@sjcrh/proteinpaint-types 2.112.1-0 → 2.114.0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-FMW25T52.js";
+} from "./chunk-66XSFQPI.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -7,22 +7,22 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-TXZQ56TX.js";
+} from "./chunk-KRHYG2ZZ.js";
 import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-4CCAF4O5.js";
+} from "./chunk-JNEIQWTE.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-A72XYNKT.js";
+} from "./chunk-BEXUBE5A.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-ZFUF4XMD.js";
+} from "./chunk-T3NOHXOJ.js";
 import {
   tilePayload,
   validTileRequest,
@@ -37,12 +37,12 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-ES6BRZ4L.js";
+} from "./chunk-7AQB3YHO.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-GHAIGRB7.js";
+} from "./chunk-PR7XHL4T.js";
 import {
   rootTermPayload,
   validRootTermRequest,
@@ -87,17 +87,17 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-2WZPM25H.js";
+} from "./chunk-WVBWDL2B.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-7Z3AE4AY.js";
+} from "./chunk-H45GALYV.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NPVDG36X.js";
+} from "./chunk-OSHG443J.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -112,7 +112,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-KHPBBU43.js";
+} from "./chunk-BNOGQYXG.js";
 import {
   hicGenomePayload,
   validHicGenomeRequest,
@@ -192,7 +192,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-GGKNEHME.js";
+} from "./chunk-XDRUNGOV.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -207,7 +207,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-FMW25T52.js";
+} from "./chunk-66XSFQPI.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-2WZPM25H.js";
+} from "./chunk-WVBWDL2B.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-7Z3AE4AY.js";
+} from "./chunk-H45GALYV.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NPVDG36X.js";
+} from "./chunk-OSHG443J.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-KHPBBU43.js";
+} from "./chunk-BNOGQYXG.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-ES6BRZ4L.js";
+} from "./chunk-7AQB3YHO.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-GHAIGRB7.js";
+} from "./chunk-PR7XHL4T.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-TXZQ56TX.js";
+} from "./chunk-KRHYG2ZZ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-4CCAF4O5.js";
+} from "./chunk-JNEIQWTE.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-A72XYNKT.js";
+} from "./chunk-BEXUBE5A.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-ZFUF4XMD.js";
+} from "./chunk-T3NOHXOJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.112.1-0",
+  "version": "2.114.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -92,12 +92,23 @@ type bcfMafFile = {
 	maffile: string
 }
 
-type SnvindelByRange = {
-	/** if true, served from gdc. no other parameters TODO change to src='gdc/native' */
-	gdcapi?: boolean
+type SnvindelByIsoform = {
+	/** if true, served from gdc. no other parameters */
+	gdcapi?: true
+	/** getter function to retrieve data. dynamically added or ds-supplied
+	first argument is required and allow for 2 additional ones
+	*/
+	get?: (f: any, f2?: any, f3?: any) => void
+	/** if true, all tw from one client query must be processed via one call to snvindel.byisoform.get()
+	and no longer processes each tw by calling mayGetGeneVariantData()
+	*/
+	processTwsInOneQuery?: true
+}
 
+type SnvindelByRange = {
+	/** if true, served from gdc. no other parameters */
+	gdcapi?: true
 	//local ds can have following different setup
-
 	/** one single bcf file */
 	bcffile?: string
 	/** one bcf file per chr */
@@ -106,8 +117,8 @@ type SnvindelByRange = {
 	bcfMafFile?: bcfMafFile
 	/** allow to apply special configurations to certain INFO fields of the bcf file */
 	infoFields?: InfoFieldEntry[]
-	/** if true, bcf or chr2bcf uses string sample name in header. to be used during this migrating so the code can deal with old files with integer sample ids and new ones; TODO once all datasets are migrated, delete the flag */
-	tempflag_sampleNameInVcfHeader?: boolean
+	/** getter function to retrieve data. dynamically added or ds-supplied */
+	get?: (f: any) => void
 }
 
 type URLEntry = {
@@ -202,7 +213,7 @@ type Filter = {
 
 type VariantFilter = {
 	opts: { joinWith: string[] }
-	filter: Filter
+	filter?: Filter
 	terms: FilterTermEntry[]
 }
 
