@sjcrh/proteinpaint-types 2.189.0 → 2.190.0

package/src/dataset.ts

@@ -1,2188 +0,0 @@
-import type { Mclass } from './Mclass.ts'
-import type { BaseTerm } from './terms/term.ts'
-import type { CategoryKey } from './terms/termCollection.ts'
-import type { WSImage } from './routes/samplewsimages.ts'
-import type { WSISample } from './routes/wsisamples.ts'
-import type { SaveWSIAnnotationRequest } from './routes/saveWSIAnnotation.ts'
-import type { DeleteWSITileSelectionRequest } from './routes/deleteWSITileSelection.ts'
-import type { Prediction } from './routes/aiProjectSelectedWSImages.ts'
-
-/*** General usage types ***/
-type FileObj = {
-	file: string
-}
-
-type KeyVal = {
-	k: string
-	v?: string
-}
-
-/** a set of categories about a vcf INFO field */
-export type InfoFieldCategories = {
-	/** category key from an INFO field of a vcf file */
-	[index: string]: {
-		/** Color used for rendering labels and backgrounds in the legend, tables, etc. */
-		color: string
-		/** Human readable label */
-		label?: string
-		/** Shown in the legend on label click */
-		desc: string
-		/** When .color is used as the background, denoted whether
-		 * to use 'white', 'black', or other color for the text */
-		textcolor?: string
-	}
-}
-
-type NumericFilterEntry = {
-	/** '<' or '>' for filtering */
-	side: string
-	/** value for filtering */
-	value: number
-}
-
-type AFEntry = {
-	/** human readable label */
-	name: string
-	/**  */
-	locusinfo: {
-		/** usually the data dictionary value  (e.g. AF_EXAC for ExAC frequency) */
-		key: string
-	}
-	/** key/values for filtering */
-	numericfilter: NumericFilterEntry[]
-}
-
-/** Specific allele freq info for ClinVar */
-export type ClinvarAF = {
-	[index: string]: AFEntry
-}
-
-/*** types supporting Queries type ***/
-
-type InfoFieldEntry = {
-	/** Human readable name to display */
-	name: string
-	/** vcf INFO field */
-	key: string
-	/** a set of categories about a vcf INFO field */
-	categories?: InfoFieldCategories
-	/** seperator (e.g. '&', '|' ) between join values */
-	separator?: string
-}
-
-/*
-type GenomicPositionEntry = {
-	chr: string
-	start: number
-	stop: number
-}
-*/
-
-type bcfMafFile = {
-	/** bcf file for only variants, no samples and FORMAT */
-	bcffile: string
-	/** maf file for sample mutations. bcf header contents with FORMAT and list of samples are
-	 * copied into this maf as headers followed by the maf header starting with #chr, pos, ref,
-	 * alt and sample. Each column after sample corresponds to the information in FORMAT. file
-	 * is bgzipped and tabix indexed (tabix -c"#" -s 1 -b 2 -e 2 <maf.gz>) */
-	maffile: string
-}
-
-type SnvindelByIsoform = {
-	/** if true, served from gdc. no other parameters */
-	gdcapi?: true
-	/** getter function to retrieve data. dynamically added or ds-supplied
-	first argument is required and allow for 2 additional ones
-	*/
-	get?: (f: any, f2?: any, f3?: any) => void
-	/** if true, all tw from one client query must be processed via one call to snvindel.byisoform.get()
-	and no longer processes each tw by calling mayGetGeneVariantData()
-	*/
-	processTwsInOneQuery?: true
-}
-
-type SnvindelByRange = {
-	/** if true, served from gdc. no other parameters */
-	gdcapi?: true
-	//local ds can have following different setup
-	/** one single bcf file */
-	bcffile?: string
-	/** one bcf file per chr
-	after loading, this is transformed into byrange._tk.chr2files{}, and deleted!
-	*/
-	chr2bcffile?: {
-		/** index is the chr (e.g. 'chr1', 'chr2', etc.)
-		 * value is the bcf file path */
-		[index: string]: string
-	}
-	/** bcf+maf combined */
-	bcfMafFile?: bcfMafFile
-	/** allow to apply special configurations to certain INFO fields of the bcf file */
-	infoFields?: InfoFieldEntry[]
-	/** getter function to retrieve data. dynamically added or ds-supplied */
-	get?: (f: any, f2?: any) => void
-}
-
-type URLEntry = {
-	/** base URL, including the host and possibly other queries */
-	base?: string
-	key?: string
-	namekey?: string
-	label?: string
-	url?: string
-}
-
-type SkewerRim = {
-	/** only enabled for 'format' */
-	type: string
-	/** 'origin' */
-	formatKey: string
-	/** 'somatic' or 'germline', generally germline */
-	rim1value: string
-	/** 'somatic' or 'germline', generally somatic */
-	noRimValue: string
-}
-
-type GdcApi = {
-	/** Represents the configuration for accessing the GDC API. */
-	gdcapi?: boolean
-}
-
-type AiApi = {
-	/** Represents the configuration for accessing the AI API.
-	 * For now only AI Histo is supported.
-	 */
-	aiApi?: boolean
-	source?: {
-		/** Data source for building the termdb on the fly */
-		file: string
-		/** Column header for sample ids or names */
-		sampleKey: string
-	}
-}
-
-/** configuration for api-based dictionary
-NOTE: currently used by mmrf, but may also be used
-by other api-based datasets (e.g. gdc) */
-type DictApi = {
-	// builds dictionary and sets standard
-	// helpers at ds.cohort.termdb.q{}
-	build?: (ds: any) => void
-	// gets dictionary term data
-	get?: (q: any, twLst: any, onlyChildren?: boolean, useCache?: boolean) => void
-}
-
-type SnvIndelFormat = {
-	[index: string]: {
-		/* has value for a non-GT field indicating the variant 
-		is annotated to this sample*/
-		ID: string
-		Description: string
-		/** 'R' or 1. do not parse values here based on Number="R"
-		as we don't need to compute on the format values on backend
-		client will parse the values for display */
-		Number: string | number
-		Type: string
-	}
-}
-
-type FilterValues = {
-	[index: string | number]: {
-		key?: string | number
-		label: string
-	}
-}
-
-type RangesEntry = {
-	start: number
-	startinclusive: boolean
-	stopunbounded: boolean
-}
-
-type BaseTvsFilter = {
-	isnot?: boolean
-	ranges?: RangesEntry[]
-}
-
-type TvsFilter = BaseTvsFilter & {
-	values?: (string | number | { label: string })[]
-}
-
-export type FilterTermEntry = BaseTvsFilter & {
-	id: string
-	name: string
-	type: string
-	parent_id: string | null
-	isleaf: boolean
-	values?: FilterValues
-	tvs?: TvsFilter
-	min?: number
-	max?: number
-}
-
-type FilterLstTvs = BaseTvsFilter & {
-	term: FilterTermEntry
-	values: (string | number | FilterValues)[]
-}
-
-type FilterLstEntry = {
-	type: string
-	tvs: FilterLstTvs
-}
-
-type Filter = {
-	type: string
-	join: string
-	in: boolean
-	lst?: FilterLstEntry[]
-}
-
-type VariantFilter = {
-	opts: { joinWith: string[] }
-	filter?: Filter
-	terms: FilterTermEntry[]
-}
-
-/** one set of AC and AN info fields to retrieve data for this population */
-type PopulationINFOset = {
-	/** optional term id for retrieving admix coefficient for an ancestry corresponding to this "PopulationINFOset" entry
-	for every sample carrying a variant.
