@sjcrh/proteinpaint-types 2.142.0 → 2.143.0

package/dist/termdb.sampleImages.js

@@ -2,8 +2,8 @@ import {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,
   validTermdbSampleImagesResponse
-} from "./chunk-X2CX5K24.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-U3BTVE5T.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,

package/dist/termdb.singleSampleMutation.js

@@ -2,8 +2,8 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-GGZUN2GE.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-UGYLBYUU.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,

package/dist/termdb.singlecellDEgenes.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-XEQWKMZN.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-EYKGJDKU.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,

package/dist/termdb.singlecellData.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
   validTermdbSingleCellDataResponse
-} from "./chunk-K5POIB3P.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-4ZMQ5CTL.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,

package/dist/termdb.singlecellSamples.js

@@ -2,8 +2,8 @@ import {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,
   validTermdbSingleCellSamplesResponse
-} from "./chunk-LPBYQJG4.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-XIRCL7KT.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,

package/dist/termdb.termchildren.js

@@ -2,8 +2,8 @@ import {
   termChildrenPayload,
   validTermChildrenRequest,
   validTermChildrenResponse
-} from "./chunk-HKGWC7OO.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-P25WDNMD.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termChildrenPayload,
   validTermChildrenRequest,

package/dist/termdb.termsbyids.js

@@ -2,8 +2,8 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-IR4QSJI7.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-GCAZSDCW.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,
   validTermsByIdsRequest,

package/dist/termdb.topMutatedGenes.js

@@ -2,8 +2,8 @@ import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
   validtopMutatedGeneResponse
-} from "./chunk-YGX6BZZY.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-EIJT53QB.js";
+import "./chunk-YNHC5SXO.js";
 export {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,

package/dist/termdb.topTermsByType.js

@@ -2,8 +2,8 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2VDOPTRV.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-74B7B2CV.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,8 +2,8 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-4R265LDJ.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-U3AOS5QJ.js";
+import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,

package/dist/termdb.violin.js

@@ -2,8 +2,8 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-DMJFOII6.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-MMFL6N5M.js";
+import "./chunk-YNHC5SXO.js";
 export {
   validViolinRequest,
   validViolinResponse,

package/dist/tileserver.js

@@ -2,8 +2,8 @@ import {
   tilePayload,
   validTileRequest,
   validTileResponse
-} from "./chunk-KFVYRW7D.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-HQV2A7JV.js";
+import "./chunk-YNHC5SXO.js";
 export {
   tilePayload,
   validTileRequest,

package/dist/wsimages.js

@@ -2,8 +2,8 @@ import {
   validWSImagesRequest,
   validWSImagesResponse,
   wsImagesPayload
-} from "./chunk-CQDDRHRY.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-CT6IBFVP.js";
+import "./chunk-YNHC5SXO.js";
 export {
   validWSImagesRequest,
   validWSImagesResponse,

package/dist/wsisamples.js

@@ -2,8 +2,8 @@ import {
   validWSISamplesRequest,
   validWSISamplesResponse,
   wsiSamplesPayload
-} from "./chunk-W6NLM363.js";
-import "./chunk-CNSSF43V.js";
+} from "./chunk-2744ACBX.js";
+import "./chunk-YNHC5SXO.js";
 export {
   validWSISamplesRequest,
   validWSISamplesResponse,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.142.0",
+  "version": "2.143.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1,6 +1,8 @@
 import type { Mclass } from './Mclass.ts'
 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'
 
 /*** General usage types ***/
 type FileObj = {
@@ -1039,31 +1041,41 @@ export type WSImages = {
 	/* path to the folder where sample images are stored
 	required; for both cases where image files are hosted locally, or loaded from remote via ds-supplied getter
 	*/
-	imageBySampleFolder: string
+	imageBySampleFolder?: string
+
+	aiToolImageFolder?: string
+
 	activePatchColor?: string
 	predictionColor?: Array<number>
 	annotationsColor?: Array<number>
 	tileSize?: number
-	classes?: WSIClass[]
 	uncertainty?: { color: string; label: string }[]
 
