@sjcrh/proteinpaint-types 2.78.0-0

package/src/fileOrUrl.ts

@@ -0,0 +1,15 @@
+type FileNotURL = {
+	/** File path from tp/ */
+	file: string
+	/** If file is provided, url should not be provided. Checked in validation type */
+	url?: never
+}
+
+type URLNotFile = {
+	/** If url is provided, file should not be provided. Checked in validation type */
+	file?: never
+	/** Remote file URL */
+	url: string
+}
+
+export type FileORURL = FileNotURL | URLNotFile

package/src/filter.ts

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+import { BaseValue } from './terms/term.ts'
+import { NumericTerm, NumericBin } from './terms/numeric.ts'
+import { CategoricalTerm } from './terms/categorical.ts'
+import { GeneVariantTerm } from './terms/geneVariant.ts'
+import { ConditionTerm } from './terms/condition.ts'
+
+/*
+--------EXPORTED--------
+Tvs
+LstEntry
+Filter
+
+*/
+
+/*** types supporting Tvs type ***/
+
+export type BaseTvs = {
+	join?: string //and, or
+	isnot?: boolean
+}
+
+export type CategoricalTvs = BaseTvs & {
+	term: CategoricalTerm
+	groupset_label?: string
+	values: BaseValue[]
+}
+
+export type NumericTvs = BaseTvs & {
+	term: NumericTerm
+	ranges: NumericBin[]
+	// TODO: define uncomputable values object
+	values: {
+		key: string
+		value: number
+		uncomputable: true
+		label?: string
+	}[]
+}
+
+type GradeAndChildEntry = {
+	grade: number
+	grade_label: string
+	child_id: string | undefined
+	child_label: string
+}
+
+export type ConditionTvs = BaseTvs & {
+	term: ConditionTerm
+	value_by_max_grade?: boolean
+	value_by_most_recent?: boolean
+	value_by_computable_grade?: boolean
+	grade_and_child?: GradeAndChildEntry[]
+}
+
+type GeneVariantOrigin = 'somatic' | 'germline'
+
+type SNVIndelClasses =
+	| 'M'
+	| 'E'
+	| 'F'
+	| 'N'
+	| 'S'
+	| 'D'
+	| 'I'
+	| 'P'
+	| 'L'
+	| 'Intron'
+	| 'Blank'
+	| 'WT'
+	| 'ITD'
+	| 'DEL'
+	| 'NLOSS'
+	| 'CLOSS'
+	| 'Utr3'
+	| 'Utr5'
+	| 'X'
+	| 'noncoding'
+type SNVIndelTvsValue = {
+	dt: 1
+	mclassLst: SNVIndelClasses[]
+	mclassExcludeLst: SNVIndelClasses[]
+	origin?: GeneVariantOrigin
+}
+
+type CNVClasses = 'CNV_amp' | 'CNV_losss' | 'CNV_loh' | 'Blank' | 'WT'
+type CNVTvsValue = {
+	dt: 4
+	mclassLst: CNVClasses[]
+	mclassExcludeLst: CNVClasses[]
+	origin?: GeneVariantOrigin
+}
+
+type SVClasses = 'SV' | 'Blank' | 'WT'
+type SVTvsValue = {
+	dt: 5
+	mclassLst: SVClasses[]
+	mclassExcludeLst: SVClasses[]
+	origin?: GeneVariantOrigin
+}
+
+type FusionRNAClasses = 'Fuserna' | 'Blank' | 'WT'
+type FusionTvsValue = {
+	dt: 2
+	mclassLst: FusionRNAClasses[]
+	mclassExcludeLst: FusionRNAClasses[]
+	origin?: GeneVariantOrigin
+}
+
+type GeneVariantTvsValue = SNVIndelTvsValue | CNVTvsValue | SVTvsValue | FusionTvsValue
+
+type GeneVariantTvs = BaseTvs & {
+	term: GeneVariantTerm
+	values: GeneVariantTvsValue[]
+}
+/*** types supporting Filter type ***/
+
+export type Tvs = CategoricalTvs | NumericTvs | ConditionTvs | GeneVariantTvs // | SampleLstTvs ...
+
+export type Filter = {
+	type: 'lst'
+	in?: boolean
+	join: 'and' | 'or'
+	tag?: string // client-side only
+	lst: (Filter | Tvs)[]
+}

