@sjcrh/proteinpaint-types 2.146.4-1 → 2.147.2-0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-4VEXL32Q.js";
+} from "./chunk-75GS5ZG5.js";
 import "./chunk-YNHC5SXO.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -1,3 +1,8 @@
+import {
+  validViolinRequest,
+  validViolinResponse,
+  violinPayload
+} from "./chunk-MMFL6N5M.js";
 import {
   tilePayload,
   validTileRequest,
@@ -13,6 +18,11 @@ import {
   validWSISamplesResponse,
   wsiSamplesPayload
 } from "./chunk-2744ACBX.js";
+import {
+  termdbSingleCellDEgenesPayload,
+  validTermdbSingleCellDEgenesRequest,
+  validTermdbSingleCellDEgenesResponse
+} from "./chunk-EYKGJDKU.js";
 import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
@@ -32,7 +42,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-GCAZSDCW.js";
+} from "./chunk-WL7ZVGZS.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -42,17 +52,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-74B7B2CV.js";
+} from "./chunk-KQNLROUN.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
 } from "./chunk-OZ3CVAFP.js";
 import {
-  validViolinRequest,
-  validViolinResponse,
-  violinPayload
-} from "./chunk-MMFL6N5M.js";
+  FilterTermValuesPayload,
+  validFilterTermValuesRequest,
+  validFilterTermValuesResponse
+} from "./chunk-CQXBQY2H.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
@@ -62,7 +72,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-4DNCZQOB.js";
+} from "./chunk-TTUU5XQC.js";
 import {
   ProfileFormScoresPayload,
   validProfileFormScoresRequest,
@@ -89,20 +99,20 @@ import {
   validTermdbSingleSampleMutationResponse
 } from "./chunk-UGYLBYUU.js";
 import {
-  termdbSingleCellDEgenesPayload,
-  validTermdbSingleCellDEgenesRequest,
-  validTermdbSingleCellDEgenesResponse
-} from "./chunk-EYKGJDKU.js";
+  diffExpPayload,
+  validDERequest,
+  validDEResponse
+} from "./chunk-CP26DR4V.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-NBV7HYBA.js";
+} from "./chunk-3SKFYOKV.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-5KADNZH2.js";
+} from "./chunk-RA7IEGS4.js";
 import {
   ChatPayload,
   validChatRequest,
@@ -112,7 +122,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-C246BWQE.js";
+} from "./chunk-5MGSKBUU.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -127,12 +137,12 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-G5KSPYQG.js";
+} from "./chunk-4SJC57Y6.js";
 import {
-  FilterTermValuesPayload,
-  validFilterTermValuesRequest,
-  validFilterTermValuesResponse
-} from "./chunk-CQXBQY2H.js";
+  imgPayload,
+  validimgRequest,
+  validimgResponse
+} from "./chunk-PTE2I7DF.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
@@ -152,7 +162,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-2BHWLFKE.js";
+} from "./chunk-ETMCI34A.js";
 import {
   saveWSIAnnotationPayload,
   validSaveWSIAnnotationRequest,
@@ -164,10 +174,10 @@ import {
   validSnpResponse
 } from "./chunk-7MUISZHS.js";
 import {
-  diffExpPayload,
-  validDERequest,
-  validDEResponse
-} from "./chunk-CP26DR4V.js";
+  geneLookupPayload,
+  validGeneLookupRequest,
+  validGeneLookupResponse
+} from "./chunk-K4FSDTDW.js";
 import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
@@ -204,10 +214,10 @@ import {
   validHicstatResponse
 } from "./chunk-6GKG55BT.js";
 import {
-  imgPayload,
-  validimgRequest,
-  validimgResponse
-} from "./chunk-PTE2I7DF.js";
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+} from "./chunk-75GS5ZG5.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -246,11 +256,6 @@ import {
   validGdcMafBuildRequest,
   validGdcMafBuildResponse
 } from "./chunk-2BCLGYAG.js";
-import {
-  geneLookupPayload,
-  validGeneLookupRequest,
-  validGeneLookupResponse
-} from "./chunk-K4FSDTDW.js";
 import {
   aiProjectAdminPayload,
   validAIProjectAdminRequest,
@@ -260,12 +265,17 @@ import {
   aiProjectSelectedWSImagesResponsePayload,
   validAiProjectSelectedWSImagesRequest,
   validAiProjectSelectedWSImagesResponse
-} from "./chunk-75OHIZMS.js";
+} from "./chunk-225Q2ZUA.js";
+import {
+  aiProjectTrainModelPayload,
+  validAIProjectTrainModelRequest,
+  validAIProjectTrainModelResponse
+} from "./chunk-UYJA4UM7.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-7ICZFAGK.js";
+} from "./chunk-KSVIBMFQ.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -283,11 +293,6 @@ import {
 import {
   clearWSImagesSessionsPayload
 } from "./chunk-RPX4TVMD.js";
-import {
-  CorrelationVolcanoPayload,
-  validCorrelationVolcanoRequest,
-  validCorrelationVolcanoResponse
-} from "./chunk-4VEXL32Q.js";
 import "./chunk-YNHC5SXO.js";
 export {
   ChatPayload,
@@ -299,6 +304,7 @@ export {
   ProfileScoresPayload,
   aiProjectAdminPayload,
   aiProjectSelectedWSImagesResponsePayload,
+  aiProjectTrainModelPayload,
   boxplotPayload,
   brainImagingPayload,
   brainImagingSamplesPayload,
@@ -347,6 +353,8 @@ export {
   topMutatedGenePayload,
   validAIProjectAdminRequest,
   validAIProjectAdminResponse,
+  validAIProjectTrainModelRequest,
+  validAIProjectTrainModelResponse,
   validAiProjectSelectedWSImagesRequest,
   validAiProjectSelectedWSImagesResponse,
   validBoxPlotRequest,

