@sjcrh/proteinpaint-types 2.116.1-2 → 2.118.1-1

package/dist/{chunk-EQGBEPDC.js → chunk-T2CSA2MC.js}

@@ -102,8 +102,8 @@ var validPercentileRequest = (input) => {
     const $io24 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "condition" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io4(input3.values)) && true;
     const $io25 = (input3) => "number" === typeof input3.grade && "string" === typeof input3.grade_label && (void 0 === input3.child_id || "string" === typeof input3.child_id) && "string" === typeof input3.child_label;
     const $io26 = (input3) => (void 0 === input3.join || "string" === typeof input3.join) && (void 0 === input3.isnot || "boolean" === typeof input3.isnot) && ("object" === typeof input3.term && null !== input3.term && $iu8(input3.term)) && (Array.isArray(input3.values) && input3.values.every((elem) => "object" === typeof elem && null !== elem && $iu3(elem)));
-    const $io27 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "geneVariant" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io4(input3.values)) && true && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $io6(input3.groupsetting)) && "gene" === input3.kind && "string" === typeof input3.gene && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
-    const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "geneVariant" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io4(input3.values)) && true && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $io6(input3.groupsetting)) && "coord" === input3.kind && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
+    const $io27 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "geneVariant" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io4(input3.values)) && true && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $iu4(input3.groupsetting)) && "gene" === input3.kind && "string" === typeof input3.gene && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
+    const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "geneVariant" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io4(input3.values)) && true && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $iu4(input3.groupsetting)) && "coord" === input3.kind && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
     const $io29 = (input3) => 1 === input3.dt && (Array.isArray(input3.mclassLst) && input3.mclassLst.every((elem) => "M" === elem || "E" === elem || "F" === elem || "N" === elem || "S" === elem || "D" === elem || "I" === elem || "P" === elem || "L" === elem || "Intron" === elem || "Blank" === elem || "WT" === elem || "ITD" === elem || "DEL" === elem || "NLOSS" === elem || "CLOSS" === elem || "Utr3" === elem || "Utr5" === elem || "X" === elem || "noncoding" === elem)) && (Array.isArray(input3.mclassExcludeLst) && input3.mclassExcludeLst.every((elem) => "M" === elem || "E" === elem || "F" === elem || "N" === elem || "S" === elem || "D" === elem || "I" === elem || "P" === elem || "L" === elem || "Intron" === elem || "Blank" === elem || "WT" === elem || "ITD" === elem || "DEL" === elem || "NLOSS" === elem || "CLOSS" === elem || "Utr3" === elem || "Utr5" === elem || "X" === elem || "noncoding" === elem)) && (void 0 === input3.origin || "somatic" === input3.origin || "germline" === input3.origin);
     const $io30 = (input3) => 4 === input3.dt && (Array.isArray(input3.mclassLst) && input3.mclassLst.every((elem) => "Blank" === elem || "WT" === elem || "CNV_amp" === elem || "CNV_loss" === elem || "CNV_loh" === elem || "CNV_amplification" === elem || "CNV_homozygous_deletion" === elem)) && (Array.isArray(input3.mclassExcludeLst) && input3.mclassExcludeLst.every((elem) => "Blank" === elem || "WT" === elem || "CNV_amp" === elem || "CNV_loss" === elem || "CNV_loh" === elem || "CNV_amplification" === elem || "CNV_homozygous_deletion" === elem)) && (void 0 === input3.origin || "somatic" === input3.origin || "germline" === input3.origin);
     const $io31 = (input3) => 5 === input3.dt && (Array.isArray(input3.mclassLst) && input3.mclassLst.every((elem) => "Blank" === elem || "WT" === elem || "SV" === elem)) && (Array.isArray(input3.mclassExcludeLst) && input3.mclassExcludeLst.every((elem) => "Blank" === elem || "WT" === elem || "SV" === elem)) && (void 0 === input3.origin || "somatic" === input3.origin || "germline" === input3.origin);
@@ -1134,11 +1134,11 @@ var validPercentileRequest = (input) => {
         value: input3.values
       }), true, ("object" === typeof input3.groupsetting && null !== input3.groupsetting || $report(_exceptionable2, {
         path: _path2 + ".groupsetting",
-        expected: "EnabledTermGroupSetting",
+        expected: "(EnabledTermGroupSetting | __type.o1)",
         value: input3.groupsetting
-      })) && $vo6(input3.groupsetting, _path2 + ".groupsetting", _exceptionable2) || $report(_exceptionable2, {
+      })) && $vu4(input3.groupsetting, _path2 + ".groupsetting", _exceptionable2) || $report(_exceptionable2, {
         path: _path2 + ".groupsetting",
-        expected: "EnabledTermGroupSetting",
+        expected: "(EnabledTermGroupSetting | __type.o1)",
         value: input3.groupsetting
       }), "gene" === input3.kind || $report(_exceptionable2, {
         path: _path2 + ".kind",
@@ -1215,11 +1215,11 @@ var validPercentileRequest = (input) => {
         value: input3.values
       }), true, ("object" === typeof input3.groupsetting && null !== input3.groupsetting || $report(_exceptionable2, {
         path: _path2 + ".groupsetting",
-        expected: "EnabledTermGroupSetting",
+        expected: "(EnabledTermGroupSetting | __type.o1)",
         value: input3.groupsetting
-      })) && $vo6(input3.groupsetting, _path2 + ".groupsetting", _exceptionable2) || $report(_exceptionable2, {
+      })) && $vu4(input3.groupsetting, _path2 + ".groupsetting", _exceptionable2) || $report(_exceptionable2, {
         path: _path2 + ".groupsetting",
-        expected: "EnabledTermGroupSetting",
+        expected: "(EnabledTermGroupSetting | __type.o1)",
         value: input3.groupsetting
       }), "coord" === input3.kind || $report(_exceptionable2, {
         path: _path2 + ".kind",