+	/** dynamically added on launch with built in logic */
+	saveWSIAnnotation?: (annotation: SaveWSIAnnotationRequest) => Promise<void>
+
+	/** dynamically added on launch with built in logic */
+	deleteWSIAnnotation?: (annotation: DeleteWSIAnnotationRequest) => Promise<void>
+
 	/** 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 */
 	getWSImages?: (sampleName: string) => Promise<WSImage[]>
 	/**  ds supplied */
-	getWSIPredictionPatches?: (sampleName: string, wsiImage: string) => Promise<string[]>
+	getWSIPredictionPatches?: (projectId: string, wsiImage: string) => Promise<string[]>
 	/**  ds supplied */
-	getWSIAnnotations?: (sampleName: string, wsiImage: string) => Promise<string[]>
+	getWSIAnnotations?: (projectId: string, wsiImage: string) => Promise<string[]>
 	/**  ds supplied */
 	makeGeoJson?: (sampleId: string, wsiImage: string) => void
 	/**  ds supplied */
-	getWSIPredictionOverlay?: (sampleName: string, wsiImage: string) => Promise<string | undefined>
+	getWSIPredictionOverlay?: (wsiImage: string) => Promise<string | undefined>
+	/**  ds supplied */
+	getWSIUncertaintyOverlay?: (wsiImage: string) => Promise<string | undefined>
 	/**  ds supplied */
-	getWSIUncertaintyOverlay?: (sampleName: string, wsiImage: string) => Promise<string | undefined>
+	getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
 }
 
-export type WSIClass = { id: number; shortcut: string; label: string; color: string }
+export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
 
 /*** types supporting Termdb ***/
 

package/src/index.ts

@@ -6,12 +6,14 @@ export * from './filter.ts'
 export * from './termdb.matrix.ts'
 export * from './routes/routeApi.ts'
 export * from './routes/aiProjectAdmin.ts'
+export * from './routes/aiProjectSelectedWSImages.ts'
 export * from './routes/brainImaging.ts'
 export * from './routes/brainImagingSamples.ts'
 export * from './routes/burden.ts'
 export * from './routes/clearwsisessions.ts'
 export * from './routes/correlationVolcano.ts'
 export * from './routes/dataset.ts'
+export * from './routes/deleteWSIAnnotation.ts'
 export * from './routes/dsdata.ts'
 export * from './routes/dzimages.ts'
 export * from './routes/errorResponse.ts'
@@ -32,7 +34,7 @@ export * from './routes/isoformlst.ts'
 export * from './routes/ntseq.ts'
 export * from './routes/pdomain.ts'
 export * from './routes/samplewsimages.ts'
-export * from './routes/sampleWsiAiApi.ts'
+export * from './routes/saveWSIAnnotation.ts'
 export * from './routes/snp.ts'
 export * from './routes/termdb.boxplot.ts'
 export * from './routes/termdb.categories.ts'

package/src/routes/aiProjectAdmin.ts

@@ -5,8 +5,10 @@ export type AIProjectAdminRequest = {
 	dslabel: string
 	/** list: get entire list of projects from db
 	 * admin: edit, add, or delete projects from db
+	 * filterImages: filter metadata for images
+	 * images: get images for a project
 	 */
-	for: 'list' | 'admin' | 'images'
+	for: 'list' | 'admin' | 'filterImages' | 'images'
 	/** required for 'project' and 'selection' requests */
 	project?: {
 		name: string
@@ -17,13 +19,13 @@ export type AIProjectAdminRequest = {
 	}
 }
 
