@sjcrh/proteinpaint-types 2.161.0 → 2.163.1

package/dist/{chunk-CSPVFAJ7.js → chunk-VQOCGHP2.js}

@@ -207,7 +207,7 @@ var validGRIN2Response = (input) => {
     const $io5 = (input3) => Array.isArray(input3.columns) && input3.columns.every((elem) => "object" === typeof elem && null !== elem && $io6(elem)) && (Array.isArray(input3.rows) && input3.rows.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && $io7(elem2))));
     const $io6 = (input3) => "string" === typeof input3.label && "boolean" === typeof input3.sortable;
     const $io7 = (input3) => "string" === typeof input3.value || "number" === typeof input3.value;
-    const $io8 = (input3) => "number" === typeof input3.processingTime && "number" === typeof input3.grin2Time && "number" === typeof input3.plottingTime && "number" === typeof input3.totalTime;
+    const $io8 = (input3) => "string" === typeof input3.processingTime && "string" === typeof input3.grin2Time && "string" === typeof input3.plottingTime && "string" === typeof input3.totalTime;
     const $io9 = (input3) => (void 0 === input3.totalSamples || "number" === typeof input3.totalSamples) && (void 0 === input3.processedSamples || "number" === typeof input3.processedSamples) && (void 0 === input3.failedSamples || "number" === typeof input3.failedSamples) && (void 0 === input3.failedFiles || Array.isArray(input3.failedFiles) && input3.failedFiles.every((elem) => "object" === typeof elem && null !== elem && $io10(elem))) && (void 0 === input3.totalLesions || "number" === typeof input3.totalLesions) && (void 0 === input3.processedLesions || "number" === typeof input3.processedLesions) && (void 0 === input3.unprocessedSamples || "number" === typeof input3.unprocessedSamples) && (void 0 === input3.lesionCounts || "object" === typeof input3.lesionCounts && null !== input3.lesionCounts && false === Array.isArray(input3.lesionCounts) && $io11(input3.lesionCounts));
     const $io10 = (input3) => "string" === typeof input3.sampleName && "string" === typeof input3.filePath && "string" === typeof input3.error;
     const $io11 = (input3) => (void 0 === input3.total || "number" === typeof input3.total) && (void 0 === input3.byType || "object" === typeof input3.byType && null !== input3.byType && false === Array.isArray(input3.byType) && $io12(input3.byType));
@@ -436,21 +436,21 @@ var validGRIN2Response = (input) => {
         expected: "(number | string)",
         value: input3.value
       })].every((flag) => flag);
-      const $vo8 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.processingTime || $report(_exceptionable2, {
+      const $vo8 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.processingTime || $report(_exceptionable2, {
         path: _path2 + ".processingTime",
-        expected: "number",
+        expected: "string",
         value: input3.processingTime
-      }), "number" === typeof input3.grin2Time || $report(_exceptionable2, {
+      }), "string" === typeof input3.grin2Time || $report(_exceptionable2, {
         path: _path2 + ".grin2Time",
-        expected: "number",
+        expected: "string",
         value: input3.grin2Time
-      }), "number" === typeof input3.plottingTime || $report(_exceptionable2, {
+      }), "string" === typeof input3.plottingTime || $report(_exceptionable2, {
         path: _path2 + ".plottingTime",
-        expected: "number",
+        expected: "string",
         value: input3.plottingTime
-      }), "number" === typeof input3.totalTime || $report(_exceptionable2, {
+      }), "string" === typeof input3.totalTime || $report(_exceptionable2, {
         path: _path2 + ".totalTime",
-        expected: "number",
+        expected: "string",
         value: input3.totalTime
       })].every((flag) => flag);
       const $vo9 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.totalSamples || "number" === typeof input3.totalSamples || $report(_exceptionable2, {

package/dist/grin2.js

@@ -2,7 +2,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-CSPVFAJ7.js";
+} from "./chunk-VQOCGHP2.js";
 import "./chunk-YNHC5SXO.js";
 export {
   GRIN2Payload,

package/dist/index.js

@@ -217,7 +217,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-CSPVFAJ7.js";
+} from "./chunk-VQOCGHP2.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.161.0",
+  "version": "2.163.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -384,19 +384,12 @@ type SvFusion = {
 }
 