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-CNR46KGX.js";
+} from "./chunk-53UNFIIG.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-I3U2T7HV.js";
+} from "./chunk-JYO2T4HZ.js";
 import {
   topMutatedGenePayload,
   validTopMutatedGeneRequest,
@@ -12,17 +12,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-KZIZMP7Y.js";
+} from "./chunk-OL4OMJSP.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-7GSVLBKZ.js";
+} from "./chunk-ROPNHRVV.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-ZPN2DV5E.js";
+} from "./chunk-DL4UYYVE.js";
 import {
   tilePayload,
   validTileRequest,
@@ -42,7 +42,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-EQGBEPDC.js";
+} from "./chunk-T2CSA2MC.js";
 import {
   rootTermPayload,
   validRootTermRequest,
@@ -87,17 +87,17 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-PTYGGJLG.js";
+} from "./chunk-4U546XOJ.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-C7DJDPLP.js";
+} from "./chunk-JOGEIPHA.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NESPJ4GG.js";
+} from "./chunk-J6SJ4M3S.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -112,12 +112,12 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-GS37E7DB.js";
+} from "./chunk-KG7UDG6M.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-M26XQDA4.js";
+} from "./chunk-GI4NNB34.js";
 import {
   hicstatPayload,
   validHicstatRequest,
@@ -197,7 +197,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-KBTAXZM4.js";
+} from "./chunk-GD3KAF6V.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -212,7 +212,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-CNR46KGX.js";
+} from "./chunk-53UNFIIG.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-PTYGGJLG.js";
+} from "./chunk-4U546XOJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-C7DJDPLP.js";
+} from "./chunk-JOGEIPHA.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NESPJ4GG.js";
+} from "./chunk-J6SJ4M3S.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-GS37E7DB.js";
+} from "./chunk-KG7UDG6M.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-M26XQDA4.js";
+} from "./chunk-GI4NNB34.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-EQGBEPDC.js";
+} from "./chunk-T2CSA2MC.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-I3U2T7HV.js";
+} from "./chunk-JYO2T4HZ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-KZIZMP7Y.js";
+} from "./chunk-OL4OMJSP.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

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

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-ZPN2DV5E.js";
+} from "./chunk-DL4UYYVE.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.116.1-2",
+  "version": "2.118.1-1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -522,33 +522,57 @@ type TrackLst = {
 	activeTracks: string[]
 }
 
+/** cnv segments are queried by coordinates, and can be filtered by segment length and/or value
+configs for types of cnv data
+- log(ratio)
+	{
+		cnvMaxLength:10000000
+		cnvGainCutoff:5
+		cnvLossCutoff:-5
+	}
+- copy number
+	{
+		cnvMaxLength:1000000
+		cnvMaxCopynumber:10
+		cnvMinCopynumber:1
+	}
+important: presence of filtering properties indiate the type of cnv quantification
+and will trigger rendering of ui controls
+*/
 type CnvSegment = {
-	byrange: CnvSegmentByRange
+	/** ds supplied ordynamically added getter */
+	get?: (q: any) => any
+	/** either file or get is required. file is bgzipped with columns:
+	1. chr
+	2. start, 0-based
+	3. stop
+	4. {"dt": 4, "mattr": {"origin": "somatic"}, "sample": "3332", "value": -1.0}
+	*/
+	file?: string
+
 	/****** rendering parameters ****
-not used as query parameter to filter segments
-value range for color scaling. default to 5. cnv segment value>this will use solid color
-*/
+	not used as query parameter to filter segments
+	value range for color scaling. default to 5. cnv segment value>this will use solid color
+	*/
 	absoluteValueRenderMax?: number
 	gainColor?: string
 	lossColor?: string
 
