@sjcrh/proteinpaint-types 2.141.0 → 2.143.0

package/src/terms/geneExpression.ts

@@ -1,4 +1,4 @@
-import type { PresetNumericBins, NumericBaseTerm, NumTWTypes } from '../index.ts'
+import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
 
 /*
 --------EXPORTED--------
@@ -7,16 +7,30 @@ GeneExpressionTermWrapper
 GeneExpressionTermSettingInstance
 */
 
-export type GeneExpressionTerm = NumericBaseTerm & {
+type Gene = {
+	kind?: 'gene'
 	gene: string
-	name: string
-	type: 'geneExpression'
-	bins?: PresetNumericBins
-	// temporarily allowing chr/start/stop to support
-	// legacy fpkm files
+	// 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 GeneExpressionTW = NumTWTypes & { term: GeneExpressionTerm }
+type Coord = {
+	kind?: 'coord'
+	gene?: string
+	chr: string
+	start: number
+	stop: number
+}
+
+export type GeneExpressionTerm = NumericBaseTerm & {
+	type: 'geneExpression'
+	bins?: PresetNumericBins
+} & (Gene | Coord)
+
+export type GeneExpressionTW = NumTW & { term: GeneExpressionTerm }
+
+export type RawGeneExpTW = RawNumTW & { term: GeneExpressionTerm & { name?: string } }

package/src/terms/metaboliteIntensity.ts

@@ -1,4 +1,4 @@
-import type { NumericBaseTerm, PresetNumericBins, NumTWTypes } from '../index.ts'
+import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
 
 /*
 --------EXPORTED--------
@@ -8,11 +8,21 @@ MetaboliteIntensityTermSettingInstance
 */
 
 export type MetaboliteIntensityTerm = NumericBaseTerm & {
-	name?: string
+	name: string
 	type: 'metaboliteIntensity'
 	metabolite: string
 	bins?: PresetNumericBins
 	unit?: string
 }
 
-export type MetaboliteIntensityTW = NumTWTypes & { term: MetaboliteIntensityTerm }
+export type MetaboliteIntensityTW = NumTW & { term: MetaboliteIntensityTerm }
+
+type RawMetabolitIntensityTerm = {
+	type: 'metaboliteIntensity'
+	metabolite: string
+	name?: string
+	bins?: PresetNumericBins
+	unit?: string
+}
+
+export type RawMetaboliteIntensityTW = RawNumTW & { term: RawMetabolitIntensityTerm }

package/src/terms/numeric.ts

@@ -63,6 +63,7 @@ export type StartUnboundedBin = {
 	stopinclusive?: boolean
 	stopunbounded?: false
 	label?: string
+	range?: string // alternative bin label
 }
 
 export type StopUnboundedBin = {
@@ -72,6 +73,7 @@ export type StopUnboundedBin = {
 	startunbounded?: false
 	stopinclusive?: false // cannot include an infinite bound
 	label?: string
+	range?: string // alternative bin label
 }
 
 // TODO??? should separate a fully bounded bin by startinclusive, stopinclusive
@@ -84,10 +86,13 @@ export type FullyBoundedBin = {
 	stopinclusive?: boolean
 	stopunbounded?: false
 	label?: string
+	range?: string // alternative bin label
 }
 
 export type NumericBin = StartUnboundedBin | FullyBoundedBin | StopUnboundedBin
 
+export type RangeEntry = NumericBin | { value: number; label: string }
+
 export type RegularNumericBinConfig = MinBaseQ & {
 	type: 'regular-bin' // another concrete value being assigned, instead of `string`
 	//regular-sized bins
@@ -209,7 +214,7 @@ export type NumTWSpline = BaseTW & {
 	q: SplineNumericQ
 }
 
