@sjcrh/proteinpaint-types 2.132.0 → 2.132.1-0

package/dist/{chunk-45AF7AQH.js → chunk-7YC2GEEO.js}

@@ -452,9 +452,10 @@ var validRunGRIN2Request = (input) => {
 var validRunGRIN2Response = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && true && true && (void 0 === input3.rustResult || "object" === typeof input3.rustResult && null !== input3.rustResult && $io1(input3.rustResult));
+    const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && true && true && (void 0 === input3.rustResult || "object" === typeof input3.rustResult && null !== input3.rustResult && $io1(input3.rustResult)) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io4(input3.timing));
     const $io1 = (input3) => Array.isArray(input3.successful_data) && input3.successful_data.every((elem) => Array.isArray(elem) && elem.every((elem2) => "string" === typeof elem2)) && (Array.isArray(input3.failed_files) && input3.failed_files.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && ("object" === typeof input3.summary && null !== input3.summary && ("number" === typeof input3.summary.total_files && "number" === typeof input3.summary.successful_files && "number" === typeof input3.summary.failed_files));
     const $io2 = (input3) => "string" === typeof input3.case_id && "string" === typeof input3.data_type && "string" === typeof input3.error_type && "string" === typeof input3.error_details && "number" === typeof input3.attempts_made;
+    const $io4 = (input3) => "number" === typeof input3.rustProcessingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.totalTime;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -480,6 +481,14 @@ var validRunGRIN2Response = (input) => {
         path: _path2 + ".rustResult",
         expected: "(RustGRIN2Result | undefined)",
         value: input3.rustResult
+      }), void 0 === input3.timing || ("object" === typeof input3.timing && null !== input3.timing || $report(_exceptionable2, {
+        path: _path2 + ".timing",
+        expected: "(__type | undefined)",
+        value: input3.timing
+      })) && $vo4(input3.timing, _path2 + ".timing", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".timing",
+        expected: "(__type | undefined)",
+        value: input3.timing
       })].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.successful_data) || $report(_exceptionable2, {
         path: _path2 + ".successful_data",
@@ -560,6 +569,19 @@ var validRunGRIN2Response = (input) => {
         expected: "number",
         value: input3.failed_files
       })].every((flag) => flag);
+      const $vo4 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.rustProcessingTime || $report(_exceptionable2, {
+        path: _path2 + ".rustProcessingTime",
+        expected: "number",
+        value: input3.rustProcessingTime
+      }), "number" === typeof input3.grin2Time || $report(_exceptionable2, {
+        path: _path2 + ".grin2Time",
+        expected: "number",
+        value: input3.grin2Time
+      }), "number" === typeof input3.totalTime || $report(_exceptionable2, {
+        path: _path2 + ".totalTime",
+        expected: "number",
+        value: input3.totalTime
+      })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "RunGRIN2Response",

package/dist/{chunk-3VVALC2P.js → chunk-QHN3YO6Q.js}

@@ -58,7 +58,7 @@ var validCategoriesRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $join = import_typia.createValidate.join;
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu5(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io12(input3.filter)) && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true;
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "string" === typeof input3.embedder && ("object" === typeof input3.tw && null !== input3.tw && $iu5(input3.tw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io12(input3.filter)) && true && (void 0 === input3.currentGeneNames || Array.isArray(input3.currentGeneNames) && input3.currentGeneNames.every((elem) => "string" === typeof elem)) && true;
     const $io1 = (input3) => (void 0 === input3.id || "string" === typeof input3.id) && (void 0 === input3.$id || "string" === typeof input3.$id) && (void 0 === input3.isAtomic || true === input3.isAtomic) && true && (void 0 === input3.settings || "object" === typeof input3.settings && null !== input3.settings && false === Array.isArray(input3.settings) && $io2(input3.settings)) && true && (void 0 === input3.minNumSamples || "number" === typeof input3.minNumSamples) && true && ("CatTWValues" === input3.type || "CatTWPredefinedGS" === input3.type || "CatTWCustomGS" === input3.type) && ("object" === typeof input3.q && null !== input3.q && false === Array.isArray(input3.q) && $iu6(input3.q)) && ("object" === typeof input3.term && null !== input3.term && $io15(input3.term));
     const $io2 = (input3) => Object.keys(input3).every((key) => {
       const value = input3[key];
@@ -356,7 +356,7 @@ var validCategoriesRequest = (input) => {
         path: _path2 + ".filter",
         expected: "(Filter | undefined)",
         value: input3.filter
-      }), void 0 === input3.currentGeneNames || (Array.isArray(input3.currentGeneNames) || $report(_exceptionable2, {
+      }), true, void 0 === input3.currentGeneNames || (Array.isArray(input3.currentGeneNames) || $report(_exceptionable2, {
         path: _path2 + ".currentGeneNames",
         expected: "(Array<string> | undefined)",
         value: input3.currentGeneNames

