@sjcrh/proteinpaint-types 2.121.0 → 2.124.0

package/dist/{chunk-HURSYPTO.js → chunk-D5OG676D.js}

@@ -65,7 +65,7 @@ var validSampleWSImagesResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.sampleWSImages) && input3.sampleWSImages.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
-    const $io1 = (input3) => "string" === typeof input3.filename && (void 0 === input3.overlays || Array.isArray(input3.overlays) && input3.overlays.every((elem) => "string" === typeof elem)) && "string" === typeof input3.metadata;
+    const $io1 = (input3) => "string" === typeof input3.filename && (void 0 === input3.overlays || Array.isArray(input3.overlays) && input3.overlays.every((elem) => "string" === typeof elem)) && (void 0 === input3.zoomInPoints || Array.isArray(input3.zoomInPoints) && input3.zoomInPoints.every((elem) => Array.isArray(elem) && (elem.length === 2 && "number" === typeof elem[0] && "number" === typeof elem[1]))) && "string" === typeof input3.metadata;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -104,6 +104,37 @@ var validSampleWSImagesResponse = (input) => {
         path: _path2 + ".overlays",
         expected: "(Array<string> | undefined)",
         value: input3.overlays
+      }), void 0 === input3.zoomInPoints || (Array.isArray(input3.zoomInPoints) || $report(_exceptionable2, {
+        path: _path2 + ".zoomInPoints",
+        expected: "(Array<[number, number]> | undefined)",
+        value: input3.zoomInPoints
+      })) && input3.zoomInPoints.map((elem, _index3) => (Array.isArray(elem) || $report(_exceptionable2, {
+        path: _path2 + ".zoomInPoints[" + _index3 + "]",
+        expected: "[number, number]",
+        value: elem
+      })) && ((elem.length === 2 || $report(_exceptionable2, {
+        path: _path2 + ".zoomInPoints[" + _index3 + "]",
+        expected: "[number, number]",
+        value: elem
+      })) && [
+        "number" === typeof elem[0] || $report(_exceptionable2, {
+          path: _path2 + ".zoomInPoints[" + _index3 + "][0]",
+          expected: "number",
+          value: elem[0]
+        }),
+        "number" === typeof elem[1] || $report(_exceptionable2, {
+          path: _path2 + ".zoomInPoints[" + _index3 + "][1]",
+          expected: "number",
+          value: elem[1]
+        })
+      ].every((flag) => flag)) || $report(_exceptionable2, {
+        path: _path2 + ".zoomInPoints[" + _index3 + "]",
+        expected: "[number, number]",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".zoomInPoints",
+        expected: "(Array<[number, number]> | undefined)",
+        value: input3.zoomInPoints
       }), "string" === typeof input3.metadata || $report(_exceptionable2, {
         path: _path2 + ".metadata",
         expected: "string",

package/dist/index.js

@@ -147,7 +147,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-HURSYPTO.js";
+} from "./chunk-D5OG676D.js";
 import {
   snpPayload,
   validSnpRequest,

package/dist/samplewsimages.js

@@ -2,7 +2,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-HURSYPTO.js";
+} from "./chunk-D5OG676D.js";
 import "./chunk-CNSSF43V.js";
 export {
   sampleWSImagesPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.121.0",
+  "version": "2.124.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -600,9 +600,20 @@ type CnvSegment = {
 	cnvMaxCopynumber?: number
 	 */
 
-	/** if cnv is using qualitative categories. ui will show checkboxes for each category that's present
-	cnvCategories?:string[]
+	/** quick fix for gdc cnv tool:
+	if not set, mds3 tk & matrix will load cnv segments and show them together with ssm & fusion
+	if set: 
+		- for mds3 tk loading via mds3.load.js, only when tk.hardcodeCnvOnly=true, this will be loaded and shown
+		- 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
+		}
+	}
 }
 
 /*
@@ -946,6 +957,8 @@ export type WSImages = {
 	getWSImages?: (sampleName: string) => Promise<WSImage[]>
 	/**  ds supplied */
 	getWSIAnnotations?: (sampleName: string, wsiImage: string) => Promise<string[]>
+	/**  ds supplied */
+	getZoomInPoints?: (sampleName: string, wsiImage: string) => Promise<Array<[number, number]>>
 }
 
 /*** types supporting Termdb ***/
@@ -1166,9 +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"
@@ -1278,7 +1294,7 @@ type Termdb = {
 	/** Terms */
 	termIds?: TermIds
 	/** if true, backend is allowed to send sample names to client in charts */
-	displaySampleIds?: boolean
+	displaySampleIds?: (clientAuthResult: any) => boolean
 	converSampleIds?: boolean
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
@@ -1428,8 +1444,8 @@ 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[]
+	//terms  are shown in the dictionary based on term and user role.
+	isTermVisible?: (clientAuthResult: any, id: string) => boolean
 }
 
 type SampleType = {
@@ -1964,11 +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/routes/samplewsimages.ts

@@ -14,6 +14,7 @@ export type SampleWSImagesResponse = {
 export type WSImage = {
 	filename: string
 	overlays?: Array<string>
+	zoomInPoints?: Array<[number, number]>
 	metadata: string
 }