package/src/genome.ts

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+import { Cohort } from './dataset.ts'
+
+/********* server/genome ********
+ 
+--------EXPORTED--------
+MinGenome
+Genome
+
+*/
+
+type GeneDb = {
+	dbfile: string
+}
+
+type TermDbs = {
+	[key: string]: TermDbsEntry
+}
+
+type TermDbsEntry = {
+	label: string
+	cohort: Cohort
+}
+
+type DbStatement = {
+	dbfile: string
+	statement: string
+}
+
+type Snp = {
+	bigbedfile: string
+}
+
+type FimoMotif = {
+	db: string
+	annotationfile: string
+}
+
+type TrackCategoryEntry = {
+	color: string
+	label: string
+}
+
+type TrackCategories = {
+	[index: string]: TrackCategoryEntry | undefined
+}
+
+type Track = {
+	__isgene?: boolean
+	translatecoding?: boolean
+	file: string
+	type: string
+	name: string
+	categories?: TrackCategories
+	stackheight?: number
+	stackspace?: number
+	vpad?: number
+	color?: string
+	onerow?: boolean
+}
+
+type DefaultCoord = {
+	chr: string
+	start: number
+	stop: number
+	gene?: string
+}
+
+type GeneSet = {
+	name: string
+	lst: string[]
+}
+
+type HicEnzymeFragment = {
+	enzyme: string
+	file: string
+}
+
+type HicDomainSetEntry = {
+	name: string
+	longname: string
+	file: string
+}
+
+type HicDomainSet = {
+	[index: string]: HicDomainSetEntry
+}
+
+type HicDomainGrpEntry = {
+	name: string
+	reference: string
+	sets: HicDomainSet
+}
+
+type HicDomainGroups = {
+	[index: string]: HicDomainGrpEntry
+}
+
+type HicDomain = {
+	[index: string]: HicDomainGroups
+}
+
+//Separated to force g.tracks as required, see hgvirus.ts
+export type MinGenome = {
+	isMinGenome?: boolean
+	species: string
+	genomefile: string
+	genedb: GeneDb
+	defaultcoord: DefaultCoord
+	hicenzymefragment?: HicEnzymeFragment[]
+	majorchr: string
+}
+
+export type Genome = MinGenome & {
+	termdbs?: TermDbs
+	proteindomain?: DbStatement
+	repeatmasker?: DbStatement
+	snp?: Snp
+	fimo_motif?: FimoMotif
+	tracks?: Track[]
+	geneset?: GeneSet[]
+	hicdomain?: HicDomain
+	minorchr?: string
+}

package/src/index.ts

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+// please list in alphanumeric order
+export * from './genome.ts'
+export * from './dataset.ts'
+export * from './termsetting.ts'
+export * from './filter.ts'
+export * from './routes/brainImaging.ts'
+export * from './routes/burden.ts'
+export * from './routes/dzimages.ts'
+export * from './routes/errorResponse.ts'
+export * from './routes/filter.gdc.ts'
+export * from './routes/gdc.maf.ts'
+export * from './routes/gdc.mafBuild.ts'
+export * from './routes/gdc.topMutatedGenes.ts'
+export * from './routes/genelookup.ts'
+export * from './routes/genesetEnrichment.ts'
+export * from './routes/genesetOverrepresentation.ts'
+export * from './routes/healthcheck.ts'
+export * from './routes/hicdata.ts'
+export * from './routes/hicgenome.ts'
+export * from './routes/hicstat.ts'
+export * from './routes/sampledzimages.ts'
+export * from './routes/samplewsimages.ts'
+export * from './routes/termdb.categories.ts'
+export * from './routes/termdb.cluster.ts'
+export * from './routes/termdb.DE.ts'
+export * from './routes/termdb.getdescrstats.ts'
+export * from './routes/termdb.getnumericcategories.ts'
+export * from './routes/termdb.getpercentile.ts'
+export * from './routes/termdb.getrootterm.ts'
+export * from './routes/termdb.getSampleImages.ts'
+export * from './routes/termdb.gettermchildren.ts'
+export * from './routes/termdb.getSampleImages.ts'
+export * from './routes/termdb.getTopTermsByType.ts'
+export * from './routes/termdb.singlecellData.ts'
+export * from './routes/termdb.singlecellDEgenes.ts'
+export * from './routes/termdb.singlecellSamples.ts'
+export * from './routes/termdb.singleSampleMutation.ts'
+export * from './routes/termdb.termsbyids.ts'
+export * from './routes/termdb.topVariablyExpressedGenes.ts'
+export * from './routes/termdb.violin.ts'
+export * from './routes/wsimages.ts'
+export * from './terms/categorical.ts'
+export * from './terms/condition.ts'
+export * from './terms/numeric.ts'
+export * from './terms/geneVariant.ts'
+export * from './terms/geneExpression.ts'
+export * from './terms/metaboliteIntensity.ts'
+export * from './terms/singleCellCellType.ts'
+export * from './terms/singleCellGeneExpression.ts'
+export * from './terms/snp.ts'
+export * from './terms/snps.ts'
+export * from './terms/samplelst.ts'
+export * from './terms/q.ts'
+export * from './terms/term.ts'
+export * from './terms/tw.ts'
+export * from './vocab.ts'

