@sjcrh/proteinpaint-types 2.169.0 → 2.170.1

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-LXW2FSLR.js";
+} from "./chunk-MH3TDIL4.js";
 import "./chunk-YNHC5SXO.js";
 export {
   CorrelationVolcanoPayload,

package/dist/grin2.js

@@ -2,7 +2,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-VQOCGHP2.js";
+} from "./chunk-YCURJJSC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   GRIN2Payload,

package/dist/healthcheck.js

@@ -2,7 +2,7 @@ import {
   healthcheckPayload,
   validHealthCheckRequest,
   validHealthCheckResponse
-} from "./chunk-FTPYJPUB.js";
+} from "./chunk-FK7OCBPT.js";
 import "./chunk-YNHC5SXO.js";
 export {
   healthcheckPayload,

package/dist/index.js

@@ -7,17 +7,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-GZKTMVAU.js";
+} from "./chunk-HDED6K55.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-EBPGV76U.js";
+} from "./chunk-33FYSH3O.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-OLXOQLZH.js";
+} from "./chunk-GNLX5NQ5.js";
 import {
   tilePayload,
   validTileRequest,
@@ -72,7 +72,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-C27KCAQH.js";
+} from "./chunk-CUU7POGC.js";
 import {
   termdbCohortsPayload,
   validTermdbCohortsRequest,
@@ -82,7 +82,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-ZXPLL3NT.js";
+} from "./chunk-53QZTLJK.js";
 import {
   FilterTermValuesPayload,
   validFilterTermValuesRequest,
@@ -92,12 +92,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-OLWNM7QP.js";
+} from "./chunk-MJEQEGN4.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-5F24QFE7.js";
+} from "./chunk-BPDR66LV.js";
 import {
   ProfileFormScoresPayload,
   validProfileFormScoresRequest,
@@ -132,22 +132,22 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-PZHVYGSD.js";
+} from "./chunk-A5Z4YYMF.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-MCL6EDOS.js";
+} from "./chunk-ZAMM6EMS.js";
 import {
   ChatPayload,
   validChatRequest,
   validChatResponse
-} from "./chunk-GIPUG4HD.js";
+} from "./chunk-447IAMTQ.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-CC32XCET.js";
+} from "./chunk-UQNHLAZN.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -217,12 +217,12 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-VQOCGHP2.js";
+} from "./chunk-YCURJJSC.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,
   validHealthCheckResponse
-} from "./chunk-FTPYJPUB.js";
+} from "./chunk-FK7OCBPT.js";
 import {
   hicdataPayload,
   validHicdataRequest,
@@ -239,7 +239,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-LXW2FSLR.js";
+} from "./chunk-MH3TDIL4.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -297,7 +297,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-5OMJAZK4.js";
+} from "./chunk-QL6YSLN6.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-PZHVYGSD.js";
+} from "./chunk-A5Z4YYMF.js";
 import "./chunk-YNHC5SXO.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-MCL6EDOS.js";
+} from "./chunk-ZAMM6EMS.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.chat.js

@@ -2,7 +2,7 @@ import {
   ChatPayload,
   validChatRequest,
   validChatResponse
-} from "./chunk-GIPUG4HD.js";
+} from "./chunk-447IAMTQ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   ChatPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-CC32XCET.js";
+} from "./chunk-UQNHLAZN.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-ZXPLL3NT.js";
+} from "./chunk-53QZTLJK.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-OLWNM7QP.js";
+} from "./chunk-MJEQEGN4.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-5F24QFE7.js";
+} from "./chunk-BPDR66LV.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-C27KCAQH.js";
+} from "./chunk-CUU7POGC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-GZKTMVAU.js";
+} from "./chunk-HDED6K55.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-EBPGV76U.js";
+} from "./chunk-33FYSH3O.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-OLXOQLZH.js";
+} from "./chunk-GNLX5NQ5.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.169.0",
+  "version": "2.170.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1596,12 +1596,18 @@ keep this setting here for reason of:
 }
 
