@sjcrh/proteinpaint-types 2.189.0 → 2.190.0

package/src/routes/termdb.violinBox.ts

@@ -1,230 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { TermWrapper } from '../terms/tw.ts'
-import type { Filter } from '../filter.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-import type { DescrStats } from './termdb.descrstats.ts'
-
-/** Common properties shared by both violin and box plots */
-type CommonProps = {
-	/** numeric tw to fetch numeric data. tw.q.mode must be continuous */
-	tw: TermWrapper
-	dslabel: string
-	genome: string
-	/** overlay tw for multiple violins/boxplots */
-	overlayTw?: TermWrapper
-	/** tw to divide to multiple charts */
-	divideTw?: TermWrapper
-	/** mass filter */
-	filter?: Filter
-	/** read-only invisible filter */
-	filter0?: any
-	/** TODO: Needs description FIXME delete */
-	currentGeneNames?: string[]
-	/** if true, use log scale; if false or undefined, use linear scale */
-	isLogScale?: boolean
-}
-
-/** Request type for violin plots with required violin-specific parameters */
-export type ViolinRequest = CommonProps & {
-	/** Indicates the type of chart to render */
-	plotType: 'violin'
-	/** A number representing the dimension perpendicular to the violin spread */
-	axisHeight?: number
-	/** A string representing the type of symbol used on the plot */
-	datasymbol?: string
-	/** A number representing the device's pixel ratio */
-	devicePixelRatio: number
-	/** If true, uses KDE method to build plot */
-	isKDE?: boolean
-	/** A string with two possible values: 'horizontal' or 'vertical' */
-	orientation: string
-	/** A number representing the radius of the data symbols */
-	radius: number
-	/** A number representing the right margin */
-	rightMargin?: number
-	/** Term may be scaled from regression analysis */
-	scale?: any
-	/** A number representing the width of the stroke */
-	strokeWidth?: number
-	/** A number representing the width of the SVG box */
-	svgw: number
-	/** Number of bins to build the plot. Default is 20. */
-	ticks?: number
-}
-
-/** Request type for box plots with required box-specific parameters */
-export type BoxRequest = CommonProps & {
-	/** Indicates the type of chart to render */
-	plotType: 'box'
-	/** sort plots by median value */
-	orderByMedian?: boolean
-	/** Remove outliers from the plot */
-	removeOutliers?: boolean
-	/** If true, show association tests table */
-	showAssocTests?: boolean
-}
-
-/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */
-export type ViolinBoxRequest = ViolinRequest | BoxRequest
-
-export type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse
-
-/** Type guard to check if response is an ErrorResponse */
-export function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {
-	return 'error' in response && 'status' in response
-}
-
-/** Type guard to check if response is a BoxPlotResponse */
-export function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {
-	return !isErrorResponse(response) && 'charts' in response && 'descrStats' in response
-}
-
-/** Type guard to check if response is a ViolinResponse */
-export function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {
-	return !isErrorResponse(response) && 'min' in response && 'max' in response
-}
-
-/** Violin response types */
-interface BinsEntries {
-	x0: number
-	x1: number
-	density: number
-}
-
-interface ValuesEntries {
-	id: string
-	label: string
-	value: number
-}
-
-interface PValueEntries {
-	value?: string
-	html?: string
-}
-
-type ViolinDensity = {
-	bins: BinsEntries[]
-	densityMax: number
-	densityMin: number
-}
-
-export type ViolinPlotEntry = {
-	color: string
-	chartId: string
-	density: ViolinDensity
-	label: string
-	plotValueCount: number
-	seriesId: string
-	src: string
-	summaryStats: ValuesEntries[]
-}
-
-export type ViolinResponse = {
-	bins: { [index: string]: any }
-	charts: {
-		[index: string]: {
-			chartId: string
-			plots: ViolinPlotEntry[]
-			pvalues?: PValueEntries[][]
-		}
-	}
-	min: number
-	max: number
-	uncomputableValues: { [index: string]: number }[] | null
-	descrStats?: DescrStats
-}
-
-/** Boxplot response types */
-export type BoxPlotData = {
-	w1: number | undefined
-	w2: number | undefined
-	p05: number
-	p25: number
-	p50: number
-	p75: number
-	p95: number
-	iqr: number
-	out: { value: number }[]
-}
-
-export type BoxPlotEntry = {
-	boxplot: BoxPlotData & { label: string }
-	color?: string
-	descrStats: DescrStats
-	isHidden?: boolean
-	key: string
-	seriesId?: string
-}
-
-export type BoxPlotChartEntry = {
-	chartId: string
-	plots: BoxPlotEntry[]
-	sampleCount: number
-	wilcoxon?: [{ value: string }, { value: string }, { html: string }][]
-}
-
-export type BoxPlotResponse = {
-	absMin?: number
-	absMax?: number
-	bins?: {
-		[index: string]: any
-	}
-	charts: {
-		[chartId: string]: BoxPlotChartEntry
-	}
-	descrStats: DescrStats
-	uncomputableValues: { label: string; value: number }[] | null
-}
-
-export const violinBoxPayload: RoutePayload = {
-	request: {
-		typeId: 'ViolinBoxRequest'
-	},
-	response: {
-		typeId: 'ViolinBoxResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					plotType: 'violin',
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					tw: {
-						term: { id: 'aaclassic_5', type: 'float' },
-						q: { mode: 'continuous' }
-					},
-					devicePixelRatio: 2,
-					svgw: 200,
-					orientation: 'horizontal',
-					datasymbol: 'rug',
-					radius: 5,
-					isLogScale: false
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		},
-		{
-			request: {
-				body: {
-					plotType: 'box',
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					tw: {
-						term: { id: 'agedx', type: 'float' },
-						q: { mode: 'continuous' }
-					},
-					overlayTw: {
-						term: { id: 'sex', type: 'categorical' }
-					},
-					orderByMedian: true
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/tileserver.ts