package/dist/gdc.grin2.js

@@ -5,7 +5,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-45AF7AQH.js";
+} from "./chunk-7YC2GEEO.js";
 import "./chunk-CNSSF43V.js";
 export {
   gdcGRIN2listPayload,

package/dist/index.js

@@ -112,7 +112,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-3VVALC2P.js";
+} from "./chunk-QHN3YO6Q.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
@@ -175,7 +175,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-45AF7AQH.js";
+} from "./chunk-7YC2GEEO.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-3VVALC2P.js";
+} from "./chunk-QHN3YO6Q.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.132.0",
+  "version": "2.132.1-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -910,6 +910,13 @@ type Mds3Queries = {
 	snvindel?: SnvIndelQuery
 	svfusion?: SvFusion
 	cnv?: CnvSegmentQuery
+	/** gene-level cnv, only available on gdc; query by gene symbol, ds must define getter
+	 */
+	geneCnv?: {
+		bygene: {
+			get: (q: any) => any
+		}
+	}
 	trackLst?: TrackLst
 	ld?: LdQuery
 	defaultCoord?: string
@@ -928,11 +935,6 @@ type Mds3Queries = {
 		file: string
 	}
 	singleCell?: SingleCellQuery
-	geneCnv?: {
-		bygene?: {
-			gdcapi: true
-		}
-	}
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
 	/** depreciated. replaced by WSImages */
@@ -2034,6 +2036,23 @@ export type Mds3 = BaseMds & {
 	validate_filter0?: (f: any) => void
 	ssm2canonicalisoform?: GdcApi
 	variant2samples?: Variant2Samples
+	/** disables switching to genomic mode for the protein view mds3 tk of this ds
+	works by preventing block gmmode menu from showing "genomic" option
+	is only passed via mds3 adhoc ds copy, but not termdbConfig
+	for lack of a better place to put this attribute, as it's not appropriate to put in queries.snvindel{}
+	as snvindel is optional so even a cnv-only ds can disable genomic mode
+	*/
+	noGenomicMode4lollipopTk?: true
+	/** if ds.queries{} exists, server launch adds this convenient getter to wrap multiple queries data types
+	 */
+	mayGetGeneVariantData?: (f: any) => void
+	/** optional key-value pairs to pass to genomic queries getter when called in mayGetGeneVariantData() 
+	- only used in mayGetGeneVariantData! not in mds3.load.js
+	- for now only passed to snvindel.*.get and not yet other data types; add when needed
+	the param contents will be assessed by ds specific getter
+	this is serverside only, not passed to termdbConfig
+	*/
+	mayGetGeneVariantDataParam?: { [key: string]: any }
 	// !!! TODO: improve these type definitions below !!!
 	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any

package/src/routes/gdc.grin2.ts

@@ -160,8 +160,17 @@ export type RunGRIN2Response = {
 	download?: any
 	/** Table of top genes indentified by analysis */
 	topGeneTable?: any
-	/** Data from Rust for making the failed files div */
+	/** Data from Rust for making the analysis summary div */
 	rustResult?: RustGRIN2Result
+	/** Timing info from nodejs */
+	timing?: {
+		/** Time taken to run Rust processing */
+		rustProcessingTime: number
+		/** Time taken to run GRIN2 processing */
+		grin2Time: number
+		/** Total time taken for the entire run */
+		totalTime: number
+	}
 }
 /**
  * Route payload definitions for type checking

package/src/routes/termdb.categories.ts

@@ -9,6 +9,7 @@ export type CategoriesRequest = {
 	/** termwrapper object */
 	tw: TermWrapper
 	filter?: Filter
+	filter0?: any
 	/** quick fix only for gdc */
 	currentGeneNames?: string[]
 	/** optional property added by mds3 tk, to limit to cases mutated in this region */

package/src/vocab.ts

@@ -13,6 +13,7 @@ VocabApi
 
 export type VocabApi = {
 	termdbConfig: any
+	state?: any
 	//Methods
 	cacheTermQ: (term: Term, q: any) => any
 	findTerm: (f: string, activeCohort: number, usecase: UseCase, x: string) => { lst: Term[] }