@sjcrh/proteinpaint-types 2.84.0 → 2.85.0

package/src/routes/healthcheck.ts

@@ -1,57 +0,0 @@
-/**
- * for documentation only, to signify integer: not type-checked statically
- */
-type int = number
-
-/**
- * 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]: int
-	}
-}
-
-/**
- * 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
-}

package/src/routes/hicdata.ts

@@ -1,37 +0,0 @@
-import type { FileORURL } from '../fileOrUrl.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 Item = [
-	/** 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: Item[]
-}

package/src/routes/hicgenome.ts

@@ -1,22 +0,0 @@
-import type { BaseHicRequest, Item } from './hicdata.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: Item[]
-	}[]
-	/** Error message to display on the client, if applicable */
-	error?: string
-}

package/src/routes/hicstat.ts

@@ -1,45 +0,0 @@
-type HicstatRequestWithFile = {
-	/** HiC file path from tp/ */
-	file: string
-	/** If file is provided, url should not be provided. Checked in validation type */
-	url?: never
-}
-
-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[]
-}

package/src/routes/sampledzimages.ts

@@ -1 +0,0 @@
-export type * from './dzimages.ts'

package/src/routes/samplewsimages.ts

@@ -1,15 +0,0 @@
-export type GetSampleWSImagesRequest = {
-	genome: string
-	dslabel: string
-	sample_id: string
-	wsimage: string
-}
-
-export type GetSampleWSImagesResponse = {
-	sampleWSImages: string[]
-}
-
-export type WSImage = {
-	filename: string
-	metadata: string
-}

package/src/routes/termdb.DE.ts

@@ -1,44 +0,0 @@
-export type DERequest = {
-	/** Genome build name */
-	genome: string
-	/** dataset label */
-	dslabel: string
-	/* Object containing two arrays of RNA seq count for DE analysis */
-	samplelst: any //{number[]; number[];}
-	/** Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset */
-	min_count: number
-	/** Minimum total read count required for each sample */
-	min_total_count: number
-	/** Storage_type for storing data. Will deprecate text files */
-	storage_type: 'text' | 'HDF5'
-	/** Method of DE used wilcoxon/edgeR */
-	method?: string
-}
-
-export type ExpressionInput = {
-	/** Case samples separated by , */
-	case: string
-	/** Control samples separated by , */
-	control: string
-	/** data_type instructs rust to carry out differential gene expression analysis */
-	data_type: 'do_DE'
-	/** File containing raw gene counts for DE analysis */
-	input_file: string
-	/** Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset */
-	min_count: number
-	/** Minimum total read count required for each sample */
-	min_total_count: number
-	/** Type of storage file: HDF5 or text. Text will be deprecated in the future */
-	storage_type: 'HDF5' | 'text'
-}
-
-export type DEResponse = {
-	/** Array containing objects of each gene containing foldchange, gene name, gene symbol, original pvalue, adjusted pvalue */
-	data: string
-	/** Effective sample size for group 1 */
-	sample_size1: number
-	/** Effective sample size for group 2 */
-	sample_size2: number
-	/** Method of DE used wilcoxon/edgeR */
-	method: string
-}

package/src/routes/termdb.boxplot.ts

@@ -1,49 +0,0 @@
-export type BoxPlotRequest = {
-	//TOOD: define request
-	tw: any
-}
-
-export type BoxPlotResponse = {
-	/** Absolute min value for all plots */
-	absMin: number
-	/** Absolute max value for all plots */
-	absMax: number
-	/** Longest label length for all plots */
-	maxLabelLgth: number
-	plots: BoxPlotEntry[]
-}
-
-type BoxPlotEntry = {
-	boxplot: BoxPlotData
-	/** Label to show */
-	label: string
-	// /** Number of samples */
-	// plotValueCount: number
-	/** TODO: Is this needed? */
-	values: number[]
-	/** Lowest min for the scale domain */
-	min: number
-	/** Highest max for the scale domain */
-	max: number
-}
-
-type BoxPlotData = {
-	/** Min/1st whisker value */
-	w1: number
-	/** Max/2nd whisker value */
-	w2: number
-	/** 5% */
-	p05: number
-	/** 25% */
-	p25: number
-	/** 50% */
-	p50: number
-	/** 75% */
-	p75: number
-	/** 95% */
-	p95: number
-	/** Interquartile region */
-	iqr: number
-	/** Outliers */
-	out: { value: number }[]
-}

