@sjcrh/proteinpaint-types 2.137.1 → 2.137.2-1

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-M7HKDHB3.js";
+} from "./chunk-PAQX4HYF.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -7,17 +7,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-C32XALTH.js";
+} from "./chunk-SUL2XLYM.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-UG7RYMCA.js";
+} from "./chunk-6H6TQ3MA.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-G5SBQR25.js";
+} from "./chunk-YGOZU46P.js";
 import {
   tilePayload,
   validTileRequest,
@@ -72,22 +72,22 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AKJWBIUV.js";
+} from "./chunk-7YFANJ2A.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-MLAGM7F5.js";
+} from "./chunk-MDPMNCMV.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-HF2D3UVQ.js";
+} from "./chunk-CBPDONEQ.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-OQVYIYZL.js";
+} from "./chunk-657TS66W.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -102,17 +102,17 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-3P6M5ZNJ.js";
+} from "./chunk-IE3MSHTB.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-B2FSTXLW.js";
+} from "./chunk-FMSTAFII.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-DA6B77HN.js";
+} from "./chunk-6LRQCE3E.js";
 import {
   ntseqPayload,
   validNtseqRequest,
@@ -235,7 +235,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-BS7BYTYZ.js";
+} from "./chunk-QCGBPQ7S.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -257,7 +257,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-M7HKDHB3.js";
+} from "./chunk-PAQX4HYF.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-MLAGM7F5.js";
+} from "./chunk-MDPMNCMV.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-HF2D3UVQ.js";
+} from "./chunk-CBPDONEQ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-OQVYIYZL.js";
+} from "./chunk-657TS66W.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-3P6M5ZNJ.js";
+} from "./chunk-IE3MSHTB.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-B2FSTXLW.js";
+} from "./chunk-FMSTAFII.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-DA6B77HN.js";
+} from "./chunk-6LRQCE3E.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AKJWBIUV.js";
+} from "./chunk-7YFANJ2A.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-C32XALTH.js";
+} from "./chunk-SUL2XLYM.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-UG7RYMCA.js";
+} from "./chunk-6H6TQ3MA.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-G5SBQR25.js";
+} from "./chunk-YGOZU46P.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.137.1",
+  "version": "2.137.2-1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -743,14 +743,13 @@ export type SingleCellGeneExpressionGdc = {
 }
 
 export type SingleCellSamples = {
-	/** if missing refer to the samples as 'sample', this provides override e.g. 'case' */
 	/** logic to decide sample table columns (the one shown on singlecell app ui, displaying a table of samples with sc data)
 	a sample table will always have a sample column, to show sample.sample value
 	- use uiLabels.Sample to customize the name of the first column
 	- the other two properties allow to declare additional columns to be shown in table, that are for display only
 	when sample.experiments[] are used, a last column of experiment id will be auto added
 	*/
-	/** any columns to be added to sample table. each is a term id */
+	/** any columns to be added to sample table. each is a term id, limited to categorical/numeric dictionary terms */
 	sampleColumns?: { termid: string }[]
 	/** used on client but not on ds */
 	experimentColumns?: { label: string }[]
@@ -803,7 +802,9 @@ type SingleCellPlot = {
 	/** value is display as plot name on ui and also used as identifier for a plot, must be unique */
 	name: string
 	/** folder in which per-sample files are stored.
-	each file is a tabular text file with all cells (rows) from that sample.
+	- each file is a tabular text file with all cells (rows) from that sample. each file is named by the sample and includes optional suffix
+	- folder must only contain per-sample files! files with names that cannot be matched to sample will crash dataset. this improves debugging
+
 	all files must have same set of columns:
 	- 1st column is cell barcode
 	- x/y coordinate column number is defined in coordsColumns{x,y} below

package/src/terms/geneVariant.ts

@@ -1,4 +1,4 @@
-import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet } from '../index.ts'
+import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet, FilterGroup } from '../index.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 // q types
@@ -10,18 +10,16 @@ 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 GvValuesQ = GvBaseQ & { type: 'values' }
+export type GvPredefinedGsQ = GvBaseQ & { type: 'predefined-groupset'; predefined_groupset_idx: number }
 export type GvCustomGsQ = GvBaseQ & { type: 'custom-groupset'; customset: BaseGroupSet }
 