-	this is required when sets[].length>1
-	this should not be set when sets[].length=1 */
-	key?: string
-	/** required info field */
-	infokey_AC: string
-	/** required info field */
-	infokey_AN: string
-}
-
-/* define method to retrieve allele AC/AN in a population, by using bcf INFO fields; population could be ancestry-stratified
-two types of population are supported:
-- ancestry-stratified
-  allowto_adjust_race can be set to true
-  sets[] has >1 elements
-- not stratified
-  allowto_adjust_race cannot be set to true
-  sets[] has only 1 element
-*/
-type Population = {
-	/** for identifying this element */
-	key: string
-	/** display, in fact it can replace key since label should also be unique*/
-	label: string
-	/** allow to set to true for race-stratified population, will adjust population AC/AN values based on admix coefficient for the dataset's cohort variants
-	 * supposed to be "read-only" attribute and not modifiable in runtime */
-	allowto_adjust_race?: boolean
-	/** when above is true, this flag is flip switch for this adjustion */
-	adjust_race?: boolean
-	/** if AC/AN of the population is ancestry-stratified, will be multiple elements of this array; otherwise just one */
-	sets: PopulationINFOset[]
-}
-
-/** primarily for prebuilding germline genetic association for survivorship portal
-part of state of genomeBrowser plot
-allowing for user modification
-*/
-type SnvindelComputeDetails = {
-	/** in each element, type corresponds to same key in groups[]
-	used for rendering choices in group data types; but content is read-only and should not be part of state
-	*/
-	groupTypes: {
-		type: string
-		name: string
-	}[]
-	/** a type of computing decides numeric values for each variant displayed in tk
-	computing type is also determined by number of groups
-	if only 1 group:
-		 type=info: use numeric info field
-		 type=filter: use AF
-		 type=population: use AF
-	if there're two groups:
-		 both types are "filter": allow AF diff or fisher
-		 "filter" and "population": allow AF diff or fisher
-		 else: value difference
-	*/
-	groups: (SnvindelComputeGroup_filter | SnvindelComputeGroup_population | SnvindelComputeGroup_info)[]
-	/** define lists of group-comparison methods to compute one numerical value per variant
-	 */
-	groupTestMethods: {
-		/** method name. used both for display and identifier. cannot supply hardcoded values here as breaks tsc */
-		name: string
-		/** optional custom text to put on mds3 tk y axis */
-		axisLabel?: string
-	}[]
-	/** array index of groupTestMethods[] */
-	groupTestMethodsIdx: number
-}
-/** supplies a pp filter (or filter by cohort) to restrict to a subset of samples from which to compute AF for each variant.
-the filter will be user-modifiable
-*/
-type SnvindelComputeGroup_filter = {
-	// FIXME type value can only be 'filter' but breaks tsc
-	type: string //'filter'
-	/** a given filter applied to all cohorts */
-	//filter?: object
-	/** filter per cohort. use either filter or filterByCohort */
-	filterByCohort?: { [key: string]: object }
-}
-/** a choice from snvindel.populations[]
- */
-type SnvindelComputeGroup_population = {
-	type: string //'population'
-	/** used to identify corresponding population element */
-	key: string
-	/** redundant, should be copied over from snvindel.populations[] */
-	label: string
-	/** if true, can adjust race. may copy over instead of duplicating? */
-	allowto_adjust_race: boolean
-	/** if true, race adjustion is being applied */
-	adjust_race: boolean
-}
-type SnvindelComputeGroup_info = {
-	type: string //'info'
-	/** numerical INFO field name from bcf, allows to retrieve numeric values for each variant in tk */
-	infoKey: string
-}
-
-/** a data type under ds.queries{} */
-type SnvIndelQuery = {
-	forTrack?: boolean
-	/** allow to query data by either isoform or range; either or both can be used; cannot be both missing */
-	byisoform?: SnvindelByIsoform
-	/** query data by range */
-	byrange?: SnvindelByRange
-
-	infoUrl?: URLEntry[]
-	skewerRim?: SkewerRim
-	format4filters?: string[]
-	format?: SnvIndelFormat
-	variant_filter?: VariantFilter
-	mafFilter?: VariantFilter
-	populations?: Population[]
-	/** NOTE **
-this definition can appear either in queries.snvindel{} or termdb{}
-so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig cannot be made */
-	ssmUrl?: UrlTemplateSsm
-	m2csq?: {
-		gdcapi?: boolean
-		by: string
-	}
-	allowSNPs?: boolean
-	vcfid4skewerName?: boolean
-	/** config on computing variant data and show as a custom mds3 tk */
-	details?: SnvindelComputeDetails
-	/** set to true to show mds3 tk by default when the ds have other genome browser track types besides this snvindel tk
-	if ds has only snvindel tk, then the tk will always be shown and no need to set this
-	*/
-	shown?: boolean
-}
-
-type SvFusion = {
-	byrange?: {
-		/** gz BED file path for sv fusion data: chr \t start \t stop \t {}
-		will only contain events with coordinates in both breakpoints
-		TODO use string sample name
-		*/
-		file?: string
-	}
-	byname?: {
-		/** file paths for sv fusion TXT data. will contain events lacking breakpoint coordinates and can only be matched by gene names
-		should be tab seperated values with the following fields: (should leave as blank for values unknown)
-		gene_a	refseq_a	chr_a	position_a	strand_a	gene_b	refseq_b	chr_b	position_b	strand_b	origin	sample_name	fusion_gene	event_type(fusion or sv)
-		TODO use string sample name
-		*/
-		file?: string
-	}
-	/** list of dt values to indicate if this ds has sv, fusion, or both */
-	dtLst: number[]
-}
-
-type SingleSampleMutationQuery = {
-	/** ds supplied getter
-	returns same json array as native. see example below
-	*/
-	get?: (f: any) => void
-	/** which property of client mutation object to retrieve sample identifier for querying single sample data with */
-	sample_id_key: string
-	/** disco plot will be launched when singleSampleMutation is enabled. supply customization options here */
-	discoPlot?: {
-		/** if true, disco plot will hide chrM, due to reason e.g. this dataset doesn't have data on chrM */
-		skipChrM?: true
-		/** if true, filter mutations by predefined geneset by default */
-		prioritizeGeneLabelsByGeneSets?: true
-	}
-	/** rest of properties are required for native ds without ds-supplied getter
-	TODO migrate gdc to get() and delete .src=native
-	*/
-	src?: 'native' | 'gdcapi' | string
-	/** only required for src=native
-	folder contains a set of files, one file per sample, file named by sample name
-	each file contains a stringified json array of mutation/cnv/sv entries (aka mlst). see example
-	https://github.com/stjude/proteinpaint/blob/master/server/test/tp/files/hg38/TermdbTest/mutationpersample/3318
-	*/
-	folder?: string
-}
-
-type NIdataQuery = {
-	/** Reference obj for NI data query. */
-	Ref1: NIdataQueryRef
-}
-
-type NIdataQueryRef = {
-	/** file path for the reference file */
-	referenceFile: string
-	/** file path for the sample file */
-	samples: string
-	/** Parameters for slice indices in the mass brain imaging plot */
-	parameters?: NIdataQueryRefParams
-	/** optional terms to show as table columns and annotate samples */
-	sampleColumns?: { termid: string }[]
-}
-
-type NIdataQueryRefParams = {
-	/** index of slice for default sagittal plane */
-	l: number
-	/** index of slice for default coronal plane */
-	f: number
-	/** index of slice for default axial plane */
-	t: number
-}
-
-/** used for the gene set edit ui */
-export type GeneArgumentEntry = {
-	/** Dom element id
-	 * Use the cooresponding parameter name as the id
-	 */
-	id: string
-	/** label/prompt for the checkbox, input, etc. */
-	label: string
-	/** Optional: Creates subtext below the main label */
-	sublabel?: string
-	/** 'boolean' has two options.
