@sjcrh/proteinpaint-types 2.181.0 → 2.183.0

package/src/dataset.ts

@@ -708,22 +708,33 @@ export type MetaboliteIntensityQueryNative = {
 export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
 
 /** the proteomics query */
-type CohortConfig = {
-	file: string
-	filter?: Tvs[]
-	overlayTerm?: BaseTerm
+type ProteomeFilter = {
+	columnIdx: number
+	columnValue: string | number
 }
-type AssayWithCohorts = {
-	cohorts: {
-		[cohortName: string]: CohortConfig
-	}
+
+type ProteomeCohortConfig = {
+	cohortName: string
+	controlFilter: ProteomeFilter[]
+	caseFilter: ProteomeFilter[]
+}
+
+type ProteomeAssayConfig = {
+	columnIdx: number
+	columnValue: string | number
+	cohorts: ProteomeCohortConfig[]
+	/** optional PTM type for PTM assay type */
+	PTMType?: string
+	/** optional specific mclass override for PTM assay type */
+	mclassOverride?: Mclass
 }
-type AssayConfig = AssayWithCohorts
 
 export type ProteomeAbundanceQuery = {
+	/** database file path */
+	dbfile?: string
 	/** document structure */
 	assays: {
-		[assayName: string]: AssayConfig
+		[assayName: string]: ProteomeAssayConfig
 	}
 	samples?: number[]
 	/** _proteins,used to dynamically built cache of protein names to speed up search */
@@ -731,6 +742,8 @@ export type ProteomeAbundanceQuery = {
 	get?: (param: any) => void
 	find?: (param: string[]) => void
 	bins?: { [index: string]: any }
+	/** set of control sample IDs returned from get() query */
+	controlSampleIds?: Set<string>
 }
 
 /** the geneExpression query
@@ -1053,10 +1066,7 @@ type Mds3Queries = {
 		src: 'native'
 		file: string
 	}
-	proteome?: {
-		/** whole proteome abundance */
-		assays?: { [assayType: string]: AssayConfig }
-	}
+	proteome?: ProteomeAbundanceQuery
 	singleCell?: SingleCellQuery
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
@@ -1445,6 +1455,12 @@ if missing, name is value of m[url.namekey], as used in url itself (e.g. snp rsi
 	linkText?: string
 }
 
+export type GetSamplesOpts = {
+	filter: any // pp filter
+	filter0: any // mmrf filter
+	ds: any
+}
+
 /*** type of ds.cohort.termdb{} ***/
 export type Termdb = {
 	/** Terms */
@@ -1477,7 +1493,7 @@ export type Termdb = {
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: (clientAuthResult: any) => boolean
 	/** get samples that match supplied filter */
-	getSamples?: (filter: any, ds: any) => Promise<Set<any>>
+	getSamples?: (opts: GetSamplesOpts) => Promise<Set<any>>
 	converSampleIds?: boolean
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
@@ -1660,14 +1676,15 @@ keep this setting here for reason of:
 type TermCollectionBase = {
 	/** human readable name as well as unique identifier for this collection */
 	name: string
-	/** array of dictionary term ids belonging to this collection */
-	termIds: string[]
+	/** array of dictionary term ids belonging to this collection.
+	 *  Optional for custom (non-dictionary) collections where termlst[] is the primary source. */
+	termIds?: string[]
 	/** full term objects corresponding to termIds[]; populated by server on dataset init,
 	 * sent to client so fill() can resolve member term names without extra requests */
 	termlst?: BaseTerm[]
 	/** array of branch term ids belonging to this collection,
 	 * may be used as state.tree.expandedTermIds[] option to termdb appInit() */
-	branchIds: string[]
+	branchIds?: string[]
 	propsByTermId: {
 		[termId: string]: any
 	}

package/src/index.ts

@@ -50,6 +50,7 @@ export * from './routes/termdb.dmr.ts'
 export * from './routes/termdb.isoformAvailability.ts'
 export * from './routes/termdb.numericcategories.ts'
 export * from './routes/termdb.percentile.ts'
+export * from './routes/termdb.proteome.ts'
 export * from './routes/termdb.runChart.ts'
 export * from './routes/termdb.rootterm.ts'
 export * from './routes/termdb.termchildren.ts'

package/src/routes/termdb.proteome.ts

@@ -0,0 +1,13 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type TermdbProteomeRequest = any
+export type TermdbProteomeResponse = any
+
+export const termdbProteomePayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbProteomeRequest'
+	},
+	response: {
+		typeId: 'TermdbProteomeResponse'
+	}
+}

package/src/terms/dnaMethylation.ts

@@ -3,16 +3,25 @@ import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } fr
 export type DnaMethylationQ = NumericQ & { dt?: number }
 
 export type DnaMethylationTerm = NumericBaseTerm & {
-	/** term.id: plan to be concatenated string value "chr:start-stop" */
-	/** term.name: can be user-assigned */
 	type: 'dnaMethylation'
+	/** concatenated string value "chr:start-stop" */
+	id?: string
 	chr: string
 	start: number
 	stop: number
+	/** Type used to categorize the genomic feature */
+	genomicFeatureType: 'gene' | 'promoter' | 'region' | 'enhancer'
 	bins?: PresetNumericBins
 }
 
-export type RawDnaMethylationTerm = DnaMethylationTerm & { name?: string }
+export type RawDnaMethylationTerm = DnaMethylationTerm & {
+	/** Name of the genomic feature, e.g., gene name or promoter id/name, etc.
+	 * Different than .name, which includes the genomic coordinates and unit,
+	 * and is used for display purposes.*/
+	featureName?: string
+	name?: string
+	unit?: string
+}
 
 export type DnaMethylationTW = NumTW & { term: DnaMethylationTerm }
 

package/src/terms/termCollection.ts

@@ -10,7 +10,7 @@ type BaseTermCollection = BaseTerm & {
 	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[]. 
+	/** 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 */
@@ -20,6 +20,10 @@ type BaseTermCollection = BaseTerm & {
 			[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 & {
@@ -60,6 +64,7 @@ export type RawNumericTermCollection = {
 		}
 	}
 	numerators?: string[]
+	isCustom?: boolean
 }
 
 /** Pre-fill shape for a categorical termCollection (memberType set by TermCollection.fill()) */
@@ -75,6 +80,7 @@ export type RawCategoricalTermCollection = {
 		}
 	}
 	categoryKeys?: CategoryKey[]
+	isCustom?: boolean
 }
 
 export type RawTermCollection = RawNumericTermCollection | RawCategoricalTermCollection