@sjcrh/proteinpaint-types 2.140.1 → 2.142.0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-IDP5KXE6.js";
+} from "./chunk-MVMUZSLL.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-BWLSDIHM.js";
+} from "./chunk-IR4QSJI7.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -12,17 +12,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-WKT3H4P4.js";
+} from "./chunk-2VDOPTRV.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-ECF6WSOD.js";
+} from "./chunk-4R265LDJ.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-PPFFVFUI.js";
+} from "./chunk-DMJFOII6.js";
 import {
   tilePayload,
   validTileRequest,
@@ -82,7 +82,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-EWON4FG5.js";
+} from "./chunk-SMVDKR2O.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -97,7 +97,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-2WLN6PMW.js";
+} from "./chunk-GDM7YUXH.js";
 import {
   FilterTermValuesPayload,
   validFilterTermValuesRequest,
@@ -107,12 +107,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-AADDTYUL.js";
+} from "./chunk-3BQ57P2P.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-ZA3FDGAD.js";
+} from "./chunk-SOM5WKDM.js";
 import {
   ProfileFormScoresPayload,
   validProfileFormScoresRequest,
@@ -152,12 +152,12 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XXHHUIEV.js";
+} from "./chunk-3L3ASC3B.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-FZJ3E7JA.js";
+} from "./chunk-CEDL2QZT.js";
 import {
   GRIN2Payload,
   validGRIN2Request,
@@ -245,7 +245,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-KS74VVON.js";
+} from "./chunk-FVBXC7SY.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -267,7 +267,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-IDP5KXE6.js";
+} from "./chunk-MVMUZSLL.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XXHHUIEV.js";
+} from "./chunk-3L3ASC3B.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-FZJ3E7JA.js";
+} from "./chunk-CEDL2QZT.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-EWON4FG5.js";
+} from "./chunk-SMVDKR2O.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-2WLN6PMW.js";
+} from "./chunk-GDM7YUXH.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-AADDTYUL.js";
+} from "./chunk-3BQ57P2P.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-ZA3FDGAD.js";
+} from "./chunk-SOM5WKDM.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-BWLSDIHM.js";
+} from "./chunk-IR4QSJI7.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-WKT3H4P4.js";
+} from "./chunk-2VDOPTRV.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-ECF6WSOD.js";
+} from "./chunk-4R265LDJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-PPFFVFUI.js";
+} from "./chunk-DMJFOII6.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,13 +1,12 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.140.1",
+  "version": "2.142.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",
   "module": "src/index.ts",
   "exports": {
     ".": "./src/index.ts",
-    "./updated": "./src/terms/updated-types.ts",
     "./routes/*": "./src/routes/*",
     "./checkers": "./dist/index.js"
   },

package/src/dataset.ts

@@ -740,6 +740,8 @@ export type GeneExpressionQueryNative = {
 	geneExpression2bins?: { [index: string]: any }
 	/** gene expression unit (e.g. 'FPKM') */
 	unit?: string
+	/** temporary h5 file format flag */
+	newformat?: boolean
 }
 
 export type GeneExpressionQuery = GeneExpressionQueryGdc | GeneExpressionQueryNative
@@ -1152,8 +1154,8 @@ type Scatterplots = {
 type CorrelationVolcano = {
 	/** fixed feature, is one numeric term */
 	feature: {
-		/** later expand to other types */
-		termType: 'geneExpression'
+		/** array of allowed term types for feature tw */
+		termTypes: string[]
 	}
 	/** list of numeric variables to be compared against fixed feature*/
 	variables: {

package/src/genome.ts

@@ -50,7 +50,7 @@ type TrackCategories = {
 	[index: string]: TrackCategoryEntry | undefined
 }
 
-type Track = {
+export type Track = {
 	__isgene?: boolean
 	translatecoding?: boolean
 	file: string
@@ -64,7 +64,7 @@ type Track = {
 	onerow?: boolean
 }
 
