@sjcrh/proteinpaint-types 2.83.0 → 2.85.0

package/src/terms/samplelst.ts

@@ -1,41 +0,0 @@
-import { BaseTerm, BaseQ } from './term.ts'
-import { TermWrapper } from './tw.ts'
-import { TermSettingInstance } from '../termsetting.ts'
-
-/*
---------EXPORTED--------
-SampleLstTermValues
-SampleLstQ
-SampleLstTerm
-SampleLstTW
-SampleLstSettingInstance
-
-*/
-
-export type SampleLstTermValues = {
-	[index: string | number]: {
-		name: string
-		inuse: boolean
-		list: { sampleId: string; sample: string }[]
-		values: any
-	}
-}
-
-export type SampleLstQ = BaseQ & {
-	groups: SampleLstTermValues
-}
-
-export type SampleLstTerm = BaseTerm & {
-	values: SampleLstTermValues
-}
-
-export type SampleLstTW = TermWrapper & {
-	q: SampleLstQ
-	term: SampleLstTerm
-}
-
-//temporary, will eventually change to SampleLstHandler
-export type SampleLstTermSettingInstance = TermSettingInstance & {
-	q: SampleLstQ
-	term: SampleLstTerm
-}

package/src/terms/singleCellCellType.ts

@@ -1,22 +0,0 @@
-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

@@ -1,28 +0,0 @@
-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

@@ -1,28 +0,0 @@
-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

@@ -1,110 +0,0 @@
-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

@@ -1,184 +0,0 @@
-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

@@ -1,38 +0,0 @@
-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

@@ -1,9 +0,0 @@
-// 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

@@ -1,197 +0,0 @@
-// 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
-	/** whether or not opt is invalid */
-	invalid?: boolean
-	/** message displayed when opt is invalid */
-	invalidMsg?: string
-}
-
-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
-}