@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/routes/grin2.ts

@@ -1,173 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { Filter } from '../filter.ts'
-
-/** GRIN2 request */
-export type GRIN2Request = {
-	/** Genome build identifier (e.g., 'hg38', 'hg19') */
-	genome: string
-
-	/** Dataset label within the genome */
-	dslabel: string
-
-	/** Device pixel ratio for rendering */
-	devicePixelRatio?: number
-
-	/** Desired plot width in pixels (default: 1000) */
-	width?: number
-
-	/** Desired plot height in pixels (default: 400) */
-	height?: number
-
-	/** Radius of the PNG rendered dots (default: 2) */
-	pngDotRadius?: number
-
-	/** Lesion type colors */
-	lesionTypeColors?: any
-
-	/** Threshold for q-values to be included as interactive dots, have significance indicators in the table and tooltips */
-	qValueThreshold?: number
-
-	/** Log cutoff for Manhattan plot rendering before we scale the y-axis (default: 40).
-	 * This is not user defined but rather a constant defined in #shared/manhattan.js.
-	 * Sending it with request for consistency. In future we will allow user to set scale value or disable scaling if they wish */
-	logCutoff?: number
-
-	/** Maximum number of points to cap the dynamic y-axis in Manhattan plots */
-	maxCappedPoints: number
-
-	/** Absolute maximum cap for the y-axis in Manhattan plots regardless of its data distribution */
-	hardCap: number
-
-	/** Bin size for Manhattan plot histogram bin size. Used in the calculation of dynamic y-axis capping process (default: 10) */
-	binSize: number
-
-	/** pp filter */
-	filter?: Filter
-
-	/** Options for filtering SNV/indel file content */
-	snvindelOptions?: {
-		/** Minimum total depth of returned SNV/indel files */
-		minTotalDepth?: number // Default: 10
-		/** Minimum alternate allele count of returned SNV/indel files */
-		minAltAlleleCount?: number // Default: 2
-		/** String array of consequence types to include */
-		consequences?: string[]
-		/** Maximum mutation count cutoff for highly mutated scenarios */
-		hyperMutator?: number // Default: 1000
-		/** Number of bases to include as 5' flank around the mutation position */
-		fivePrimeFlankSize?: number
-		/** Number of bases to include as 3' flank around the mutation position */
-		threePrimeFlankSize?: number
-		/** MAF filter object (tvslst) to filter mutations by allele frequency */
-		mafFilter?: Filter
-	}
-
-	/** Options for filtering CNV file content */
-	cnvOptions?: {
-		/** Threshold for copy number loss detection */
-		lossThreshold?: number // Default: -0.4
-		/** Threshold for copy number gain detection */
-		gainThreshold?: number // Default: 0.3
-		/** Maximum segment length to include (0 = no filter) */
-		maxSegLength?: number // Default: 0
-		/** Hypermutator max cut off for CNVs per case */
-		hyperMutator?: number // Default: 500
-		/** Number of bases to include as 5' flank around the segment position */
-		fivePrimeFlankSize?: number
-		/** Number of bases to include as 3' flank around the segment position */
-		threePrimeFlankSize?: number
-	}
-
-	/** Options for filtering fusion file content */
-	fusionOptions?: {
-		/** Number of bases to include as 5' flank around the fusion position */
-		fivePrimeFlankSize?: number
-		/** Number of bases to include as 3' flank around the fusion position */
-		threePrimeFlankSize?: number
-	}
-
-	/** Options for filtering structural variant file content */
-	svOptions?: {
-		/** Number of bases to include as 5' flank around the sv position */
-		fivePrimeFlankSize?: number
-		/** Number of bases to include as 3' flank around the sv position */
-		threePrimeFlankSize?: number
-	}
-	maxGenesToShow?: number // Default: 500
-}
-
-/** Simple Interface to store the complex plot data from the rust Manhattan plot */
-interface grin2PlotData {
-	points: Array<{
-		x: number // X-axis position (base pair/genomic position in the pixel space)
-		y: number // Y-axis position (-log10(q-value) in the pixel space)
-		color: string // Point color (hexadecimal string representing a color for mutation type)
-		type: string // Mutation type (e.g., 'mutation', 'loss', 'gain', 'fusion', 'sv')
-		gene: string // Gene symbol
-		chrom: string // Chromosome in the form of <chrX>
-		start: number // Starting position of this chromosome in base pairs/genomic coordinates. Used in hover table
-		end: number // Ending position of this chromosome in base pairs/genomic coordinates
-		pos: number // Mid-point of this chromosome in base pairs/genomic coordinates
-		nsubj: number // Number of subjects with this mutation. Used for hover table subject count
-	}>
-	chrom_data: Record<
-		// Data for chromosome labels and positioning on the x-axis
-		string,
-		{
-			start: number
-			size: number
-			center: number
-		}
-	>
-	total_genome_length: number // Gives us the full length of the genome so we can easily append x buffer space when building d3 x-axis
-	has_capped_points: boolean // Whether we have capped the y-axis due to q-values exceeding the cap
-}
-
-/**
- * Response for GRIN2 analysis run
- */
-export type GRIN2Response = {
-	/** Status of the analysis */
-	status: 'success' | 'error'
-	/** Error message if status is 'error' */
-	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 */
-	topGeneTable?: {
-		/** Column definitions with labels and sort capabilities */
-		columns: Array<{
-			label: string
-			sortable: boolean
-		}>
-		/** Data rows with gene information and statistics */
-		rows: Array<
-			Array<{
-				value: string | number
-			}>
-		>
-	}
-
-	stats?: {
-		lst: Array<{
-			name: string
-			rows: string[][]
-		}>
-	}
-}
-
-/**
- * Route payload definitions for type checking
- */
-export const GRIN2Payload: RoutePayload = {
-	request: {
-		typeId: 'GRIN2Request'
-	},
-	response: {
-		typeId: 'GRIN2Response'
-	}
-}

