@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/routes/termdb.sampleScatter.ts

@@ -1,60 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-//TermWrapper defined in client/types/terms/tw.ts
-//Do not use #types TermWrapper here as it will be deprecated
-export type TermdbSampleScatterRequest = {
-	genome: string
-	dslabel: string
-	colorTW?: any //TermWrapper
-	shapeTW?: any //TermWrapper
-	divideByTW?: any //TermWrapper
-	scaleDotTW?: any //TermWrapper
-	coordTWs?: any[] //TermWrapper[]
-	plotName?: string
-	filter?: any
-	filter0?: any
-	chartType?: string
-	singleCellPlot?: any
-	colorColumn?: any
-	excludeOutliers?: any
-}
-
-export type ScatterSample = {
-	category: string
-	sample: string
-	info?: { [index: string]: any }
-	shape: string
-	x: number
-	y: number
-	z: number
-}
-
-type ColorObject = { color: string; sampleCount: number; key: string }
-export type ColorLegendEntry = [string, ColorObject]
-export type ColorMap = { [index: string]: ColorObject }
-
-type ShapeObject = { shape: number; sampleCount: number; key: string }
-export type ShapeLegendEntry = [string, ShapeObject]
-export type ShapeMap = { [index: string]: ShapeObject }
-
-type ScatterResult = {
-	[index: string]: {
-		colorLegend: ColorLegendEntry[]
-		samples: ScatterSample[]
-		shapeLegend: ShapeLegendEntry[]
-	}
-}
-
-export type TermdbSampleScatterResponse = {
-	range: { xMin: number; xMax: number; yMin: number; yMax: number }
-	result: ScatterResult
-}
-
-export const termdbSampleScatterPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSampleScatterRequest'
-	},
-	response: {
-		typeId: 'TermdbSampleScatterResponse'
-	}
-}

package/src/routes/termdb.singleSampleMutation.ts

@@ -1,51 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type TermdbSingleSampleMutationRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** sample id, allow string or number; for native ds, sample name in number will be cast into string */
-	sample: string | number
-}
-type ValidResponse = {
-	/** List of mutation data points from this sample TODO change to type of M elements */
-	mlst: object[]
-	/** total number of items for each dt, useful to indicate snvindel limited to 10k for a hypermutator */
-	dt2total?: { dt: number; total: number }[]
-	/** declares presence of alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
-	key: dt value
-	value: array of objects, each is a distinct set of data points for this dt
-		on ui, selecting an object will allow to show this data in disco plot
-		each is identified by either nameHtml or name
-	*/
-	alternativeDataByDt?: {
-		[index: number]: {
-			/** hyperlink */
-			nameHtml?: string
-			/** name in text */
-			name?: string
-			/** one set of data must have this flag set to true to indicate its data is already present in ValidResponse.mlst */
-			inuse?: boolean
-			/** required list of events from this data */
-			mlst: object[]
-			/** optional info about this source */
-			attrs?: {
-				[index: string]: string
-			}
-		}[]
-	}
-}
-
-export type TermdbSingleSampleMutationResponse = ErrorResponse | ValidResponse
-
-export const termdbSingleSampleMutationPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSingleSampleMutationRequest'
-	},
-	response: {
-		typeId: 'TermdbSingleSampleMutationResponse'
-	}
-	// examples: []
-}

package/src/routes/termdb.singlecellDEgenes.ts

@@ -1,50 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { ErrorResponse } from './errorResponse.ts'
-import type { DataEntry, VolcanoData, VolcanoRenderRequest } from './termdb.DE.js'
-
-export type TermdbSingleCellDEgenesRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** Sample identifier
-	 * for GDC the value is "seurat.analysis.tsv" file UUID
-	 * rather than sample name, derived from the eID. The file
-	 * contains the analysis results for an experiment.
-	 *
-	 * Eventually, all requests will use the object and
-	 * **not** the string format.*/
-	sample: string | { sID: string; eID: string }
-	/** column name to provide cell groups/clustering,
-	 * for which DE genes are precomputed.  */
-	termId: string
-	/** User selected cell group/cluster, corresponds to termId,
-	 * for which DE genes will be returned to client */
-	categoryName: string
-	/** Parameters for the server-side `volcano` Rust renderer. Always required — the
-	 * server always returns a rendered PNG plus the threshold-passing rows. */
-	volcanoRender: VolcanoRenderRequest
-}
-
-export type SingleCellDEEntry = DataEntry & {
-	/** gene name */
-	gene_name: string
-}
-
-export type HasDataResponse = {
-	/** The volcano payload — per-gene interactive dots + PNG + extents + totals.
-	 * See VolcanoData for details. */
-	data: VolcanoData<SingleCellDEEntry>
-}
-
-export type TermdbSingleCellDEgenesResponse = ErrorResponse | HasDataResponse
-
-export const termdbSingleCellDEgenesPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSingleCellDEgenesRequest'
-	},
-	response: {
-		typeId: 'TermdbSingleCellDEgenesResponse'
-	}
-	// examples: []
-}

