@sjcrh/proteinpaint-types 2.177.0 → 2.178.0

package/src/terms/term.ts

@@ -47,7 +47,7 @@ export type BaseTerm = {
 	}
 }
 
-// NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, and other non-dict terms
+// NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, wholeProteomeAbundance, and other non-dict terms
 export type Term = BaseTerm &
 	(NumericTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm | QualTerm | TermCollection)
 

package/src/terms/termCollection.ts

@@ -1,17 +1,20 @@
 import type { BaseTerm, BaseTW, MinBaseQ } from '../index.ts'
 
 /*
-For term type 'snp'
+For term type 'termCollection'
 */
+export type CategoryKey = { key: string; shown: boolean }
 
-export type TermCollection = BaseTerm & {
+type BaseTermCollection = BaseTerm & {
 	name: string
 	collectionId?: string
 	type: 'termCollection'
-	// may be queried from backend, but should be available in frontend for termsetting edit menu
-	/** the full list of term.ids that are available in this collection */
+	/** 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[]
-	numerators?: string[]
+	/** TODO purpose */
 	newTvs?: boolean
 	propsByTermId: {
 		[termId: string]: {
@@ -20,42 +23,111 @@ export type TermCollection = BaseTerm & {
 	}
 }
 
-export type RawTermCollection = TermCollection & {
+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[]
+}
+
+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'
-	termlst: BaseTerm[]
+	memberType?: 'numeric'
+	name?: string
+	collectionId?: string
+	termIds?: string[]
+	termlst?: BaseTerm[]
 	propsByTermId?: {
 		[termId: string]: {
 			[prop: string]: any
 		}
 	}
+	numerators?: string[]
 }
 
-export type TermCollectionQValues = MinBaseQ & {
-	mode: 'continuous' // | 'discrete'
+/** Pre-fill shape for a categorical termCollection (memberType set by TermCollection.fill()) */
+export type RawCategoricalTermCollection = {
+	type?: 'termCollection'
+	memberType?: 'categorical'
+	name?: string
+	collectionId?: string
+	termIds?: string[]
+	termlst?: BaseTerm[]
+	propsByTermId?: {
+		[termId: string]: {
+			[prop: string]: any
+		}
+	}
+	categoryKeys?: CategoryKey[]
+}
+
+export type RawTermCollection = RawNumericTermCollection | RawCategoricalTermCollection
+
+/** Q shape for numeric (continuous) termCollection wrappers */
+export type TermCollectionQCont = MinBaseQ & {
+	mode: 'continuous'
 	type: 'values'
-	// groupValuesBy: 'sampleId' | 'termId'
 	/** 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 = TermCollectionQValues
+export type TermCollectionQ = TermCollectionQCont | TermCollectionQQual
 
-export type TermCollectionTWValues = BaseTW & {
-	type: 'TermCollectionTWValues'
-	term: TermCollection
-	q: TermCollectionQValues
+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 = TermCollectionTWValues
+export type TermCollectionTW = TermCollectionTWCont | TermCollectionTWQual
+
+export type RawTermCollectionTWCont = {
+	type?: 'TermCollectionTWCont'
+	term: RawNumericTermCollection
+	q?: TermCollectionQCont
+}
 
-export type RawTermCollectionTWValues = /*TermCollectionTW &*/ {
-	type?: 'TermCollectionTWValues' | 'termCollection' // deprecated
-	term: RawTermCollection
-	q: TermCollectionQValues
+export type RawTermCollectionTWQual = {
+	type?: 'TermCollectionTWQual'
+	term: RawCategoricalTermCollection
+	q?: TermCollectionQQual
 }
 
 // TODO: may add different termCollection TW types here
-export type RawTermCollectionTW = RawTermCollectionTWValues
+export type RawTermCollectionTW = RawTermCollectionTWCont | RawTermCollectionTWQual

package/src/terms/wholeProteomeAbundance.ts

@@ -0,0 +1,30 @@
+import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
+
+/*
+--------EXPORTED--------
+ProteomeTermWrapper
+ProteomeTermSettingInstance
+
+*/
+
+export type WholeProteomeAbundanceTerm = NumericBaseTerm & {
+	id?: string
+	name: string
+	type: 'wholeProteomeAbundance'
+	protein: string
+	bins?: PresetNumericBins
+	unit?: string
+}
+
+export type WholeProteomeAbundanceTW = NumTW & { term: WholeProteomeAbundanceTerm }
+
+export type RawWholeProteomeAbundanceTerm = NumericBaseTerm & {
+	id?: string
+	type: 'wholeProteomeAbundance'
+	protein: string
+	name?: string
+	bins?: PresetNumericBins
+	unit?: string
+}
+
+export type RawWholeProteomeAbundanceTW = RawNumTW & { term: RawWholeProteomeAbundanceTerm }