-type DefaultCoord = {
+export type DefaultCoord = {
 	chr: string
 	start: number
 	stop: number

package/src/index.ts

@@ -61,6 +61,7 @@ export * from './routes/wsimages.ts'
 export * from './routes/wsisamples.ts'
 export * from './terms/categorical.ts'
 export * from './terms/condition.ts'
+export * from './terms/date.ts'
 export * from './terms/numeric.ts'
 export * from './terms/geneVariant.ts'
 export * from './terms/geneExpression.ts'

package/src/terms/categorical.ts

@@ -71,10 +71,6 @@ export type CatTWValues = BaseTW & {
 	term: CategoricalTerm
 	q: ValuesQ
 	type: 'CatTWValues'
-	// do not use this boolean flag, defined here only to help illustrate
-	// in tw/test/fake/app.js why this is type check error prone and
-	// less preferred than a discriminant prop that also works at runtime
-	isCatTWValues?: true
 }
 
 export type CatTWPredefinedGS = BaseTW & {
@@ -82,10 +78,6 @@ export type CatTWPredefinedGS = BaseTW & {
 	term: CategoricalTerm
 	q: PredefinedGroupSettingQ
 	type: 'CatTWPredefinedGS'
-	// do not use this boolean flag, defined here only to help illustrate
-	// in tw/test/fake/app.js why this is type check error prone and
-	// less preferred than a discriminant prop that also works at runtime
-	isCatTWPredefiendGS?: true
 }
 
 export type CatTWCustomGS = BaseTW & {

package/src/terms/condition.ts

@@ -1,5 +1,5 @@
-import type { BaseTerm, BaseQ, TermValues } from './term.ts'
-import type { TermWrapper } from './tw.ts'
+import type { BaseTerm, BaseQ, TermValues, BaseTW } from './term.ts'
+//import type { TermWrapper } from './tw.ts'
 
 /**
  * @category TW
@@ -37,7 +37,8 @@ export type ConditionTerm = BaseTerm & {
  * @group Termdb
  * @category TW
  */
-export type ConditionTW = TermWrapper & {
+export type ConditionTW = BaseTW & {
+	type: 'ConditionTW'
 	term: ConditionTerm
 	q: ConditionQ //replace the generic Q with specific condition Q
 }

package/src/terms/date.ts

@@ -0,0 +1,20 @@
+import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
+
+/*
+--------EXPORTED--------
+DateTerm
+DateTW
+DateTermSettingInstance
+*/
+
+export type DateTerm = NumericBaseTerm & {
+	name: string
+	type: 'date'
+	bins?: PresetNumericBins
+}
+
+export type DateTW = NumTW & { term: DateTerm }
+
+type RawDateTerm = DateTerm & { name?: string }
+
+export type RawDateTW = RawNumTW & { term: RawDateTerm }

package/src/terms/geneExpression.ts

@@ -1,5 +1,4 @@
-import type { BaseTW, PresetNumericBins, NumericBaseTerm, NumericQ } from '../index.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
+import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
 
 /*
 --------EXPORTED--------
@@ -8,25 +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 = BaseTW & {
-	q: NumericQ
-	term: GeneExpressionTerm
-	type: string
+type Coord = {
+	kind?: 'coord'
+	gene?: string
+	chr: string
+	start: number
+	stop: number
 }
 
-export type GeneExpressionTermSettingInstance = TermSettingInstance & {
-	q: NumericQ
-	term: GeneExpressionTerm
-}
+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/geneVariant.ts

@@ -3,6 +3,8 @@ import type { TermSettingInstance } from '../termsetting.ts'
 