package/src/routes/termdb.categories.ts

@@ -1,26 +0,0 @@
-import type { Filter } from '../filter.ts'
-import type { TermWrapper } from '../terms/tw.ts'
-
-export type getcategoriesRequest = {
-	genome: string
-	dslabel: string
-	embedder: string
-	/** termwrapper object */
-	tw: TermWrapper
-	filter?: Filter
-	/** quick fix only for gdc */
-	currentGeneNames?: string[]
-	/** optional property added by mds3 tk, to limit to cases mutated in this region */
-	rglst?: any
-}
-
-interface entries {
-	samplecount: number
-	key: string
-	label: string
-}
-
-export type getcategoriesResponse = {
-	lst: entries[]
-	orderedLabels?: []
-}

package/src/routes/termdb.cluster.ts

@@ -1,86 +0,0 @@
-import { ErrorResponse } from './errorResponse.ts'
-import { Filter } from '../filter.ts'
-import { Term } from '../terms/term.ts'
-import { GeneExpressionTerm } from '../terms/geneExpression.ts'
-import { MetaboliteIntensityTerm } from '../terms/metaboliteIntensity.ts'
-import { NumericDictTerm } from '../terms/numeric.ts'
-
-export type Gene = {
-	/** gene symbol, required */
-	gene: string
-	/** optionally, client may supply chr/start/stop; if missing, backend code may add them when processing native dataset */
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-type TermdbClusterRequestBase = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** cluster method */
-	clusterMethod: string
-	/** distance method */
-	distanceMethod: string
-	/** pp filter */
-	filter?: Filter
-	/** todo gdc filter */
-	filter0?: any
-}
-
-export type TermdbClusterRequestGeneExpression = TermdbClusterRequestBase & {
-	/** Data type */
-	dataType: 'geneExpression'
-	/** List of terms */
-	terms: GeneExpressionTerm[]
-}
-
-export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
-	/** Data type */
-	dataType: 'metaboliteIntensity'
-	/** List of terms */
-	terms: MetaboliteIntensityTerm[]
-}
-
-export type TermdbClusterRequestNumericDictTerm = TermdbClusterRequestBase & {
-	/** Data type */
-	dataType: 'numericDictTerm'
-	/** List of terms */
-	terms: NumericDictTerm[]
-}
-
-export type TermdbClusterRequest =
-	| TermdbClusterRequestGeneExpression
-	| TermdbClusterRequestMetabolite
-	| TermdbClusterRequestNumericDictTerm
-
-export type Hclust = {
-	merge: { n1: number; n2: number }[]
-	height: { height: number }[]
-	order: { name: string }[]
-	inputOrder: string[]
-}
-export type Clustering = {
-	row: Hclust
-	col: Hclust
-	matrix: number[][]
-}
-
-// response with clustering result of multiple gene/rows
-export type ValidResponse = {
-	/**  */
-	clustering: Clustering
-	/**  */
-	byTermId: { [index: string]: any }
-	/**  */
-	bySampleId: { [index: string]: any }
-}
-
-//response of just 1 gene, thus unable to do clustering
-export type SingletermResponse = {
-	term: Term
-	data: any
-}
-
-export type TermdbClusterResponse = ErrorResponse | ValidResponse | SingletermResponse

package/src/routes/termdb.getSampleImages.ts

@@ -1,14 +0,0 @@
-export type TermdbGetSampleImagesRequest = {
-	genome: string
-	/** Ds label */
-	dslabel: string
-	sampleId: number
-}
-
-export type Image = {
-	src: any
-}
-
-export type TermdbGetSampleImagesResponse = {
-	images: Image[]
-}

