@sjcrh/proteinpaint-types 2.83.0 → 2.85.0

package/src/routes/termdb.topVariablyExpressedGenes.ts

@@ -1,45 +0,0 @@
-//import GdcFilter0 from './filter.gdc'
-import type { Filter } from '../filter.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type TermdbTopVariablyExpressedGenesRequest = {
-	/** Ref genome */
-	genome: string
-	/** Ds label */
-	dslabel: string
-	/** Number of top genes requested */
-	maxGenes: number
-	/** optional param defined by dataset. if to scan all or subset of genes */
-	geneSet?: {
-		/** Indicates the geneset to return
-		 * all - all genes
-		 * custom - user defined list of genes
-		 * msigdb - msigdb geneset
-		 */
-		type: 'all' | 'custom' | 'msigdb'
-		/** Sent as null for 'all' types. Otherwise a list of gene symbols */
-		geneList: string[] | null
-	}
-	/** optional parameter defined in gdc dataset. not used for non-gdc ds */
-	min_median_log2_uqfpkm?: number
-	/** filter extreme values (in native implementation): true/false */
-	filter_extreme_values?: number
-	/** min_count of fpkm when filter_extreme_values (in native implementation) = true */
-	min_count?: number
-	/** min_total_count of fpkm when filter_extreme_values (in native implementation) = true */
-	min_total_count?: number
-	/** Filter type: variance/inter-quartile region (in native implementation) */
-	rank_type?: {
-		type: 'var' | 'iqr'
-	}
-	filter?: Filter
-	/** JSON, optional GDC cohort filter to restrict cases */
-	filter0?: any //GdcFilter0
-}
-
-type ValidResponse = {
-	/** Array of gene names TODO may change element to objs */
-	genes: string[]
-}
-
-export type TermdbTopVariablyExpressedGenesResponse = ErrorResponse | ValidResponse

package/src/routes/termdb.violin.ts

@@ -1,74 +0,0 @@
-import type { Filter } from '../filter.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type getViolinRequest = {
-	genome: string
-	dslabel: string
-	embedder: string
-	/** main tw to fetch numeric data to show in violin */
-	tw: any
-	/** optional tw to divide tw data into multiple violins and show under one axis */
-	divideTw?: any
-	/** A number representing the device's pixel ratio, which may be used for rendering quality adjustments */
-	devicePixelRatio: number
-	/** optional mass filter */
-	filter?: Filter
-	/** optional read-only invisible filter TODO GdcFilter0 */
-	filter0?: any
-	/** A number representing the width of the SVG (Scalable Vector Graphics) box, used for rendering the chart */
-	svgw: number
-	/** A string with two possible values: 'horizontal' or 'vertical', indicating the orientation of the chart, either horizontal or vertical */
-	orientation: 'horizontal' | 'vertical'
-	/** A string representing the type of symbol used on the plot, which can be either 'circles' or 'rugs' */
-	datasymbol: string
-	/** A number representing the radius of the data symbols rendered on the plot */
-	radius: number
-	/** A number representing the width of the stroke used to generate the data symbols (data symbols are rendered on the server side) */
-	strokeWidth: number
-	/** A number representing the dimension perpendicular to the violin spread (the height of the axis) */
-	axisHeight: number
-	/** A number representing the right margin of the chart or plot */
-	rightMargin: number
-	/** A string representing a unit of measurement (e.g., 'log' for log scale) */
-	unit: string
-	/** ?? */
-	isKDE: boolean
-}
-
-interface binsEntries {
-	x0: number
-	x1: number
-	density: number
-}
-interface valuesEntries {
-	id: string
-	label: string
-	value: number
-}
-
-interface pvalueEntries {
-	value?: string
-	html?: string
-}
-
-type plot = {
-	label: string
-	plotValueCount: number
-	src: string
-	bins: binsEntries[]
-	densityMax: number
-	biggestBin: number
-	summaryStats: {
-		values: valuesEntries[]
-	}
-}
-
-export type getViolinResponse = ValidResponse | ErrorResponse
-
-type ValidResponse = {
-	min: number
-	max: number
-	plots: plot[]
-	pvalues?: pvalueEntries[][]
-	uncomputableValueObj: any
-}

package/src/routes/wsimages.ts

@@ -1,12 +0,0 @@
-export type GetWSImagesRequest = {
-	genome: string
-	dslabel: string
-	sampleId: string
-	wsimage: string
-}
-
-export type GetWSImagesResponse = {
-	sessionId: string
-	slide_dimensions: number[]
-	status: string
-}