-export type AIProjectAdminResponse =
-	| {
-			status: 'ok' | 'error'
-			error?: string
-			data?: { cols: any[]; rows: any[]; images: string[] }[]
-	  }
-	| string[]
+export type AIProjectAdminResponse = {
+	status: 'ok' | 'error'
+	projectId?: number
+	images: string[]
+	error?: string
+	data?: { cols: any[]; rows: any[]; images: string[] }[]
+}
 
 export const aiProjectAdminPayload: RoutePayload = {
 	request: {

package/src/routes/aiProjectSelectedWSImages.ts

@@ -0,0 +1,23 @@
+import type { RoutePayload } from './routeApi.ts'
+import type { WSImage } from './samplewsimages.ts'
+
+export type AiProjectSelectedWSImagesRequest = {
+	genome: string
+	dslabel: string
+	projectId: number
+	wsimagesFilenames: Array<string>
+}
+
+export type AiProjectSelectedWSImagesResponse = {
+	// TODO create a type for WSImage with AI project specific fields
+	wsimages: WSImage[]
+}
+
+export const aiProjectSelectedWSImagesResponsePayload: RoutePayload = {
+	request: {
+		typeId: 'AiProjectSelectedWSImagesRequest'
+	},
+	response: {
+		typeId: 'AiProjectSelectedWSImagesResponse'
+	}
+}

package/src/routes/deleteWSIAnnotation.ts

@@ -0,0 +1,23 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type DeleteWSIAnnotationRequest = {
+	genome: string
+	dslabel: string
+	projectId: number
+	annotation: any
+	wsimage: string
+}
+
+export type DeleteWSIAnnotationResponse = {
+	status: string
+	error?: string
+}
+
+export const deleteWSIAnnotationPayload: RoutePayload = {
+	request: {
+		typeId: 'DeleteWSIAnnotationRequest'
+	},
+	response: {
+		typeId: 'DeleteWSIAnnotationResponse'
+	}
+}

package/src/routes/grin2.ts

@@ -17,6 +17,15 @@ export type GRIN2Request = {
 	/** Dataset label within the genome */
 	dslabel: string
 
+	/** Device pixel ratio for rendering */
+	devicePixelRatio?: number
+
+	/** Desired plot width in pixels (default: 1000) */
+	plot_width?: number
+
+	/** Desired plot height in pixels (default: 400) */
+	plot_height?: number
+
 	/** Filter from existing PP infrastructure */
 	filter?: any // Filter object passed to get_samples(filter, ds)
 
@@ -51,6 +60,37 @@ export type GRIN2Request = {
 	}
 }
 
+/** Simple Interface to store the complex plot data from the python Manhattan plot */
+interface grin2PlotData {
+	points: Array<{
+		x: number
+		y: number
+		svg_x: number
+		svg_y: number
+		color: string
+		type: string
+		gene: string
+		chrom: string
+		pos: number
+		q_value: number
+	}>
+	chrom_data: Record<
+		string,
+		{
+			start: number
+			size: number
+			center: number
+		}
+	>
+	y_axis_scaled: boolean
+	scale_factor: number
+	total_genome_length: number
+	plot_width: number
+	plot_height: number
+	device_pixel_ratio: number
+	dpi: number
+}
+
 /**
  * Response for GRIN2 analysis run
  */
@@ -61,6 +101,8 @@ export type GRIN2Response = {
 	error?: string
 	/** Base64-encoded PNG Manhattan plot image */
 	pngImg?: string
+	/** Plot data for the Manhattan plot */
+	plotData?: grin2PlotData
 	/** Download status/info */
 	download?: any
 	/** Sortable table of top genes identified by GRIN2 */

package/src/routes/samplewsimages.ts

@@ -13,11 +13,13 @@ export type SampleWSImagesResponse = {
 }
 
 export type WSImage = {
+	id?: number
 	filename: string
-	overlays?: Array<string>
+	// TODO remove when it's verified
+	annotationsAndPredictionsOverlay?: string
 	predictionLayers?: Array<string>
-	metadata: string
-	annotationsData?: Array<Annotation>
+	metadata?: string
+	annotations?: Array<Annotation>
 	predictions?: Array<Prediction>
 	classes?: Array<WSIClass>
 	/** ds defined uncertainity labels and colors */

