@sjcrh/proteinpaint-types 2.145.1-1 → 2.146.0

package/dist/{chunk-6SOULHNE.js → chunk-V2TEJZ2V.js}

@@ -73,7 +73,7 @@ var validBoxPlotRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $join = import_typia.createValidate.join;
-    const $io0 = (input3) => "object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw) && "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.isLogScale && "boolean" === typeof input3.orderByMedian && (void 0 === input3.overlayTw || "object" === typeof input3.overlayTw && null !== input3.overlayTw && $iu6(input3.overlayTw)) && (void 0 === input3.divideTw || "object" === typeof input3.divideTw && null !== input3.divideTw && $iu6(input3.divideTw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && true;
+    const $io0 = (input3) => "object" === typeof input3.tw && null !== input3.tw && $iu6(input3.tw) && "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.isLogScale && "boolean" === typeof input3.orderByMedian && (void 0 === input3.overlayTw || "object" === typeof input3.overlayTw && null !== input3.overlayTw && $iu6(input3.overlayTw)) && (void 0 === input3.divideTw || "object" === typeof input3.divideTw && null !== input3.divideTw && $iu6(input3.divideTw)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io6(input3.filter)) && true && true && (void 0 === input3.removeOutliers || "boolean" === typeof input3.removeOutliers);
     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 && ("object" === typeof input3.term && null !== input3.term && $io3(input3.term)) && ("object" === typeof input3.q && null !== input3.q && $io40(input3.q)) && "CatTWValues" === input3.type;
     const $io2 = (input3) => Object.keys(input3).every((key) => {
       const value = input3[key];
@@ -371,7 +371,11 @@ var validBoxPlotRequest = (input) => {
         path: _path2 + ".filter",
         expected: "(Filter | undefined)",
         value: input3.filter
-      }), true, true].every((flag) => flag);
+      }), true, true, void 0 === input3.removeOutliers || "boolean" === typeof input3.removeOutliers || $report(_exceptionable2, {
+        path: _path2 + ".removeOutliers",
+        expected: "(boolean | undefined)",
+        value: input3.removeOutliers
+      })].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.id || "string" === typeof input3.id || $report(_exceptionable2, {
         path: _path2 + ".id",
         expected: "(string | undefined)",
@@ -4172,7 +4176,7 @@ var validBoxPlotResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $join = import_typia.createValidate.join;
-    const $io0 = (input3) => (void 0 === input3.absMin || "number" === typeof input3.absMin) && (void 0 === input3.absMax || "number" === typeof input3.absMax) && ("object" === typeof input3.charts && null !== input3.charts && false === Array.isArray(input3.charts) && $io1(input3.charts)) && (null === input3.uncomputableValues || Array.isArray(input3.uncomputableValues) && input3.uncomputableValues.every((elem) => "object" === typeof elem && null !== elem && $io8(elem))) && true;
+    const $io0 = (input3) => (void 0 === input3.absMin || "number" === typeof input3.absMin) && (void 0 === input3.absMax || "number" === typeof input3.absMax) && ("object" === typeof input3.charts && null !== input3.charts && false === Array.isArray(input3.charts) && $io1(input3.charts)) && (null === input3.uncomputableValues || Array.isArray(input3.uncomputableValues) && input3.uncomputableValues.every((elem) => "object" === typeof elem && null !== elem && $io8(elem))) && true && true;
     const $io1 = (input3) => Object.keys(input3).every((key) => {
       const value = input3[key];
       if (void 0 === value)
@@ -4226,7 +4230,7 @@ var validBoxPlotResponse = (input) => {
         path: _path2 + ".uncomputableValues",
         expected: "(Array<__type>.o2 | null)",
         value: input3.uncomputableValues
-      }), true].every((flag) => flag);
+      }), true, true].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
         const value = input3[key];
         if (void 0 === value)