package/src/routes/healthcheck.ts

@@ -1,80 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type HealthCheckRequest = {
-	dslabel?: string
-}
-
-/**
- * Information aboute the server build version and dates,
- * including the date when the server was last launched
- */
-export type VersionInfo = {
-	pkgver: string
-	codedate: string
-	launchdate: string
-	deps: {
-		[pkgName: string]: {
-			/** the version as found in node_modules/[package]/package.json */
-			installed?: string
-			/** the version as entered in the project's package.dependencies */
-			entry?: string
-		}
-	}
-}
-
-type BuildByGenome = {
-	[index: string]: GenomeBuildInfo
-}
-
-export type GenomeBuildInfo = {
-	genedb: DbInfo
-	termdbs?: {
-		[index: string]: DbInfo
-	}
-}
-
-type DbInfo = {
-	buildDate: string // "unknown" or a Date-convertible string
-	tables?: {
-		[index: string]: number
-	}
-}
-
-/**
- * Server status and data related to it's health
- */
-export type HealthCheckResponse = {
-	status: 'ok' | 'error'
-	genomes: BuildByGenome
-	versionInfo: VersionInfo
-	byDataset?: {
-		[dslabel: string]: any
-	}
-	auth?: {
-		errors?: string[]
-	}
-	w?: number[]
-	rs?: number
-	dsInitStatus: any[]
-}
-
-export const healthcheckPayload: RoutePayload = {
-	request: {
-		typeId: 'HealthCheckRequest'
-	},
-	response: {
-		typeId: 'HealthCheckResponse'
-	},
-	examples: [
-		{
-			request: { body: {} }
-			//response: {}
-		},
-		{
-			request: {
-				body: { dsLabel: 'TermdbTest' }
-			}
-			//response: {}
-		}
-	]
-}