package/dist/samplewsimages.js

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

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-NBV7HYBA.js";
+} from "./chunk-3SKFYOKV.js";
 import "./chunk-YNHC5SXO.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-5KADNZH2.js";
+} from "./chunk-RA7IEGS4.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-C246BWQE.js";
+} from "./chunk-5MGSKBUU.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-G5KSPYQG.js";
+} from "./chunk-4SJC57Y6.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-4DNCZQOB.js";
+} from "./chunk-TTUU5XQC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-GCAZSDCW.js";
+} from "./chunk-WL7ZVGZS.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-74B7B2CV.js";
+} from "./chunk-KQNLROUN.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.146.4-1",
+  "version": "2.147.2-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -3,6 +3,7 @@ import type { WSImage } from './routes/samplewsimages.ts'
 import type { WSISample } from './routes/wsisamples.ts'
 import type { SaveWSIAnnotationRequest } from './routes/saveWSIAnnotation.ts'
 import type { DeleteWSIAnnotationRequest } from './routes/deleteWSIAnnotation.ts'
+import type { Prediction } from './routes/aiProjectSelectedWSImages.ts'
 
 /*** General usage types ***/
 type FileObj = {
@@ -1068,15 +1069,15 @@ export type WSImages = {
 	/** either ds supplied or dynamically added on launch with built in logic */
 	getWSImages?: (sampleName: string) => Promise<WSImage[]>
 	/**  ds supplied */
-	getWSIPredictionPatches?: (projectId: string, wsiImage: string) => Promise<string[]>
+	getWSIPredictionPatches?: (projectId: string, wsiImage: string) => Promise<Prediction[]>
 	/**  ds supplied */
 	getWSIAnnotations?: (projectId: string, wsiImage: string) => Promise<string[]>
 	/**  ds supplied */
-	getWSIPredictionOverlay?: (wsiImage: string) => Promise<string | undefined>
-	/**  ds supplied */
-	getWSIUncertaintyOverlay?: (wsiImage: string) => Promise<string | undefined>
+	getPredictionLayers?: (projectId: string, wsiImage: string) => Promise<Map<string, string> | undefined>
 	/**  ds supplied */
 	getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
+	/**  ds supplied */
+	retrainModel?: (projectId: string) => Promise<void>
 }
 
 export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
@@ -1420,17 +1421,19 @@ export type Termdb = {
 	 * in order to minimize the ease of extracting identifiable information from aggregate data
 	 * in server response
 	 *
-	 * q            :   req.query as processed through app middleware (pre-parsed, may have req.body props, __protectec__, etc)
-	 *
-	 * data{
-	 *   sampleCount:   the number of samples with matching data from one or more queried terms
-	 * }
-	 *
 	 * returns: {minSampleSize, canAccess}, see below
 	 */
 	checkAccessToSampleData?: (
+		/** req.query as processed through app middleware (pre-parsed, may have req.body props, __protectec__, etc) */
 		q: any,
-		data: { sampleCount: number }
+		data: {
+			/** the number of samples with matching data from one or more queried terms */
+			sampleCount: number
+			/** option to specify sample names that is accessible to the current user,
+			 * not using sample ID since portal embedder and token generator does not
+			 * know the internal sample ID-to-name mapping */
+			sampleNames?: string[]
+		}
 	) => {
 		/** the required minimum sample size for the current user,
 		 * may be dependent on login status or other context
@@ -1597,7 +1600,7 @@ keep this setting here for reason of:
 	}
 	//terms  are shown in the dictionary based on term and user role.
 	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
-	getAdditionalFilter?: (clientAuthResult: any, term: any) => Filter | undefined
+	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
 }
 