 // q types
 export type GvBaseQ = MinBaseQ & {
+	// TODO: may uncomment below if q.mode is required in downstream code
+	// mode?: 'discrete' // may support 'continuous' for CNV?
 	cnvGainCutoff?: number
 	cnvMaxLength?: number
 	cnvMinAbsValue?: number
@@ -12,6 +14,7 @@ export type GvBaseQ = MinBaseQ & {
 type RawGvValuesQ = GvBaseQ & { type?: 'values' }
 type RawGvPredefinedGsQ = GvBaseQ & { type: 'predefined-groupset'; predefined_groupset_idx?: number }
 type RawGvCustomGsQ = GvBaseQ & { type: 'custom-groupset'; customset?: BaseGroupSet }
+export type RawGvQ = RawGvValuesQ | RawGvPredefinedGsQ | RawGvCustomGsQ
 
 export type GvValuesQ = GvBaseQ & { type: 'values' }
 export type GvPredefinedGsQ = GvBaseQ & { type: 'predefined-groupset'; predefined_groupset_idx: number }

package/src/terms/metaboliteIntensity.ts

@@ -1,31 +1,28 @@
-import type { TermWrapper } from './tw.ts'
-import type { BaseQ } from './term.ts'
-import type { NumericTerm } from './numeric.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
+import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
 
 /*
 --------EXPORTED--------
-MetaboliteIntensityQ
 MetaboliteIntensityTermWrapper
 MetaboliteIntensityTermSettingInstance
 
 */
 
-export type MetaboliteIntensityQ = BaseQ & {
-	mode: 'continuous'
+export type MetaboliteIntensityTerm = NumericBaseTerm & {
+	name: string
+	type: 'metaboliteIntensity'
+	metabolite: string
+	bins?: PresetNumericBins
+	unit?: string
 }
 
-export type MetaboliteIntensityTW = TermWrapper & {
-	q: MetaboliteIntensityQ
-	term: MetaboliteIntensityTerm
-}
+export type MetaboliteIntensityTW = NumTW & { term: MetaboliteIntensityTerm }
 
-export type MetaboliteIntensityTerm = NumericTerm & {
+type RawMetabolitIntensityTerm = {
+	type: 'metaboliteIntensity'
 	metabolite: string
-	bins: any
+	name?: string
+	bins?: PresetNumericBins
+	unit?: string
 }
 
-export type MetaboliteIntensityTermSettingInstance = TermSettingInstance & {
-	q: MetaboliteIntensityQ
-	term: MetaboliteIntensityTerm
-}
+export type RawMetaboliteIntensityTW = RawNumTW & { term: RawMetabolitIntensityTerm }

package/src/terms/numeric.ts

@@ -1,4 +1,13 @@
-import type { MinBaseQ, BaseTW, TermValues, BaseTerm, GeneExpressionTerm } from '../index.ts'
+import type {
+	MinBaseQ,
+	BaseTW,
+	TermValues,
+	BaseTerm,
+	GeneExpressionTerm,
+	MetaboliteIntensityTerm,
+	DateTerm,
+	SsGSEATerm
+} from '../index.ts'
 
 export type RawRegularBin = Partial<RegularNumericBinConfig> & { preferredBins?: string }
 
@@ -38,12 +47,12 @@ export type NumericBaseTerm = BaseTerm & {
 
 export type NumericDictTerm = NumericBaseTerm & {
 	id?: string
-	type: 'integer' | 'float' | 'date'
+	type: 'integer' | 'float'
 	bins: PresetNumericBins
 	values?: TermValues
 }
 
-export type NumericTerm = NumericDictTerm | GeneExpressionTerm
+export type NumericTerm = NumericDictTerm | GeneExpressionTerm | MetaboliteIntensityTerm | DateTerm | SsGSEATerm
 
 export type StartUnboundedBin = {
 	// where possible, assign a concrete value (true) when it is known in advance,
@@ -101,25 +110,6 @@ export type CustomNumericBinConfig = MinBaseQ & {
 	preferredBins?: 'median'
 }
 