package/src/routes/hicdata.ts

@@ -1,48 +0,0 @@
-import type { FileORURL } from '../fileOrUrl.ts'
-import type { RoutePayload } from './routeApi.ts'
-
-export type BaseHicRequest = FileORURL & {
-	/** Value relates to the 1st parameter of straw tool, which accepts 'observed', 'expected', 'oe', 'norm', and 'distance' */
-	matrixType: 'observed' | 'expected' | 'oe' | 'log(oe)'
-	/** Either a base pair or fragment resolution calculated from the array*/
-	resolution: number
-	/** Normalization method, an option read from the file or NONE */
-	nmeth: string
-}
-
-export type HicdataRequest = BaseHicRequest & {
-	/** Position of first locus, in the format of chr:start:stop */
-	pos1: string
-	/** Position of second locus, in the format of chr:start:stop */
-	pos2: string // portal code must validate pos1 and pos2 values, to prevent xxx:456-321
-	/** If is in fragment resolution */
-	isfrag?: boolean
-	/** Minimum value cutoff */
-	mincutoff?: number
-}
-
-/** Item typed for documentation/explanation purposes*/
-export type XYZCoord = [
-	/** position 1, x coordinate */
-	number,
-	/** position 2, y coordinate */
-	number,
-	/** inter-loci contact value */
-	number
-]
-
-export type HicdataResponse = {
-	/** Error message to display on the client, if applicable */
-	error?: string
-	items: XYZCoord[]
-}
-
-export const hicdataPayload: RoutePayload = {
-	request: {
-		typeId: 'HicdataRequest'
-	},
-	response: {
-		typeId: 'HicdataResponse'
-	}
-	// examples: []
-}

package/src/routes/hicgenome.ts

@@ -1,50 +0,0 @@
-import type { BaseHicRequest, XYZCoord } from './hicdata.ts'
-import type { RoutePayload } from './routeApi.ts'
-
-export type HicGenomeRequest = BaseHicRequest & {
-	/** Entire chromosome list read from the file (see hicstate) */
-	chrlst: string[]
-	/** window location */
-	embedder: string
-	/** whether or not the file contains 'chr' for the chromosomes */
-	nochr: boolean
-}
-
-export type HicGenomeResponse = {
-	data: {
-		/** First chromosome */
-		lead: string
-		/** Second chromosome */
-		follow: string
-		items: XYZCoord[]
-	}[]
-	/** Error message to display on the client, if applicable */
-	error?: string
-}
-
-export const hicGenomePayload: RoutePayload = {
-	request: {
-		typeId: 'HicGenomeRequest'
-	},
-	response: {
-		typeId: 'HicGenomeResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					embedder: 'localhost',
-					url: 'https://proteinpaint.stjude.org/ppdemo/hg19/hic/hic_demo.hic',
-					matrixType: 'observed',
-					nmeth: 'NONE',
-					pos1: '3',
-					pos2: '2',
-					resolution: 1000000
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/hicstat.ts

@@ -1,57 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type HicstatRequestWithFile = {
-	/** HiC file path from tp/ */
-	file: string
-	/** If file is provided, url should not be provided. Checked in validation type */
-	url?: never
-}
-
-export type HicstatRequestWithUrl = {
-	/** If url is provided, file should not be provided. Checked in validation type */
-	file?: never
-	/** Remote HiC file URL */
-	url: string
-}
-
-export type HicstatRequest = HicstatRequestWithFile | HicstatRequestWithUrl
-
-/** Checks if a file or url is present before proceeding */
-type RequireFileOrUrl<T> = T extends HicstatRequestWithFile | HicstatRequestWithUrl
-	? T
-	: { error: 'Either "file" or "url" must be provided' }
-
-export type HicstatRequestWithValidation = RequireFileOrUrl<HicstatRequest>
-
-export type HicstatResponse = {
-	/** Version number pulled from the header. Only hic versions 7-9 are acceptable */
-	version: 7 | 8 | 9
-	/**genome identifer */
-	'Genome ID': string
-	/** k:v of chrs and a position */
-	Chromosomes: {
-		/** Index of chr 1 through 22 */
-		[index: number]: number
-		All: number
-		X: number
-		Y: number
-		M: number
-	}
-	/** Orders Chromosomes keys (see above) */
-	chrorder: number[]
-	/** bins for base pair resolutions */
-	'Base pair-delimited resolutions': number[]
-	/** bins for fragment resolutions */
-	'Fragment-delimited resolutions': number[]
-	normalization: string[]
-}
-
-export const hicstatPayload: RoutePayload = {
-	request: {
-		typeId: 'HicstatRequest'
-	},
-	response: {
-		typeId: 'HicstatResponse'
-	}
-	// examples: []
-}