-export type GvQ = GvValuesQ | GvCustomGsQ
+export type GvQ = GvValuesQ | GvPredefinedGsQ | GvCustomGsQ
 
 // term types
-type GvBaseTerm = BaseTerm & {
-	type: 'geneVariant'
-}
-
 export type GvGene = {
 	kind: 'gene'
 	gene: string
@@ -40,17 +38,17 @@ export type GvCoord = {
 	stop: number
 }
 
-export type RawGvTerm = GvBaseTerm &
-	(GvGene | GvCoord) & {
-		groupsetting?: TermGroupSetting
-		childTerms?: DtTerm[]
-	}
+type GvBaseTerm = BaseTerm & { type: 'geneVariant' } & (GvGene | GvCoord)
+
+export type RawGvTerm = GvBaseTerm & {
+	groupsetting?: TermGroupSetting
+	childTerms?: DtTerm[]
+}
 
-export type GvTerm = GvBaseTerm &
-	(GvGene | GvCoord) & {
-		groupsetting: TermGroupSetting
-		childTerms: DtTerm[]
-	}
+export type GvTerm = GvBaseTerm & {
+	groupsetting: TermGroupSetting
+	childTerms: DtTerm[]
+}
 
 // tw types
 export type RawGvValuesTW = BaseTW & {
@@ -59,6 +57,12 @@ export type RawGvValuesTW = BaseTW & {
 	q: RawGvValuesQ
 }
 
+export type RawGvPredefinedGsTW = BaseTW & {
+	type?: 'GvPredefinedGsTW'
+	term: RawGvTerm
+	q: RawGvPredefinedGsQ
+}
+
 export type RawGvCustomGsTW = BaseTW & {
 	type?: 'GvCustomGsTW'
 	term: RawGvTerm
@@ -71,21 +75,27 @@ export type GvValuesTW = BaseTW & {
 	q: GvValuesQ
 }
 
+export type GvPredefinedGsTW = BaseTW & {
+	type: 'GvPredefinedGsTW'
+	term: GvTerm
+	q: GvPredefinedGsQ
+}
+
 export type GvCustomGsTW = BaseTW & {
 	type: 'GvCustomGsTW'
 	term: GvTerm
 	q: GvCustomGsQ
 }
 
-export type RawGvTW = RawGvValuesTW | RawGvCustomGsTW
-export type GvTW = GvValuesTW | GvCustomGsTW
+export type RawGvTW = RawGvValuesTW | RawGvPredefinedGsTW | RawGvCustomGsTW
+export type GvTW = GvValuesTW | GvPredefinedGsTW | GvCustomGsTW
 
 // termsetting types
 export type GeneVariantTermSettingInstance = TermSettingInstance & {
 	q: GvQ
 	term: GvTerm
 	category2samplecount: any
-	groupSettingInstance?: any
+	groups: FilterGroup[] // will store groups created in edit UI
 }
 
 // miscellaneous types

package/src/terms/term.ts

@@ -136,22 +136,14 @@ type Groupset = {
 	name: string
 	is_grade?: boolean
 	is_subcondition?: boolean
-	id?: string // to identify groupset, used by geneVariant term
+	dt?: number // dt of groupset, used by geneVariant term
 } & BaseGroupSet
 
-export type EnabledTermGroupSetting = {
-	disabled?: false | boolean // can remove boolean fallback once common.js is converted to .ts and can declare `disabled: false as const`
-	lst: Groupset[]
+export type TermGroupSetting = {
+	disabled: boolean // true when term has <= 2 values, otherwise false
+	lst?: Groupset[] // array of predefined groupsets
 }
 
-export type TermGroupSetting =
-	| EnabledTermGroupSetting
-	| {
-			/** disabled=false when groupsetting is not applicable for term (e.g., when term has only two categories) */
-			disabled: true | boolean // can remove boolean fallback once common.js is converted to .ts and can declare `disabled: true as const`
-			lst?: []
-	  }
-
 /*** types supporting termwrapper ***/
 
 export type BaseTW = {