package/src/terms/categorical.ts

@@ -1,106 +0,0 @@
-import {
-	BaseTerm,
-	TermValues,
-	GroupSettingQ,
-	ValuesQ,
-	TermGroupSetting,
-	BaseTW,
-	PredefinedGroupSettingQ,
-	CustomGroupSettingQ
-} from './term.ts'
-import { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
-import { TermSettingInstance } from '../termsetting.ts'
-
-/**
- * A raw categorical term q object, before filling-in
- *
- * test:CategoricalQ:
- *
- * @category TW
- */
-
-export type RawCatTWValues = BaseTW & {
-	type?: 'CatTWValues'
-	/** must already exist, for dictionary terms, TwRouter.fill() will use mayHydrateDictTwLst() */
-	term: CategoricalTerm
-	q: RawValuesQ
-}
-
-export type RawCatTWPredefinedGS = BaseTW & {
-	type?: 'CatTWPredefinedGS'
-	term: CategoricalTerm
-	q: RawPredefinedGroupsetQ
-}
-
-export type RawCatTWCustomGS = BaseTW & {
-	type?: 'CatTWCustomGS'
-	term: CategoricalTerm
-	q: RawCustomGroupsetQ
-}
-
-export type RawCatTW = RawCatTWValues | RawCatTWPredefinedGS | RawCatTWCustomGS
-
-export type CategoricalBaseQ = MinBaseQ & {
-	mode?: 'discrete' | 'binary'
-}
-
-export type CategoricalQ = GroupSettingQ | ValuesQ
-
-export type CategoricalTerm = BaseTerm & {
-	type: 'categorical'
-	values: TermValues
-	groupsetting: TermGroupSetting
-}
-
-/**
- * A categorical term wrapper object
- *
- * @group Termdb
- * @category TW
- */
-
-export type CategoricalTW = BaseTW & {
-	//id: string
-	type: 'CatTWValues' | 'CatTWPredefinedGS' | 'CatTWCustomGS'
-	q: CategoricalQ
-	term: CategoricalTerm
-}
-
-export type CatTWValues = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: ValuesQ
-	type: 'CatTWValues'
-	// do not use this boolean flag, defined here only to help illustrate
-	// in tw/test/fake/app.js why this is type check error prone and
-	// less preferred than a discriminant prop that also works at runtime
-	isCatTWValues?: true
-}
-
-export type CatTWPredefinedGS = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: PredefinedGroupSettingQ
-	type: 'CatTWPredefinedGS'
-	// do not use this boolean flag, defined here only to help illustrate
-	// in tw/test/fake/app.js why this is type check error prone and
-	// less preferred than a discriminant prop that also works at runtime
-	isCatTWPredefiendGS?: true
-}
-
-export type CatTWCustomGS = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: CustomGroupSettingQ
-	type: 'CatTWCustomGS'
-}
-
-export type CatTWTypes = CatTWValues | CatTWPredefinedGS | CatTWCustomGS
-
-export type CategoricalTermSettingInstance = TermSettingInstance & {
-	q: CategoricalQ
-	term: CategoricalTerm
-	category2samplecount: any
-	validateGroupsetting: () => { text: string; bgcolor?: string }
-	error?: string
-}

package/src/terms/condition.ts

@@ -1,55 +0,0 @@
-import { BaseTerm, BaseQ, TermValues } from './term.ts'
-import { TermWrapper } from './tw.ts'
-
-/**
- * @category TW
- */
-
-export type ConditionQ = BaseQ & {
-	mode: 'discrete' | 'binary' | 'cuminc' | 'cox'
-	type?: 'values'
-	bar_by_children?: boolean // 'true' if term is not a leaf and has subconditions
-	bar_by_grade?: boolean /* 'true' for barchart. Always 'true' for cuminc and logistic/cox outcome (children terms are not allowed for those cases)
-	when 'true', 'value_by_*' flags are effective.*/
-	breaks?: number[] /*
-	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'
-	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 ConditionTerm = BaseTerm & {
-	type: 'condition'
-	values: TermValues
-}
-
-/**
- * @group Termdb
- * @category TW
- */
-export type ConditionTW = TermWrapper & {
-	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
-}
-*/