-	/*** filtering parameters ***
-default max length setting to restrict to focal events; if missing show all */
+	/** filter segments by max length to restrict to focal events; set to -1 to show all
+	allow to be missing, in such case will always show all */
 	cnvMaxLength?: number
 
-	/** TODO define value type, if logratio, or copy number */
-
-	/** following two cutoffs only apply to log ratio, cnv gain value is positive, cnv loss value is negative
-if cnv is gain, skip if value<this cutoff */
+	/** if cnv is quantified as log(ratio) or similar, must set these two properties
+	filter segments by following two cutoffs only apply to log ratio, cnv gain value is positive, cnv loss value is negative
+	*/
+	/** if value>0, skip if value<this cutoff, set to a large value e.g. 100 for not filtering */
 	cnvGainCutoff?: number
-	/** if cnv is loss, skip if value>this cutoff */
+	/** if value<0, skip if value>this cutoff, set to a large negative value e.g. -100 for not filtering */
 	cnvLossCutoff?: number
-}
-
-type CnvSegmentByRange = {
-	src: 'native' | 'gdcapi' | string
-	/** only for src=native */
-	file?: string
+	/** TODO if cnv is quantified as integer copy number, must set these properties; do not use for log(ratio)
+	 */
+	cnvMinCopynumber?: number
+	cnvMaxCopynumber?: number
 }
 
 /*
@@ -1370,6 +1394,8 @@ keep this setting here for reason of:
 		/** colors for a category multivalues */
 		[index: string]: { [index: string]: string }
 	}
+	//terms that are not shown in the dictionary tree unless the user is admin. If there is no authentication the terms listes are always hidden
+	hiddenTermIds?: string[]
 }
 
 type SampleType = {
@@ -1477,6 +1503,7 @@ export type Cohort = {
 	/** if present, supplies premade scatter plots */
 	scatterplots?: Scatterplots
 	termdb: Termdb
+	hiddenTermIds?: string[]
 }
 
 /** Customizations specific to the mass nav component */

package/src/terms/geneVariant.ts

@@ -1,12 +1,4 @@
-import type {
-	MinBaseQ,
-	BaseTerm,
-	EnabledTermGroupSetting,
-	BaseTW,
-	GroupSettingQ,
-	ValuesQ,
-	TermValues
-} from '../index.ts'
+import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, GroupSettingQ, ValuesQ, TermValues } from '../index.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 export type GeneVariantBaseQ = MinBaseQ & {
@@ -23,7 +15,7 @@ export type GeneVariantQ = GeneVariantBaseQ & (ValuesQ | GroupSettingQ)
 
 type GeneVariantBaseTerm = BaseTerm & {
 	type: 'geneVariant'
-	groupsetting: EnabledTermGroupSetting
+	groupsetting: TermGroupSetting
 }
 
 export type GeneVariantGeneTerm = GeneVariantBaseTerm & {

package/src/vocab.ts

@@ -1,7 +1,7 @@
-import { TermWrapper } from './terms/tw.ts'
-import { Term } from './terms/term.ts'
-import { Filter } from './filter.ts'
-import { UseCase } from './termsetting.ts'
+import type { TermWrapper } from './terms/tw.ts'
+import type { Term } from './terms/term.ts'
+import type { Filter } from './filter.ts'
+import type { UseCase } from './termsetting.ts'
 
 /*
 --------EXPORTED--------
@@ -16,7 +16,7 @@ export type VocabApi = {
 	//Methods
 	cacheTermQ: (term: Term, q: any) => any
 	findTerm: (f: string, activeCohort: number, usecase: UseCase, x: string) => { lst: Term[] }
-	getCategories: (term: Term, filer: Filter, body?: any) => any
+	getCategories: (term: Term, filter?: Filter, body?: any) => any
 	getCustomTermQLst: (f: Term) => any
 	getPercentile: (term_id: string | number, percentile_lst: number[], filter?: Filter) => any
 	getterm: (f: any) => Term