-	 * 	- If .options[] is provided, it creates a 'submenu', a checkbox
-	 * 		that expands to show additional inputs when checked. .options[]
-	 * 		in this case is GeneArgumentEntry[]
-	 *  - If !.options[] is provided, it creates a checkbox
-	 * 'string' creates a checked checkbox if a .value is provided
-	 * 'number' creates a text number input
-	 * 'radio' creates a radio buttons, see options[] */
-	type: 'boolean' | 'string' | 'number' | 'radio'
-	/** value of the input or checkbox
-	 * required if type is string. Otherwise, optional
-	 */
-	value?:
-		| string
-		| boolean
-		| number
-		| {
-				type: string
-				value: string[] | null
-		  }
-	options?: {
-		/** Type of dom element to render underneath the radio
-		 * 'text': creates a text area input
-		 * 'tree': launches termdb app and the tree
-		 * 'boolean': No element is created
-		 *
-		 * boolean is the default type
-		 */
-		type: 'text' | 'tree' | 'boolean' | string
-		/** value used to construct the server argument
-		 * also the element id in the gene set edit ui
-		 */
-		value: number | string
-		/** radio label */
-		label: string
-		/** Optional: smaller text that appears underneath the label */
-		sublabel?: string
-	}[]
-}
-
-type TopVariablyExpressedGenesQuery = {
-	/** ds supplied getter. if not, dynamically adds one during launch */
-	getGenes?: (f: any) => void
-	/** Specifies the dom element rendered in the menu */
-	arguments?: GeneArgumentEntry[]
-}
-
-type TopMutatedGenes = {
-	/** ds supplied getter. if not, dynamically adds one during launch */
-	get?: (f: any) => void
-	/** Specifies the dom element rendered in the menu */
-	arguments?: GeneArgumentEntry[]
-}
-
-/** setup for a set of genome browser tracks and/or facet tables, that can be selected for genomebrowser display
- */
-type TrackLst = {
-	/** path to legacy json file containing a long array of 1 or more facets
-
-	[
-	  {
-		 "isfacet": true,
-		 "name": "PEDDEP Prepilot",
-		 "tracks": [
-		   {
-			 name:str // required. used as *identifer* for a track
-			 sample:str // required. should match with a sample in db!
-			 assay:str // required. free string not controlled in dictionary yet. if missing the track won't appear in facet table
-			 type:str // properties inherent for each custom track
-			 file:str
-		   },
-		   ... more tk
-		 ]
-	  },
-	  { ... 2nd facet table }
-	]
-
-	*/
-	jsonFile: string
-
-	/*
-	alternative format that's easier to maintain than a giant json file
-	facetFiles:[
-		{
-			// name of this facet table
-			name: str
-			// a tabular file with columns "tkname/assay/sample/path/json"; last column json provides any customization for a track
-			// e.g. "Track 1 \t h3k4me3 \t sample1 \t path/to/file.bw \t {"scale":{..}}"
-			tabFile: string
-		}
-	]
-	*/
-
-	/** list of track names to show by default, should be found in json file
-	in json content above, allow a name to be shared by multiple tracks!
-	in such case, all tracks identified by given name will show/hide altogether
-	*/
-	activeTracks: string[]
-}
-
-/** cnv segments are queried by coordinates, and can be filtered by segment length and/or value
-configs for types of cnv data
-
-- log(ratio)
-	{
-		cnvMaxLength:10000000
-		cnvGainCutoff:5
-		cnvLossCutoff:-5
-	}
-- copy number
-	{
-		cnvMaxLength:1000000
-		cnvMaxCopynumber:10
-		cnvMinCopynumber:1
-	}
-- qualitative categories
-	{
-		cnvMaxLength?:? // abscent if ds doesn't allow filtering by max length (e.g. segments are actually gene bodies)
-		//cnvCategories:['CNV_amp', 'CNV_loss'] // "CNV_amplification" and "CNV_homozygous_deletion" are optional depending on ds
-	}
-	may not need to declare cnvCategories[];
-	cnv edit ui rendering can be entirely based on actual server-returned gene cnv data
-	e.g. if CNV_amplification is present from getCategories() or cnv data, show its checkbox, otherwise do not show checkbox
-
-important: presence of filtering properties indiate the type of cnv quantification
-and will trigger rendering of ui controls
-*/
-type CnvSegmentQuery = {
-	/** ds supplied or dynamically added getter
-	todo properly type input/output
-	returns:
-		{
-			cnvs:[]
-				{ chr, start, stop, value?, class, samples[], occurrence=1, ssm_id }
-			cnvMsg:string
-		}
-	*/
-	get?: (q: any) => any
-	/** either file or get is required. file is bgzipped with columns:
-	1. chr
-	2. start, 0-based
-	3. stop
-	4. {"dt": 4, "mattr": {"origin": "somatic"}, "sample": "3332", "value": -1.0}
-	   "value" can be logratio (minus/positive number), copy number (non-negative integer), or qualitative call (gain/loss)
-	*/
-	file?: string
-
-	/****** rendering parameters ****
-	not used as query parameter to filter segments
-	value range for color scaling. default to 5. cnv segment value>this will use solid color
-	*/
-	absoluteValueRenderMax?: number
-	gainColor?: string
-	lossColor?: string
-
-	/** filter segments by max length to restrict to focal events;
-	samples with all events filtered out should be treated as wildtype
-	set to -1 to show all as a convenient solution, thus no need for UI to show a checkbox for filterbylength or not
-	allow to be missing, in such case will always show all */
-	cnvMaxLength?: number
-
-	/// quick fix: following sets of properties are mutually exclusive. TODO may improve with "type" property
-
-	/** presence of these properties indicate cnv is quantified as log(ratio) or similar
-	filter segments by following two cutoffs only apply to log ratio, cnv gain value is positive, cnv loss value is negative
-	samples with all events filtered out should be treated as wildtype
-
-	- if m.value>0, skip m if m.value<this cutoff
-	- set to 0 to not filtering and show all gain events
-	- set to a large value e.g. 99 to hide all gain events
-	*/
-	cnvGainCutoff?: number
-	/*
-	- if m.value<0, skip m if m.value>this cutoff
-	- set to 0 to not filtering and show all loss events
-	- set to a large negative value e.g. -99 to hide all loss events
-	*/
-	cnvLossCutoff?: number
-
-	/** presence of these properties indicate cnv is quantified as integer copy number
-	* not in use yet *
-	enable when there's such data
-	cnvMinCopynumber?: number
-	cnvMaxCopynumber?: number
-	 */
-
-	/** quick fix for gdc cnv tool:
-	if not set, mds3 tk & matrix will load cnv segments and show them together with ssm & fusion
-	if set: 
-		- for mds3 tk loading via mds3.load.js, only when tk.hardcodeCnvOnly=true, this will be loaded and shown
-		- for others using mayGetGeneVariantData(), this is always disabled, as request won't have this flag
-	*/
-	requiresHardcodeCnvOnlyFlag?: true
-
-	/** CNV cutoffs (such as cnvGainCutoff, cnvLossCutoff, cnvMaxLength) that are applied to specific genes */
-	cnvCutoffsByGene?: {
-		[geneName: string]: {
-			[key: string]: any
-		}
-	}
-
-	/** in mds3 tk view and gdc cnv tool, when number of segments from view region exceeds this cutoff, it's piled up into density view to speed up
-	overrides default 1000
-	this cutoff does not apply to other uses beyond mds3 tk, including matrix and geneVariant
-	*/
-	densityViewCutoff?: number
-
-	/** this cutoff is applied in ds.queries.cnv.get(), in that up to this number of segments will be returned
-	overrides default 10k
-	this applies to matrix, geneVariant, and mds3 tk
-	todo there lacks a way for getter to message downstream code of exceeding limit
-	*/
-	maxReturnCutoff?: number
-}
-
-/*
-no longer used!!