-// |
-// {
-// 	type?: 'custom-bin'
-// 	mode?: 'discrete' | 'binary'
-// 	// since ts will allow NumericBin[] to be empty,
-// 	// use this workaround to define a non-empty array
-// 	lst?: [NumericBin, ...NumericBin[]]
-// }
-
-/*export type NumericQ = BaseQ & {
-	// termType: 'float' | 'integer' -- converts to 'numeric'
-	preferredBins?: 'median' | 'less' | 'default'
-	modeBinaryCutoffType: 'normal' | 'percentile'
-	modeBinaryCutoffPercentile?: number
-	knots?: any //[]?
-	scale?: number //0.1 | 0.01 | 0.001
-	rounding: string
-}*/
-
 export type PresetNumericBins = {
 	default: RegularNumericBinConfig | CustomNumericBinConfig
 	less: RegularNumericBinConfig | CustomNumericBinConfig
@@ -219,7 +209,7 @@ 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/snp.ts

@@ -1,5 +1,4 @@
-import type { TermWrapper } from './tw.ts'
-import type { BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
+import type { BaseTW, BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 /*
@@ -8,11 +7,6 @@ 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
@@ -22,6 +16,12 @@ export type SnpTerm = BaseTerm & {
 	groupsetting: TermGroupSetting
 }
 
+export type SnpTW = BaseTW & {
+	type: 'SnpTW'
+	q: SnpQ
+	term: SnpTerm
+}
+
 export type SnpTermSettingInstance = TermSettingInstance & {
 	q: SnpQ
 	term: SnpTerm

package/src/terms/snps.ts

@@ -72,6 +72,7 @@ export type SnpsTerm = BaseTerm & {
 }
 
 export type SnpsTW = BaseTW & {
+	type: 'SnpsTW'
 	q: SnpsQ
 	term: SnpsTerm
 }

package/src/terms/ssGSEA.ts

@@ -1,6 +1,4 @@
-import type { TermWrapper } from './tw.ts'
-import type { NumericTerm, NumericQ } from './numeric.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
+import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } from './numeric.ts'
 
 /*
 duplicated from geneExpression.ts
@@ -8,19 +6,17 @@ duplicated from geneExpression.ts
 
 export type SsGSEAQ = NumericQ & { dt?: number }
 
-export type SsGSEATW = TermWrapper & {
-	q: SsGSEAQ
-	term: SsGSEATerm
-}
-
-export type SsGSEATerm = NumericTerm & {
+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 SsGSEATermSettingInstance = TermSettingInstance & {
-	q: SsGSEAQ
-	term: SsGSEATerm
-}
+export type SsGSEATW = NumTW & { term: SsGSEATerm }
+
+export type RawSsGSEATW = RawNumTW & { term: SsGSEATerm }

package/src/terms/tw.ts

@@ -1,14 +1,19 @@
-import type { BaseQ, BaseTW, Term } from './term.ts'
-import type { CategoricalQ, CategoricalTW } from './categorical.ts'
-import type { NumericQ, NumericTW } from './numeric.ts'
 import type { SnpsQ, SnpsTW } from './snps.ts'
-import type { ConditionQ } from './condition.ts'
+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 { NumTW, NumericQ } from './numeric.ts'
+import type { GvTW, GvQ } from './geneVariant.ts'
 
-export type TermWrapper = CategoricalTW | NumericTW | SnpsTW | (BaseTW & { term: Term; q: Q })
+export type TermWrapper = CatTWTypes | NumTW | GvTW | ConditionTW | SnpsTW | SnpTW
+
+export type Q = CategoricalQ | NumericQ | GvQ | ConditionQ | SnpsQ | SnpQ | SampleLstQ // | 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 Q = BaseQ | CategoricalQ | ConditionQ | NumericQ | SampleLstQ | SnpsQ
 
 export type RawTW =
 	//{ id: string } | RawCatTW

package/src/terms/updated-types.ts

@@ -1,10 +0,0 @@
-// temporary code file to hold updated type definitions
-// as part of the tw router/handler refactor
-
-import type { CatTWTypes, CategoricalQ } from './categorical.ts'
-import type { NumTWTypes, NumericQ } from './numeric.ts'
-import type { GvTW, GvQ } from './geneVariant.ts'
-
-export type TermWrapper = CatTWTypes | NumTWTypes | GvTW
-
-export type Q = CategoricalQ | NumericQ | GvQ // | other q