package/src/routes/brainImaging.ts

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+export type GetBrainImagingRequest = {
+	/** 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
+	/** a user-defined brain template label in dataset file, such as Ref1, Ref2 */
+	refKey: string
+	/** when true will only return all the samples that have NIdata */
+	samplesOnly?: boolean
+	/** the slice index of sagittal, coronal and axial planes*/
+	l?: string
+	f?: string
+	t?: string
+	/** the sample names selected by the users to plot on brain template */
+	selectedSampleFileNames?: string[]
+}
+
+export type GetBrainImagingResponse = {
+	/** the brain imaging plot */
+	brainImage: string
+}

package/src/routes/burden.ts

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+import { createValidate } from 'typia'
+
+export type BurdenRequest = {
+	/** 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
+	/** the diagnosis group:
+	 * 1= "Acute lymphoblastic leukemia (ALL)"
+	 * 2= "Acute Myeloid Leukemia (AML)"
+	 * 3= "Hodgkin lymphoma (HL)"
+	 * 4= "Non-Hodgkin lymphoma (NHL)"
+	 * 5= "Central nervous system (CNS)"
+	 * 6= "Bone tumor (BT)"
+	 * 7= "Soft Tissue Sarcoma (STS)"
+	 * 8= "Wilms tumor (WT)"
+	 * 9= "Neuroblastoma (NB)"
+	 * 10= "Retinoblastoma (Rb)"
+	 * 11= "Germ cell tumor (GCT)"
+	 */
+	diaggrp: number
+	/** sex: 0=Female, 1=Male */
+	sex: number
+	/** race or ethnicity: 1=Yes, 0=No */
+	white: number
+	/** Age of diagnosis, in years */
+	agedx: number
+	/** bleomycin: a chemotherapy treatment drug, mg/m^2 */
+	bleo: number
+	/** Etoposide: a chemotherapy treatment drug, mg/m^2 */
+	etop: number
+	/** Cisplatin: a chemotherapy treatment drug, mg/m^2 */
+	cisp: number
+	/** Carboplatin: a class of chemotherapy treatment drugs, mg/m^2 */
+	carbo: number
+	/** Steriods: a class of chemotherapy treatment drugs, mg/m^2 */
+	steriod: number
+	/** Vincristine: a chemotherapy treatment drug, mg/m^2 */
+	vcr: number
+	/** High-dose methothrexate: a chemotherapy treatment drug, mg/m^2 */
+	hdmtx: number
+	/** Intrathecal methothrexate: a chemotherapy treatment drug, mg/m^2 */
+	itmt: number
+	/** Cyclophosphamide: a chemotherapy treatment drug, mg/m^2 */
+	ced: number
+	/** Anthracycline: a chemotherapy treatment drug, mg/m^2 */
+	dox: number
+	/** Heart radiation, Gy */
+	heart: number
+	/** Brain radiation, Gy */
+	brain: number
+	/** Abdominal radiation, Gy */
+	abd: number
+	/** Pelvic radiation, Gy */
+	pelvis: number
+	/** Chest radiation, Gy */
+	chest: number
+}
+
+export type BurdenResponse = {
+	status: string
+	keys: string[]
+	rows: number[][]
+}
+
+export const validBurdenRequest = createValidate<BurdenRequest>()
+export const validBurdenResponse = createValidate<BurdenResponse>()