package/dist/index.js

@@ -1,3 +1,8 @@
+import {
+  tilePayload,
+  validTileRequest,
+  validTileResponse
+} from "./chunk-HQV2A7JV.js";
 import {
   validWSImagesRequest,
   validWSImagesResponse,
@@ -8,6 +13,11 @@ import {
   validWSISamplesResponse,
   wsiSamplesPayload
 } from "./chunk-2744ACBX.js";
+import {
+  termdbSingleCellDataPayload,
+  validTermdbSingleCellDataRequest,
+  validTermdbSingleCellDataResponse
+} from "./chunk-4ZMQ5CTL.js";
 import {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,
@@ -44,10 +54,10 @@ import {
   violinPayload
 } from "./chunk-MMFL6N5M.js";
 import {
-  tilePayload,
-  validTileRequest,
-  validTileResponse
-} from "./chunk-HQV2A7JV.js";
+  numericCategoriesPayload,
+  validNumericCategoriesRequest,
+  validNumericCategoriesResponse
+} from "./chunk-4MLQS6N7.js";
 import {
   percentilePayload,
   validPercentileRequest,
@@ -83,21 +93,21 @@ import {
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
 } from "./chunk-EYKGJDKU.js";
-import {
-  termdbSingleCellDataPayload,
-  validTermdbSingleCellDataRequest,
-  validTermdbSingleCellDataResponse
-} from "./chunk-4ZMQ5CTL.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-6SOULHNE.js";
+} from "./chunk-V2TEJZ2V.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
 } from "./chunk-5KADNZH2.js";
+import {
+  ChatPayload,
+  validChatRequest,
+  validChatResponse
+} from "./chunk-DBSRGRXR.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
@@ -123,11 +133,6 @@ import {
   validFilterTermValuesRequest,
   validFilterTermValuesResponse
 } from "./chunk-CQXBQY2H.js";
-import {
-  numericCategoriesPayload,
-  validNumericCategoriesRequest,
-  validNumericCategoriesResponse
-} from "./chunk-4MLQS6N7.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
@@ -147,7 +152,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-PPPSDO6G.js";
+} from "./chunk-2BHWLFKE.js";
 import {
   saveWSIAnnotationPayload,
   validSaveWSIAnnotationRequest,
@@ -255,7 +260,7 @@ import {
   aiProjectSelectedWSImagesResponsePayload,
   validAiProjectSelectedWSImagesRequest,
   validAiProjectSelectedWSImagesResponse
-} from "./chunk-NO2EZKW4.js";
+} from "./chunk-75OHIZMS.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
@@ -285,6 +290,7 @@ import {
 } from "./chunk-4VEXL32Q.js";
 import "./chunk-YNHC5SXO.js";
 export {
+  ChatPayload,
   CorrelationVolcanoPayload,
   FilterTermValuesPayload,
   GRIN2Payload,
@@ -353,6 +359,8 @@ export {
   validBurdenResponse,
   validCategoriesRequest,
   validCategoriesResponse,
+  validChatRequest,
+  validChatResponse,
   validClearWSImagesSessionsRequest,
   validClearWSImagesSessionsResponse,
   validCorrelationVolcanoRequest,

package/dist/samplewsimages.js

@@ -2,7 +2,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-PPPSDO6G.js";
+} from "./chunk-2BHWLFKE.js";
 import "./chunk-YNHC5SXO.js";
 export {
   sampleWSImagesPayload,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-6SOULHNE.js";
+} from "./chunk-V2TEJZ2V.js";
 import "./chunk-YNHC5SXO.js";
 export {
   boxplotPayload,

package/dist/termdb.chat.js

@@ -0,0 +1,11 @@
+import {
+  ChatPayload,
+  validChatRequest,
+  validChatResponse
+} from "./chunk-DBSRGRXR.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  ChatPayload,
+  validChatRequest,
+  validChatResponse
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.145.1-1",
+  "version": "2.146.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1011,8 +1011,14 @@ type Mds3Queries = {
 	DZImages?: DZImages
 	WSImages?: WSImages
 	images?: Images
+	chat?: any
 }
 
+/** chat app support
+type Chat = {
+}
+ */
+
 /** non-zoom small images
 iamge file to sample mapping is stored in images table
 */
@@ -1066,8 +1072,6 @@ export type WSImages = {
 	/**  ds supplied */
 	getWSIAnnotations?: (projectId: string, wsiImage: string) => Promise<string[]>
 	/**  ds supplied */
-	makeGeoJson?: (sampleId: string, wsiImage: string) => void
-	/**  ds supplied */
 	getWSIPredictionOverlay?: (wsiImage: string) => Promise<string | undefined>
 	/**  ds supplied */
 	getWSIUncertaintyOverlay?: (wsiImage: string) => Promise<string | undefined>

package/src/index.ts

@@ -22,7 +22,6 @@ export * from './routes/gdc.maf.ts'
 export * from './routes/gdc.mafBuild.ts'
 export * from './routes/gdc.grin2.ts'
 export * from './routes/grin2.ts'
-export * from './routes/termdb.topMutatedGenes.ts'
 export * from './routes/genelookup.ts'
 export * from './routes/genesetEnrichment.ts'
 export * from './routes/genesetOverrepresentation.ts'
@@ -30,6 +29,7 @@ export * from './routes/healthcheck.ts'
 export * from './routes/hicdata.ts'
 export * from './routes/hicgenome.ts'
 export * from './routes/hicstat.ts'
+export * from './routes/img.ts'
 export * from './routes/isoformlst.ts'
 export * from './routes/ntseq.ts'
 export * from './routes/pdomain.ts'
@@ -38,6 +38,7 @@ export * from './routes/saveWSIAnnotation.ts'
 export * from './routes/snp.ts'
 export * from './routes/termdb.boxplot.ts'
 export * from './routes/termdb.categories.ts'
+export * from './routes/termdb.chat.ts'
 export * from './routes/termdb.cluster.ts'
 export * from './routes/termdb.cohort.summary.ts'
 export * from './routes/termdb.cohorts.ts'
@@ -48,13 +49,13 @@ export * from './routes/termdb.percentile.ts'
 export * from './routes/termdb.rootterm.ts'
 export * from './routes/termdb.termchildren.ts'
 export * from './routes/termdb.sampleImages.ts'
-export * from './routes/img.ts'
 export * from './routes/termdb.singlecellData.ts'
 export * from './routes/termdb.singlecellDEgenes.ts'
 export * from './routes/termdb.singlecellSamples.ts'
 export * from './routes/termdb.singleSampleMutation.ts'
 export * from './routes/termdb.termsbyids.ts'
 export * from './routes/termdb.termchildren.ts'
+export * from './routes/termdb.topMutatedGenes.ts'
 export * from './routes/termdb.topTermsByType.ts'
 export * from './routes/termdb.topVariablyExpressedGenes.ts'
 export * from './routes/termdb.violin.ts'