 type SingleSampleMutationQuery = {
-	/** for native ds, each file should contain a stringified json array with elements below
-	see file server/test/tp/files/hg38/TermdbTest/mutationpersample/3318 for example
-	for non-native ds, the getter should return an json array with same structure
+	/** ds supplied getter
+	returns same json array as native. see example below
 	*/
-	src: 'native' | 'gdcapi' | string
-	/** which property of client mutation object to retrieve sample identifier for
-	 * querying single sample data with */
+	get?: (f: any) => void
+	/** which property of client mutation object to retrieve sample identifier for querying single sample data with */
 	sample_id_key: string
-	/** only required for src=native
-	folder contains a set of files, one file per sample, file named by sample name
-	each file contains a stringified json array of mutation/cnv/sv entries (aka mlst)
-	*/
-	folder?: string
 	/** disco plot will be launched when singleSampleMutation is enabled. supply customization options here */
 	discoPlot?: {
 		/** if true, disco plot will hide chrM, due to reason e.g. this dataset doesn't have data on chrM */
@@ -404,6 +397,16 @@ type SingleSampleMutationQuery = {
 		/** if true, filter mutations by predefined geneset by default */
 		prioritizeGeneLabelsByGeneSets?: true
 	}
+	/** rest of properties are required for native ds without ds-supplied getter
+	TODO migrate gdc to get() and delete .src=native
+	*/
+	src?: 'native' | 'gdcapi' | string
+	/** only required for src=native
+	folder contains a set of files, one file per sample, file named by sample name
+	each file contains a stringified json array of mutation/cnv/sv entries (aka mlst). see example
+	https://github.com/stjude/proteinpaint/blob/master/server/test/tp/files/hg38/TermdbTest/mutationpersample/3318
+	*/
+	folder?: string
 }
 
 type NIdataQuery = {
@@ -1405,6 +1408,12 @@ export type Termdb = {
 	}
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: (clientAuthResult: any) => boolean
+	/** ds-supplied async callback to build dictionary
+	argument: dataset object
+	sets termdb.q{}
+	no return
+	*/
+	buildDictionary?: (ds: any) => void
 	converSampleIds?: boolean
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
@@ -1566,6 +1575,25 @@ keep this setting here for reason of:
 	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
 	hiddenIds?: string[]
 	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
+	/** collections of numeric dictionary terms that are related and can be used together in some plots
+	 */
+	numericTermCollections?: NumericTermCollection[]
+}
+
+type NumericTermCollection = {
+	/** human readable name for this collection */
+	name: string
+	/** array of dictionary numeric term ids belonging to this collection */
+	termIds: string[]
+	/** array of branch term ids belonging to this collection */
+	branchIds: string[]
+	/** preconfigured cohort-level plots for this collection */
+	plots?: {
+		/** name of this plot */
+		name: string
+		/** json file path of this plot */
+		file: string
+	}[]
 }
 
 type SampleType = {
@@ -1605,6 +1633,8 @@ type Variant2Samples = GdcApi & {
 	variantkey: string
 	twLst?: Tw[]
 	sunburst_twLst?: Tw[]
+	/** ds-supplied getter */
+	getMutatedSamples?: (q: any, ds: any) => void
 }
 
 type MutationSet = {
@@ -1781,7 +1811,6 @@ export type Mds = BaseMds & {
 	cohort?: any
 	queries?: any
 	mutationAttribute?: any
-	dbFile?: string
 	version?: { label: string; link: string }
 	gene2mutcount?: any
 	locusAttribute?: any
@@ -1917,6 +1946,21 @@ export type Mds3 = BaseMds & {
 		data during post-processing */
 		postProcessDtFilter?: boolean
 	}
+	demoJwtInput?: {
+		[role: string]: {
+			datasets?: string[]
+			clientAuthResult?: // sjcares, panMB, SJLife
+			| ClientAuthResult
+				// profile
+				| {
+						[cohort: string]: ClientAuthResult
+				  }
+			// below will be assigned by /demoToken route handler if not specified
+			iat?: number // jwt issued at time, unix time in seconds
+			exp?: number // jwt expiration, unix time in seconds
+			email?: string
+		}
+	}
 	// !!! TODO: improve these type definitions below !!!
 	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any
@@ -1925,6 +1969,12 @@ export type Mds3 = BaseMds & {
 	}
 }
 
+export type ClientAuthResult = {
+	role?: string
+	datasets?: string[]
+	sites?: string[]
+}
+
 export type Mds3WithCohort = Mds3 & {
 	cohort: Cohort
 }

package/src/routes/grin2.ts

@@ -148,13 +148,13 @@ export type GRIN2Response = {
 	/** Timing info for the analysis */
 	timing?: {
 		/** Time taken to run data processing */
-		processingTime: number
+		processingTime: string
 		/** Time taken to run GRIN2 processing */
-		grin2Time: number
+		grin2Time: string
 		/** Time taken to run Manhattan plot generation */
-		plottingTime: number
+		plottingTime: string
 		/** Total time taken for the entire run */
-		totalTime: number
+		totalTime: string
 	}
 	/** Detailed processing summary */
 	processingSummary?: {