package/src/routes/saveWSIAnnotation.ts

@@ -0,0 +1,24 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type SaveWSIAnnotationRequest = {
+	genome: string
+	dslabel: string
+	coordinates: [number, number]
+	classId: number
+	projectId: number
+	wsimage: string
+}
+
+export type SaveWSIAnnotationResponse = {
+	status: 'ok' | 'error'
+	error?: string
+}
+
+export const saveWSIAnnotationPayload: RoutePayload = {
+	request: {
+		typeId: 'SaveWSIAnnotationRequest'
+	},
+	response: {
+		typeId: 'SaveWSIAnnotationResponse'
+	}
+}

package/src/routes/termdb.boxplot.ts

@@ -15,6 +15,8 @@ export type BoxPlotRequest = {
 	orderByMedian: boolean
 	/** term2 */
 	overlayTw?: TermWrapper
+	/** term0 */
+	divideTw?: TermWrapper
 	filter?: Filter
 	filter0?: any
 	__protected__: any
@@ -25,11 +27,31 @@ export type BoxPlotResponse = {
 	absMin?: number
 	/** Absolute max value for all plots */
 	absMax?: number
-	plots: BoxPlotEntry[]
+	/** Charts data */
+	charts: {
+		[chartId: string]: BoxPlotChartEntry
+	}
 	/** Categories not shown in the final plot */
 	uncomputableValues: { label: string; value: number }[] | null
+	error?: any
+}
+
+// chart containing a set of boxplots
+export type BoxPlotChartEntry = {
+	/** Chart ID */
+	chartId: string
+	/** Boxplot data within the chart */
+	plots: BoxPlotEntry[]
+	/** svg of chart, necessary for svg download */
+	svg?: any
+	/** Copied from BoxPlotResponse, necessary for
+	ViewModel to process chart data */
+	absMin?: number
+	absMax?: number
+	uncomputableValues?: { label: string; value: number }[] | null
 }
 
+// individual boxplot
 export type BoxPlotEntry = {
 	boxplot: BoxPlotData & { label: string }
 	/** color matching the value/category color */

package/src/routes/termdb.violin.ts

@@ -14,7 +14,9 @@ export type ViolinRequest = {
 	/** A number representing the device's pixel ratio, which may be used for
 	 * rendering quality adjustments */
 	devicePixelRatio: number
-	/** optional tw to divide tw data into multiple violins and show under one axis */
+	/** optional overlay tw, will generate multiple violin plots */
+	overlayTw?: any
+	/** optional divide tw, will generate multiple charts, each of which will contain violin plots */
 	divideTw?: any
 	/** Reference label (i.e. short label) for the ds */
 	dslabel: string
@@ -81,7 +83,7 @@ export type ViolinPlotEntry = {
 	/** Color to render */
 	color: string
 	density: ViolinDensity
-	divideTwBins: any
+	overlayTwBins: any
 	/** Text for label */
 	label: string
 	/** Number of samples/cases/patients/etc. */

package/src/routes/wsimages.ts

@@ -3,8 +3,9 @@ import type { RoutePayload } from './routeApi.js'
 export type WSImagesRequest = {
 	genome: string
 	dslabel: string
-	sampleId: string
+	sampleId?: string
 	wsimage: string
+	aiProjectId?: number
 }
 
 export type WSImagesResponse = {

package/src/termdb.matrix.ts

@@ -23,6 +23,8 @@ type CategoryEntry = {
 	samplecount: number
 }
 
+// TODO: need to add a discriminant property (e.g. ".kind") to
+// distinguish between ValidGetDataResponse and { error: string }
 export type ValidGetDataResponse = {
 	samples: {
 		[index: string | number]: SampleEntry

package/src/terms/categorical.ts

@@ -7,7 +7,7 @@ import type {
 	BaseTW,
 	PredefinedGroupSettingQ,
 	CustomGroupSettingQ
-} from './term.ts'
+} from '../index.ts'
 import type { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
@@ -89,8 +89,9 @@ export type CatTWCustomGS = BaseTW & {
 
