@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/terms/snps.ts

@@ -1,111 +0,0 @@
-import type { BaseTW, MinBaseQ, BaseTerm } from '../index.ts'
-import type { TermSettingInstance, InstanceDom, UseCase } from '../termsetting.ts'
-import type { VocabApi } from '../vocab.ts'
-import type { Tvs, Filter } from '../filter.ts'
-
-/*
---------EXPORTED--------
-SnpsQ
-SnpsEntry
-SnpsTerm
-SnpsTW
-SnpsVocabApi
-SnpsTermSettingInstance
-
-*/
-
-type RestrictAncestry = {
-	name: string
-	tvs: Tvs
-}
-
-export type SnpsQ = MinBaseQ & {
-	// 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 & {
-	type: 'SnpsTW'
-	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/ssGSEA.ts

@@ -1,26 +0,0 @@
-import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } from './numeric.ts'
-
-/*
-duplicated from geneExpression.ts
-*/
-
-export type SsGSEAQ = NumericQ & { dt?: number }
-
-export type SsGSEATerm = NumericBaseTerm & {
-	/** term.id: geneset db term id for native term, and cache file name for custom term */
-	/** term.name: geneset db term name for native term, and user-defined name for custom term */
-	/** custom term has list of gene names used for computing score */
-	genes?: string[]
-	name: string
-	type: 'ssGSEA'
-	bins?: PresetNumericBins
-	unit?: string
-}
-
-export type RawSsGSEATerm = SsGSEATerm & {
-	name?: string
-}
-
-export type SsGSEATW = NumTW & { term: SsGSEATerm }
-
-export type RawSsGSEATW = RawNumTW & { term: SsGSEATerm }

package/src/terms/term.ts

@@ -1,60 +0,0 @@
-import type { Filter } from '../filter.js'
-import type { ConditionTerm } from './condition.js'
-import type { NumericTerm } from './numeric.js'
-import type { GvTerm } from './geneVariant.js'
-import type { SampleLstTerm } from './samplelst.js'
-import type { SnpsTerm } from './snps.js'
-import type { QualTerm } from './qualitative.ts'
-import type { TermCollection } from './termCollection.ts'
-
-/**
- * @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 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
-	/** Do not build .values{} when building termdb. Used for 
-	making categorical term with empty .values{} in TermdbTest */
-	skipValuesBuild?: boolean
-	valueConversion?: {
-		fromUnit: string
-		toUnit: string
-		scaleFactor: string
-	}
-}
-
-// NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, proteomeAbundance, and other non-dict terms
-export type Term = BaseTerm &
-	(NumericTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm | QualTerm | TermCollection)
-
-/*** types supporting Term types ***/
-
-export type Subconditions = {
-	[index: string | number]: {
-		label: string
-	}
-}