-file content is a probe-by-sample matrix, values are signals
-for a given region, the median signal from probes in the region is used to make a gain/loss call for each sample
-this is alternative to CnvSegmentQuery
-
-type Probe2Cnv = {
-	file: string
-}
-*/
-
-type RnaseqGeneCount = {
-	/** Name of the HDF5 file */
-	file: string
-	samplesFile?: string
-	/** Storage_type for storing data (HDF5) */
-	storage_type: 'HDF5'
-}
-
-/** the metabolite query */
-export type MetaboliteIntensityQueryNative = {
-	src: 'native' | string
-	file: string
-	samples?: number[]
-	/** _metabolites,used to dynamically built cache of metabolite names to speed up search */
-	_metabolites?: string[]
-	get?: (param: any) => void
-	find?: (param: string[]) => void
-	metaboliteIntensity2bins?: { [index: string]: any }
-}
-
-export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
-
-/** the proteomics query */
-type ProteomeFilter = {
-	columnIdx: number
-	columnValue: string | number
-}
-
-type ProteomeCohortConfig = {
-	prior: { d0: number; s0sq: number }
-	controlFilter: ProteomeFilter[]
-	caseFilter: ProteomeFilter[]
-	DAPfile?: string
-}
-
-type ProteomeAssayConfig = {
-	columnIdx: number
-	columnValue: string | number
-	cohorts: {
-		[cohortName: string]: ProteomeCohortConfig
-	}
-	/** optional PTM type for PTM assay type */
-	PTMType?: string
-	/** optional specific mclass override for PTM assay type */
-	mclassOverride?: Mclass
-}
-
-export type ProteomeAbundanceQuery = {
-	/** database file path */
-	dbfile?: string
-	/** organism-keyed structure (new format) */
-	organisms?: {
-		[organism: string]: {
-			overlayTerm: BaseTerm
-			columnIdx: number
-			columnValue?: string
-			/** genome assembly name for this organism, e.g. 'hg38' or 'mm10' */
-			genomeName?: string
-			assays: {
-				[assayName: string]: ProteomeAssayConfig
-			}
-		}
-	}
-	/** flat assays structure (legacy format) */
-	assays?: {
-		[assayName: string]: ProteomeAssayConfig
-	}
-	samples?: number[]
-	/** _proteins,used to dynamically built cache of protein names to speed up search */
-	_proteins?: string[]
-	get?: (param: any) => void
-	find?: (param: string[]) => void
-	bins?: { [index: string]: any }
-	/** set of control sample IDs returned from get() query */
-	controlSampleIds?: Set<string>
-}
-
-/** the geneExpression query
-three possibilities
-{ src: 'native', file }
-{ src: 'gdcapi' } // dynamically add get()
-{ src: 'gdcapi', get } // ds supplied get
-*/
-export type GeneExpressionQuery = {
-	src: 'native' | 'gdcapi' // when gdc getter can become supplied, will remove src
-	/** either ds-supplied or dynamically added getter */
-	get?: (param: any, ds: any) => void
-	/** bgzip-compressed, tabix-index file.
-	first line must be "#chr \t start \t stop \t gene \t sample1 \t ..."
-	(required when src=native and no ds-supplied getter)
-	*/
-	file?: string
-	/** dynamically added during server launch, list of sample integer IDs from file */
-	samples?: number[]
-	/** dynamically added flag during launch */
-	nochr?: boolean
-	/** This dictionary is used to store/cache the default bins calculated for a geneExpression term when initialized in the fillTermWrapper */
-	geneExpression2bins?: { [index: string]: any }
-	/** gene expression unit (e.g. 'FPKM') */
-	unit?: string
-}
-
-/** Isoform expression query — either .get() or .file is needed.
- *  availableItems is populated at startup from the HDF5 item dataset
- *  so the client can filter isoform selection lists. */
-export type IsoformExpressionQuery = {
-	/** ds-supplied or dynamically added getter */
-	get?: (param: any, ds: any) => void
-	/** HDF5 file with ENST IDs as row keys */
-	file?: string
-	/** dynamically added during server launch, list of sample integer IDs from file */
-	samples?: number[]
-	/** cache for default bins per isoform */
-	geneExpression2bins?: { [index: string]: any }
-	/** expression unit (e.g. 'TPM') */
-	unit?: string
-	/** ENST IDs available in the HDF5 file, populated during server validation */
-	availableItems?: string[]
-}
-
-export type SingleCellGeneExpressionNative = {
-	src: 'native'
-	/** path to HDF5 files. for now only HDF5 is supported.
-	each is a gene-by-cell matrix for a sample, with ".h5" suffix. missing files are detected and handled */
-	folder: string
-	/** dynamically added getter */
-	get?: (q: any) => any
-	/** cached gene exp bins */
-	sample2gene2expressionBins?: { [sample: string]: { [gene: string]: any } }
-	/** gene expression unit (e.g. 'FPKM') */
-	unit?: string
-}
-
-export type SingleCellGeneExpressionGdc = {
-	src: 'gdcapi'
-	/** gene expression unit (e.g. 'FPKM') */
-	unit?: string
-}
-
-export type SingleCellSamples = {
-	/** logic to decide sample table columns (the one shown on singlecell app ui, displaying a table of samples with sc data)
-	a sample table will always have a sample column, to show sample.sample value
-	- use uiLabels.Sample to customize the name of the first column
-	- the other two properties allow to declare additional columns to be shown in table, that are for display only
-	when sample.experiments[] are used, a last column of experiment id will be auto added
-	*/
-	/** any columns to be added to sample table. each is a term id, limited to categorical/numeric dictionary terms */
-	sampleColumns?: { termid: string }[]
-	/** used on client but not on ds */
-	experimentColumns?: { label: string }[]
-	/** getter function to return list of samples with single-cell data
-	is either ds-supplied, to enclose ds-specific query details (gdc)
-	or is missing, to be added at launch with built-in logic (samples are found by looking through singleCell.data.plots[].folder)
-	*/
-	get?: (q: any) => any
-	/** extra label to show along with sample, must be a term id as in sampleColumns[] and allow to retrieve value from sample object */
-	extraSampleTabLabel?: string
-}
-
-type SingleCellDataBase = {
-	/** when a sample has multiple tsne plots, this flag allows allows all plots to share one cell type legend */
-	sameLegend?: boolean
-	/** name of ref cells? */
-	refName?: string
-	/** dynamically added getter */
-	get?: (q: any) => any
-	/** width and height of the plots */
-	settings?: { [key: string]: any }
-	/** In development
-	 * Replacing colorColumns in gdc plot objs.*/
-	twLst?: object[]
-}
-
-export type SingleCellDataGdc = SingleCellDataBase & {
-	src: 'gdcapi'
-	plots: GDCSingleCellPlot[]
-}
-
-export type SingleCellDEgeneGdc = {
-	src: 'gdcapi'
-	/** termId = Column name.
-this must be the colorColumn from one of the plots. In the client app, as soon as the plot data loads and maps renders, client finds the cell groups based on this columnName value, and shows a drop down of these groups on UI. user selects a group, and passes it as request body to backend to get DE genes for this group
-*/
-	termId: string
-}
-
-type GDCSingleCellPlot = {
-	name: string
-	colorColumns: ColorColumn[]
-	coordsColumns: { x: number; y: number }
-	/** if true the plot is shown by default. otherwise hidden
-	 * Will not be needed when the singleCellPlot is deprecated.*/
-	selected?: boolean
-}
-
-type ColorColumn = {
-	/** 0-based column number in the tabular file */
-	index?: number
-	/** name of the column */
-	name: string
-	/** column values (categories) to color mapping */
-	colorMap?: { [index: string]: string }
-	aliases?: { [index: string]: string }
-}
-
-/** defines a tsne type of plot for cells from one sample */
-type SingleCellPlot = {
-	/** value is display as plot name on ui and also used as identifier for a plot, must be unique */
-	name: string
-	/** folder in which per-sample files are stored.
-	- each file is a tabular text file with all cells (rows) from that sample. each file is named by the sample and includes optional suffix
-	- folder must only contain per-sample files! files with names that cannot be matched to sample will crash dataset. this improves debugging
-
-	all files must have same set of columns:
-	- 1st column is cell barcode
-	- x/y coordinate column number is defined in coordsColumns{x,y} below
-	- additional columns for cell annotations, corresponds to colorColumns
-	*/
-	folder: string
-	/** 0-based column number for x/y coordinate for this plot */
-	coordsColumns: { x: number; y: number }
-	/** optional suffix to locate the file for a sample, via ${folder}/${sampleName}${fileSuffix}
-	assumes that file name always start with sample name.
-	if not introduce filePrefix
-	*/
-	fileSuffix?: string
-	/** list of columns in tabular text file that define cell categories and can be used to color the cells in the plot. must have categorical values
-	 */
-	colorColumns: ColorColumn[]
-	/** if true the plot is shown by default. otherwise hidden.