package/src/routes/termdb.singlecellData.ts

@@ -1,75 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type Cell = {
-	/** Cell id or barcode */
-	cellId: string
-	/** X coord of the cell */
-	x: number
-	/** Y coord of the cell */
-	y: number
-	/** Z coord of the cell, should be present for all cells and trigger 3d plot   */
-	z?: number
-	/** The cell may have different classifications, e.g. by cell type, CNV, FUSION, etc. */
-	category: string
-	/** Gene expression data for this cell */
-	geneExp?: number
-}
-
-export type Plot = {
-	/** name of the plot */
-	name: string
-	/** List of cells with gene expression */
-	expCells: Cell[]
-	/** List of cells with no gene expression, if no gene provided all cells will be here */
-	noExpCells: Cell[]
-	colorColumns: string[]
-	colorBy: string
-	colorMap: any
-}
-
-export type TermdbSingleCellDataRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** Sample name for which the sc results will be shown.
-	for GDC the value is "seurat.analysis.tsv" file UUID rather than any sample name. the file contains the analysis results for an experiment */
-	sample: { eID?: string; sID: string }
-	/** List of plot names from this sample to request data for */
-	plots: string[]
-	/** check plot availability for this sample, will not return actual plot data and speed up */
-	checkPlotAvailability?: boolean
-	/** Gene name to retrieve expression data for all cells of the given sample, and to overlay on maps */
-	gene?: string
-	/** in each plot, what Column name to color by 
-	key: plot.name, value: column name
-	if missing, use default setting of the plot
-	*/
-	// colorBy?: { [key: string]: string }
-	colorBy?: string
-	colorMap?: { [key: string]: string }
-	singleCellPlot?: any
-}
-
-export type HasdataResponse = {
-	/** List of plots from singlecell experiment of this sample */
-	plots: Plot[]
-}
-
-export type NodataResponse = {
-	/** Flag to indicate no sc data for this sample */
-	nodata: boolean
-}
-
-export type TermdbSingleCellDataResponse = NodataResponse | ErrorResponse | HasdataResponse
-
-export const termdbSingleCellDataPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSingleCellDataRequest'
-	},
-	response: {
-		typeId: 'TermdbSingleCellDataResponse'
-	}
-	// examples: []
-}

package/src/routes/termdb.singlecellSamples.ts

@@ -1,50 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type SingleCellSample = {
-	/** Sample name, required */
-	sample: string
-	/** optional list of sc data files available for this sample, gdc-specific
-	if available:
-		each row of sample table will infact be one experiment.
-		selecting one will use its experimentID as "sample" value in request parameter
-		each experiment may have additional fields that may be displayed in table. see singleCell.samples.experimentColumns[]
-
-	if no exp, then each sample will just have one experiment identifiable by its sample name, and this name is used in request
-	*/
-	[key: string]: any //sample column/term value
-	experiments?: {
-		sampleName: any
-		experimentID?: string
-	}[]
-	isMetaResult?: boolean // whether this sample is a meta result. if so, sample name is from plot.sampleId or plot.name and experimentID is not used
-	// a sample may have additional fields that will be displayed in table, see singleCell.samples.sampleColumns[]
-}
-
-export type TermdbSingleCellSamplesRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	//filter0?: Filter0 // for gdc
-}
-type ValidResponse = {
-	/** List of sample names with singlecell data */
-	samples: SingleCellSample[]
-	metaResults?: {
-		/** identifier of one result */
-		name: string
-	}[]
-}
-
-export type TermdbSingleCellSamplesResponse = ErrorResponse | ValidResponse
-
-export const termdbSingleCellSamplesPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSingleCellSamplesRequest'
-	},
-	response: {
-		typeId: 'TermdbSingleCellSamplesResponse'
-	}
-	// examples: []
-}

package/src/routes/termdb.termchildren.ts

@@ -1,49 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type TermChildrenRequest = {
-	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
-	genome: string
-	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
-	dslabel: string
-	embedder: string
-	get_children: number
-	tid: string
-}
-
-interface Entries {
-	name: string
-	id: string
-	isleaf: boolean
-	included_types: string[]
-	child_types: string[]
-}
-
-export type TermChildrenResponse = {
-	lst: Entries[]
-}
-
-export const termChildrenPayload: RoutePayload = {
-	request: {
-		typeId: 'TermChildrenRequest'
-	},
-	response: {
-		typeId: 'TermChildrenResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					embedder: 'localhost',
-					get_children: 1,
-					cohortValues: 'ABC',
-					tid: 'GO:0000001'
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/termdb.termsbyids.ts