package/src/terms/termCollection.ts

@@ -1,139 +0,0 @@
-import type { BaseTerm, BaseTW, MinBaseQ } from '../index.ts'
-
-/*
-For term type 'termCollection'
-*/
-export type CategoryKey = { key: string; shown: boolean }
-
-type BaseTermCollection = BaseTerm & {
-	name: string
-	type: 'termCollection'
-	/** list of term.ids that are available in this collection. this is used in request payload and server side */
-	termIds?: string[]
-	/** list of term objs corresponding to termIds[].
-	this is generated on server init, and sent to client, so client has easy access to show name of every term */
-	termlst: BaseTerm[]
-	/** TODO purpose */
-	newTvs?: boolean
-	propsByTermId: {
-		[termId: string]: {
-			[prop: string]: any
-		}
-	}
-	/** When true, member terms are non-dictionary terms (e.g. isoformExpression).
-	 *  getData() expands them into individual tws for existing handlers, then
-	 *  reconstitutes the grouped shape after data is returned. */
-	isCustom?: boolean
-}
-
-export type NumericTermCollection = BaseTermCollection & {
-	/**
-	 * Copies ds.cohort.termdb.termCollections[].type ('numeric' | 'categorical').
-	 * Allows client code using the term to know the collection kind without looking up config.
-	 */
-	memberType: 'numeric'
-	/** the sum of numerator values will be divided by the sum of values for all terms,
-	 *  to be used for sorting matrix sample columns */
-	numerators?: string[]
-	/** optional transformation. app specific
-	 */
-	valueTransform?: { offset?: number }
-}
-
-export type CategoricalTermCollection = BaseTermCollection & {
-	/**
-	 * Copies ds.cohort.termdb.termCollections[].type ('numeric' | 'categorical').
-	 * Allows client code using the term to know the collection kind without looking up config.
-	 */
-	memberType: 'categorical'
-	categoryKeys: CategoryKey[]
-}
-
-export type TermCollection = NumericTermCollection | CategoricalTermCollection
-
-/** Pre-fill shape for a numeric termCollection (memberType set by TermCollection.fill()) */
-export type RawNumericTermCollection = {
-	type?: 'termCollection'
-	memberType?: 'numeric'
-	name?: string
-	termIds?: string[]
-	termlst?: BaseTerm[]
-	propsByTermId?: {
-		[termId: string]: {
-			[prop: string]: any
-		}
-	}
-	numerators?: string[]
-	isCustom?: boolean
-}
-
-/** Pre-fill shape for a categorical termCollection (memberType set by TermCollection.fill()) */
-export type RawCategoricalTermCollection = {
-	type?: 'termCollection'
-	memberType?: 'categorical'
-	name?: string
-	termIds?: string[]
-	termlst?: BaseTerm[]
-	propsByTermId?: {
-		[termId: string]: {
-			[prop: string]: any
-		}
-	}
-	categoryKeys?: CategoryKey[]
-	isCustom?: boolean
-}
-
-export type RawTermCollection = RawNumericTermCollection | RawCategoricalTermCollection
-
-/** Q shape for numeric (continuous) termCollection wrappers */
-export type TermCollectionQCont = MinBaseQ & {
-	mode: 'continuous'
-	type: 'values'
-	/** a selection of term.ids for the current termwrapper, selected from term.lst */
-	lst: string[]
-	/** the sum of numerator values divided by the sum of all values will be used
-	 * to sort matrix sample columns */
-	numerators?: string[]
-}
-
-/** Q shape for categorical (qualitative) termCollection wrappers */
-export type TermCollectionQQual = MinBaseQ & {
-	mode: 'discrete'
-	type: 'values'
-	/** a selection of term.ids for the current termwrapper, selected from term.lst */
-	lst: string[]
-	categoryKeys?: CategoryKey[]
-}
-
-// TODO: may add different q types below
-export type TermCollectionQ = TermCollectionQCont | TermCollectionQQual
-
-export type TermCollectionTWCont = BaseTW & {
-	type: 'TermCollectionTWCont'
-	term: NumericTermCollection
-	q: TermCollectionQCont
-}
-
-export type TermCollectionTWQual = BaseTW & {
-	type: 'TermCollectionTWQual'
-	term: CategoricalTermCollection
-	q: TermCollectionQQual
-}
-
-// TODO: may add different termCollection TW types here
-export type TermCollectionTW = TermCollectionTWCont | TermCollectionTWQual
-
-export type RawTermCollectionTWCont = BaseTW & {
-	type?: 'TermCollectionTWCont'
-	term: RawNumericTermCollection
-	q?: TermCollectionQCont
-}
-
-export type RawTermCollectionTWQual = BaseTW & {
-	type?: 'TermCollectionTWQual'
-	term: RawCategoricalTermCollection
-	q?: TermCollectionQQual
-}
-
-// TODO: may add different termCollection TW types here
-export type RawTermCollectionTW = RawTermCollectionTWCont | RawTermCollectionTWQual

package/src/terms/tw.ts

@@ -1,64 +0,0 @@
-import type { SnpsQ, SnpsTW } from './snps.ts'
-import type { ConditionQ, ConditionTW, RawConditionTW } from './condition.ts'
-import type { SampleLstQ } from './samplelst.ts'
-import type { NumTW, NumericQ, RawNumTW } from './numeric.ts'
-import type { GvTW, GvQ, RawGvTW } from './geneVariant.ts'
-import type { QualTW, QualQ, RawQualTW } from './qualitative.ts'
-import type { TermCollectionTW, TermCollectionQ, RawTermCollectionTW } from './termCollection.ts'
-
-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
-	values?: { [key: string]: any }
-}
-
-export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW | TermCollectionTW
-
-export type Q = NumericQ | GvQ | ConditionQ | SnpsQ | SampleLstQ | QualQ | TermCollectionQ // | other q
-
-//export type TermWrapper = CategoricalTW | NumericTW | SnpsTW | (BaseTW & { term: Term; q: Q })
-export type TwLst = TermWrapper[]
-
-//export type Q = BaseQ | CategoricalQ | ConditionQ | NumericQ | SampleLstQ | SnpsQ
-
-export type RawDictTW = BaseTW & {
-	id: string
-	term?: undefined
-	q?: any
-}
-
-export type RawTW = RawDictTW | RawQualTW | RawNumTW | RawGvTW | RawConditionTW | RawTermCollectionTW
-//{ 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/termsetting.ts

@@ -1,201 +0,0 @@
-// TODO: will deprecate this code, should use client/termsetting/types.ts instead
-import type { VocabApi } from './vocab.ts'
-import type { TermWrapper, Q } from './terms/tw.ts'
-import type { Term } from './terms/term.ts'
-import type { 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 = {
-	/** Set the max number of characters in a pill
-	 * before the pill name is truncated. */
-	abbrCutoff?: number
-	activeCohort?: number
-	/** array of term objects to show in the tree but not clickable */
-	disable_terms?: Term[]
-	// This is not used anywhere.
-	// Ok to remove?
-	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?: Term[]
-	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
-}