@sjcrh/proteinpaint-types 2.86.0 → 2.87.1

package/src/routes/gdc.topMutatedGenes.ts

@@ -0,0 +1,37 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type GdcTopMutatedGeneRequest = {
+	/** to restrict to CGC genes */
+	geneFilter?: 'CGC'
+	/** max number of genes to return */
+	maxGenes?: number
+	/** gdc cohort filter */
+	filter0?: object
+}
+
+export type GdcGene = {
+	/** 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 GdcTopMutatedGeneResponse = {
+	genes: GdcGene[]
+}
+
+export const gdcTopMutatedGenePayload: RoutePayload = {
+	request: {
+		typeId: 'GdcTopMutatedGeneRequest'
+	},
+	response: {
+		typeId: 'GdcTopMutatedGeneResponse'
+	}
+	//examples: []
+}

package/src/routes/genelookup.ts

@@ -0,0 +1,22 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type GeneLookupRequest = {
+	input: string
+	genome: string
+	deep: boolean
+}
+
+export type GeneLookupResponse = {
+	error?: string
+	hits: string[]
+}
+
+export const geneLookupPayload: RoutePayload = {
+	request: {
+		typeId: 'GeneLookupRequest'
+	},
+	response: {
+		typeId: 'GeneLookupResponse'
+	}
+	//examples: []
+}

package/src/routes/genesetEnrichment.ts

@@ -0,0 +1,60 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type GenesetEnrichmentRequest = {
+	/** Sample genes to be queried */
+	genes: string[]
+	/** Background genes against which the sample genes will be queried */
+	fold_change: number[]
+	/** Filter non-coding genes */
+	filter_non_coding_genes: boolean
+	/** Genome build */
+	genome: string
+	/** Type of GO to be queried e.g MF, CC, BP */
+	geneSetGroup: string
+	/** Gene set name whose enrichment score is to be profiled */
+	geneset_name?: string
+	/** Pickle file to be queried for generating gsea image of a particular geneset */
+	pickle_file?: string
+}
+
+type pathway_attributes = {
+	/** Absolute enrichment score */
+	es: number
+	/** Normalized enrichment score */
+	nes: number
+	/** Size of gene set */
+	geneset_size: number
+	/** Leading edge genes */
+	leading_edge: string
+	/** pvalue */
+	pvalue: number
+	/** sidak (multiple testing correction) */
+	sidak: number
+	/** false discovery rate */
+	fdr: number
+}
+
+type gsea_result = {
+	/** array of pathway_attributes */
+	data: pathway_attributes[]
+	/** file name of pickle file containing the stored gsea result in cache directory */
+	pickle_file: string
+}
+
+/** Pass gsea image to client side */
+type gsea_image = any
+
+export type GenesetEnrichmentResponse = {
+	/** gsea result or an image (for plotting) is sent to client side */
+	pathway: gsea_result | gsea_image
+}
+
+export const genesetEnrichmentPayload: RoutePayload = {
+	request: {
+		typeId: 'GenesetEnrichmentRequest'
+	},
+	response: {
+		typeId: 'GenesetEnrichmentResponse'
+	}
+	//examples: []
+}

package/src/routes/genesetOverrepresentation.ts

@@ -0,0 +1,48 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type GenesetOverrepresentationRequest = {
+	/**  Sample genes to be queried */
+	sample_genes: string
+	/** Background genes against which the sample genes will be queried. if missing will use all protein-coding genes, available in gene db */
+	background_genes?: string
+	/** Genome build */
+	genome: string
+	/** msigdb branch term name. all genesets under this branch will be analyzed */
+	geneSetGroup: string
+	/** Boolean variable describing if non-coding genes should be filtered */
+	filter_non_coding_genes: boolean
+}
+
+export type GenesetOverrepresentationResponse = {
+	/** Name of pathway */
+	pathway_name: string
+	/** Original p-value */
+	p_value_original: number
+	/** Adjusted p-value */
+	p_value_adjusted: number
+}
+
+export type gene_overrepresentation_input = {
+	/** Input sample genes */
+	sample_genes: string
+	/** Input background genes */
+	background_genes?: string
+	/** Path to msigdb */
+	msigdb: string
+	/** Name of Gene Set Group */
+	gene_set_group: string
+	/** Path to gene db */
+	genedb: string
+	/** Boolean variable describing if non-coding genes should be filtered */
+	filter_non_coding_genes: boolean
+}
+
+export const genesetOverrepresentationPayload: RoutePayload = {
+	request: {
+		typeId: 'GenesetOverrepresentationRequest'
+	},
+	response: {
+		typeId: 'GenesetOverrepresentationResponse'
+	}
+	// examples: []
+}