 type SampleType = {

package/src/index.ts

@@ -7,6 +7,7 @@ export * from './termdb.matrix.ts'
 export * from './routes/routeApi.ts'
 export * from './routes/aiProjectAdmin.ts'
 export * from './routes/aiProjectSelectedWSImages.ts'
+export * from './routes/aiProjectTrainModel.ts'
 export * from './routes/brainImaging.ts'
 export * from './routes/brainImagingSamples.ts'
 export * from './routes/burden.ts'
@@ -69,6 +70,7 @@ export * from './terms/numeric.ts'
 export * from './terms/geneVariant.ts'
 export * from './terms/geneExpression.ts'
 export * from './terms/metaboliteIntensity.ts'
+export * from './terms/qualitative.ts'
 export * from './terms/singleCellCellType.ts'
 export * from './terms/singleCellGeneExpression.ts'
 export * from './terms/snp.ts'

package/src/routes/aiProjectSelectedWSImages.ts

@@ -24,7 +24,6 @@ export interface Annotation extends TileSelection {
 }
 
 export interface Prediction extends TileSelection {
-	type: string
 	class: string
 	uncertainty: number
 }

package/src/routes/aiProjectTrainModel.ts

@@ -0,0 +1,20 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type AIProjectTrainModelRequest = {
+	genome: string
+	dslabel: string
+	projectId?: string
+}
+
+export type AIProjectTrainModelResponse = {
+	status: 'ok' | 'error'
+}
+
+export const aiProjectTrainModelPayload: RoutePayload = {
+	request: {
+		typeId: 'AIProjectTrainModelRequest'
+	},
+	response: {
+		typeId: 'AIProjectTrainModelResponse'
+	}
+}

package/src/routes/brainImaging.ts

@@ -1,4 +1,4 @@
-import type { CategoricalTW } from '../terms/categorical.ts'
+import type { QualTW } from '../terms/qualitative.ts'
 import type { RoutePayload } from './routeApi.ts'
 
 export type BrainImagingRequest = {
@@ -15,9 +15,9 @@ export type BrainImagingRequest = {
 	/** the sample names selected by the users to plot on brain template */
 	selectedSampleFileNames: string[]
 	/* the term to divide the samples into groups */
-	divideByTW?: CategoricalTW
+	divideByTW?: QualTW
 	/* the term to color the samples based on their category */
-	overlayTW?: CategoricalTW
+	overlayTW?: QualTW
 	/* the term categories that were filtered out */
 	legendFilter?: string[]
 }

package/src/terms/categorical.ts

@@ -1,99 +1,18 @@
-import type {
-	BaseTerm,
-	TermValues,
-	GroupSettingQ,
-	ValuesQ,
-	TermGroupSetting,
-	BaseTW,
-	PredefinedGroupSettingQ,
-	CustomGroupSettingQ
-} from '../index.ts'
-import type { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
+import type { TermGroupSetting, TermValues, BaseTerm } from '../index.ts'
 
-/**
- * A raw categorical term q object, before filling-in
- *
- * test:CategoricalQ:
- *
- * @category TW
- */
-
-export type RawCatTWValues = BaseTW & {
-	type?: 'CatTWValues'
-	/** must already exist, for dictionary terms, TwRouter.fill() will use mayHydrateDictTwLst() */
-	term: CategoricalTerm
-	q: RawValuesQ
-}
-
-export type RawCatTWPredefinedGS = BaseTW & {
-	type?: 'CatTWPredefinedGS'
-	term: CategoricalTerm
-	q: RawPredefinedGroupsetQ
-}
-
-export type RawCatTWCustomGS = BaseTW & {
-	type?: 'CatTWCustomGS'
-	term: CategoricalTerm
-	q: RawCustomGroupsetQ
-}
-
-export type RawCatTW = RawCatTWValues | RawCatTWPredefinedGS | RawCatTWCustomGS
-
-export type CategoricalBaseQ = MinBaseQ & {
-	mode?: 'discrete' | 'binary'
-}
-
-export type CategoricalQ = GroupSettingQ | ValuesQ
+/*
+For term type 'snp'
+*/
 
 export type CategoricalTerm = BaseTerm & {
+	id: string
+	name?: string
 	type: 'categorical'
 	values: TermValues
 	groupsetting: TermGroupSetting
 }
 