package/src/routes/dzimages.ts

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+export type GetSampleDZImagesRequest = {
+	genome: string
+	dslabel: string
+	sample_id: string
+}
+
+export type GetSampleDZImagesResponse = {
+	sampleDZImages: string
+}

package/src/routes/errorResponse.ts

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+export type ErrorResponse = {
+	/* Status code. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status */
+	status: number
+	/* Msg */
+	error: string
+}

package/src/routes/filter.gdc.ts

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+/* the gdc cohort filter object
+is invisible on pp ui
+always used as "filter0" property in pp client code and in request to pp back
+pp does not compute on it, on pp backend, it's passed to gdc api queries
+
+FIXME type is not properly defined yet
+*/
+export type GdcFilter0 = {
+	op: string
+	// TODO: this should allow an array of objects, and/or nesting ???
+	content: {
+		field: string
+		value: string
+	}
+}

package/src/routes/gdc.maf.ts

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+//import GdcFilter0 from './filter.gdc'
+
+// an object representing gdc maf file, to be shown on client table
+
+export type File = {
+	/** A string representing the file's UUID (Universally Unique Identifier) , can be accessed via https://api.gdc.cancer.gov/data/<uuid>*/
+	id: string
+	/** A string representing a submitter ID for the case associated with this file */
+	case_submitter_id: string
+	// case uuid
+	case_uuid: string
+	/** An integer as the byte size of this file, compressed */
+	file_size: number
+	/** Array of strings, each is a sample type, for all samples involved in generating the maf file */
+	sample_types: string[]
+	/** A string representing the type of workflow used to generate or process this file */
+	//workflow_type: string
+	/** A string as the project id of the case */
+	project_id: string
+}
+
+enum ExperimentalStrategy {
+	targeted = 'Targeted Sequencing',
+	wxs = 'WXS'
+}
+
+export type GdcMafRequest = {
+	/** Name of exp strategy to get maf files for */
+	experimentalStrategy: ExperimentalStrategy
+	/** JSON, optional GDC cohort filter to restrict cases; if supplied, will only get maf files for these cases. the filter is readonly and pass to GDC API query */
+	filter0?: any
+}
+
+export type GdcMafResponse = {
+	/** List of file objects passing filter and to be displayed on client */
+	files: File[]
+	/** Total number of files found by API (in case bigger than files.length) */
+	filesTotal: number
+	/** Maximum total size of maf files allowed, for indicating on ui while selecting files */
+	maxTotalSizeCompressed: number
+}

package/src/routes/gdc.mafBuild.ts

@@ -0,0 +1,13 @@
+/*
+
+export type GdcMafBuildResponse = {
+	FIXME response is a binary stream. don't know a way to type it
+}
+*/
+
+export type GdcMafBuildRequest = {
+	/** List of input file uuids in gdc */
+	fileIdLst: string[]
+	/** List of columns in output MAF file */
+	columns: string[]
+}

package/src/routes/gdc.topMutatedGenes.ts

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+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[]
+}

package/src/routes/genelookup.ts

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+export type GeneLookupRequest = {
+	input: string
+	genome: string
+	deep: boolean
+}
+
+export type GeneLookupResponse = {
+	error?: string
+	hits: string[]
+}

package/src/routes/genesetEnrichment.ts

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+export type genesetEnrichmentRequest = {
+	/** Sample genes to be queried */
+	genes: string[]
+	/** Background genes against which the sample genes will be queried */
+	fold_change: number[]
+	/** 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
+}

package/src/routes/genesetOverrepresentation.ts

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+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
+}
+
+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
+}

package/src/routes/healthcheck.ts

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+/**
+ * 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
+}