package/src/routes/img.ts

@@ -1,23 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type imgRequest = {
-	file: string
-}
-
-export type SrcImage = {
-	src: any
-}
-
-export type imgResponse = {
-	src: string
-	size: string
-}
-
-export const imgPayload: RoutePayload = {
-	request: {
-		typeId: 'imgRequest'
-	},
-	response: {
-		typeId: 'imgResponse'
-	}
-}

package/src/routes/isoformlst.ts

@@ -1,14 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type IsoformLstRequest = any
-export type IsoformLstResponse = any
-
-export const isoformlstPayload: RoutePayload = {
-	request: {
-		typeId: 'IsoformLstRequest'
-	},
-	response: {
-		typeId: 'IsoformLstResponse'
-	}
-	//examples: []
-}

package/src/routes/ntseq.ts

@@ -1,14 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type NtseqRequest = any
-export type NtseqResponse = any
-
-export const ntseqPayload: RoutePayload = {
-	request: {
-		typeId: 'NtseqRequest'
-	},
-	response: {
-		typeId: 'NtseqResponse'
-	}
-	//examples: []
-}

package/src/routes/pdomain.ts

@@ -1,14 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type PdomainRequest = any
-export type PdomainResponse = any
-
-export const pdomainPayload: RoutePayload = {
-	request: {
-		typeId: 'PdomainRequest'
-	},
-	response: {
-		typeId: 'PdomainResponse'
-	}
-	//examples: []
-}

package/src/routes/routeApi.ts

@@ -1,47 +0,0 @@
-export type RouteApi = {
-	endpoint: string
-	methods: {
-		get?: RoutePayload
-		post?: RoutePayload
-		put?: RoutePayload
-		delete?: RoutePayload
-	}
-}
-
-export type RoutePayload = {
-	init?: RouteInit
-	request: RouteMethod
-	response: RouteMethod
-	/** if examples are not provided, will not test */
-	examples?: PayloadExample[]
-}
-export type RouteMethod = {
-	typeId: string
-	checker?: any
-}
-/* later replace actual values */
-export type Point = {
-	x: string
-	y: string | number
-}
-
-type RouteInitArg = {
-	app: any
-	genome: any
-	genomes: any
-}
-type RouteHandler = (req: any, res: any) => void
-type RouteInit = (a: RouteInitArg) => RouteHandler
-type PayloadExample = {
-	request: {
-		body: any
-	}
-	response?: {
-		header?: any
-		/**
-		 * if omitted, only payload shape is checked at runtime;
-		 * if provided, will use deep equal to check at runtime
-		 */
-		body?: any
-	}
-}

package/src/routes/samplewsimages.ts

@@ -1,44 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-import type { WSIClass } from '../dataset.ts'
-import type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'
-
-export type SampleWSImagesRequest = {
-	genome: string
-	dslabel: string
-	sample_id: string
-	wsimage: string
-}
-
-export type SampleWSImagesResponse = {
-	sampleWSImages: WSImage[]
-}
-
-export class WSImage {
-	id?: number
-	filename: string
-	metadata?: string
-	predictionLayers?: Array<string>
-	annotations?: Array<Annotation>
-	predictions?: Array<Prediction>
-	classes?: Array<WSIClass>
-	/** ds defined uncertainity labels and colors */
-	uncertainty?: any
-	/** Color to highlight active patches */
-	activePatchColor?: string
-	/** Tile size in pixels needed for AI scripts */
-	tileSize?: number
-
-	constructor(filename: string) {
-		this.filename = filename
-	}
-}
-
-export const sampleWSImagesPayload: RoutePayload = {
-	request: {
-		typeId: 'SampleWSImagesRequest'
-	},
-	response: {
-		typeId: 'SampleWSImagesResponse'
-	}
-	// examples: []
-}

package/src/routes/saveWSIAnnotation.ts

@@ -1,25 +0,0 @@
-import type { TileSelection } from '../index.ts'
-import type { RoutePayload } from './routeApi.ts'
-
-export type SaveWSIAnnotationRequest = {
-	genome: string
-	dslabel: string
-	tileSelection: TileSelection
-	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/snp.ts

@@ -1,13 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type SnpRequest = any
-export type SnpResponse = any
-
-export const snpPayload: RoutePayload = {
-	request: {
-		typeId: 'SnpRequest'
-	},
-	response: {
-		typeId: 'SnpResponse'
-	}
-}