+export type FilesByCategory = { [category: string]: { samples: string[]; color: string } }

package/src/routes/termdb.boxplot.ts

@@ -4,16 +4,16 @@ export type BoxPlotRequest = {
 }
 
 export type BoxPlotResponse = {
-	plots: BoxPlotEntry[]
 	/** Absolute min value for all plots */
 	absMin: number
 	/** Absolute max value for all plots */
 	absMax: number
 	/** Longest label length for all plots */
 	maxLabelLgth: number
+	plots: BoxPlotEntry[]
 }
 
-export type BoxPlotEntry = {
+type BoxPlotEntry = {
 	boxplot: BoxPlotData
 	/** Label to show */
 	label: string
@@ -27,14 +27,23 @@ export type BoxPlotEntry = {
 	max: number
 }
 
-export type BoxPlotData = {
+type BoxPlotData = {
+	/** Min/1st whisker value */
 	w1: number
+	/** Max/2nd whisker value */
 	w2: number
+	/** 5% */
 	p05: number
+	/** 25% */
 	p25: number
+	/** 50% */
 	p50: number
+	/** 75% */
 	p75: number
+	/** 95% */
 	p95: number
+	/** Interquartile region */
 	iqr: number
+	/** Outliers */
 	out: { value: number }[]
 }

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/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