-export type NumTWTypes = NumTWRegularBin | NumTWCustomBin | NumTWBinary | NumTWCont | NumTWSpline
+export type NumTW = NumTWRegularBin | NumTWCustomBin | NumTWBinary | NumTWCont | NumTWSpline
 export type NumTWDiscreteTypes = NumTWRegularBin | NumTWCustomBin //| NumTWBinary
 
 export type DefaultMedianQ = {

package/src/terms/q.ts

@@ -1,4 +1,5 @@
-import type { HiddenValues, GroupSettingQ, GroupEntry } from './term.ts'
+import type { CategoricalBaseQ } from './categorical.js'
+import type { Filter } from '../filter.js'
 
 // MinBaseQ is BaseQ without .mode and .type
 // MinBaseQ should eventually replace BaseQ because .mode and .type
@@ -36,3 +37,61 @@ export type RawCustomGroupsetQ = MinBaseQ & {
 	/** deprecated nested object, will be handled by reshapeLegacyTW() in TwRouter */
 	groupsetting?: { inuse?: boolean } & GroupSettingQ
 }
+
+export type HiddenValues = {
+	[index: string]: number
+}
+
+/*** types supporting termwrapper q ***/
+
+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 FilterQ = MinBaseQ & {
+	type: 'filter'
+}
+
+export type GroupSettingQ = ValuesQ | FilterQ | PredefinedGroupSettingQ | CustomGroupSettingQ
+
+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
+}
+
+export type FilterGroup = {
+	name: string
+	type: 'filter'
+	filter: Filter
+	color: string
+}
+
+export type GroupEntry = ValuesGroup | FilterGroup
+
+export type BaseGroupSet = {
+	groups: GroupEntry[]
+}
+
+type Groupset = {
+	name: string
+	is_grade?: boolean
+	is_subcondition?: boolean
+	dt?: number // dt of groupset, used by geneVariant term
+} & BaseGroupSet
+
+export type TermGroupSetting = {
+	disabled: boolean // true when term has <= 2 values, otherwise false
+	lst?: Groupset[] // array of predefined groupsets
+}

package/src/terms/samplelst.ts

@@ -1,4 +1,4 @@
-import type { BaseTerm, BaseQ } from './term.ts'
+import type { BaseTerm, MinBaseQ } from '../index.ts'
 import type { TermWrapper } from './tw.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
@@ -21,7 +21,7 @@ export type SampleLstTermValues = {
 	}
 }
 
-export type SampleLstQ = BaseQ & {
+export type SampleLstQ = MinBaseQ & {
 	groups: SampleLstTermValues
 }
 

package/src/terms/singleCellCellType.ts

@@ -1,4 +1,4 @@
-import type { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from './term.ts'
+import type { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from '../index.ts'
 import type { MinBaseQ } from './q.ts'
 
 type SingleCellCellTypeBaseQ = MinBaseQ & { mode: 'discrete' | 'binary' }

package/src/terms/snp.ts

@@ -1,11 +1,11 @@
-import type { BaseTW, BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
+import type { BaseTW, MinBaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from '../index.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 /*
 For term type 'snp'
 */
 
-export type SnpQ = BaseQ & GroupSettingQ
+export type SnpQ = MinBaseQ & GroupSettingQ
 
 export type SnpTerm = BaseTerm & {
 	chr: string

package/src/terms/snps.ts

@@ -1,4 +1,4 @@
-import type { BaseTW, BaseQ, BaseTerm } from './term.ts'
+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'
@@ -19,7 +19,7 @@ type RestrictAncestry = {
 	tvs: Tvs
 }
 
-export type SnpsQ = BaseQ & {
+export type SnpsQ = MinBaseQ & {
 	// termType: 'snplocus' | 'snplst'
 	//for snplst and snplocus term types
 	AFcutoff: number

package/src/terms/ssGSEA.ts

@@ -1,4 +1,4 @@
-import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTWTypes } from './numeric.ts'
+import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } from './numeric.ts'
 
 /*
 duplicated from geneExpression.ts
@@ -17,4 +17,6 @@ export type SsGSEATerm = NumericBaseTerm & {
 	unit?: string
 }
 