package/src/routes/healthcheck.ts

@@ -0,0 +1,79 @@
+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
+}
+
+export const healthcheckPayload: RoutePayload = {
+	request: {
+		typeId: 'HealthCheckRequest'
+	},
+	response: {
+		typeId: 'HealthCheckResponse'
+	},
+	examples: [
+		{
+			request: { body: {} }
+			//response: {}
+		},
+		{
+			request: {
+				body: { dsLabel: 'TermdbTest' }
+			}
+			//response: {}
+		}
+	]
+}

package/src/routes/hicdata.ts

@@ -0,0 +1,48 @@
+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

@@ -0,0 +1,50 @@
+import type { BaseHicRequest, XYZCoord } from './hicdata.ts'
+import { 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

@@ -0,0 +1,57 @@
+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/isoformlst.ts

@@ -0,0 +1,14 @@
+import { 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

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,14 @@
+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

@@ -0,0 +1,41 @@
+export type RouteApi = {
+	endpoint: string
+	methods: {
+		get?: RoutePayload
+		post?: 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
+}
+
+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

@@ -0,0 +1,27 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type SampleWSImagesRequest = {
+	genome: string
+	dslabel: string
+	sample_id: string
+	wsimage: string
+}
+
+export type SampleWSImagesResponse = {
+	sampleWSImages: string[]
+}
+
+export type WSImage = {
+	filename: string
+	metadata: string
+}
+
+export const sampleWSImagesPayload: RoutePayload = {
+	request: {
+		typeId: 'SampleWSImagesRequest'
+	},
+	response: {
+		typeId: 'SampleWSImagesResponse'
+	}
+	// examples: []
+}

package/src/routes/snp.ts

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

package/src/routes/termdb.DE.ts

@@ -0,0 +1,57 @@
+import type { RoutePayload } from './routeApi.js'
+
+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
+}
+
+export const diffExpPayload: RoutePayload = {
+	request: {
+		typeId: 'DERequest'
+	},
+	response: {
+		typeId: 'DEResponse'
+		// will combine this with type checker
+		//valid: (t) => {}
+	}
+}

package/src/routes/termdb.boxplot.ts

@@ -0,0 +1,78 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type BoxPlotRequest = {
+	/** Args set in TermVocab */
+	/** term1 or term */
+	tw: any
+	genome: string
+	dslabel: string
+	/** term2 */
+	overlayTw?: any
+	filter: any
+	filter0: any
+}
+
+export type BoxPlotResponse = {
+	/** Absolute min value for all plots */
+	absMin?: number
+	/** Absolute max value for all plots */
+	absMax?: number
+	plots: BoxPlotEntry[]
+	/** Categories not shown in the final plot */
+	uncomputableValues: { label: string; value: number }[] | null
+}
+
+export type BoxPlotEntry = {
+	boxplot: BoxPlotData & { label: string }
+	/** color matching the value/category color */
+	color?: string
+	descrStats: BoxPlotDescrStatsEntry[]
+	/** Pertains to an uncomputable term value and
+	 * whether or not the plot is hidden by default */
+	isHidden?: boolean
+	key: string
+	/** Formatted bins for numeric terms */
+	overlayBins?: any
+	/** Usually the same as key, but determined by the tw */
+	seriesId?: string
+}
+
+export type BoxPlotData = {
+	/** Min/1st whisker value */
+	w1: number | undefined
+	/** Max/2nd whisker value */
+	w2: number | undefined
+	/** 5% */
+	p05: number
+	/** 25% */
+	p25: number
+	/** 50%, median */
+	p50: number
+	/** 75% */
+	p75: number
+	/** 95% */
+	p95: number
+	/** Interquartile region */
+	iqr: number
+	/** Outliers */
+	out: { value: number }[]
+}
+
+export type BoxPlotDescrStatsEntry = {
+	/** Use lower case for sanity check
+	 * 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr'
+	 */
+	id: string
+	label: string
+	value: number
+}
+
+export const boxplotPayload: RoutePayload = {
+	request: {
+		typeId: 'BoxPlotRequest'
+	},
+	response: {
+		typeId: 'BoxPlotResponse'
+	}
+	//examples: []
+}