@sjcrh/proteinpaint-types 2.78.0-0

package/src/terms/singleCellCellType.ts

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+import { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from './term.ts'
+import { MinBaseQ } from './q.ts'
+
+type SingleCellCellTypeBaseQ = MinBaseQ & { mode: 'discrete' | 'binary' }
+
+export type SingleCellCellTypeQ = SingleCellCellTypeBaseQ & GroupSettingQ
+
+export type SingleCellCellTypeTerm = BaseTerm & {
+	type: 'singleCellCellType'
+	/** the cell types may be also cell attributes like CNV, Fusion, etc */
+	values: TermValues
+	/** single cell terms require a sample to read the term values, they are associated with a sample */
+	sample: string
+	/** the plot defined in the dataset contains a column with the term values for the sample, it needs to be passed to read the sample values */
+	plot: string
+	groupsetting: TermGroupSetting
+}
+
+export type SingleCellCellTypeTW = BaseTW & {
+	term: SingleCellCellTypeTerm
+	q: SingleCellCellTypeQ
+}

package/src/terms/singleCellGeneExpression.ts

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+import { TermWrapper } from './tw.ts'
+import { BaseQ } from './term.ts'
+import { GeneExpressionQ } from './geneExpression.ts'
+import { TermSettingInstance } from '../termsetting.ts'
+import { NumericTerm } from './numeric.ts'
+
+/*
+--------EXPORTED--------
+GeneExpressionQ
+GeneExpressionTermWrapper
+GeneExpressionTermSettingInstance
+
+*/
+
+export type SingleCellGeneExpressionTW = TermWrapper & {
+	q: GeneExpressionQ
+	term: SingleCellGeneExpressionTerm
+}
+
+export type SingleCellGeneExpressionTerm = NumericTerm & {
+	gene: string
+	sample: string
+}
+
+export type SingleCellGeneExpressionTermSettingInstance = TermSettingInstance & {
+	q: GeneExpressionQ
+	term: SingleCellGeneExpressionTerm
+}

package/src/terms/snp.ts

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+import { TermWrapper } from './tw.ts'
+import { BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
+import { TermSettingInstance } from '../termsetting.ts'
+
+/*
+For term type 'snp'
+*/
+
+export type SnpQ = BaseQ & GroupSettingQ
+
+export type SnpTW = TermWrapper & {
+	q: SnpQ
+	term: SnpTerm
+}
+
+export type SnpTerm = BaseTerm & {
+	chr: string
+	start: number
+	stop: number
+	ref: string
+	alt: string[]
+	groupsetting: TermGroupSetting
+}
+
+export type SnpTermSettingInstance = TermSettingInstance & {
+	q: SnpQ
+	term: SnpTerm
+}

package/src/terms/snps.ts

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+import { BaseTW, BaseQ, BaseTerm } from './term.ts'
+import { TermSettingInstance, InstanceDom, UseCase } from '../termsetting.ts'
+import { VocabApi } from '../vocab.ts'
+import { Tvs, Filter } from '../filter.ts'
+
+/*
+--------EXPORTED--------
+SnpsQ
+SnpsEntry
+SnpsTerm
+SnpsTW
+SnpsVocabApi
+SnpsTermSettingInstance
+
+*/
+
+type RestrictAncestry = {
+	name: string
+	tvs: Tvs
+}
+
+export type SnpsQ = BaseQ & {
+	// termType: 'snplocus' | 'snplst'
+	//for snplst and snplocus term types
+	AFcutoff: number
+	alleleType: number
+	cacheid: string
+	doNotRestrictAncestry: any
+	geneticModel: number
+	info_fields?: any //[] Not documented
+	missingGenotype?: number
+	numOfSampleWithAnyValidGT: number
+	restrictAncestry: RestrictAncestry
+	snp2effAle?: any
+	snp2refGrp: any //[] maybe??
+	variant_filter: Filter
+	//Position
+	chr: string
+	start: number
+	stop: number
+}
+
+type AllelesEntry = {
+	allele: string
+	count: number
+	isRef: boolean
+}
+
+export type SnpsEntry = {
+	alt2csq?: any //{} In document but not implemented?
+	altAlleles?: string[]
+	alleles?: AllelesEntry[]
+	effectAllele: boolean
+	gt2count?: {
+		k: string
+		v: string | number
+	}
+	invalid?: boolean
+	referenceAllele?: string
+	rsid: string
+	snpid: string
+	tobe_deleted?: any
+	//Position properties
+	chr?: string
+	pos?: number
+}
+
+export type SnpsTerm = BaseTerm & {
+	id: string
+	reachedVariantLimit?: boolean
+	snps?: SnpsEntry[]
+}
+
+export type SnpsTW = BaseTW & {
+	q: SnpsQ
+	term: SnpsTerm
+}
+
+type VariantFilter = {
+	active: any
+	filter: any
+	opts: any
+	terms: any
+}
+
+export type SnpsVocabApi = VocabApi & {
+	validateSnps: (f?: any) => {
+		error?: any
+		cacheid: string
+		snps: any
+		reachedVariantLimit: any
+	}
+	get_variantFilter: () => any
+}
+
+type SnpsDom = InstanceDom & {
+	input_AFcutoff_label: any
+	restrictAncestriesRow: any
+	setEffectAlleleAsHint: any
+	snplst_table: any
+}
+
+export type SnpsTermSettingInstance = TermSettingInstance & {
+	dom: SnpsDom
+	q: Partial<SnpsQ>
+	term: SnpsTerm
+	usecase: UseCase
+	variantFilter: VariantFilter
+	vocabApi: SnpsVocabApi
+}