-	 * Old implementation. Maybe deleted when singleCellPlot is deprecated.*/
-	selected?: boolean
-	/** Plot is a meta analysis result and treated differently in the UI */
-	isMetaResult?: boolean
-	/** optional for meta analysis result plots. May define the "sampleId" for the
-	 * server requests. If not provided, the file name or the plot name with the
-	 * spaces replaced with '_' is used. */
-	sampleId?: string
-}
-export type SingleCellDataNative = SingleCellDataBase & {
-	src: 'native'
-	/** available tsne type of plots for each sample */
-	plots: SingleCellPlot[]
-}
-
-export type SingleCellQuery = {
-	/** methods to identify samples with singlecell data,
-	this data allows client-side to display a table with these samples for user to choose from
-	also, sampleView uses this to determine if to invoke the sc plot for a sample
-	*/
-	samples: SingleCellSamples
-	/** defines tsne/umap type of clustering maps for each sample
-	 */
-	data: SingleCellDataGdc | SingleCellDataNative
-	metaResults?: SingleCellMetaResult[]
-	/** defines available gene-level expression values for each cell of each sample */
-	geneExpression?: SingleCellGeneExpressionGdc | SingleCellGeneExpressionNative
-	/** Precomputed top differentialy expressed genes for a cell cluster, against rest of cells */
-	DEgenes?: SingleCellDEgeneGdc
-	/** supplies per-sample images. will create a new tab on the ui. one image per sample */
-	images?: SCImages
-	/** Created on mds.init() from colorMap and alias within each plot. */
-	terms?: object[]
-}
-
-export type SingleCellMetaResult = {
-	/** identifier */
-	name: string
-	/** tsv file
-	- 1st column is cell barcode
-	- x/y coordinate column number is defined in coordsColumns{x,y} below
-	- additional columns for cell annotations, corresponds to colorColumns
-	- must have a column for sample name, to identify which sample the cell is from
-	*/
-	file: string
-	/** gene exp h5 file */
-	geneExpFile?: string
-	/** 0-based column number for x/y coordinate for this plot */
-	coordsColumns: { x: number; y: number }
-	colorColumns: ColorColumn[]
-}
-
-type SCImages = {
-	/** folder where the per-sample image files are stored, as "SCImages/<folder>/<sample>/<fileName>" */
-	folder: string
-	/** see above */
-	fileName: string
-	/**Used to name the image tab in the single cell plot */
-	label: string
-}
-
-/** genome browser LD track */
-type LdQuery = {
-	/** each track obj defines a ld track */
-	tracks: {
-		/** for displaying and identifying a track. must not duplicate */
-		name: string
-		/** relative path of ld .gz file */
-		file: string
-		/** dynamically added */
-		nochr?: boolean
-		/** if to show by default */
-		shown: boolean
-		/** max range allowed to show data */
-		viewrangelimit: number
-	}[]
-	/** color scale when LD is used to overlay on variants of a locus  */
-	overlay: {
-		/** color for r2 value 1 */
-		color_1: string
-		/** Color for r2 value 0 */
-		color_0: string
-	}
-}
-
-/** one more multiple sets of genome-wide plots per sample, e.g. dna meth probe beta values. the plot has a Y axis and shows all chromosomes. each key is one set of such plot. there could be multiple sets */
-type SingleSampleGenomeQuantification = {
-	[index: string]: {
-		/** description of this data */
-		description: string
-		/** min value of Y axis */
-		min: number
-		/** max value of Y axis */
-		max: number
-		sample_id_key: string
-		/** folder path of data files per sample */
-		folder: string
-		/** plot color for positive values */
-		positiveColor: string
-		/** plot color for negative values */
-		negativeColor: string
-		/** optionally, link the plot to singleSampleGbtk, in that clicking on the plot will luanch a detailed block view defined by singleSampleGbtk */
-		singleSampleGbtk?: string
-	}
-}
-
-/** single sample genome browser track. each key corresponds to one track. currently hardcoded to "<sampleId>.gz" bedgraph files in the folder  */
-type SingleSampleGbtk = {
-	[index: string]: {
-		/** description of this data */
-		description: string
-		/** min value of Y axis */
-		min: number
-		/** max value of Y axis */
-		max: number
-		/** */
-		sample_id_key: string
-		/** folder path of data files per sample */
-		folder: string
-	}
-}
-
-type Mds3Queries = {
-	/** (gb=genomebrowser) controls gb chart button menu genesearchbox behavior, 
-	add some additional options after a gene is found, and mode of gb launched from the menu
-
-	- "protein":
-		genesearchbox only allow searching gene and not coord
-		launched gb goes into protein-mode
-		this is used for ds with only coding mutations over some protein-coding genes, and only want to show protein view for such
-	- "genomic":
-		searching either gene/coord will result in coord
-		gb will always be in genomic mode
-		this is used for ds with genome-wide variants only shown in genomic views, but not protein view
-	- none:
-		meaning gb can be shown in either protein or genomic mode
-		when searching coord, gb goes into genomic mode
-		when searching gene, show an option in chart btn menu to select protein or genomic view
-	*/
-	gbRestrictMode?: 'protein' | 'genomic'
-	snvindel?: SnvIndelQuery
-	svfusion?: SvFusion
-	cnv?: CnvSegmentQuery
-	/** gene-level cnv, only available on gdc; query by gene symbol, ds must define getter
-	 */
-	geneCnv?: {
-		bygene: {
-			get: (q: any) => any
-		}
-	}
-	trackLst?: TrackLst
-	ld?: LdQuery
-	defaultCoord?: string
-	singleSampleMutation?: SingleSampleMutationQuery
-	NIdata?: NIdataQuery
-	geneExpression?: GeneExpressionQuery
-	isoformExpression?: IsoformExpressionQuery
-	/** single-sample gsea precomputed scores for rnaseq samples, for genesets from geneset db
-	requires genome to be equipped with geneset db
-	*/
-	ssGSEA?: {
-		/** path to h5 file, matrix of NES scores. rows are msigdb geneset ids, columns are rnaseq samples */
-		file: string
-		// in case a genome may have more than 1 geneset dbs, here may specify name of db that this result is based on */
-	}
-	/** dna methylation beta value matrix
-	 */
-	dnaMethylation?: {
-		/** path to h5 file */
-		file: string
-		/** dna methylation unit (e.g. 'Average Beta Value') */
-		unit: string
-		/** promoter-by-sample matrix, values are average M-value */
-		promoter?: {
-			/** path to h5 file */
-			file: string
-			/** unit label for promoter values (e.g. 'Average M-value') */
-			unit: string
-		}
-	}
-	rnaseqGeneCount?: RnaseqGeneCount
-	/** Used to create the top mutated genes UI in the gene
-	 * set edit ui and data requests. */
-	topMutatedGenes?: TopMutatedGenes
-	/** get top variably expressed genes */
-	topVariablyExpressedGenes?: TopVariablyExpressedGenesQuery
-	metaboliteIntensity?: {
-		src: 'native'
-		file: string
-	}
-	proteome?: ProteomeAbundanceQuery
-	singleCell?: SingleCellQuery
-	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
-	singleSampleGbtk?: SingleSampleGbtk
-	/** deprecated. replaced by WSImages */
-	DZImages?: DZImages
-	WSImages?: WSImages
-	images?: Images
-	chat?: any
-	alphaGenome?: {
-		ontologyTerm?: string // default ontology term for a dataset
-		default: {
-			gene: string
-			chromosome: string
-			position: number
-			reference: string
-			alternate: string
-			ontologyTerm: string
-			outputType: number
-		}
-	}
-}
-
-/** chat app support
-type Chat = {
-}
- */
-
-/** non-zoom small images
-iamge file to sample mapping is stored in images table
-*/
-type Images = {
-	/** folder where the per-sample image files are stored */
-	folder: string
-}
-
-/** Deprecated. deep zoom image shown via openseadragon, with precomputed tiles.
- * this is replaced by WSImages and should not be used anymore */
-export type DZImages = {
-	// type of the image, e.g. H&E
-	type: string
-	// path to the folder where sample images are stored
-	imageBySampleFolder: string
-}
-
-/** deep zoom image shown via tiatoolbox, covers any big image files including whole-slide image. 
