@sjcrh/proteinpaint-types 2.189.0 → 2.190.0

package/src/fileOrUrl.ts

@@ -1,15 +0,0 @@
-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

@@ -1,110 +0,0 @@
-import type { BaseValue } from './terms/term.ts'
-import type { NumericTerm, NumericBin } from './terms/numeric.ts'
-import type { CategoricalTerm } from './terms/categorical.ts'
-import type { DtTerm } from './terms/geneVariant.ts'
-import type { ConditionTerm } from './terms/condition.ts'
-import type { TermCollection } from './terms/termCollection.ts'
-
-/*
---------EXPORTED--------
-Tvs
-LstEntry
-Filter
-
-*/
-
-/*** types supporting Tvs type ***/
-
-export type BaseTvs = {
-	join?: string //and, or
-	isnot?: boolean
-	// Additional properties used in runtime
-	bar_by_grade?: boolean
-	bar_by_children?: boolean
-	value_by_max_grade?: boolean
-	value_by_most_recent?: boolean
-	value_by_computable_grade?: boolean
-}
-
-export type CategoricalTvs = BaseTvs & {
-	term: CategoricalTerm
-	groupset_label?: string
-	values: BaseValue[]
-	valueset?: Set<any> // Runtime property set by setDatasetAnnotations
-}
-
-export type NumericTvs = BaseTvs & {
-	term: NumericTerm
-	ranges: (NumericBin | { value: number; label?: string; name?: string })[]
-	// 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[]
-	values: { key: string | number; label?: string; [key: string]: any }[]
-}
-
-export type GeneVariantValue = {
-	key?: string
-	label?: string | number
-	value?: string
-	dt?: number
-	mclasslst?: string[]
-	mclassExcludeLst?: string[]
-	origin?: string
-}
-
-export type GeneVariantTvs = BaseTvs & {
-	term: DtTerm
-	values: GeneVariantValue[]
-	/** boolean for including not tested classes (excluded by default) */
-	includeNotTested?: boolean
-	/** boolean for excluding gene name from pill name (included by default)
-	 * used by geneVariant edit ui to exclude unnecessary gene name */
-	excludeGeneName?: boolean
-	/** FIXME following are quick fix to avoid tsc err. TODO define snvindel tsv type */
-	genotype?: 'variant' | 'nt' | 'wt'
-	mcount?: 'any' | 'single' | 'multiple' | 'all'
-	/** FIXME following are quick fix to avoid tsc err. TODO define cnv tsv type */
-	continuousCnv?: boolean
-	cnvLossCutoff?: number
-	cnvGainCutoff?: number
-	cnvMaxLength?: number
-	cnvWT?: boolean
-	fractionOverlap?: number
-}
-
-export type TermCollectionTvs = BaseTvs & {
-	term: TermCollection
-	ratio: number
-}
-
-/*** types supporting Filter type ***/
-
-export type Tvs = CategoricalTvs | NumericTvs | ConditionTvs | GeneVariantTvs | TermCollectionTvs // | SampleLstTvs ...
-
-export type Filter = {
-	type: 'tvslst'
-	in: boolean
-	join: string
-	tag?: string // client-side only
-	lst: ({ type: 'tvs'; tvs: Tvs } | Filter)[]
-	$id?: string // Optional ID property
-}

package/src/genome.ts

@@ -1,129 +0,0 @@
-import type { Cohort } from './dataset.ts'
-
-/********* server/genome ********
- 
---------EXPORTED--------
-MinGenome
-Genome
-
-*/
-
-type GeneDb = {
-	dbfile: string
-}
-
-type TermDbs = {
-	[key: string]: TermDbsEntry
-}
-
-type TermDbsEntry = {
-	label: string
-	cohort: Cohort
-	/** list of geneset groups in db; required for geneORA and gsea
-	later allow ds override so ds can enable/disable some genesets..
-	*/
-	analysisGenesetGroups: { label: string; value: string }[]
-	/** required for gsea */
-	geneORAparam: { minCutoff: number; maxCutoff: number }
-}
-
-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
-}
-
-export type Track = {
-	__isgene?: boolean
-	translatecoding?: boolean
-	file: string
-	type: string
-	name: string
-	categories?: TrackCategories
-	stackheight?: number
-	stackspace?: number
-	vpad?: number
-	color?: string
-	onerow?: boolean
-}
-
-export 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