package/src/terms/geneExpression.ts

@@ -1,32 +0,0 @@
-import { TermWrapper } from './tw.ts'
-import { NumericTerm, NumericQ } from './numeric.ts'
-import { TermSettingInstance } from '../termsetting.ts'
-
-/*
---------EXPORTED--------
-GeneExpressionQ
-GeneExpressionTermWrapper
-GeneExpressionTermSettingInstance
-
-*/
-
-export type GeneExpressionQ = NumericQ & { dt?: number }
-
-export type GeneExpressionTW = TermWrapper & {
-	q: GeneExpressionQ
-	term: GeneExpressionTerm
-}
-
-export type GeneExpressionTerm = NumericTerm & {
-	gene: string
-	// temporarily allowing chr/start/stop to support
-	// legacy fpkm files
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-export type GeneExpressionTermSettingInstance = TermSettingInstance & {
-	q: GeneExpressionQ
-	term: GeneExpressionTerm
-}

package/src/terms/geneVariant.ts

@@ -1,51 +0,0 @@
-import { MinBaseQ, BaseTerm, EnabledTermGroupSetting, BaseTW, GroupSettingQ, ValuesQ } from '../index.ts'
-import { TermSettingInstance } from '../termsetting.ts'
-
-export type GeneVariantBaseQ = MinBaseQ & {
-	cnvGainCutoff?: number
-	cnvMaxLength?: number
-	cnvMinAbsValue?: number
-	cnvLossCutoff?: number
-	exclude: string[]
-	dt?: number
-	origin?: string
-}
-
-export type GeneVariantQ = GeneVariantBaseQ & (ValuesQ | GroupSettingQ)
-
-type GeneVariantBaseTerm = BaseTerm & {
-	type: 'geneVariant'
-	groupsetting: EnabledTermGroupSetting
-}
-
-export type GeneVariantGeneTerm = GeneVariantBaseTerm & {
-	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
-}
-
-export type GeneVariantCoordTerm = GeneVariantBaseTerm & {
-	kind: 'coord'
-	chr: string
-	start: number
-	stop: number
-}
-
-export type GeneVariantTerm = GeneVariantGeneTerm | GeneVariantCoordTerm
-
-export type GeneVariantTW = BaseTW & {
-	term: GeneVariantTerm
-	q: GeneVariantQ
-}
-
-export type GeneVariantTermSettingInstance = TermSettingInstance & {
-	q: GeneVariantQ
-	term: GeneVariantTerm
-	category2samplecount: any
-	groupSettingInstance?: any
-}

package/src/terms/metaboliteIntensity.ts

@@ -1,31 +0,0 @@
-import { TermWrapper } from './tw.ts'
-import { BaseQ } from './term.ts'
-import { NumericTerm } from './numeric.ts'
-import { TermSettingInstance } from '../termsetting.ts'
-
-/*
---------EXPORTED--------
-MetaboliteIntensityQ
-MetaboliteIntensityTermWrapper
-MetaboliteIntensityTermSettingInstance
-
-*/
-
-export type MetaboliteIntensityQ = BaseQ & {
-	mode: 'continuous'
-}
-
-export type MetaboliteIntensityTW = TermWrapper & {
-	q: MetaboliteIntensityQ
-	term: MetaboliteIntensityTerm
-}
-
-export type MetaboliteIntensityTerm = NumericTerm & {
-	metabolite: string
-	bins: any
-}
-
-export type MetaboliteIntensityTermSettingInstance = TermSettingInstance & {
-	q: MetaboliteIntensityQ
-	term: MetaboliteIntensityTerm
-}