package/src/terms/term.ts

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+import { Filter } from '../filter.js'
+import { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
+import { ConditionTerm } from './condition.js'
+import { NumericTerm } from './numeric.js'
+import { GeneVariantTerm } from './geneVariant.js'
+import { SampleLstTerm } from './samplelst.js'
+import { SnpsTerm } from './snps.js'
+
+/**
+ * @param id      term.id for dictionary terms, undefined for non-dictionary terms
+ * @params $id    client-computed deterministic unique identifier, to distinguish tw with the same term but different q, that are in the same payload
+ */
+
+/*** types supporting termwrapper q ***/
+
+export type HiddenValues = {
+	[index: string]: number
+}
+
+// TODO: replace BaseQ with MinBaseQ (see below)
+// keeping BaseQ for now to not break old code
+export type BaseQ = {
+	/**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?: boolean
+	name?: string
+	mode?:
+		| 'discrete'
+		/** Binary is a special case of discrete. */
+		| 'binary'
+		| 'continuous'
+		/** Only for numeric terms in regression analysis. Requires q.knots */
+		| 'spline'
+		/** Only applies to condition term. Requires q.breaks[] to have one grade value.*/
+		| 'cuminc'
+		/** Only applies to condition term for cox regression outcome. Requires q.breaks[] to have one grade value, for event and q.timeScale.*/
+		| 'cox'
+
+	reuseId?: string
+	/** To define ways to divide up cohort based on a term, using methods specific to term types.*/
+	type?: /** Requires term.values{} to access categories for categorical term, and grade for condition term */
+	| 'values'
+		/** Applies to numeric terms */
+		| 'regular-bin'
+		/** Applies to numeric terms */
+		| 'custom-bin'
+		/** Applies to categorical, condition, geneVariant, and singleCellCellType terms */
+		| 'predefined-groupset'
+		/** Applies to categorical, condition, geneVariant, and singleCellCellType terms */
+		| 'custom-groupset'
+		/** Applies to samplelst terms */
+		| 'custom-samplelst'
+}
+
+export type ValuesQ = CategoricalBaseQ & {
+	type: 'values'
+}
+
+export type PredefinedGroupSettingQ = CategoricalBaseQ & {
+	type: 'predefined-groupset'
+	predefined_groupset_idx: number
+}
+
+export type CustomGroupSettingQ = CategoricalBaseQ & {
+	type: 'custom-groupset'
+	customset: BaseGroupSet
+}
+
+export type GroupSettingQ = ValuesQ | PredefinedGroupSettingQ | CustomGroupSettingQ
+
+/*** types supporting termwrapper term ***/
+
+export type BaseValue = {
+	key?: string
+	uncomputable?: boolean
+	label?: string | number
+	order?: string
+	color?: string
+	group?: number
+	filter?: Filter
+}
+
+export type TermValues = {
+	[key: string | number]: BaseValue
+}
+
+export type BaseTerm = {
+	id: string
+	name: string
+	type: string
+	child_types?: string[]
+	hashtmldetail?: boolean
+	included_types?: string[]
+	isleaf?: boolean
+	values?: TermValues
+}
+
+export type Term = BaseTerm &
+	(NumericTerm | CategoricalTerm | ConditionTerm | GeneVariantTerm | SampleLstTerm | SnpsTerm)
+
+export type ValuesGroup = {
+	name: string
+	type: 'values' | string // can remove boolean fallback once problematic js files are converted to .ts and can declare `type: 'values' as const`
+	values: { key: number | string; label: string }[]
+	uncomputable?: boolean // if true, do not include this group in computations
+}
+
+// TODO: determine if this is used
+export type FilterGroup = {
+	name: string
+	type: 'filter'
+	filter: Filter
+}
+
+export type GroupEntry = ValuesGroup | FilterGroup
+
+export type BaseGroupSet = {
+	groups: GroupEntry[]
+}
+
+type Groupset = {
+	name: string
+	is_grade?: boolean
+	is_subcondition?: boolean
+} & BaseGroupSet
+
+export type EnabledTermGroupSetting = {
+	disabled?: false | boolean // can remove boolean fallback once common.js is converted to .ts and can declare `disabled: false as const`
+	lst: Groupset[]
+}
+
+export type TermGroupSetting =
+	| EnabledTermGroupSetting
+	| {
+			/** disabled=false when groupsetting is not applicable for term (e.g., when term has only two categories) */
+			disabled: true | boolean // can remove boolean fallback once common.js is converted to .ts and can declare `disabled: true as const`
+			lst?: []
+	  }
+
+/*** types supporting termwrapper ***/
+
+export type BaseTW = {
+	id?: string
+	$id?: string
+	isAtomic?: true
+	// plot-specific customizations that are applied to a tw copy
+	// todo: should rethink these
+	legend?: any
+	settings?: {
+		[key: string]: any
+	}
+	sortSamples?: any
+	minNumSamples?: number
+	valueFilter?: any
+}
+
+/*** types supporting Term types ***/
+
+export type Subconditions = {
+	[index: string | number]: {
+		label: string
+	}
+}
+
+/*** other types ***/
+
+export type RangeEntry = {
+	//Used binconfig.lst[] and in tvs.ranges[]
+	start?: number
+	startunbounded?: boolean
+	startinclusive?: boolean
+	stop?: number
+	stopunbounded?: boolean
+	stopinclusive?: boolean
+	label?: string //for binconfig.lst[]
+	value?: string //for tvs.ranges[]
+	range?: any //No idea what this is
+}