@@ -1,94 +0,0 @@
-// 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 './termdb.matrix.ts'
-export * from './routes/routeApi.ts'
-export * from './routes/aiProjectAdmin.ts'
-export * from './routes/aiProjectSelectedWSImages.ts'
-export * from './routes/aiProjectTrainModel.ts'
-export * from './routes/brainImaging.ts'
-export * from './routes/brainImagingSamples.ts'
-export * from './routes/burden.ts'
-export * from './routes/clearwsisessions.ts'
-export * from './routes/correlationVolcano.ts'
-export * from './routes/dataset.ts'
-export * from './routes/deleteWSITileSelection.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.grin2.ts'
-export * from './routes/grin2.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/img.ts'
-export * from './routes/isoformlst.ts'
-export * from './routes/ntseq.ts'
-export * from './routes/pdomain.ts'
-export * from './routes/routeApi.ts'
-export * from './routes/samplewsimages.ts'
-export * from './routes/saveWSIAnnotation.ts'
-export * from './routes/snp.ts'
-export * from './routes/termdb.categories.ts'
-export * from './routes/termdb.chat2.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.dapVolcano.ts'
-export * from './routes/termdb.diffMeth.ts'
-export * from './routes/termdb.descrstats.ts'
-export * from './routes/termdb.dmr.ts'
-export * from './routes/termdb.isoformAvailability.ts'
-export * from './routes/termdb.numericcategories.ts'
-export * from './routes/termdb.percentile.ts'
-export * from './routes/termdb.proteome.ts'
-export * from './routes/termdb.runChart.ts'
-export * from './routes/termdb.rootterm.ts'
-export * from './routes/termdb.termchildren.ts'
-export * from './routes/termdb.sampleImages.ts'
-export * from './routes/termdb.sampleScatter.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.topMutatedGenes.ts'
-export * from './routes/termdb.topTermsByType.ts'
-export * from './routes/termdb.topVariablyExpressedGenes.ts'
-export * from './routes/termdb.violinBox.ts'
-export * from './routes/tileserver.ts'
-export * from './routes/wsimages.ts'
-export * from './routes/wsisamples.ts'
-export * from './terms/categorical.ts'
-export * from './terms/condition.ts'
-export * from './terms/date.ts'
-export * from './terms/numeric.ts'
-export * from './terms/geneVariant.ts'
-export * from './terms/geneExpression.ts'
-export * from './terms/isoformExpression.ts'
-export * from './terms/metaboliteIntensity.ts'
-export * from './terms/proteomeAbundance.ts'
-export * from './terms/qualitative.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/ssGSEA.ts'
-export * from './terms/dnaMethylation.ts'
-export * from './terms/q.ts'
-export * from './terms/term.ts'
-export * from './terms/termCollection.ts'
-export * from './terms/tw.ts'
-export * from './vocab.ts'

package/src/routes/aiProjectAdmin.ts

@@ -1,37 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type AIProjectAdminRequest = {
-	genome: string
-	dslabel: string
-	/** list: get entire list of projects from db
-	 * admin: edit, add, or delete projects from db
-	 * filterImages: filter metadata for images
-	 * images: get images for a project
-	 */
-	for: 'list' | 'admin' | 'filterImages' | 'images'
-	/** required for 'project' and 'selection' requests */
-	project?: {
-		name: string
-		id?: number
-		filter?: string
-		classes?: any[]
-		images?: string[]
-	}
-}
-
-export type AIProjectAdminResponse = {
-	status: 'ok' | 'error'
-	projectId?: number
-	images: string[]
-	error?: string
-	data?: { cols: any[]; rows: any[]; images?: string[]; selectedImages?: string[] }[]
-}
-
-export const aiProjectAdminPayload: RoutePayload = {
-	request: {
-		typeId: 'AIProjectAdminRequest'
-	},
-	response: {
-		typeId: 'AIProjectAdminResponse'
-	}
-}