@@ -310,12 +321,10 @@ type SnvindelComputeGroup_info = {
 /** a data type under ds.queries{} */
 type SnvIndelQuery = {
 	forTrack?: boolean
-	/** allow to query data by either isoform or range
-	 * isoform query is only used for gdc api
-	 */
-	byisoform?: GdcApi
+	/** allow to query data by either isoform or range; either or both can be used; cannot be both missing */
+	byisoform?: SnvindelByIsoform
 	/** query data by range */
-	byrange: SnvindelByRange
+	byrange?: SnvindelByRange
 
 	infoUrl?: URLEntry[]
 	skewerRim?: SkewerRim
@@ -579,6 +588,8 @@ export type GeneExpressionQueryNative = {
 	samples?: number[]
 	/** dynamically added flag during launch */
 	nochr?: boolean
+	/** if true, the file is in HDF5 format */
+	hdf5File?: boolean
 	/** dynamically added getter */
 	get?: (param: any) => void
 	/** This dictionary is used to store/cache the default bins calculated for a geneExpression term when initialized in the fillTermWrapper */
@@ -1215,9 +1226,14 @@ keep this setting here for reason of:
 		ssm?: UrlTemplateSsm | UrlTemplateSsm[]
 	}
 
-	q?: {
+	/** ds-defined or dynamically created */
+	termtypeByCohort?: any
+	/** ds-defined or dynamically created callbacks 
+	{
 		getSupportedChartTypes: (a: any) => any
 	}
+	*/
+	q?: any
 	termMatch2geneSet?: any
 	mclass?: Mclass
 	lollipop?: any
@@ -1354,7 +1370,7 @@ export type Cohort = {
 	/** if present, means correlation volcano plot analysis is enabled */
 	correlationVolcano?: CorrelationVolcano
 	cumburden?: CumBurdenData
-	db: FileObj
+	db?: FileObj
 	/** customize the default chart to open on mass ui when there's no charts. if
 	 * missing it opens dictionary ui */
 	defaultChartType?: string
@@ -1783,7 +1799,7 @@ export type Mds3 = BaseMds & {
 	queries?: Mds3Queries
 	cohort?: Cohort
 	isSupportedChartOverride?: isSupportedChartCallbacks
-	// TODO: termdb should be nested under cohort
+	// TODO FIXME nest termdb under cohort
 	termdb?: Termdb
 	validate_filter0?: (f: any) => void
 	ssm2canonicalisoform?: GdcApi

package/src/routes/termdb.DE.ts

@@ -46,6 +46,10 @@ export type ExpressionInput = {
 	conf2_mode?: 'continuous' | 'discrete'
 	/** Number of variable genes to be included for DE analysis (optional) */
 	VarGenes?: number
+	/** The methodology used for differential gene expression: wilcoxon, edgeR and limma */
+	DE_method: 'wilcoxon' | 'limma' | 'edgeR'
+	/** Cutoff for when mds plot will be generated for edgeR and limma test */
+	mds_cutoff: number
 }
 
 export type DEResponse = {

package/src/routes/termdb.cluster.ts

@@ -82,8 +82,13 @@ export type ValidResponse = {
 	byTermId: { [index: string]: any }
 	/**  */
 	bySampleId: { [index: string]: any }
-	/** list of term names that are excluded from analysis for lacking any numerical data */
-	removedHierClusterTerms?: string[]
+	/** list of term names that are excluded from analysis, one reason per set, for client display */
+	removedHierClusterTerms?: {
+		/** reason for skipping */
+		text: string
+		/** list of skipped item names */
+		lst: string[]
+	}[]
 }
 