 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
+	q: CategoricalQ & { mode: 'binary' | 'discrete' }
 	term: CategoricalTerm
 	category2samplecount: any
 	validateGroupsetting: () => { text: string; bgcolor?: string }

package/src/terms/condition.ts

@@ -1,18 +1,16 @@
-import type { BaseTerm, BaseQ, TermValues, BaseTW } from './term.ts'
+import type { BaseTerm, MinBaseQ, TermValues, BaseTW } from '../index.ts'
 //import type { TermWrapper } from './tw.ts'
 
 /**
  * @category TW
  */
 
-export type ConditionQ = BaseQ & {
+export type ConditionGradeQ = MinBaseQ & {
 	mode: 'discrete' | 'binary' | 'cuminc' | 'cox'
-	type?: 'values'
-	bar_by_children?: boolean // 'true' if term is not a leaf and has subconditions
-	bar_by_grade?: boolean /* 'true' for barchart. Always 'true' for cuminc and logistic/cox outcome (children terms are not allowed for those cases)
-	when 'true', 'value_by_*' flags are effective.*/
-	breaks?: number[] /*
-	Breaks grades into groups
+	valueFor: 'grade'
+	bar_by_grade: true
+	/**
+		Breaks grades into groups
 		Array length=1, will break grades to 2 groups. 
 			E.g. [3] divides to [-1,0,1,2,], [3,4,5]
 			Allowed for both conditionModes "discrete/binary"
@@ -22,12 +20,23 @@ export type ConditionQ = BaseQ & {
 			Only allowed for conditionMode="discrete" but not "binary"
 	*/
 	timeScale: 'age' | 'time'
+	breaks?: number[]
 	value_by_max_grade?: boolean //'false' if bar_by_children is 'true'
 	value_by_most_recent?: boolean //'false' if bar_by_children is 'true'
 	value_by_computable_grade?: boolean //'true' if bar_by_children is 'true'
 	groups?: any // TODO: should use a defined type
 }
 
+export type ConditionChildrenQ = MinBaseQ & {
+	mode: 'discrete'
+	valueFor: 'children'
+	bar_by_children: true
+	groups?: any // TODO: should use a defined type
+}
+
+// TODO: should implement the expected property combinations as distinct types
+export type ConditionQ = ConditionGradeQ | ConditionChildrenQ
+
 export type ConditionTerm = BaseTerm & {
 	type: 'condition'
 	values: TermValues
@@ -54,3 +63,11 @@ export type ConditionTermSettingInstance = TermSettingInstance & {
 	refGrp: any
 }
 */
+
+export type RawConditionTW = ConditionTW & {
+	q: {
+		valueFor?: 'grade' | 'children'
+		bar_by_children?: true
+		bar_by_grade?: true
+	}
+}

package/src/terms/numeric.ts

@@ -63,6 +63,7 @@ export type StartUnboundedBin = {
 	stopinclusive?: boolean
 	stopunbounded?: false
 	label?: string
+	range?: string // alternative bin label
 }
 
 export type StopUnboundedBin = {
@@ -72,6 +73,7 @@ export type StopUnboundedBin = {
 	startunbounded?: false
 	stopinclusive?: false // cannot include an infinite bound
 	label?: string
+	range?: string // alternative bin label
 }
 
 // TODO??? should separate a fully bounded bin by startinclusive, stopinclusive
@@ -84,10 +86,13 @@ export type FullyBoundedBin = {
 	stopinclusive?: boolean
 	stopunbounded?: false
 	label?: string
+	range?: string // alternative bin label
 }
 
 export type NumericBin = StartUnboundedBin | FullyBoundedBin | StopUnboundedBin
 
+export type RangeEntry = NumericBin | { value: number; label: string }
+
 export type RegularNumericBinConfig = MinBaseQ & {
 	type: 'regular-bin' // another concrete value being assigned, instead of `string`
 	//regular-sized bins