@@ -1,14 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type TileRequest = any
-export type TileResponse = any
-
-export const tilePayload: RoutePayload = {
-	request: {
-		typeId: 'TileRequest'
-	},
-	response: {
-		typeId: 'TileResponse'
-	}
-	// examples: []
-}

package/src/routes/wsimages.ts

@@ -1,34 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type WSImagesRequest = {
-	genome: string
-	dslabel: string
-	sampleId?: string
-	wsimage: string
-	aiProjectId?: number
-}
-
-export type WSImagesResponse = {
-	// TileServer image session id
-	wsiSessionId?: string
-	overlays?: Array<PredictionOverlay>
-	slide_dimensions: number[]
-	mpp: number[]
-	status: string
-	error?: string
-}
-
-export type PredictionOverlay = {
-	layerNumber: string
-	predictionOverlayType: string
-}
-
-export const wsImagesPayload: RoutePayload = {
-	request: {
-		typeId: 'WSImagesRequest'
-	},
-	response: {
-		typeId: 'WSImagesResponse'
-	}
-	// examples: []
-}

package/src/routes/wsisamples.ts

@@ -1,25 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type WSISamplesRequest = {
-	genome: string
-	dslabel: string
-}
-
-export type WSISamplesResponse = {
-	samples: Array<WSISample>
-	error?: string
-}
-
-export type WSISample = {
-	sampleId: string
-	wsimages: Array<string>
-}
-
-export const wsiSamplesPayload: RoutePayload = {
-	request: {
-		typeId: 'WSISamplesRequest'
-	},
-	response: {
-		typeId: 'WSISamplesResponse'
-	}
-}

package/src/termdb.matrix.ts

@@ -1,57 +0,0 @@
-/******* server/src/termdb.matrix.js is ~not~ a route *****
- * getData() is used frequently in other routes or typescript files.
- * Although the original file is 1) not ts and 2) not a route, a type
- * is still needed when func used in other ts files.
- *
- * Use this type for that purpose.
- */
-
-type SampleEntry = {
-	/** stringified integer sample id  */
-	sample: string | number
-} & {
-	/** key and values for terms, separated by tw.$id */
-	[index: string]: {
-		key: number
-		value: number
-	}
-}
-
-type CategoryEntry = {
-	key: string
-	label: string
-	samplecount: number
-}
-
-// TODO: need to add a discriminant property (e.g. ".kind") to
-// distinguish between ValidGetDataResponse and { error: string }
-export type ValidGetDataResponse = {
-	samples: {
-		[index: string | number]: SampleEntry
-	}
-	/** Metadata */
-	refs: {
-		/** metadata about terms
-		 * Index is <tw.$id> */
-		byTermId: Record<
-			string,
-			{
-				keyOrder?: any
-				/** CTE.bins */
-				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)
-		[sample integer id]: {label: [string sample name for display], ...} 
-		May return as an empty object. */
-		bySampleId: Record<string, { label: string }> | object
-	}
-	sampleType?: any
-}
-
-export type GetDataResponse = ValidGetDataResponse | { error: string }