 type NumericTermCollection = {
-	/** human readable name for this collection */
+	/** collection id */
+	id?: string
+	/** human readable name for this collection, may be as collection id if missing */
 	name: string
 	/** array of dictionary numeric term ids belonging to this collection */
 	termIds: string[]
-	/** array of branch term ids belonging to this collection */
+	/** array of branch term ids belonging to this collection,
+	 * may be used as state.tree.expandedTermIds[] option to termdb appInit() */
 	branchIds: string[]
+	propsByTermId: {
+		[termId: string]: any
+	}
 	/** preconfigured cohort-level plots for this collection */
 	plots?: {
 		/** name of this plot */

package/src/filter.ts

@@ -3,6 +3,7 @@ import type { NumericTerm, NumericBin } from './terms/numeric.ts'
 import type { CategoricalTerm } from './terms/categorical.ts'
 import type { DtTerm } from './terms/geneVariant.ts'
 import type { ConditionTerm } from './terms/condition.ts'
+import type { TermCollection } from './terms/termCollection.ts'
 
 /*
 --------EXPORTED--------
@@ -62,9 +63,14 @@ type GeneVariantTvs = BaseTvs & {
 	excludeGeneName?: boolean
 }
 
+export type TermCollectionTvs = BaseTvs & {
+	term: TermCollection
+	ratio: number
+}
+
 /*** types supporting Filter type ***/
 
-export type Tvs = CategoricalTvs | NumericTvs | ConditionTvs | GeneVariantTvs // | SampleLstTvs ...
+export type Tvs = CategoricalTvs | NumericTvs | ConditionTvs | GeneVariantTvs | TermCollectionTvs // | SampleLstTvs ...
 
 export type Filter = {
 	type: 'tvslst'

package/src/index.ts

@@ -80,5 +80,6 @@ export * from './terms/samplelst.ts'
 export * from './terms/ssGSEA.ts'
 export * from './terms/q.ts'
 export * from './terms/term.ts'
+export * from './terms/termCollection.ts'
 export * from './terms/tw.ts'
 export * from './vocab.ts'

package/src/routes/grin2.ts

@@ -35,6 +35,11 @@ export type GRIN2Request = {
 	/** Threshold for q-values to be included as interactive dots */
 	qValueThreshold?: number
 
+	/** Log cutoff for Manhattan plot rendering before we scale the y-axis (default: 40).
+	 * This is not user defined but rather a constant defined in #shared/manhattan.js.
+	 * Sending it with request for consistency. In future we will allow user to set scale value or disable scaling if they wish */
+	logCutoff?: number
+
 	/** Filter from existing PP infrastructure */
 	filter?: any // Filter object passed to get_samples(filter, ds)
 

package/src/routes/healthcheck.ts

@@ -55,6 +55,7 @@ export type HealthCheckResponse = {
 	}
 	w?: number[]
 	rs?: number
+	dsInitStatus: any[]
 }
 
 export const healthcheckPayload: RoutePayload = {

package/src/routes/termdb.boxplot.ts

@@ -31,7 +31,11 @@ export type BoxPlotResponse = {
 	absMin?: number
 	/** Absolute max value for all plots */
 	absMax?: number
-	/** Charts data */
+	/** Bins for overlay and/or divide terms */
+	bins?: {
+		[index: string]: any
+	}
+	/** Charts data. chartId corresponds the divide by term value*/
 	charts: {
 		[chartId: string]: BoxPlotChartEntry
 	}
@@ -66,7 +70,7 @@ export type BoxPlotEntry = {
 	isHidden?: boolean
 	key: string
 	/** Formatted bins for numeric terms */
-	overlayBins?: any
+	overlayTwBins?: any
 	/** Usually the same as key, but determined by the tw */
 	seriesId?: string
 }