-image file to sample mapping is stored in wsimages table
-*/
-export type WSImages = {
-	db?: { file: string }
-	// type of the image, e.g. H&E
-	type: string
-
-	/* path to the folder where sample images are stored
-	required; for both cases where image files are hosted locally, or loaded from remote via ds-supplied getter
-	*/
-	imageBySampleFolder?: string
-
-	aiToolImageFolder?: string
-
-	activePatchColor?: string
-	predictionColor?: Array<number>
-	annotationsColor?: Array<number>
-	tileSize?: number
-	uncertainty?: { color: string; label?: string }[]
-
-	/** dynamically added on launch with built in logic */
-	saveWSIAnnotation?: (annotation: SaveWSIAnnotationRequest) => Promise<void>
-
-	/** dynamically added on launch with built in logic */
-	deleteWSIAnnotation?: (annotation: DeleteWSITileSelectionRequest) => Promise<void>
-
-	/** dynamically added on launch with built in logic - returns all image filenames for a project */
-	getAllWSImages?: (projectId: string) => Promise<string[]>
-
-	/** either ds supplied or dynamically added on launch with built in logic (retrieve the sample list from the wsimages table) */
-	getSamples?: () => Promise<Array<WSISample>>
-	/** either ds supplied or dynamically added on launch with built in logic */
-	getWSImages?: (sampleName: string) => Promise<WSImage[]>
-	/**  ds supplied */
-	getWSIPredictionPatches?: (projectId: string, wsiImage: string) => Promise<Prediction[]>
-	/**  ds supplied */
-	getWSIAnnotations?: (projectId: string, wsiImage: string) => Promise<string[]>
-	/**  ds supplied */
-	getPredictionLayers?: (projectId: string, wsiImage: string) => Promise<Map<string, string> | undefined>
-	/**  ds supplied */
-	getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
-	/**  ds supplied */
-	retrainModel?: (projectId: string, wsimages: string[]) => Promise<void>
-	/**  ds supplied */
-	selectWSIImages?: () => Promise<string[]>
-}
-
-export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
-
-/*** types supporting Termdb ***/
-
-type TermIds = {
-	[index: string]: string
-}
-
-type SelectCohortValuesEntry = {
-	keys: string[]
-	label: string
-	shortLabel: string
-	isdefault?: boolean
-	note?: string
-}
-
-export type SelectCohortEntry = {
-	/** subcohort term in db. uses hardcoded type=multivalue */
-	term: { id: string; type: string }
-	/** Title above the cohort introduction/content in the about tab */
-	title?: string
-	/** Text above radio cohort options in the about tab. */
-	prompt: string
-	values: SelectCohortValuesEntry[]
-	/** cohort-related static html shown in about tab */
-	description?: string
-	descriptionByCohort?: { [index: string]: string }
-	/** If the description is dependent on the user's role, 
-	define this callback to return description based on auth
-	returns a static description
-	*/
-	descriptionByUser?: (auth: any) => string
-	/** similar to descriptionByUser but returns an object with one description per cohort,
-	about tab will switch description based on user-selected cohort
-	*/
-	descriptionByCohortBasedOnUserRole?: (auth: any) => object
-	/** subtext shown at the very bottom of the cohort/about tab subheader */
-	asterisk?: string
-	//The profile has clearOnChange. The terms used in the plots are not always the same for the profile.
-	//Therefore when switching cohorts, it is necessary to delete the plots opened and the global filter
-	clearOnChange?: { [index: string]: boolean }
-}
-
-type MissingAccess = {
-	message: string
-	links: { [index: string]: string }
-}
-
-type DataDownloadCatch = {
-	helpLink: string
-	missingAccess: MissingAccess
-	jwt: { [index: string]: string }
-}
-
-type ScatterPlotsEntry = {
-	name: string
-	description?: string
-	descriptionShort?: string
-	dimension: number
-	file: string
-	coordsColumns?: { x: number; y: number; z?: number }
-	settings?: { [index: string]: any }
-	/** by default the dots are called "samples" on the plot, use this to call it by diff name e.g. "cells" */
-	sampleType?: string
-	/** a termsetting to supply dot color */
-	colorTW?: { id: string }
-	/** a termsetting to supply dot shape */
-	shapeTW?: { id: string } // TODO replace with tw type
-	colorColumn?: ColorColumn
-	/** provide a sampletype term to filter for specific type of samples for subjects with multiple samples and show in the plot.
-e.g. to only show D samples from all patients
-this is limited to only one term and doesn't allow switching between multiple terms
-*/
-	sampleCategory?: {
-		/** categorical term like "sampleType" which describes types of multiple samples from the same subject */
-		tw: { id: string }
-		/** default category */
-		defaultValue: string
-		/** order of categories */
-		order: string[]
-	}
-}
-
-type Scatterplots = {
-	/** 
-	if defined:
-		ds-supplied getter, arg is clientAuthResult, returns list of plot available for this request based on auth
-		here plots[] array is still needed! so on loading a plot the server can find the matching plot by requested name
-	if not defined:
-		entire plots[] is always send to client
-	*/
-	get?: (clientAuthResult: any) => ScatterPlotsEntry[]
-	/** hardcoded plots */
-	plots: ScatterPlotsEntry[]
-}
-
-/** this plot compares correlation of one feature against a bunch of variables across samples
- */
-type CorrelationVolcano = {
-	/** fixed feature, is one numeric term */
-	feature: {
-		/** array of allowed term types for feature tw */
-		termTypes: string[]
-	}
-	/** list of numeric variables to be compared against fixed feature*/
-	variables: {
-		/** later can expand */
-		type: 'dictionaryTerm'
-		/** when type=dictionaryTerm, is array of numeric term ids */
-		termIds?: string[]
-	}
-}
-
-/** Configurations for box plots */
-type BoxPlots = {
-	/** If true, allows user to 'remove outliers' from burger menu */
-	removeOutliers: boolean
-}
-
-type UiLabels = {
-	[propName: string]: string | { label: string; [otherAttr: string]: string }
-}
-
-type TieBreakerFilterValuesEntry = {
-	dt: number
-}
-
-type TieBreakerFilter = {
-	values: TieBreakerFilterValuesEntry[]
-}
-
-type TieBreakersEntry = {
-	by: string
-	order?: (string | number)[]
-	filter?: TieBreakerFilter
-}
-
-type SortPriorityEntry = {
-	types: string[]
-	tiebreakers: TieBreakersEntry[]
-}
-
-type SurvivalSettings = {
-	/** The max time-to-event to be displayed in plot, hide all the samples with Time-to-Event longer than this maxTimeToEvent */
-	maxTimeToEvent?: number
-	/** The time unit (years, months, weeks, or days) displayed in the x-axis of survival plot */
-	timeUnit?: string
-	/** The number of raw survival data's time units that make up one year, e.g., 12 for months */
-	numUnitInOneYear?: number
-	/** the customized x-axis tick values of survival plot */
-	xTickValues?: number[]
-}
-
-type RegressionSettings = {
-	/** Disclaimer message shown under the cofficient table when
-	 * regression type is cox. */
-	coxDisclaimer?: string
-	/** disable interactions */
-	disableInteractions?: boolean
-	/** hide type III statistics table in results */
-	hideType3?: boolean
-	/** hide statistical tests table in results */
-	hideTests?: boolean
-}
-
-type MatrixSettings = {
-	maxSample?: number
-	svgCanvasSwitch?: number
-	cellEncoding?: string
-	cellbg?: string
-	controlLabels?: UiLabels
-	sortSamplesBy?: string
-	sortPriority?: SortPriorityEntry[]
-	ignoreCnvValues?: boolean
-	geneVariantCountSamplesSkipMclass?: string[]
-	/** all the truncating mutations exist in the dataset */
-	truncatingMutations?: string[]
-	/** all the protein-changing mutations mutations exist in the dataset */
-	proteinChangingMutations?: string[]
-	/** all the mutation classes exist in the dataset */
-	mutationClasses?: string[]
-	/** all the CNV classes exist in the dataset */
-	CNVClasses?: string[]
-	/** all the synonymous mutations exist in the dataset */
-	synonymousMutations?: string[]
-	showHints?: string[]
-	displayDictRowWithNoValues?: boolean