package/src/terms/categorical.ts

@@ -1,18 +0,0 @@
-import type { TermGroupSetting, TermValues, BaseTerm } from '../index.ts'
-
-/*
-For term type 'snp'
-*/
-
-export type CategoricalTerm = BaseTerm & {
-	id: string
-	name?: string
-	type: 'categorical'
-	values: TermValues
-	groupsetting: TermGroupSetting
-}
-
-export type RawCategoricalTerm = CategoricalTerm & {
-	groupsetting?: TermGroupSetting
-	values?: TermValues
-}

package/src/terms/condition.ts

@@ -1,73 +0,0 @@
-import type { BaseTerm, MinBaseQ, TermValues, BaseTW } from '../index.ts'
-//import type { TermWrapper } from './tw.ts'
-
-/**
- * @category TW
- */
-
-export type ConditionGradeQ = MinBaseQ & {
-	mode: 'discrete' | 'binary' | 'cuminc' | 'cox'
-	valueFor: 'grade'
-	bar_by_grade: true
-	/**
-		Breaks grades into groups
-		Array length=1, will break grades to 2 groups. 
-			E.g. [3] divides to [-1,0,1,2,], [3,4,5]
-			Allowed for both conditionModes "discrete/binary"
-		Array length=2, break to 3 groups. 
-			E.g. [1,2] divides to [-1,0], [1], [2,3,4,5]
-			E.g. [1,3] divides to [-1,0], [1,2], [3,4,5]
-			Only allowed for conditionMode="discrete" but not "binary"
-	*/
-	timeScale: 'age' | 'time'
-	breaks?: number[]
-	value_by_max_grade?: boolean //'false' if bar_by_children is 'true'
-	value_by_most_recent?: boolean //'false' if bar_by_children is 'true'
-	value_by_computable_grade?: boolean //'true' if bar_by_children is 'true'
-	groups?: any // TODO: should use a defined type
-}
-
-export type ConditionChildrenQ = MinBaseQ & {
-	mode: 'discrete'
-	valueFor: 'children'
-	bar_by_children: true
-	groups?: any // TODO: should use a defined type
-}
-
-// TODO: should implement the expected property combinations as distinct types
-export type ConditionQ = ConditionGradeQ | ConditionChildrenQ
-
-export type ConditionTerm = BaseTerm & {
-	type: 'condition'
-	values: TermValues
-}
-
-/**
- * @group Termdb
- * @category TW
- */
-export type ConditionTW = BaseTW & {
-	type: 'ConditionTW'
-	term: ConditionTerm
-	q: ConditionQ //replace the generic Q with specific condition Q
-}
-
-/**
- * @group Termdb
- * @category TW
- */
-/*
-export type ConditionTermSettingInstance = TermSettingInstance & {
-	q: ConditionQ
-	category2samplecount: { key: string; label: string; count: number }[]
-	refGrp: any
-}
-*/
-
-export type RawConditionTW = ConditionTW & {
-	q: {
-		valueFor?: 'grade' | 'children'
-		bar_by_children?: true
-		bar_by_grade?: true
-	}
-}

package/src/terms/date.ts

@@ -1,20 +0,0 @@
-import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
-
-/*
---------EXPORTED--------
-DateTerm
-DateTW
-DateTermSettingInstance
-*/
-
-export type DateTerm = NumericBaseTerm & {
-	name: string
-	type: 'date'
-	bins?: PresetNumericBins
-}
-
-export type DateTW = NumTW & { term: DateTerm }
-
-export type RawDateTerm = DateTerm & { name?: string }
-
-export type RawDateTW = RawNumTW & { term: RawDateTerm }

package/src/terms/dnaMethylation.ts

@@ -1,28 +0,0 @@
-import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } from './numeric.ts'
-
-export type DnaMethylationQ = NumericQ & { dt?: number }
-
-export type DnaMethylationTerm = NumericBaseTerm & {
-	type: 'dnaMethylation'
-	/** concatenated string value "chr:start-stop" */
-	id?: string
-	chr: string
-	start: number
-	stop: number
-	/** Type used to categorize the genomic feature */
-	genomicFeatureType: 'gene' | 'promoter' | 'region' | 'enhancer'
-	bins?: PresetNumericBins
-}
-
-export type RawDnaMethylationTerm = DnaMethylationTerm & {
-	/** Name of the genomic feature, e.g., gene name or promoter id/name, etc.
-	 * Different than .name, which includes the genomic coordinates and unit,
-	 * and is used for display purposes.*/
-	featureName?: string
-	name?: string
-	unit?: string
-}
-
-export type DnaMethylationTW = NumTW & { term: DnaMethylationTerm }
-
-export type RawDnaMethylationTW = RawNumTW & { term: RawDnaMethylationTerm }

