@sjcrh/proteinpaint-types 2.86.0 → 2.87.1

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

@@ -0,0 +1,125 @@
+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

@@ -0,0 +1,123 @@
+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

@@ -0,0 +1,67 @@
+// please list in alphanumeric order, include file extension
+export * from './genome.ts'
+export * from './dataset.ts'
+export * from './termsetting.ts'
+export * from './filter.ts'
+export * from './routes/routeApi.ts'
+export * from './routes/brainImaging.ts'
+export * from './routes/brainImagingSamples.ts'
+export * from './routes/burden.ts'
+export * from './routes/dataset.ts'
+export * from './routes/dsdata.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/isoformlst.ts'
+export * from './routes/ntseq.ts'
+export * from './routes/pdomain.ts'
+export * from './routes/samplewsimages.ts'
+export * from './routes/snp.ts'
+export * from './routes/termdb.boxplot.ts'
+export * from './routes/termdb.categories.ts'
+export * from './routes/termdb.cluster.ts'
+export * from './routes/termdb.cohort.summary.ts'
+export * from './routes/termdb.cohorts.ts'
+export * from './routes/termdb.DE.ts'
+export * from './routes/termdb.descrstats.ts'
+export * from './routes/termdb.numericcategories.ts'
+export * from './routes/termdb.percentile.ts'
+export * from './routes/termdb.rootterm.ts'
+export * from './routes/termdb.termchildren.ts'
+export * from './routes/termdb.sampleImages.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.termchildren.ts'
+export * from './routes/termdb.topTermsByType.ts'
+export * from './routes/termdb.topVariablyExpressedGenes.ts'
+export * from './routes/termdb.violin.ts'
+export * from './routes/tileserver.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

@@ -0,0 +1,47 @@
+import type { CategoricalTW } from '../terms/categorical.ts'
+import type { RoutePayload } from './routeApi.ts'
+
+export type BrainImagingRequest = {
+	/** 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
+	/** 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[]
+	/* the term to divide the samples into groups */
+	divideByTW?: CategoricalTW
+	/* the term to color the samples based on their category */
+	overlayTW?: CategoricalTW
+	/* the term categories that were filtered out */
+	legendFilter?: string[]
+}
+
+export type BrainImagingResponse = {
+	/** the brain imaging plot */
+	brainImage: string
+	plane?: any
+	legend?: {
+		[key: string]: {
+			color: string
+			maxLength: number
+			crossedOut: boolean
+		}
+	}
+}
+
+export type FilesByCategory = { [category: string]: { samples: string[]; color: string } }
+
+export const brainImagingPayload: RoutePayload = {
+	request: {
+		typeId: 'BrainImagingRequest'
+	},
+	response: {
+		typeId: 'BrainImagingResponse'
+	}
+}

package/src/routes/brainImagingSamples.ts

@@ -0,0 +1,25 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type BrainImagingSamplesRequest = {
+	/** 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
+}
+
+export type BrainImagingSamplesResponse = {
+	samples: BrainSample[]
+}
+
+export type BrainSample = { [key: string]: string }
+
+export const brainImagingSamplesPayload: RoutePayload = {
+	request: {
+		typeId: 'BrainImagingSamplesRequest'
+	},
+	response: {
+		typeId: 'BrainImagingSamplesResponse'
+	}
+}

package/src/routes/burden.ts

@@ -0,0 +1,111 @@
+import type { RoutePayload } from './routeApi.js'
+
+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
+}
+
+// tentative code for migrating api code from `server/routes` code
+export type BurdenResponse = {
+	status: string
+	keys: string[]
+	rows: number[][]
+}
+
+// tentative code to generate runtime "type" checkers, requires tsx/bundler to have transform for typia createValidate to work
+// export const validBurdenRequest = createValidate<BurdenRequest>()
+// export const validBurdenResponse = createValidate<BurdenResponse>()
+
+export const burdenPayload: RoutePayload = {
+	request: {
+		typeId: 'BurdenRequest'
+	},
+	response: {
+		typeId: 'BurdenResponse'
+	},
+	examples: [
+		{
+			request: {
+				body: {
+					genome: 'hg38',
+					// TODO: !!! use hg38-test and TermdbTest !!!
+					dslabel: 'SJLife',
+					diaggrp: 5,
+					sex: 1,
+					white: 1,
+					agedx: 1,
+					bleo: 0,
+					etop: 0,
+					cisp: 0,
+					carbo: 0,
+					steriod: 0,
+					vcr: 0,
+					hdmtx: 0,
+					itmt: 0,
+					ced: 0,
+					dox: 0,
+					heart: 0,
+					brain: 0,
+					abd: 0,
+					pelvis: 0,
+					chest: 0
+				}
+			},
+			response: {
+				header: { status: 200 }
+			}
+		}
+	]
+}

package/src/routes/dataset.ts

@@ -0,0 +1,14 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type DatasetRequest = any
+export type DatasetResponse = any
+
+export const datasetPayload: RoutePayload = {
+	request: {
+		typeId: 'DatasetRequest'
+	},
+	response: {
+		typeId: 'DatasetResponse'
+	}
+	// examples: []
+}

package/src/routes/dsdata.ts

@@ -0,0 +1,14 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type DsDataRequest = any
+export type DsDataResponse = any
+
+export const dsDataPayload: RoutePayload = {
+	request: {
+		typeId: 'DsDataRequest'
+	},
+	response: {
+		typeId: 'DsDataResponse'
+	}
+	// examples: []
+}

package/src/routes/dzimages.ts

@@ -0,0 +1,25 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type DZImagesRequest = {
+	genome: string
+	dslabel: string
+	file: string
+
+	// params: {
+	// 	[key: string]: any
+	// }
+	sampleId?: string
+	sample_id?: string
+}
+
+export type DZImagesResponse = string
+
+export const dzImagesPayload: RoutePayload = {
+	request: {
+		typeId: 'DZImagesRequest'
+	},
+	response: {
+		typeId: 'DZImagesResponse'
+	}
+	// examples: []
+}

package/src/routes/errorResponse.ts

@@ -0,0 +1,6 @@
+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

@@ -0,0 +1,15 @@
+/* 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

@@ -0,0 +1,52 @@
+import type { RoutePayload } from './routeApi.js'
+//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
+}
+
+export const gdcMafPayload: RoutePayload = {
+	request: {
+		typeId: 'GdcMafRequest'
+	},
+	response: {
+		typeId: 'GdcMafResponse'
+	}
+	//examples: []
+}

package/src/routes/gdc.mafBuild.ts

@@ -0,0 +1,20 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type GdcMafBuildRequest = {
+	/** List of input file uuids in gdc */
+	fileIdLst: string[]
+	/** List of columns in output MAF file */
+	columns: string[]
+}
+
+export type GdcMafBuildResponse = any
+
+export const GdcMafPayload: RoutePayload = {
+	request: {
+		typeId: 'GdcMafBuildRequest'
+	},
+	response: {
+		typeId: 'GdcMafBuildResponse'
+	}
+	//examples: []
+}