package/src/terms/tw.ts

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+import { BaseQ, BaseTW, Term } from './term.ts'
+import { CategoricalQ, CategoricalTW } from './categorical.ts'
+import { NumericQ, NumericTW } from './numeric.ts'
+import { SnpsQ, SnpsTW } from './snps.ts'
+import { ConditionQ } from './condition.ts'
+import { GeneVariantQ } from './geneVariant.ts'
+import { SampleLstQ } from './samplelst.ts'
+
+export type TermWrapper = CategoricalTW | NumericTW | SnpsTW | (BaseTW & { term: Term; q: Q })
+export type TwLst = TermWrapper[]
+
+export type Q = BaseQ | CategoricalQ | ConditionQ | NumericQ | GeneVariantQ | SampleLstQ | SnpsQ
+
+export type RawTW =
+	//{ id: string } | RawCatTW
+	//
+	// BELOW TYPE IS NOT TESTED, only being used to compare tsc type checking behavior
+	// between non-union versus type-unions, which way is easier to code against
+	{
+		id?: string
+		term?: {
+			type: 'categorical' | 'condition'
+			[key: string | number]: any
+		}
+		q?: {
+			//predefined_groupset_idx?: number
+			//customset?: any
+			[key: string]: any
+			//type?: string //'custom-groupset' |
+			//customset?: any
+		}
+		isAtomic?: true
+		$id?: string
+	}
+
+export interface TwHandler {
+	render?: (opts?: any) => void
+}

package/src/terms/updated-types.ts

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+// temporary code file to hold updated type definitions
+// as part of the tw router/handler refactor
+
+import { CatTWTypes, CategoricalQ } from './categorical.ts'
+import { NumTWTypes, NumericQ } from './numeric.ts'
+
+export type TermWrapper = CatTWTypes | NumTWTypes
+
+export type Q = CategoricalQ | NumericQ // | other q

