@sjcrh/proteinpaint-types 2.163.0 → 2.164.0

package/dist/aiProjectSelectedWSImages.js

@@ -2,7 +2,7 @@ import {
   aiProjectSelectedWSImagesResponsePayload,
   validAiProjectSelectedWSImagesRequest,
   validAiProjectSelectedWSImagesResponse
-} from "./chunk-225Q2ZUA.js";
+} from "./chunk-C6EUYXHJ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   aiProjectSelectedWSImagesResponsePayload,

package/dist/{chunk-225Q2ZUA.js → chunk-C6EUYXHJ.js}

@@ -74,7 +74,7 @@ var validAiProjectSelectedWSImagesResponse = (input) => {
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.wsimages) && input3.wsimages.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
     const $io1 = (input3) => (void 0 === input3.id || "number" === typeof input3.id) && "string" === typeof input3.filename && (void 0 === input3.metadata || "string" === typeof input3.metadata) && (void 0 === input3.predictionLayers || Array.isArray(input3.predictionLayers) && input3.predictionLayers.every((elem) => "string" === typeof elem)) && (void 0 === input3.annotations || Array.isArray(input3.annotations) && input3.annotations.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.predictions || Array.isArray(input3.predictions) && input3.predictions.every((elem) => "object" === typeof elem && null !== elem && $io3(elem))) && (void 0 === input3.classes || Array.isArray(input3.classes) && input3.classes.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && true && (void 0 === input3.activePatchColor || "string" === typeof input3.activePatchColor) && (void 0 === input3.tileSize || "number" === typeof input3.tileSize);
-    const $io2 = (input3) => "string" === typeof input3["class"] && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
+    const $io2 = (input3) => "string" === typeof input3["class"] && (void 0 === input3.timestamp || "string" === typeof input3.timestamp) && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
     const $io3 = (input3) => "string" === typeof input3["class"] && "number" === typeof input3.uncertainty && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
     const $io4 = (input3) => "number" === typeof input3.id && "string" === typeof input3.key_shortcut && "string" === typeof input3.label && "string" === typeof input3.color;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
@@ -184,6 +184,10 @@ var validAiProjectSelectedWSImagesResponse = (input) => {
         path: _path2 + '["class"]',
         expected: "string",
         value: input3["class"]
+      }), void 0 === input3.timestamp || "string" === typeof input3.timestamp || $report(_exceptionable2, {
+        path: _path2 + ".timestamp",
+        expected: "(string | undefined)",
+        value: input3.timestamp
       }), (Array.isArray(input3.zoomCoordinates) || $report(_exceptionable2, {
         path: _path2 + ".zoomCoordinates",
         expected: "[number, number]",

package/dist/{chunk-ETMCI34A.js → chunk-ZFEV22KC.js}

@@ -66,7 +66,7 @@ var validSampleWSImagesResponse = (input) => {
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.sampleWSImages) && input3.sampleWSImages.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
     const $io1 = (input3) => (void 0 === input3.id || "number" === typeof input3.id) && "string" === typeof input3.filename && (void 0 === input3.metadata || "string" === typeof input3.metadata) && (void 0 === input3.predictionLayers || Array.isArray(input3.predictionLayers) && input3.predictionLayers.every((elem) => "string" === typeof elem)) && (void 0 === input3.annotations || Array.isArray(input3.annotations) && input3.annotations.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.predictions || Array.isArray(input3.predictions) && input3.predictions.every((elem) => "object" === typeof elem && null !== elem && $io3(elem))) && (void 0 === input3.classes || Array.isArray(input3.classes) && input3.classes.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && true && (void 0 === input3.activePatchColor || "string" === typeof input3.activePatchColor) && (void 0 === input3.tileSize || "number" === typeof input3.tileSize);
-    const $io2 = (input3) => "string" === typeof input3["class"] && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
+    const $io2 = (input3) => "string" === typeof input3["class"] && (void 0 === input3.timestamp || "string" === typeof input3.timestamp) && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
     const $io3 = (input3) => "string" === typeof input3["class"] && "number" === typeof input3.uncertainty && (Array.isArray(input3.zoomCoordinates) && (input3.zoomCoordinates.length === 2 && "number" === typeof input3.zoomCoordinates[0] && "number" === typeof input3.zoomCoordinates[1]));
     const $io4 = (input3) => "number" === typeof input3.id && "string" === typeof input3.key_shortcut && "string" === typeof input3.label && "string" === typeof input3.color;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
@@ -176,6 +176,10 @@ var validSampleWSImagesResponse = (input) => {
         path: _path2 + '["class"]',
         expected: "string",
         value: input3["class"]
+      }), void 0 === input3.timestamp || "string" === typeof input3.timestamp || $report(_exceptionable2, {
+        path: _path2 + ".timestamp",
+        expected: "(string | undefined)",
+        value: input3.timestamp
       }), (Array.isArray(input3.zoomCoordinates) || $report(_exceptionable2, {
         path: _path2 + ".zoomCoordinates",
         expected: "[number, number]",

package/dist/index.js

@@ -187,7 +187,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-ETMCI34A.js";
+} from "./chunk-ZFEV22KC.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,
@@ -277,7 +277,7 @@ import {
   aiProjectSelectedWSImagesResponsePayload,
   validAiProjectSelectedWSImagesRequest,
   validAiProjectSelectedWSImagesResponse
-} from "./chunk-225Q2ZUA.js";
+} from "./chunk-C6EUYXHJ.js";
 import {
   aiProjectTrainModelPayload,
   validAIProjectTrainModelRequest,

package/dist/samplewsimages.js

@@ -2,7 +2,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-ETMCI34A.js";
+} from "./chunk-ZFEV22KC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   sampleWSImagesPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.163.0",
+  "version": "2.164.0",
   "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 = {
@@ -1047,6 +1050,9 @@ export type WSImages = {
 	/** dynamically added on launch with built in logic */
 	deleteWSIAnnotation?: (annotation: DeleteWSIAnnotationRequest) => Promise<void>
 
+	/** dynamically added on launch with built in logic - returns all image filenames for a project */
+	getAllWSImages?: (projectId: string) => Promise<string[]>
+
 	/** either ds supplied or dynamically added on launch with built in logic (retrieve the sample list from the wsimages table) */
 	getSamples?: () => Promise<Array<WSISample>>
 	/** either ds supplied or dynamically added on launch with built in logic */
@@ -1572,6 +1578,25 @@ 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 = {
@@ -1611,6 +1636,8 @@ type Variant2Samples = GdcApi & {
 	variantkey: string
 	twLst?: Tw[]
 	sunburst_twLst?: Tw[]
+	/** ds-supplied getter */
+	getMutatedSamples?: (q: any, ds: any) => void
 }
 
 type MutationSet = {
@@ -1922,6 +1949,21 @@ 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
@@ -1930,6 +1972,12 @@ export type Mds3 = BaseMds & {
 	}
 }
 
+export type ClientAuthResult = {
+	role?: string
+	datasets?: string[]
+	sites?: string[]
+}
+
 export type Mds3WithCohort = Mds3 & {
 	cohort: Cohort
 }

package/src/routes/aiProjectSelectedWSImages.ts

@@ -21,6 +21,7 @@ export interface TileSelection {
 
 export interface Annotation extends TileSelection {
 	class: string
+	timestamp?: string
 }
 
 export interface Prediction extends TileSelection {