@sjcrh/proteinpaint-types 2.123.0 → 2.125.0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-K7P6C6KU.js";
+} from "./chunk-LVXO4MLR.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AGSW7G4T.js";
+} from "./chunk-O4RAE6UJ.js";
 import {
   topMutatedGenePayload,
   validTopMutatedGeneRequest,
@@ -12,17 +12,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-NCFUZ5VV.js";
+} from "./chunk-2S4T3WUF.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-SQBZAOWB.js";
+} from "./chunk-7IRM7OKB.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-RX5EB2HL.js";
+} from "./chunk-VSNV3MLV.js";
 import {
   tilePayload,
   validTileRequest,
@@ -42,7 +42,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-3ZT4UCFM.js";
+} from "./chunk-BXPSDGWG.js";
 import {
   rootTermPayload,
   validRootTermRequest,
@@ -87,17 +87,17 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XPOHYEAY.js";
+} from "./chunk-537XOM43.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZMOSABYP.js";
+} from "./chunk-GZCIY2WK.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-F64WJMRL.js";
+} from "./chunk-DJCPG2RT.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -112,12 +112,12 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-5XRJ5ATE.js";
+} from "./chunk-YOS2YTCE.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-LBGUOJR3.js";
+} from "./chunk-5O422YU6.js";
 import {
   hicstatPayload,
   validHicstatRequest,
@@ -197,7 +197,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-QMWUUGEK.js";
+} from "./chunk-CJC7ZHSZ.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -212,7 +212,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-K7P6C6KU.js";
+} from "./chunk-LVXO4MLR.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XPOHYEAY.js";
+} from "./chunk-537XOM43.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZMOSABYP.js";
+} from "./chunk-GZCIY2WK.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-F64WJMRL.js";
+} from "./chunk-DJCPG2RT.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-5XRJ5ATE.js";
+} from "./chunk-YOS2YTCE.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-LBGUOJR3.js";
+} from "./chunk-5O422YU6.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-3ZT4UCFM.js";
+} from "./chunk-BXPSDGWG.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AGSW7G4T.js";
+} from "./chunk-O4RAE6UJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-NCFUZ5VV.js";
+} from "./chunk-2S4T3WUF.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-SQBZAOWB.js";
+} from "./chunk-7IRM7OKB.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-RX5EB2HL.js";
+} from "./chunk-VSNV3MLV.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.123.0",
+  "version": "2.125.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -607,6 +607,13 @@ type CnvSegment = {
 		- for others using mayGetGeneVariantData(), this is always disabled, as request won't have this flag
 	*/
 	requiresHardcodeCnvOnlyFlag?: true
+
+	/** CNV cutoffs (such as cnvGainCutoff, cnvLossCutoff, cnvMaxLength) that are applied to specific genes */
+	cnvCutoffsByGene?: {
+		[geneName: string]: {
+			[key: string]: any
+		}
+	}
 }
 
 /*
@@ -1172,9 +1179,12 @@ type Matrix = {
 	settings?: MatrixSettings
 	/** matrix-specific mclass override? */
 	mclass?: Mclass
-	// TODO: improve definitions below
+	/** filter to hide entire legend group, e.g. hide all CNV */
 	legendGrpFilter?: any
+	/** filter to hide categories or mclass, e.g. hide male, hide MISSENSE */
 	legendValueFilter?: any
+	/** matrix criteria for a CNV alteration */
+	cnvCutoffs?: any
 }
 
 // specific hierCluster type settings, should be named as "dataTYpe + Cluster"
@@ -1970,11 +1980,6 @@ export type Mds3 = BaseMds & {
 	// !!! TODO: improve these type definitions below !!!
 	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any
-	customTwQByType?: {
-		[termType: string]: {
-			[key: string]: any
-		}
-	}
 	getHealth?: (ds: any) => {
 		[key: string]: any
 	}

package/src/genome.ts

@@ -19,6 +19,12 @@ type TermDbs = {
 type TermDbsEntry = {
 	label: string
 	cohort: Cohort
+	/** list of geneset groups in db; required for geneORA and gsea
+	later allow ds override so ds can enable/disable some genesets..
+	*/
+	analysisGenesetGroups: { label: string; value: string }[]
+	/** required for gsea */
+	geneORAparam: { minCutoff: number; maxCutoff: number }
 }
 
 type DbStatement = {

package/src/terms/geneVariant.ts

@@ -94,6 +94,7 @@ export type DtTerm = {
 	query: string
 	name: string
 	name_noOrigin: string
+	geneVariantTerm?: RawGvTerm
 	parent_id: any
 	isleaf: boolean
 	type: string