@sjcrh/proteinpaint-types 2.84.0 → 2.86.0

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

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

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

@@ -1,57 +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 './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.boxplot.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

@@ -1,42 +0,0 @@
-import { CategoricalTW } from '../terms/categorical.ts'
-
-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
-	/** 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
-}
-
-export type GetBrainImagingSamplesRequest = {
-	/** 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 GetBrainImagingSamplesResponse = {
-	samples: BrainSample[]
-}
-
-export type BrainSample = { [key: string]: string }
-
-export type GetBrainImagingResponse = {
-	/** the brain imaging plot */
-	brainImage: string
-}
-
-export type FilesByCategory = { [category: string]: { samples: string[]; color: string } }

package/src/routes/burden.ts

@@ -1,69 +0,0 @@
-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
-}
-
-// 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
-export const validBurdenRequest = createValidate<BurdenRequest>()
-export const validBurdenResponse = createValidate<BurdenResponse>()

package/src/routes/dzimages.ts

@@ -1,9 +0,0 @@
-export type GetSampleDZImagesRequest = {
-	genome: string
-	dslabel: string
-	sample_id: string
-}
-
-export type GetSampleDZImagesResponse = {
-	sampleDZImages: string
-}

package/src/routes/errorResponse.ts

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

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

@@ -1,41 +0,0 @@
-//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

@@ -1,13 +0,0 @@
-/*
-
-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

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

@@ -1,10 +0,0 @@
-export type GeneLookupRequest = {
-	input: string
-	genome: string
-	deep: boolean
-}
-
-export type GeneLookupResponse = {
-	error?: string
-	hits: string[]
-}

package/src/routes/genesetEnrichment.ts

@@ -1,46 +0,0 @@
-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

@@ -1,36 +0,0 @@
-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
-}