-	/** allow to add two buttons (CNV and mutation) to control panel for selecting
-	 * mclasses displayed on oncoMatrix */
-	addMutationCNVButtons?: boolean
-	/** this is now computed from sortPriority[x].tiebreakers.find(tb =>
-	 * tb.filter?.values[0]?.dt === 1) ... */
-	sortByMutation?: string
-	/** this is now computed from sortPriority[x].tiebreakers.find(tb =>
-	 * tb.filter?.values[0]?.dt === 4).isOrdered */
-	sortByCNV?: boolean
-	cnvUnit?: 'log2ratio' | 'segmedian'
-	/** whether to show white cell border for SNVindel in oncoPrint mode */
-	oncoPrintSNVindelCellBorder?: boolean
-	/** use a geneset edit UI without or with initial radio inputs */
-	genesetEditUiVersion?: '' | 'withTabs'
-}
-
-type NumericDictTermClusterSettings = {
-	/** default hiercluster group name */
-	termGroupName?: string
-	zScoreTransformation?: boolean
-	colorScale?: string
-}
-
-type Matrix = {
-	/** alternative name, e.g. the plot is called "oncomatrix" in gdc; by default it's called "matrix" */
-	appName?: string
-	/** default settings for matrix plot */
-	settings?: MatrixSettings
-	/** matrix-specific mclass override? */
-	mclass?: Mclass
-	/** filter to hide entire legend group, e.g. hide all CNV */
-	legendGrpFilter?: any
-	/** filter to hide categories or mclass, e.g. hide male, hide MISSENSE */
-	legendValueFilter?: any
-	/** local filter to limit samples in matrix/hiercluster, merged with this.state.termfilter.filter when querying server */
-	filter?: any
-	/** matrix criteria for a CNV alteration */
-	cnvCutoffs?: any
-}
-
-// specific hierCluster type settings, should be named as "dataType + Cluster"
-type NumericDictTermCluster = {
-	/** alternative name, e.g. the plot is called "drug sensitivity" in ALL-pharmacotyping; by default it's called "Numeric Dictionary Term cluster" */
-	appName?: string
-	/** default settings for numericDictTermCluster plot */
-	settings?: NumericDictTermClusterSettings
-	/** list of numeric term ids that will be excluded from the numeric dictionary term cluster, add to usecase.detail to exclude terms*/
-	exclude?: string[]
-	/** list of pre-built numericDictTermcluster plots */
-	plots?: NumericDictTermClusterPlotsEntry[]
-}
-
-type NumericDictTermClusterPlotsEntry = {
-	name: string
-	file: string
-	settings?: {
-		[key: string]: any
-	}
-	/** helper function to get plot config from saved session file */
-	getConfig?: (f: any) => void
-}
-
-type Survival = {
-	/** default settings for survival plot */
-	settings?: SurvivalSettings
-}
-
-type Regression = {
-	/** default settings for regression */
-	settings?: RegressionSettings
-}
-
-type MatrixPlotsEntry = {
-	name: string
-	file: string
-	settings?: {
-		[key: string]: any
-	}
-	getConfig?: (f: any) => void
-}
-
-type MatrixPlots = {
-	plots: MatrixPlotsEntry[]
-}
-
-type AllowCaseDetails = {
-	sample_id_key: string
-	terms: string[]
-}
-
-type MultipleTestingCorrection = {
-	method: string
-	skipLowSampleSize: boolean
-}
-
-type TvsTerm = {
-	id: string
-	type: string
-	name: string
-}
-
-type TvsValues = {
-	key?: string
-	label?: string
-}
-
-type Tvs = {
-	term: TvsTerm
-	values: TvsValues[]
-}
-
-type RestrictAncestriesEntry = {
-	name: string
-	tvs: Tvs
-	PCcount: number
-
-	// TODO declare that either PCTermId or PCBySubcohort is required
-	PCTermId?: string
-	PCBySubcohort?: {
-		[subcohortId: string]: any
-	}
-}
-
-/*
-base type for deriving new types with new attributes
-
-*/
-type UrlTemplateBase = {
-	/** must end with '/' */
-	base: string
-	namekey: string
-	defaultText?: string
-}
-export type UrlTemplateSsm = UrlTemplateBase & {
-	/** to create separate link, but not directly on chr.pos.ref.alt string.
-	name of link is determined by either namekey or linkText. former allows to retrieve a name per m that's different from chr.pos.xx */
-	shownSeparately?: boolean
-	/** optional name of link, if set, same name will be used for all links. e.g. "ClinVar".
-if missing, name is value of m[url.namekey], as used in url itself (e.g. snp rsid) */
-	linkText?: string
-}
-
-export type GetSamplesOpts = {
-	filter: any // pp filter
-	filter0: any // mmrf filter
-	ds: any
-}
-
-/*** type of ds.cohort.termdb{} ***/
-export type Termdb = {
-	/** Terms */
-	termIds?: TermIds
-	/**
-	 * Check for the required minimum number of samples with data as queried with getData() or other code,
-	 * in order to minimize the ease of extracting identifiable information from aggregate data
-	 * in server response
-	 *
-	 * returns: {minSize, canAccess}, see below
-	 */
-	checkAccessToSampleData?: (
-		/** req.query as processed through app middleware (pre-parsed, may have req.body props, __protectec__, etc) */
-		q: any,
-		data: {
-			/** the number of samples or sites with matching data from one or more queried terms */
-			count: number
-			/** option to specify sample names or sites that are accessible to the current user,
-			 */
-			names?: string[]
-		}
-	) => {
-		/** the required minimum size for the current user to access certain data,
-		 * may be dependent on login status or other context
-		 * */
-		minSize: number
-		/** whether downstreadm backend code can proceed */
-		canAccess: boolean
-	}
-	/** if true, backend is allowed to send sample names to client in charts */
-	displaySampleIds?: (clientAuthResult: any) => boolean
-	/** get samples that match supplied filter */
-	getSamples?: (opts: GetSamplesOpts) => Promise<Set<any>>
-	converSampleIds?: boolean
-	alwaysShowBranchTerms?: boolean
-	minimumSampleAllowed4filter?: number
-	minTimeSinceDx?: number
-	timeUnit?: string
-	ageEndOffset?: number
-	cohortStartTimeMsg?: string
-	alwaysRefillCategoricalTermValues?: boolean
-	restrictAncestries?: RestrictAncestriesEntry[]
-	/** Cohort specific */
-	selectCohort?: SelectCohortEntry
-	/* When a dataset uses login this property allows to configure the login logic */
-	invalidTokenErrorHandling?: {
-		//Affected charts contains the list of charts that require a login, if * is present, all charts require a login
-		affectedCharts: string[]
-		//Error message that will be displayed in the UI when the login fails or the token is invalid
-		errorMessage: string
-	}
-
-	/** quick fix to convert category values from a term to lower cases for comparison (case insensitive comparison)
-for gdc, graphql and rest apis return case-mismatching strings for the same category e.g. "Breast/breast"
-keep this setting here for reason of:
-- in mds3.gdc.js, when received all-lowercase values from graphql, it's hard to convert them to Title case for comparison
-- mds3.variant2samples consider this setting, allows to handle other datasets of same issue
-  */
-	useLower?: boolean
-	matrix?: Matrix
-	numericDictTermCluster?: NumericDictTermCluster
-	survival?: Survival
-	regression?: Regression
-	logscaleBase2?: boolean
-	plotConfigByCohort?: PlotConfigByCohort
-	/** Functionality */
-	dataDownloadCatch?: DataDownloadCatch
-	helpPages?: URLEntry[]
-	multipleTestingCorrection?: MultipleTestingCorrection
-	urlTemplates?: {
-		/** gene link definition */
-		gene?: UrlTemplateBase
-		/** sample link definition */
-		sample?: UrlTemplateBase
-		/** ssm link definition */
-		ssm?: UrlTemplateSsm | UrlTemplateSsm[]
-		/** allow to add link to "Experiment" field of singlecell app sample table */
-		scrnaExperimentId?: UrlTemplateBase
-	}
-
-	termtypeByCohort?: any // FIXME see below
-	/** TODO not declared due to tsc err
-	ds-defined or dynamically created. the array has an extra "nested" property
-	only describes dictionary terms,
-	non-dict terms are dynamically generated in getAllowedTermTypes() of termdb.config.ts based on query types
-	termtypeByCohort?: {
-		cohort: string
-		termType: string
-		termCount: number
-	}[] & {
-		nested: {
-			[cohort: string]: {
-				[termType: string]: number
-			}
-		}
-	}
-	*/
-
-	/** ds defined add on to termtypeByCohort; note that this is not cohort-specific!