-/**
- * A categorical term wrapper object
- *
- * @group Termdb
- * @category TW
- */
-
-export type CategoricalTW = BaseTW & {
-	//id: string
-	type: 'CatTWValues' | 'CatTWPredefinedGS' | 'CatTWCustomGS'
-	q: CategoricalQ
-	term: CategoricalTerm
-}
-
-export type CatTWValues = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: ValuesQ
-	type: 'CatTWValues'
-}
-
-export type CatTWPredefinedGS = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: PredefinedGroupSettingQ
-	type: 'CatTWPredefinedGS'
-}
-
-export type CatTWCustomGS = BaseTW & {
-	//id: string
-	term: CategoricalTerm
-	q: CustomGroupSettingQ
-	type: 'CatTWCustomGS'
-}
-
-export type CatTWTypes = CatTWValues | CatTWPredefinedGS | CatTWCustomGS
-
-// TODO: should not need this once TermSettingInstance is replaced with simply using the class as the type
-export type CategoricalTermSettingInstance = TermSettingInstance & {
-	q: CategoricalQ & { mode: 'binary' | 'discrete' }
-	term: CategoricalTerm
-	category2samplecount: any
-	validateGroupsetting: () => { text: string; bgcolor?: string }
-	error?: string
+export type RawCategoricalTerm = CategoricalTerm & {
+	groupsetting?: TermGroupSetting
+	values?: TermValues
 }

package/src/terms/date.ts

@@ -15,6 +15,6 @@ export type DateTerm = NumericBaseTerm & {
 
 export type DateTW = NumTW & { term: DateTerm }
 
-type RawDateTerm = DateTerm & { name?: string }
+export type RawDateTerm = DateTerm & { name?: string }
 
 export type RawDateTW = RawNumTW & { term: RawDateTerm }

package/src/terms/geneExpression.ts

@@ -33,4 +33,6 @@ export type GeneExpressionTerm = NumericBaseTerm & {
 
 export type GeneExpressionTW = NumTW & { term: GeneExpressionTerm }
 
-export type RawGeneExpTW = RawNumTW & { term: GeneExpressionTerm & { name?: string } }
+export type RawGeneExpTerm = GeneExpressionTerm & { name?: string }
+
+export type RawGeneExpTW = RawNumTW & { term: RawGeneExpTerm }

package/src/terms/metaboliteIntensity.ts

@@ -8,6 +8,7 @@ MetaboliteIntensityTermSettingInstance
 */
 
 export type MetaboliteIntensityTerm = NumericBaseTerm & {
+	id?: string
 	name: string
 	type: 'metaboliteIntensity'
 	metabolite: string
@@ -17,7 +18,8 @@ export type MetaboliteIntensityTerm = NumericBaseTerm & {
 
 export type MetaboliteIntensityTW = NumTW & { term: MetaboliteIntensityTerm }
 
-type RawMetabolitIntensityTerm = {
+export type RawMetaboliteIntensityTerm = NumericBaseTerm & {
+	id?: string
 	type: 'metaboliteIntensity'
 	metabolite: string
 	name?: string
@@ -25,4 +27,4 @@ type RawMetabolitIntensityTerm = {
 	unit?: string
 }
 
-export type RawMetaboliteIntensityTW = RawNumTW & { term: RawMetabolitIntensityTerm }
+export type RawMetaboliteIntensityTW = RawNumTW & { term: RawMetaboliteIntensityTerm }

package/src/terms/numeric.ts

@@ -46,12 +46,16 @@ export type NumericBaseTerm = BaseTerm & {
 }
 
 export type NumericDictTerm = NumericBaseTerm & {
-	id?: string
+	id: string
 	type: 'integer' | 'float'
 	bins: PresetNumericBins
 	values?: TermValues
 }
 
+export type RawNumericDictTerm = NumericDictTerm & {
+	id?: string
+}
+
 export type NumericTerm = NumericDictTerm | GeneExpressionTerm | MetaboliteIntensityTerm | DateTerm | SsGSEATerm
 
 export type StartUnboundedBin = {

package/src/terms/q.ts

@@ -1,4 +1,4 @@
-import type { CategoricalBaseQ } from './categorical.js'
+//import type { CategoricalQ } from './q.ts'
 import type { Filter } from '../filter.js'
 
 // MinBaseQ is BaseQ without .mode and .type
@@ -18,6 +18,10 @@ export type MinBaseQ = {
 	reuseId?: string
 }
 
+export type CategoricalBaseQ = MinBaseQ & {
+	mode?: 'discrete' | 'binary'
+}
+
 export type RawValuesQ = MinBaseQ & { type?: 'values'; mode?: 'binary' }
 
 export type RawPredefinedGroupsetQ = MinBaseQ & {