-export type SsGSEATW = NumTWTypes & { term: SsGSEATerm }
+export type SsGSEATW = NumTW & { term: SsGSEATerm }
+
+export type RawSsGSEATW = RawNumTW & { term: SsGSEATerm }

package/src/terms/term.ts

@@ -1,5 +1,5 @@
 import type { Filter } from '../filter.js'
-import type { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
+import type { CategoricalTerm } from './categorical.js'
 import type { ConditionTerm } from './condition.js'
 import type { NumericTerm } from './numeric.js'
 import type { GvTerm } from './geneVariant.js'
@@ -11,75 +11,6 @@ import type { SnpsTerm } from './snps.js'
  * @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'
-		/** Applies to geneVariant term */
-		| 'filter'
-}
-
-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 FilterQ = BaseQ & {
-	type: 'filter'
-}
-
-export type GroupSettingQ = ValuesQ | FilterQ | PredefinedGroupSettingQ | CustomGroupSettingQ
-
 /*** types supporting termwrapper term ***/
 
 export type BaseValue = {
@@ -110,57 +41,9 @@ export type BaseTerm = {
 	skipValuesBuild?: boolean
 }
 
+// NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, and other non-dict terms
 export type Term = BaseTerm & (NumericTerm | CategoricalTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm)
 
-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
-}
-
-export type FilterGroup = {
-	name: string
-	type: 'filter'
-	filter: Filter
-	color: string
-}
-
-export type GroupEntry = ValuesGroup | FilterGroup
-
-export type BaseGroupSet = {
-	groups: GroupEntry[]
-}
-
-type Groupset = {
-	name: string
-	is_grade?: boolean
-	is_subcondition?: boolean
-	dt?: number // dt of groupset, used by geneVariant term
-} & BaseGroupSet
-
-export type TermGroupSetting = {
-	disabled: boolean // true when term has <= 2 values, otherwise false
-	lst?: Groupset[] // array of predefined groupsets
-}
-
-/*** 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 = {
@@ -168,18 +51,3 @@ export type Subconditions = {
 		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

@@ -3,10 +3,25 @@ import type { SnpQ, SnpTW } from './snp.ts'
 import type { ConditionQ, ConditionTW } from './condition.ts'
 import type { SampleLstQ } from './samplelst.ts'
 import type { CatTWTypes, CategoricalQ } from './categorical.ts'
-import type { NumTWTypes, NumericQ } from './numeric.ts'
+import type { NumTW, NumericQ } from './numeric.ts'
 import type { GvTW, GvQ } from './geneVariant.ts'
 
-export type TermWrapper = CatTWTypes | NumTWTypes | GvTW | ConditionTW | SnpsTW | SnpTW
+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
+}
+
+export type TermWrapper = CatTWTypes | NumTW | GvTW | ConditionTW | SnpsTW | SnpTW
 
 export type Q = CategoricalQ | NumericQ | GvQ | ConditionQ | SnpsQ | SnpQ | SampleLstQ // | other q
 

package/dist/sampleWsiAiApi.js

@@ -1,11 +0,0 @@
-import {
-  sampleWsiAiApiPayload,
-  validSampleWSIAiApiRequest,
-  validSampleWSIAiApiResponse
-} from "./chunk-XJU4JALX.js";
-import "./chunk-CNSSF43V.js";
-export {
-  sampleWsiAiApiPayload,
-  validSampleWSIAiApiRequest,
-  validSampleWSIAiApiResponse
-};

package/src/routes/sampleWsiAiApi.ts

@@ -1,21 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type SampleWSIAiApiRequest = {
-	index: number
-	confirmed: boolean
-	class: number | null
-}
-
-export type SampleWSIAiApiResponse = {
-	status: 'ok' | 'error'
-	error?: string
-}
-
-export const sampleWsiAiApiPayload: RoutePayload = {
-	request: {
-		typeId: 'SampleWSIAiApiRequest'
-	},
-	response: {
-		typeId: 'SampleWSIAiApiResponse'
-	}
-}