package/src/routes/aiProjectSelectedWSImages.ts

@@ -13,6 +13,22 @@ export type AiProjectSelectedWSImagesResponse = {
 	wsimages: WSImage[]
 }
 
+// TODO move to another class
+export interface TileSelection {
+	zoomCoordinates: [number, number]
+	class?: string
+}
+
+export interface Annotation extends TileSelection {
+	class: string
+}
+
+export interface Prediction extends TileSelection {
+	type: string
+	class: string
+	uncertainty: number
+}
+
 export const aiProjectSelectedWSImagesResponsePayload: RoutePayload = {
 	request: {
 		typeId: 'AiProjectSelectedWSImagesRequest'

package/src/routes/samplewsimages.ts

@@ -1,5 +1,6 @@
 import type { RoutePayload } from './routeApi.ts'
 import type { WSIClass } from '../dataset.ts'
+import type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'
 
 export type SampleWSImagesRequest = {
 	genome: string
@@ -12,13 +13,11 @@ export type SampleWSImagesResponse = {
 	sampleWSImages: WSImage[]
 }
 
-export type WSImage = {
+export class WSImage {
 	id?: number
 	filename: string
-	// TODO remove when it's verified
-	annotationsAndPredictionsOverlay?: string
-	predictionLayers?: Array<string>
 	metadata?: string
+	predictionLayers?: Array<string>
 	annotations?: Array<Annotation>
 	predictions?: Array<Prediction>
 	classes?: Array<WSIClass>
@@ -28,23 +27,10 @@ export type WSImage = {
 	activePatchColor?: string
 	/** Tile size in pixels needed for AI scripts */
 	tileSize?: number
-}
-
-export type Annotation = {
-	zoomCoordinates: [number, number]
-	class: string
-}
-
-export type Prediction = {
-	zoomCoordinates: [number, number]
-	type: string
-	class: string
-	uncertainty: number
-}
 
-export type TileSelection = {
-	zoomCoordinates: [number, number]
-	class?: string
+	constructor(filename: string) {
+		this.filename = filename
+	}
 }
 
 export const sampleWSImagesPayload: RoutePayload = {

package/src/routes/termdb.boxplot.ts

@@ -20,6 +20,7 @@ export type BoxPlotRequest = {
 	filter?: Filter
 	filter0?: any
 	__protected__: any
+	removeOutliers?: boolean
 }
 
 export type BoxPlotResponse = {
@@ -34,6 +35,7 @@ export type BoxPlotResponse = {
 	/** Categories not shown in the final plot */
 	uncomputableValues: { label: string; value: number }[] | null
 	error?: any
+	descrStats: any
 }
 
 // chart containing a set of boxplots

package/src/routes/termdb.chat.ts

@@ -0,0 +1,58 @@
+import type { Filter } from '../filter.ts'
+import type { RoutePayload } from './routeApi.js'
+
+/** */
+export type ChatRequest = {
+	genome: string
+	dslabel: string
+	filter?: Filter
+	filter0?: any // gdc
+	/** user prompt */
+	prompt: string
+	__protected__: any
+}
+
+export type numeric_filter = {
+	lower: number
+	upper: number
+}
+
+export type categorical_filter = {
+	name: string
+}
+
+export type filter_variable = {
+	name: string
+	variable_type: 'float' | 'categories'
+	cutoff: numeric_filter | categorical_filter
+}
+
+export type summary = {
+	group_categories: string
+	overlay?: string
+	divide_by?: string
+	filter?: filter_variable
+}
+
+export type plot = {
+	/** Different chart types currently supported by the AI chatbot, will add types for the other charts when they will be implemented */
+	chartType: summary | 'survival' | 'hierarchial' | 'snv_indel' | 'cnv' | 'variant_calling' | 'none' | 'dge'
+}
+
+export type ChatResponse = {
+	type: 'html' | 'plot'
+	/** when type=html, this value is set meaning server returns a chat response */
+	html?: string
+	/** when type=plot. value is json */
+	plot?: any
+}
+
+export const ChatPayload: RoutePayload = {
+	request: {
+		typeId: 'ChatRequest'
+	},
+	response: {
+		typeId: 'ChatResponse'
+	}
+	//examples: []
+}