package/src/termsetting.ts

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+// TODO: will deprecate this code, should use client/termsetting/types.ts instead
+import { VocabApi } from './vocab.ts'
+import { TermWrapper, Q } from './terms/tw.ts'
+import { Term } from './terms/term.ts'
+import { Filter } from './filter.ts'
+
+/*
+
+!!! 
+	For shared/types: 
+	- Declare only the types that are used in the request and response payloads, or in *both* client and server-side code
+	- Do not track client or server-specific type declarations here, those belong in the corresponding workspace code 
+!!!
+
+--------EXPORTED--------
+Dom
+Api
+NoTermPromptOptsEntry
+UseCase
+SampleCountsEntry
+Handler
+PillData
+TermSettingOpts
+InstanceDom
+TermSettingInstance
+
+*/
+
+/*** types supporting TermSettingOpts & PillData types ***/
+
+export type Dom = {
+	holder: Selection
+	tip: any //TODO Menu type??
+	tip2: any //same as above
+	nopilldiv?: Selection
+	pilldiv?: Selection
+	btnDiv?: Selection
+}
+
+export type NoTermPromptOptsEntry = {
+	isDictionary?: boolean
+	termtype?: string
+	text?: string
+	html?: string
+	q?: Q
+}
+
+type NumericContEditOptsEntry = {
+	scale: string
+	transform: string
+}
+
+export type UseCase = {
+	target: string
+	detail?: string //Maybe?
+	regressionType?: string //Maybe?
+	term1type?: string //Maybe? not documented
+}
+
+type DefaultQ4fillTW = {
+	[index: string]: Q
+}
+
+export type SampleCountsEntry = {
+	key: string
+	value: number //This maybe a string???
+	label?: string //Not documented?? in key or no?
+}
+
+export type Handler = {
+	getPillName: (d: any) => string
+	getPillStatus: (f?: any) => any
+	showEditMenu: (div: Selection) => void
+	validateQ?: (d: Q) => void
+	postMain?: () => void
+}
+
+type BaseTermSettingOpts = {
+	//Optional
+	abbrCutoff?: number
+	activeCohort?: number
+	disable_terms?: string[]
+	handler: Handler
+	noTermPromptOptions?: NoTermPromptOptsEntry[]
+}
+
+export type PillData = BaseTermSettingOpts & {
+	$id?: string
+	doNotHideTipInMain: boolean
+	dom: Dom
+	error?: string
+	filter?: Filter
+	q?: Q
+	sampleCounts?: SampleCountsEntry[]
+	term?: Term
+}
+
+export type TermSettingOpts = BaseTermSettingOpts & {
+	//Required
+	holder: any
+	vocabApi: VocabApi
+	//Optional
+	$id?: string
+	buttons?: string[] //replace, delete, info
+	defaultQ4fillTW?: DefaultQ4fillTW
+	menuOptions: string //all, edit, replace, remove
+	menuLayout?: string //horizonal, all
+	numericEditMenuVersion?: string[]
+	geneVariantEditMenuOnlyGrp?: boolean
+	numericContinuousEditOptions?: NumericContEditOptsEntry[]
+	placeholder?: string
+	placeholderIcon?: string //default '+'
+	renderAs: string //none
+	tip?: any //TODO: Menu type?
+	use_bins_less?: boolean
+	usecase?: UseCase
+	debug?: boolean | number //true or 1
+	//'snplocus' types
+	genomeObj?: any
+
+	//vocab??
+
+	// required callback function. argument is the updated termwrapper object
+	callback: (f: TermWrapper | null) => void
+
+	// ?
+	customFillTw?: (f: TermWrapper) => void
+
+	// to pass in purpose and context-specific arguments that will be merged to client request parameters
+	getBodyParams?: () => any
+}
+
+/*** types supporting TermSettingInstance type ***/
+
+export type InstanceDom = {
+	//Separate from the Dom outlined in termsetting.ts?????
+	//Required
+	holder: any
+	tip: any //TODO Menu type??
+	tip2: any //same as above
+	nopilldiv?: any
+	pilldiv?: any
+	btnDiv?: any
+	//Optional
+	customBinBoundaryInput?: any
+	customBinBoundaryPercentileCheckbox?: any
+	customBinLabelInput?: any
+	customBinRanges?: any
+	cutoff_div?: any
+	num_holder?: any
+	pill_termname?: any
+	rangeAndLabelDiv?: any
+}
+
+export type TermSettingInstance = {
+	activeCohort?: number
+	clickNoPillDiv?: any
+	dom: InstanceDom
+	doNotHideTipInMain?: boolean
+	disable_terms?: string[]
+	durations: { exit: number }
+	filter?: Filter
+	handler?: Handler
+	handlerByType?: { [index: string]: Handler }
+	hasError?: boolean
+	noTermPromptOptions?: NoTermPromptOptsEntry[]
+	opts: TermSettingOpts
+	placeholder: string | undefined
+	q: Q
+	term: Term
+	usecase?: UseCase
+	vocabApi: VocabApi
+
+	//Methods
+	/*
+	TODOs: 
+		- Move specifc methods to their own intersection instance type within in termsetting/handler/*.ts, out of main type
+	*/
+	cancelGroupsetting?: () => void
+	enterPill?: () => void
+	exitPill?: () => void
+	initUI: () => void
+	removeTerm?: () => void
+	runCallback: (f?: any) => any
+	setHandler?: (f: string) => any
+	showGeneSearch: (clickedElem: Element | null, event: MouseEvent) => void
+	showMenu: (event: MouseEvent, clickedElem: string | null, menuHolder: any) => void
+	showReuseMenu?: (div: any) => void
+	showTree: (holder: Selection, event?: MouseEvent) => void
+	tabCallback?: (event: any, tab: any) => void
+	updatePill?: () => void
+	updateUI: () => void
+}