package/src/routes/termdb.getTopTermsByType.ts

@@ -1,21 +0,0 @@
-//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[]
-}

package/src/routes/termdb.getdescrstats.ts

@@ -1,31 +0,0 @@
-import type { Filter } from '../filter.ts'
-import type { TermWrapper } from '../terms/tw.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type getdescrstatsRequest = {
-	/** genome label in the serverconfig.json */
-	genome: string
-	/** dataset label for the given genome */
-	dslabel: string
-	embedder: string
-	/** wrapper of a numeric term, q.mode can be any as getData() will always pull sample-level values for summarizing */
-	tw: TermWrapper
-	/** if true, the (violin) plot is in log scale and must exclude 0-values from the stat */
-	logScale?: boolean
-	/** optional pp filter */
-	filter?: Filter
-	/** optional gdc filter */
-	filter0?: any
-}
-
-interface entries {
-	id: string
-	label: string
-	value: number
-}
-
-type ValidResponse = {
-	values: entries[]
-}
-
-export type getdescrstatsResponse = ValidResponse | ErrorResponse

package/src/routes/termdb.getnumericcategories.ts

@@ -1,21 +0,0 @@
-import type { Filter } from '../filter.ts'
-
-export type getnumericcategoriesRequest = {
-	/** 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 */
-	tid: string
-	filter?: Filter
-}
-
-interface entries {
-	value: number
-	samplecount: number
-}
-
-export type getnumericcategoriesResponse = {
-	lst: entries[]
-}

package/src/routes/termdb.getpercentile.ts

@@ -1,17 +0,0 @@
-import type { Filter } from '../filter.ts'
-
-export type getpercentileRequest = {
-	/** 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
-	getpercentile: number[]
-	/** term id string */
-	tid: string
-	filter: Filter
-}
-
-export type getpercentileResponse = {
-	values: number[]
-}

package/src/routes/termdb.getrootterm.ts

@@ -1,22 +0,0 @@
-export type getroottermRequest = {
-	/** 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
-	default_rootterm: number
-	cohortValues: string
-	treeFilter: string
-}
-
-interface entries {
-	name: string
-	id: string
-	isleaf: boolean
-	included_types: string[]
-	child_types: string[]
-}
-
-export type getroottermResponse = {
-	lst: entries[]
-}

package/src/routes/termdb.gettermchildren.ts

@@ -1,21 +0,0 @@
-export type gettermchildrenRequest = {
-	/** 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 gettermchildrenResponse = {
-	lst: entries[]
-}

package/src/routes/termdb.singleSampleMutation.ts

@@ -1,18 +0,0 @@
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type TermdbSingleSampleMutationRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** sample id */
-	sample: string
-}
-type ValidResponse = {
-	/** List of mutation data points from this sample TODO change to type of M elements */
-	mlst: object[]
-	/** */
-	dt2total?: { dt: number; total: number }[]
-}
-
-export type TermdbSingleSampleMutationResponse = ErrorResponse | ValidResponse

package/src/routes/termdb.singlecellDEgenes.ts

@@ -1,30 +0,0 @@
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type TermdbSinglecellDEgenesRequest = {
-	/** Genome id */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** Sample name
-	for GDC the value is "seurat.analysis.tsv" file UUID rather than sample name. the file contains the analysis results for an experiment
-	*/
-	sample: string
-	/** column name to provide cell groups/clustering, for which DE genes are precomputed.  */
-	columnName: string
-	/** User selected cell group/cluster, corresponds to columnName, for which DE genes will be returned to client */
-	categoryName: string
-}
-
-export type HasDataResponse = {
-	/** list of significant DE genes for the given category in the sample */
-	genes: {
-		/** gene name */
-		name: string
-		/** adjusted p-value */
-		p_val_adj: number
-		/** log foldchange */
-		avg_log2FC: number
-	}[]
-}
-
-export type TermdbSinglecellDEgenesResponse = ErrorResponse | HasDataResponse

package/src/routes/termdb.singlecellData.ts

@@ -1,58 +0,0 @@
-import { 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[]
-	/** Column name to color by, e.g Cell type, CNV, Fusion */
-	colorBy: string
-	colorColumns: string[]
-	colorMap?: { [key: string]: string }
-}
-
-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[]
-	/** Gene name to retrieve expression data for all cells of the given sample, and to overlay on maps */
-	gene?: string
-}
-
-export type HasdataResponse = {
-	/** List of plots from singlecell experiment of this sample */
-	plots: Plot[]
-
-	/** Terms used to annotate cells */
-	//terms: Term[]
-}
-
-export type NodataResponse = {
-	/** Flag to indicate no sc data for this sample */
-	nodata: boolean
-}
-
-export type TermdbSinglecellDataResponse = NodataResponse | ErrorResponse | HasdataResponse