@sjcrh/proteinpaint-types 2.145.2 → 2.146.1

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,
@@ -83,11 +93,6 @@ import {
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
 } from "./chunk-EYKGJDKU.js";
-import {
-  termdbSingleCellDataPayload,
-  validTermdbSingleCellDataRequest,
-  validTermdbSingleCellDataResponse
-} from "./chunk-4ZMQ5CTL.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
@@ -98,6 +103,11 @@ import {
   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.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": "2.145.2",
+  "version": "2.146.1",
   "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>
@@ -1299,6 +1303,8 @@ type Matrix = {
 	legendGrpFilter?: any
 	/** filter to hide categories or mclass, e.g. hide male, hide MISSENSE */
 	legendValueFilter?: any
+	/** local filter to limit samples in matrix/hiercluster, merged with this.state.termfilter.filter when querying server */
+	localFilter?: any
 	/** matrix criteria for a CNV alteration */
 	cnvCutoffs?: any
 }

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.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: []
+}