package/src/routes/termdb.violin.ts

@@ -82,13 +82,13 @@ type ViolinDensity = {
 export type ViolinPlotEntry = {
 	/** Color to render */
 	color: string
+	chartId: string
 	density: ViolinDensity
-	overlayTwBins: any
 	/** Text for label */
 	label: string
 	/** Number of samples/cases/patients/etc. */
 	plotValueCount: number
-	/** Cooresponds to the tw.$id */
+	/** Corresponds to the tw.$id */
 	seriesId: string
 	/** Plot image to display */
 	src: string
@@ -99,12 +99,20 @@ export type ViolinPlotEntry = {
 export type ViolinResponse = ValidResponse | ErrorResponse
 
 type ValidResponse = {
+	/** Bins used for each term
+	 * Used for listing samples, filtering, etc.*/
+	bins: { [index: string]: any }
+	charts: {
+		[index: string]: {
+			chartId: string
+			plots: ViolinPlotEntry[]
+			pvalues?: PValueEntries[][]
+		}
+	}
 	/** Absolute min value for all plots */
 	min: number
 	/** Absolute max value for all plots */
 	max: number
-	plots: ViolinPlotEntry[]
-	pvalues?: PValueEntries[][]
 	uncomputableValues: { [index: string]: number }[] | null
 }
 

package/src/terms/term.ts

@@ -5,6 +5,7 @@ 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
@@ -47,7 +48,8 @@ export type BaseTerm = {
 }
 
 // NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, and other non-dict terms
-export type Term = BaseTerm & (NumericTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm | QualTerm)
+export type Term = BaseTerm &
+	(NumericTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm | QualTerm | TermCollection)
 
 /*** types supporting Term types ***/
 

package/src/terms/termCollection.ts

@@ -0,0 +1,52 @@
+import type { BaseTerm, BaseTW, MinBaseQ } from '../index.ts'
+
+/*
+For term type 'snp'
+*/
+
+export type TermCollection = 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 */
+	lst?: string[]
+	termlst?: any[] // TODO: choose either lst or termlst
+	numerators?: string[]
+	newTvs?: boolean
+}
+
+export type RawTermCollection = TermCollection & {
+	type?: 'termCollection'
+	termlst?: string[]
+}
+
+export type TermCollectionQValues = MinBaseQ & {
+	mode: 'continuous' // | 'discrete'
+	type: 'values'
+	// groupValuesBy: 'sampleId' | 'termId'
+	/** a selection of term.ids for the current termwrapper, selected from term.lst */
+	lst: string[]
+	numerators?: string[]
+}
+
+// TODO: may add different q types below
+export type TermCollectionQ = TermCollectionQValues
+
+export type TermCollectionTWValues = BaseTW & {
+	type: 'TermCollectionTWValues'
+	term: TermCollection
+	q: TermCollectionQValues
+}
+
+// TODO: may add different termCollection TW types here
+export type TermCollectionTW = TermCollectionTWValues
+
+export type RawTermCollectionTWValues = /*TermCollectionTW &*/ {
+	type?: 'TermCollectionTWValues' | 'termCollection' // deprecated
+	term: RawTermCollection
+	q: TermCollectionQValues
+}
+
+// TODO: may add different termCollection TW types here
+export type RawTermCollectionTW = RawTermCollectionTWValues

package/src/terms/tw.ts

@@ -4,6 +4,7 @@ import type { SampleLstQ } from './samplelst.ts'
 import type { NumTW, NumericQ } from './numeric.ts'
 import type { GvTW, GvQ } from './geneVariant.ts'
 import type { QualTW, QualQ } from './qualitative.ts'
+import type { TermCollectionTW, TermCollectionQ } from './termCollection.ts'
 
 export type BaseTW = {
 	id?: string
@@ -20,9 +21,9 @@ export type BaseTW = {
 	valueFilter?: any
 }
 
-export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW
+export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW | TermCollectionTW
 
-export type Q = NumericQ | GvQ | ConditionQ | SnpsQ | SampleLstQ | QualQ // | other q
+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[]