package/src/terms/geneExpression.ts

@@ -1,38 +0,0 @@
-import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
-
-/*
---------EXPORTED--------
-GeneExpressionTerm
-GeneExpressionTermWrapper
-GeneExpressionTermSettingInstance
-*/
-
-type Gene = {
-	kind?: 'gene'
-	gene: string
-	// chr,start,stop should exist together as a separate type called
-	// 'Coord', but hard to code as atomic `& Coord` because it may
-	// need to be filled in
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-type Coord = {
-	kind?: 'coord'
-	gene?: string
-	chr: string
-	start: number
-	stop: number
-}
-
-export type GeneExpressionTerm = NumericBaseTerm & {
-	type: 'geneExpression'
-	bins?: PresetNumericBins
-} & (Gene | Coord)
-
-export type GeneExpressionTW = NumTW & { term: GeneExpressionTerm }
-
-export type RawGeneExpTerm = GeneExpressionTerm & { name?: string }
-
-export type RawGeneExpTW = RawNumTW & { term: RawGeneExpTerm }

package/src/terms/geneVariant.ts

@@ -1,132 +0,0 @@
-import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet } from '../index.ts'
-
-// q types
-export type GvBaseQ = MinBaseQ & {
-	// TODO: may uncomment below if q.mode is required in downstream code
-	// mode?: 'discrete' // may support 'continuous' for CNV?
-	cnvGainCutoff?: number
-	cnvMaxLength?: number
-	cnvMinAbsValue?: number
-	cnvLossCutoff?: number
-}
-
-type RawGvValuesQ = GvBaseQ & { type?: 'values' }
-type RawGvPredefinedGsQ = GvBaseQ & {
-	type: 'predefined-groupset'
-	predefined_groupset_idx?: number
-	dtLst?: any[] // dts to query
-}
-type RawGvCustomGsQ = GvBaseQ & {
-	type: 'custom-groupset'
-	customset?: BaseGroupSet
-	dtLst?: any[] // dts to query
-}
-export type RawGvQ = RawGvValuesQ | RawGvPredefinedGsQ | RawGvCustomGsQ
-
-export type GvValuesQ = GvBaseQ & { type: 'values' }
-export type GvPredefinedGsQ = GvBaseQ & {
-	type: 'predefined-groupset'
-	predefined_groupset_idx: number
-	dtLst: any[] // dts to query
-}
-export type GvCustomGsQ = GvBaseQ & {
-	type: 'custom-groupset'
-	customset: BaseGroupSet
-	dtLst: any[] // dts to query
-}
-
-export type GvQ = GvValuesQ | GvPredefinedGsQ | GvCustomGsQ
-
-// term types
-type Gene = {
-	kind: 'gene'
-	gene: string
-	// chr,start,stop should exist together as a separate type called
-	// 'Coord', but hard to code as atomic `& Coord` because it may
-	// need to be filled in
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-type Coord = {
-	kind: 'coord'
-	chr: string
-	start: number
-	stop: number
-}
-
-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
-	childTerms?: DtTerm[]
-}
-
-export type GvTerm = GvBaseTerm & {
-	groupsetting: TermGroupSetting
-	childTerms: DtTerm[]
-}
-
-// tw types
-export type RawGvValuesTW = BaseTW & {
-	type?: 'GvValuesTW'
-	term: RawGvTerm
-	q: RawGvValuesQ
-}
-
-export type RawGvPredefinedGsTW = BaseTW & {
-	type?: 'GvPredefinedGsTW'
-	term: RawGvTerm
-	q: RawGvPredefinedGsQ
-}
-
-export type RawGvCustomGsTW = BaseTW & {
-	type?: 'GvCustomGsTW'
-	term: RawGvTerm
-	q: RawGvCustomGsQ
-}
-
-export type GvValuesTW = BaseTW & {
-	type: 'GvValuesTW'
-	term: GvTerm
-	q: GvValuesQ
-}
-
-export type GvPredefinedGsTW = BaseTW & {
-	type: 'GvPredefinedGsTW'
-	term: GvTerm
-	q: GvPredefinedGsQ
-}
-
-export type GvCustomGsTW = BaseTW & {
-	type: 'GvCustomGsTW'
-	term: GvTerm
-	q: GvCustomGsQ
-}
-
-export type RawGvTW = RawGvValuesTW | RawGvPredefinedGsTW | RawGvCustomGsTW
-export type GvTW = GvValuesTW | GvPredefinedGsTW | GvCustomGsTW
-
-// miscellaneous types
-export type DtTerm = {
-	id: string
-	query: string
-	name: string
-	name_noOrigin: string
-	parentTerm?: RawGvTerm
-	parent_id: any
-	isleaf: boolean
-	type: string
-	dt: number
-	origin?: string
-	values: TermValues
-}