package/src/terms/numeric.ts

@@ -1,253 +0,0 @@
-import { MinBaseQ, BaseTW, TermValues, BaseTerm } from '../index.ts'
-
-export type RawRegularBin = Partial<RegularNumericBinConfig> & { preferredBins?: string }
-
-export type RawNumTWRegularBin = BaseTW & {
-	type?: 'NumTWRegularBin'
-	term: NumericTerm
-	q: RawRegularBin
-}
-
-export type RawCustomBin = Partial<CustomNumericBinConfig> & { preferredBins?: string }
-
-export type RawNumTWCustomBin = BaseTW & {
-	type?: 'NumTWCustomBin'
-	term: NumericTerm
-	q: RawCustomBin
-}
-
-export type RawNumTWCont = BaseTW & {
-	type?: 'NumTWCont'
-	term: NumericTerm
-	q: ContinuousNumericQ
-}
-
-export type RawNumTWSpline = BaseTW & {
-	type?: 'NumTWSpline'
-	term: NumericTerm
-	q: SplineNumericQ
-}
-
-export type RawNumTW = RawNumTWCustomBin | RawNumTWRegularBin | RawNumTWCont | RawNumTWSpline
-
-export type NumericTerm = BaseTerm & {
-	id?: string
-	// these concrete term.type values make it clear that only these are numeric,
-	// "categorical", "condition", and other term.types are not included in this union
-	type: 'integer' | 'float' | 'geneExpression' | 'metaboliteIntensity'
-	bins: PresetNumericBins
-	values?: TermValues
-	unit?: string
-	/*densityNotAvailable?: boolean //Not used?
-	logScale?: string | number
-	max?: number
-	min?: number
-	name?: string
-	skip0forPercentile?: boolean
-	tvs?: Tvs
-	values?: TermValues
-	unit?: string
-	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
-	startunbounded: true
-	startinclusive?: false // cannot include an infinite bound
-	stop: number
-	stopinclusive?: boolean
-	stopunbounded?: false
-	label?: string
-}
-
-export type StopUnboundedBin = {
-	start: number
-	stopunbounded: true
-	startinclusive?: boolean
-	startunbounded?: false
-	stopinclusive?: false // cannot include an infinite bound
-	label?: string
-}
-
-// TODO??? should separate a fully bounded bin by startinclusive, stopinclusive
-// since neighboring bins must not contain the same boundary value
-export type FullyBoundedBin = {
-	startunbounded?: false
-	startinclusive?: boolean
-	start: number
-	stop: number
-	stopinclusive?: boolean
-	stopunbounded?: false
-	label?: string
-}
-
-export type NumericBin = StartUnboundedBin | FullyBoundedBin | StopUnboundedBin
-
-export type RegularNumericBinConfig = MinBaseQ & {
-	type: 'regular-bin' // another concrete value being assigned, instead of `string`
-	//regular-sized bins
-	mode?: 'discrete'
-	bin_size: number
-	// first_bin.stop is always required
-	first_bin: StartUnboundedBin | FullyBoundedBin
-
-	// if last_bin?.start is set, then a fixed last bin is used; otherwise it's not fixed and computed from data
-	last_bin?: StopUnboundedBin | FullyBoundedBin
-	label_offset?: number
-}
-
-export type CustomNumericBinConfig = MinBaseQ & {
-	type: 'custom-bin'
-	mode?: 'discrete' | 'binary'
-	// since ts will allow NumericBin[] to be empty,
-	// use this workaround to define a non-empty array
-	lst: [NumericBin, ...NumericBin[]]
-	preferredBins?: 'median'
-}
-
-// |
-// {
-// 	type?: 'custom-bin'
-// 	mode?: 'discrete' | 'binary'
-// 	// since ts will allow NumericBin[] to be empty,
-// 	// use this workaround to define a non-empty array
-// 	lst?: [NumericBin, ...NumericBin[]]
-// }
-
-/*export type NumericQ = BaseQ & {
-	// termType: 'float' | 'integer' -- converts to 'numeric'
-	preferredBins?: 'median' | 'less' | 'default'
-	modeBinaryCutoffType: 'normal' | 'percentile'
-	modeBinaryCutoffPercentile?: number
-	knots?: any //[]?
-	scale?: number //0.1 | 0.01 | 0.001
-	rounding: string
-}*/
-
-export type PresetNumericBins = {
-	default: RegularNumericBinConfig | CustomNumericBinConfig
-	less: RegularNumericBinConfig | CustomNumericBinConfig
-	label_offset?: number
-	label_offset_ignored?: boolean
-	rounding?: string
-	min?: number
-	max?: number
-}
-
-export type BinnedNumericQ = RegularNumericBinConfig | CustomNumericBinConfig
-
-export type DiscreteNumericQ = BinnedNumericQ //&
-// MinBaseQ & {
-// 	mode: 'discrete' | 'binary'
-// }
-
-// TODO: test with live code that defines an actual binary q object
-export type BinaryNumericQ = MinBaseQ & {
-	mode: 'binary'
-	type: 'custom-bin'
-	// tuple type with 2 members
-	lst: [StartUnboundedBin | FullyBoundedBin, StopUnboundedBin | FullyBoundedBin]
-}
-
-export type ContinuousNumericQ = MinBaseQ & {
-	mode: 'continuous'
-	// TODO: do not use a boolean, convert to a `transform: 'zscore' | ...` option
-	convert2ZScore?: boolean
-	//scale?: string
-	// todo below: q.type is expected to be undefined for now,
-	// but may be used later like in other q.modes,
-	// making type optional here makes NumericQ operations/conditions
-	// work consistently within the TermWrapper union type
-	type?: undefined
-}
-
-export type SplineNumericQ = MinBaseQ & {
-	mode: 'spline'
-	knots: {
-		value: number
-	}[]
-	// todo below: q.type is expected to be undefined for now,
-	// but may be used later like in other q.modes,
-	// making type optional here makes NumericQ operations/conditions
-	// work consistently within the TermWrapper union type
-	type?: undefined
-}
-
-export type NumericQ = DiscreteNumericQ | BinaryNumericQ | ContinuousNumericQ | SplineNumericQ
-
-export type NumericTW = BaseTW & {
-	//id: string
-	term: NumericTerm
-	q: NumericQ
-}
-
-export type NumTWDiscrete = BaseTW & {
-	type: 'NumTWDiscrete'
-	term: NumericTerm
-	q: DiscreteNumericQ
-}
-
-export type NumTWRegularBin = BaseTW & {
-	type: 'NumTWRegularBin'
-	term: NumericTerm
-	q: RegularNumericBinConfig
-}
-
-export type NumTWCustomBin = BaseTW & {
-	type: 'NumTWCustomBin'
-	term: NumericTerm
-	q: CustomNumericBinConfig
-}
-
-export type NumTWBinaryBin = BaseTW & {
-	type: 'NumTWBinaryBin'
-	term: NumericTerm
-	q: BinaryNumericQ
-}
-
-export type NumTWBinary = BaseTW & {
-	type: 'NumTWBinary'
-	term: NumericTerm
-	q: BinaryNumericQ
-}
-
-export type NumTWCont = BaseTW & {
-	type: 'NumTWCont'
-	term: NumericTerm
-	q: ContinuousNumericQ
-}
-
-export type NumTWSpline = BaseTW & {
-	type: 'NumTWSpline'
-	term: NumericTerm
-	q: SplineNumericQ
-}
-
-export type NumTWTypes = NumTWRegularBin | NumTWCustomBin | NumTWBinary | NumTWCont | NumTWSpline
-export type NumTWDiscreteTypes = NumTWRegularBin | NumTWCustomBin //| NumTWBinary
-
-export type DefaultMedianQ = {
-	isAtomic?: true
-	mode: 'discrete'
-	type: 'custom-bin'
-	preferredBins: 'median'
-	lst: []
-}
-
-export type DefaultBinnedQ = {
-	isAtomic: true
-	mode: 'discrete'
-	type: 'regular-bin' | 'custom-bin'
-	preferredBins: 'default' | 'less'
-}
-
-export type DefaultNumericQ = NumericQ | DefaultBinnedQ | DefaultMedianQ

