@sjcrh/proteinpaint-types 2.86.0 → 2.87.0

package/src/routes/termdb.termsbyids.ts

@@ -0,0 +1,26 @@
+import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+
+export type TermsByIdsRequest = {
+	/** 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
+	embedder: string
+	/** term id string */
+	ids: string[]
+}
+
+export type TermsByIdsResponse = {
+	terms: { [id: string]: TermWrapper }
+}
+
+export const termsByIdsPayload: RoutePayload = {
+	request: {
+		typeId: 'TermsByIdsRequest'
+	},
+	response: {
+		typeId: 'TermsByIdsResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.topTermsByType.ts

@@ -0,0 +1,32 @@
+import type { RoutePayload } from './routeApi.js'
+//import GdcFilter0 from './filter.gdc'
+import type { Term } from '../terms/term.ts'
+import type { Filter } from '../filter.ts'
+
+export type TermdbTopTermsByTypeRequest = {
+	/** Ref genome */
+	genome: string
+	/** Ds label */
+	dslabel: string
+	/* Term type */
+	type: string
+	/** pp filter */
+	filter?: Filter
+	/** JSON, optional GDC cohort filter to restrict cases */
+	filter0?: any //GdcFilter0
+}
+
+export type TermdbTopTermsByTypeResponse = {
+	/** Array of gene names TODO may change element to objs */
+	terms: Term[]
+}
+
+export const termdbTopTermsByTypePayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbTopTermsByTypeRequest'
+	},
+	response: {
+		typeId: 'TermdbTopTermsByTypeResponse'
+	},
+	// examples: []
+}

package/src/routes/termdb.topVariablyExpressedGenes.ts

@@ -0,0 +1,56 @@
+import type { RoutePayload } from './routeApi.js'
+//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
+
+export const termdbTopVariablyExpressedGenesPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbTopVariablyExpressedGenesRequest'
+	},
+	response: {
+		typeId: 'TermdbTopVariablyExpressedGenesResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.violin.ts

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+import type { RoutePayload } from './routeApi.js'
+import type { Filter } from '../filter.ts'
+import type { ErrorResponse } from './errorResponse.ts'
+
+export type ViolinRequest = {
+	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 ViolinResponse = ValidResponse | ErrorResponse
+
+type ValidResponse = {
+	min: number
+	max: number
+	plots: plot[]
+	pvalues?: pvalueEntries[][]
+	uncomputableValueObj: any
+}
+
+export const violinPayload: RoutePayload = {
+	request: {
+		typeId: 'ViolinRequest'
+	},
+	response: {
+		typeId: 'ViolinResponse'
+	},
+	examples: [
+		{
+			request: {
+				body: {
+					genome: 'hg38-test',
+					dslabel: 'TermdbTest',
+					embedder: 'localhost',
+					devicePixelRatio: 2.200000047683716,
+					maxThickness: 150,
+					screenThickness: 1218,
+					filter: {
+						type: 'tvslst',
+						in: true,
+						join: '',
+						lst: [
+							{
+								tag: 'cohortFilter',
+								type: 'tvs',
+								tvs: { term: { id: 'subcohort', type: 'categorical' }, values: [{ key: 'ABC', label: 'ABC' }] }
+							}
+						]
+					},
+					svgw: 227.27272234672367,
+					orientation: 'horizontal',
+					datasymbol: 'bean',
+					radius: 5,
+					strokeWidth: 0.2,
+					axisHeight: 60,
+					rightMargin: 50,
+					unit: 'abs',
+					termid: 'agedx'
+				}
+			},
+			response: {
+				header: { status: 200 }
+			}
+		}
+	]
+}

package/src/routes/tileserver.ts

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,24 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type WSImagesRequest = {
+	genome: string
+	dslabel: string
+	sampleId: string
+	wsimage: string
+}
+
+export type WSImagesResponse = {
+	sessionId?: string
+	slide_dimensions: number[]
+	status: string
+}
+
+export const wsImagesPayload: RoutePayload = {
+	request: {
+		typeId: 'WSImagesRequest'
+	},
+	response: {
+		typeId: 'WSImagesResponse'
+	}
+	// examples: []
+}

package/src/terms/categorical.ts

@@ -0,0 +1,106 @@
+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

@@ -0,0 +1,55 @@
+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

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+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

@@ -0,0 +1,51 @@
+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

@@ -0,0 +1,31 @@
+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
+}