 //response of just 1 gene, thus unable to do clustering

package/src/terms/geneVariant.ts

@@ -1,5 +1,13 @@
-import { MinBaseQ, BaseTerm, EnabledTermGroupSetting, BaseTW, GroupSettingQ, ValuesQ } from '../index.ts'
-import { TermSettingInstance } from '../termsetting.ts'
+import type {
+	MinBaseQ,
+	BaseTerm,
+	EnabledTermGroupSetting,
+	BaseTW,
+	GroupSettingQ,
+	ValuesQ,
+	TermValues
+} from '../index.ts'
+import type { TermSettingInstance } from '../termsetting.ts'
 
 export type GeneVariantBaseQ = MinBaseQ & {
 	cnvGainCutoff?: number
@@ -49,3 +57,16 @@ export type GeneVariantTermSettingInstance = TermSettingInstance & {
 	category2samplecount: any
 	groupSettingInstance?: any
 }
+
+export type DtTerm = {
+	id: string
+	name: string
+	parent_id: any
+	isleaf: boolean
+	type: string
+	dt: number
+	origin?: string
+	values?: TermValues
+	min?: number
+	max?: number
+}

package/src/terms/term.ts

@@ -1,10 +1,10 @@
-import { Filter } from '../filter.js'
-import { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
-import { ConditionTerm } from './condition.js'
-import { NumericTerm } from './numeric.js'
-import { GeneVariantTerm } from './geneVariant.js'
-import { SampleLstTerm } from './samplelst.js'
-import { SnpsTerm } from './snps.js'
+import type { Filter } from '../filter.js'
+import type { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
+import type { ConditionTerm } from './condition.js'
+import type { NumericTerm } from './numeric.js'
+import type { GeneVariantTerm } from './geneVariant.js'
+import type { SampleLstTerm } from './samplelst.js'
+import type { SnpsTerm } from './snps.js'
 
 /**
  * @param id      term.id for dictionary terms, undefined for non-dictionary terms
@@ -56,6 +56,8 @@ export type BaseQ = {
 		| 'custom-groupset'
 		/** Applies to samplelst terms */
 		| 'custom-samplelst'
+		/** Applies to geneVariant term */
+		| 'filter'
 }
 
 export type ValuesQ = CategoricalBaseQ & {
@@ -72,7 +74,11 @@ export type CustomGroupSettingQ = CategoricalBaseQ & {
 	customset: BaseGroupSet
 }
 
-export type GroupSettingQ = ValuesQ | PredefinedGroupSettingQ | CustomGroupSettingQ
+export type FilterQ = BaseQ & {
+	type: 'filter'
+}
+
+export type GroupSettingQ = ValuesQ | FilterQ | PredefinedGroupSettingQ | CustomGroupSettingQ
 
 /*** types supporting termwrapper term ***/
 
@@ -99,6 +105,7 @@ export type BaseTerm = {
 	included_types?: string[]
 	isleaf?: boolean
 	values?: TermValues
+	filter?: any
 }
 
 export type Term = BaseTerm &
@@ -116,6 +123,7 @@ export type FilterGroup = {
 	name: string
 	type: 'filter'
 	filter: Filter
+	uncomputable?: boolean // if true, do not include this group in computations
 }
 
 export type GroupEntry = ValuesGroup | FilterGroup

package/src/termsetting.ts

@@ -84,8 +84,8 @@ type BaseTermSettingOpts = {
 	 * before the pill name is truncated. */
 	abbrCutoff?: number
 	activeCohort?: number
-	/** tw.term.ids */
-	disable_terms?: string[]
+	/** array of term objects to show in the tree but not clickable */
+	disable_terms?: Term[]
 	// This is not used anywhere.
 	// Ok to remove?
 	handler: Handler
@@ -165,7 +165,7 @@ export type TermSettingInstance = {
 	clickNoPillDiv?: any
 	dom: InstanceDom
 	doNotHideTipInMain?: boolean
-	disable_terms?: string[]
+	disable_terms?: Term[]
 	durations: { exit: number }
 	filter?: Filter
 	handler?: Handler