package/src/terms/q.ts

@@ -1,38 +0,0 @@
-import { HiddenValues, GroupSettingQ, GroupEntry } from './term.ts'
-
-// MinBaseQ is BaseQ without .mode and .type
-// MinBaseQ should eventually replace BaseQ because .mode and .type
-// should be specified in a term-type-specific manner
-export type MinBaseQ = {
-	/**Automatically set by fillTermWrapper()
-	Applies to barchart, survival plot, and cuminc plot.
-	Contains categories of a term to be hidden in its chart. This should only apply to client-side rendering, and should not be part of “dataName” when requesting data from server. Server will always provide a summary for all categories. It’s up to the client to show/hide categories.
-	This allows the key visibility to be stored in state, while toggling visibility will not trigger data re-request.
-	Currently termsetting menu does not manage this attribute. It’s managed by barchart legend.
-	*/
-	hiddenValues?: HiddenValues
-	/**indicates this object should not be extended by a copy-merge tool */
-	isAtomic?: true
-	name?: string
-	reuseId?: string
-}
-
-export type RawValuesQ = MinBaseQ & { type?: 'values'; mode?: 'binary' }
-
-export type RawPredefinedGroupsetQ = MinBaseQ & {
-	type: 'predefined-groupset'
-	mode?: 'binary' | 'discrete'
-	predefined_groupset_idx: number
-	/** deprecated nested object, will be handled by reshapeLegacyTW() in TwRouter */
-	groupsetting?: { inuse?: boolean } & GroupSettingQ
-}
-
-export type RawCustomGroupsetQ = MinBaseQ & {
-	type: 'custom-groupset'
-	mode?: 'binary' | 'discrete'
-	customset: {
-		groups: GroupEntry[]
-	}
-	/** deprecated nested object, will be handled by reshapeLegacyTW() in TwRouter */
-	groupsetting?: { inuse?: boolean } & GroupSettingQ
-}