package/src/routes/aiProjectSelectedWSImages.ts

@@ -1,47 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-import type { WSImage } from './samplewsimages.ts'
-import type { FlagStatusValues } from '#shared/devTs'
-
-export type AiProjectSelectedWSImagesRequest = {
-	genome: string
-	dslabel: string
-	projectId: number
-	wsimagesFilenames: Array<string>
-}
-
-export type AiProjectSelectedWSImagesResponse = {
-	// TODO create a type for WSImage with AI project specific fields
-	wsimages: WSImage[]
-}
-
-export interface FlagPredictionInfo {
-	flag: FlagStatusValues
-	timestamp: string
-}
-
-// TODO move to another class
-export interface TileSelection {
-	zoomCoordinates: [number, number]
-	class?: string
-	flag: FlagStatusValues
-	id: string
-	timestamp: string
-}
-
-export interface Annotation extends TileSelection {
-	class: string
-}
-
-export interface Prediction extends TileSelection {
-	class: string
-	uncertainty: number
-}
-
-export const aiProjectSelectedWSImagesResponsePayload: RoutePayload = {
-	request: {
-		typeId: 'AiProjectSelectedWSImagesRequest'
-	},
-	response: {
-		typeId: 'AiProjectSelectedWSImagesResponse'
-	}
-}

package/src/routes/aiProjectTrainModel.ts

@@ -1,20 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type AIProjectTrainModelRequest = {
-	genome: string
-	dslabel: string
-	projectId?: string
-}
-
-export type AIProjectTrainModelResponse = {
-	status: 'ok' | 'error'
-}
-
-export const aiProjectTrainModelPayload: RoutePayload = {
-	request: {
-		typeId: 'AIProjectTrainModelRequest'
-	},
-	response: {
-		typeId: 'AIProjectTrainModelResponse'
-	}
-}

package/src/routes/alphaGenome.ts

@@ -1,27 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type alphaGenomeRequest = {
-	genome?: string
-	dslabel?: string
-	chromosome: string
-	position: number
-	reference: string
-	alternate: string
-	ontologyTerms: string[]
-	outputType?: number
-	interval: number
-}
-
-export type alphaGenomeResponse = {
-	/** the alpha genome plot */
-	plotImage: string
-}
-
-export const alphaGenomePayload: RoutePayload = {
-	request: {
-		typeId: 'alphaGenomeRequest'
-	},
-	response: {
-		typeId: 'alphaGenomeResponse'
-	}
-}

package/src/routes/alphaGenomeTypes.ts

@@ -1,21 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type alphaGenomeTypesRequest = {
-	dslabel: string
-}
-export type alphaGenomeTypesResponse = {
-	/** the alpha genome ontology terms supported by the dataset */
-	ontologyTerms: any[]
-	/** the alpha genome output types */
-	outputTypes: any[]
-	intervals: number[]
-}
-
-export const alphaGenomeTypesPayload: RoutePayload = {
-	request: {
-		typeId: 'alphaGenomeTypesRequest'
-	},
-	response: {
-		typeId: 'alphaGenomeTypesResponse'
-	}
-}

package/src/routes/brainImaging.ts

@@ -1,47 +0,0 @@
-import type { QualTW } from '../terms/qualitative.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?: QualTW
-	/* the term to color the samples based on their category */
-	overlayTW?: QualTW
-	/* 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?: any } }
-
-export const brainImagingPayload: RoutePayload = {
-	request: {
-		typeId: 'BrainImagingRequest'
-	},
-	response: {
-		typeId: 'BrainImagingResponse'
-	}
-}

package/src/routes/brainImagingSamples.ts

@@ -1,25 +0,0 @@
-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

@@ -1,113 +0,0 @@
-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
-	/** boolean for whether to show 95% confidence interval */
-	showCI: boolean
-	/** 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 }
-			}
-		}
-	]
-}