@sjcrh/proteinpaint-types 2.78.0-0

package/src/routes/hicdata.ts

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+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

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+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

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+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

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+export type * from './dzimages.ts'

package/src/routes/samplewsimages.ts

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+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

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+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
+	/** Method of DE used wilcoxon/edgeR */
+	method?: string
+}
+
+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.categories.ts

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+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

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+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'
+
+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 TermdbClusterRequest = TermdbClusterRequestGeneExpression | TermdbClusterRequestMetabolite
+
+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

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+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

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+//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

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+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

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+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

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+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

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+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

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+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

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+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

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+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

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+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 */
+	cells: Cell[]
+	/** Column name to color by, e.g Cell type, CNV, Fusion */
+	colorBy: 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
+}
+
+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

package/src/routes/termdb.singlecellSamples.ts

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+import type { ErrorResponse } from './errorResponse.ts'
+
+export type Sample = {
+	/** 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?: { experimentID: string }[]
+
+	// 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: Sample[]
+	fields: string[]
+	columnNames: string[]
+	sameLegend?: boolean
+}
+
+export type TermdbSinglecellsamplesResponse = ErrorResponse | ValidResponse

package/src/routes/termdb.termsbyids.ts

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+import type { TermWrapper } from '../terms/tw.ts'
+
+export type gettermsbyidsRequest = {
+	/** 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 gettermsbyidsResponse = {
+	terms: { [id: string]: TermWrapper }
+}

package/src/routes/termdb.topVariablyExpressedGenes.ts

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+//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?: number
+	/** min_count of fpkm when filter_extreme_values (in native implementation) = true */
+	min_count?: number
+	/** min_total_count of fpkm when filter_extreme_values (in native implementation) = true */
+	min_total_count?: 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
+}
+
+type ValidResponse = {
+	/** Array of gene names TODO may change element to objs */
+	genes: string[]
+}
+
+export type TermdbTopVariablyExpressedGenesResponse = ErrorResponse | ValidResponse