@@ -1,26 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { TermWrapper } from '../terms/tw.ts'
-
-export type TermsByIdsRequest = {
-	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
-	genome: string
-	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
-	dslabel: string
-	embedder: string
-	/** term id string */
-	ids: string[]
-}
-
-export type TermsByIdsResponse = {
-	terms: { [id: string]: TermWrapper }
-}
-
-export const termsByIdsPayload: RoutePayload = {
-	request: {
-		typeId: 'TermsByIdsRequest'
-	},
-	response: {
-		typeId: 'TermsByIdsResponse'
-	}
-	// examples: []
-}

package/src/routes/termdb.topMutatedGenes.ts

@@ -1,51 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type topMutatedGeneRequest = {
-	genome: string
-	dslabel: string
-	/** to restrict to CGC genes */
-	geneFilter?: 'CGC'
-	/** max number of genes to return */
-	maxGenes?: number
-	/** pp filter */
-	filter?: object
-	/** gdc cohort filter */
-	filter0?: object
-	/** rest are arguments for built in query */
-	snv_mfndi?: number
-	snv_splice?: number
-	snv_utr?: number
-	snv_s?: number
-	sv?: number
-	fusion?: number
-	cnv?: number
-	cnv_ms?: { type: string; geneLst: null }
-	cnv_logratio?: { type: string; geneLst: null }
-}
-
-export type MutatedGene = {
-	/** gene symbol */
-	gene: string
-	/** optional attributes on number of mutated cases per dt */
-	mutationStat?: {
-		/** each stat object is identified by either dt or class */
-		dt?: number
-		class?: string
-		/** number of samples with alterations of this gene */
-		count: number
-	}[]
-}
-
-export type topMutatedGeneResponse = {
-	genes: MutatedGene[]
-}
-
-export const topMutatedGenePayload: RoutePayload = {
-	request: {
-		typeId: 'topMutatedGeneRequest'
-	},
-	response: {
-		typeId: 'topMutatedGeneResponse'
-	}
-	//examples: []
-}

package/src/routes/termdb.topTermsByType.ts

@@ -1,32 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-//import GdcFilter0 from './filter.gdc'
-import type { Term } from '../terms/term.ts'
-import type { Filter } from '../filter.ts'
-
-export type TermdbTopTermsByTypeRequest = {
-	/** Ref genome */
-	genome: string
-	/** Ds label */
-	dslabel: string
-	/* Term type */
-	type: string
-	/** pp filter */
-	filter?: Filter
-	/** JSON, optional GDC cohort filter to restrict cases */
-	filter0?: any //GdcFilter0
-}
-
-export type TermdbTopTermsByTypeResponse = {
-	/** Array of gene names TODO may change element to objs */
-	terms: Term[]
-}
-
-export const termdbTopTermsByTypePayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbTopTermsByTypeRequest'
-	},
-	response: {
-		typeId: 'TermdbTopTermsByTypeResponse'
-	},
-	// examples: []
-}

package/src/routes/termdb.topVariablyExpressedGenes.ts

@@ -1,54 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-//import GdcFilter0 from './filter.gdc'
-import type { Filter } from '../filter.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type TermdbTopVariablyExpressedGenesRequest = {
-	/** Ref genome */
-	genome: string
-	/** Ds label */
-	dslabel: string
-	/** Number of top genes requested */
-	maxGenes: number
-	/** optional param defined by dataset. if to scan all or subset of genes */
-	geneSet?: {
-		/** Indicates the geneset to return
-		 * all - all genes
-		 * custom - user defined list of genes
-		 * msigdb - msigdb geneset
-		 */
-		type: 'all' | 'custom' | 'msigdb'
-		/** Sent as null for 'all' types. Otherwise a list of gene symbols */
-		geneList: string[] | null
-	}
-	/** optional parameter defined in gdc dataset. not used for non-gdc ds */
-	min_median_log2_uqfpkm?: number
-	/** filter extreme values (in native implementation): true/false */
-	filter_extreme_values?: boolean | number
-	/** Filter type: variance/inter-quartile region (in native implementation) */
-	rank_type?: {
-		type: 'var' | 'iqr'
-	}
-	filter?: Filter
-	/** JSON, optional GDC cohort filter to restrict cases */
-	filter0?: any //GdcFilter0
-	/** helps ds getter */
-	ds?: any
-}
-
-type ValidResponse = {
-	/** Array of gene names TODO may change element to objs */
-	genes: string[]
-}
-
-export type TermdbTopVariablyExpressedGenesResponse = ErrorResponse | ValidResponse
-
-export const termdbTopVariablyExpressedGenesPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbTopVariablyExpressedGenesRequest'
-	},
-	response: {
-		typeId: 'TermdbTopVariablyExpressedGenesResponse'
-	}
-	// examples: []
-}