-	this is combined with termtypeByCohort in getAllowedTermTypes()
-	for now is used to support following types which lacks good way to auto generate them:
-
-	- geneVariant
-		for somatic events. works for snvindel/svfusion/cnv.
-		since all these datatypes are optional, cannot define it in snvindel.termTypes which could be missing
-		** must be defined via allowedTermTypes[] **
-
-	- snp, snplst, snplocus
-		for germline markers
-	*/
-	allowedTermTypes?: string[]
-
-	/** ds-defined or dynamically created callbacks 
-	{
-		getSupportedChartTypes: (a: any) => any
-	}
-	*/
-	q?: any
-	/** mclass override (color, label etc) */
-	mclass?: Mclass
-	lollipop?: any
-	hasAncestry?: boolean
-	/** set to true for genome-level geneset db */
-	isGeneSetTermdb?: boolean
-
-	/** method to get total sample size per category for a dict term. to use in mds3 tk sample summary
-	 */
-	termid2totalsize2?: {
-		// ds-supplied getter. if missing, should be using native termdb
-		get?: (twLst: any, q: any, combination: any, ds: any) => void
-		// gdc flag for outdated design
-		gdcapi?: true
-	}
-	/** Do not use a union here. */
-	/** TODO: should use a union to distinguish between type defs */
-	dictionary?: GdcApi & AiApi & DictApi
-	allowCaseDetails?: AllowCaseDetails
-	/** Searches the genedb alias list to return the genecode ID */
-	getGeneAlias?: (q: any, tw: any) => { gencodeId: any }
-	convertSampleId?: GdcApi
-	hierCluster?: any
-
-	/** ds customization of rules in TermTypeSelect on what term type to exclude for a usecase.
-	used by gdc in that gene exp cannot be used for filtering
-	note this applies to left-side term type tabs, but not terms in dict tree. latter is controlled by excludeTermtypeByTarget
-	*/
-	useCasesExcluded?: {
-		/** key is target name (todo restrict values), value is array of 1 or more term
-		 * types (todo restrict values) */
-		[useCaseTarget: string]: string[]
-	}
-	/** ds customization to rules in isUsableTerm(). this applies to what's showing in dict tree
-	 */
-	excludedTermtypeByTarget?: {
-		/** key is usecase target (todo restrict). value is array of term type (todo restrict) */
-		[useCaseTarget: string]: string[]
-	}
-	/** in development!
-	 * Supports the About tab in mass UI
-	 */
-	hasSampleAncestry?: boolean
-	sampleTypes?: SampleType[]
-	/** ui labels used for plot controls and tooltips */
-	uiLabels?: UiLabels
-
-	tracks?: {
-		/** allow color or shape changes in the lollipop */
-		allowSkewerChanges: boolean
-	}
-	//* specify color map per module/group of terms. Used in the profile dataset.
-	/** For example "National Context" is a profile module, that groups some multivalue terms for wich the category colors are the ones shown below: 
-	 colorMap: {
-				['*']: {
-					['Not applicable for my role']: '#aaa',
-					['Not Available/Do Not Know']: '#aaa',
-					["I don't know"]: '#aaa',
-					['Almost Never']: '#595959',
-					['Infrequently']: '#747474',
-					['No']: '#aaa'
-				},
-				['National Context']: {
-					['Almost Always']: '#15557C',
-					['Frequently']: '#1E77BB',
-					['Sometimes']: '#2FA9F4',
-					['Yes']: '#1E77BB'
-				},
-	}
-	If the colors are the same for all the categories, use the wildcard '*' to define the color for all the modules.
-	**/
-	colorMap?: {
-		/** colors for a category multivalues */
-		[index: string]: { [index: string]: string }
-	}
-	defaultTw4correlationPlot?: {
-		/** key is string as disease/survial etc, value is tw */
-		[index: string]: Tw
-	}
-	/** maximum number of genes to query in geneVariant gene set */
-	maxGeneVariantGeneSetSize?: number
-	/** (server-side) maximum number of awaited by-term queries for sample data */
-	maxConcurrentQueries?: number
-	/** (client-side) maximum number of terms that should be submitted in one fetch request in TermdbVocab.getAnnotatedSampleData() */
-	maxAnnoTermsPerClientRequest?: number
-	/** option to disable mayAddDataAvailability() based on request path and query parameters */
-	disableAssayAvailability?: (path: string, query: { [key: string]: any }) => boolean
-	//terms  are shown in the dictionary based on term and user role.
-	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
-	hiddenIds?: string[]
-	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
-	/** collections of dictionary terms (numeric or categorical) that are related and can be used together in some plots */
-	termCollections?: TermCollection[]
-	/** whether to set onlyChildren in getData() */
-	setOnlyChildren?: true
-}
-
-type TermCollectionBase = {
-	/** human readable name as well as unique identifier for this collection */
-	name: string
-	/** array of dictionary term ids belonging to this collection.
-	 *  Optional for custom (non-dictionary) collections where termlst[] is the primary source. */
-	termIds?: string[]
-	/** full term objects corresponding to termIds[]; populated by server on dataset init,
-	 * sent to client so fill() can resolve member term names without extra requests */
-	termlst?: BaseTerm[]
-	/** array of branch term ids belonging to this collection,
-	 * may be used as state.tree.expandedTermIds[] option to termdb appInit() */
-	branchIds?: string[]
-	propsByTermId: {
-		[termId: string]: any
-	}
-	/** preconfigured cohort-level plots for this collection */
-	plots?: {
-		/** name of this plot */
-		name: string
-		/** json file path of this plot */
-		file: string
-	}[]
-}
-
-type NumericTermCollection = TermCollectionBase & {
-	type: 'numeric'
-	/** optional transformations to apply to the term values when used in plots, specified by plot type */
-	valueTransformByPlots?: {
-		[chartType: string]: { offset?: number }
-	}
-}
-
-type CategoricalTermCollection = TermCollectionBase & {
-	type: 'categorical'
-	/** category values to filter on; hydrated form uses CategoryKey[] */
-	categoryKeys: CategoryKey[]
-}
-
-type TermCollection = NumericTermCollection | CategoricalTermCollection
-
-type SampleType = {
-	name: string
-	plural_name: string
-	parent_id: string
-}
-
-/** predefined configuration objects per subcohort per plot type */
-type PlotConfigByCohort = {
-	/** key is subcohort string */
-	[index: string]: {
-		/** key is plot type as in mass/charts.js */
-		[key: string]: object
-	}
-}
-
-/** modified version of termwrapper*/
-type Tw = {
-	/** short hand for using either id (dict term) or term{} */
-	id?: string
-	term?: object
-	q?: unknown
-	/** quick fix for generating URL links in mds3 tk sample table! adhoc design. may move to tw.term.baseURL and not specific to mds3 tk
-	 */
-	baseURL?: string
-	/** quick fix. such a "publication" term can have values either pmid or doi, need to generate different links
-	cannot use ds-defined callback to compute the link as the links are only generated on client
-	thus this work around for client code to apply the url-building logic
-	a doi value must be defined as "doi: 10.1038/s41408-025-01309-6", beginning with "doi: ", this allows client code to recognize it is doi;
-	otherwise it is treated as pmid and joined to pubmed link as-is
-	*/
-	pmidOrDoi?: true
-}
-
-type Variant2Samples = GdcApi & {
-	variantkey: string
-	twLst?: Tw[]
-	sunburst_twLst?: Tw[]
-	/** ds-supplied getter */
-	getMutatedSamples?: (q: any, ds: any) => void
-}
-
-type MutationSet = {
-	snvindel: string
-	cnv: string
-	fusion: string
-}
-
-/** different methods to return samples with assay availability info */
-/** using dictionary term */
-type DtAssayAvailabilityTerm = {
-	/** id of this assay term for this dt */
-	term_id: string
-	/** optional label */
-	label?: string
-	/** categories meaning the sample has this assay */
-	yes: { value: string[] }
-	/** categories meaning the sample doesn't have this assay */
-	no: { value: string[] }
-	/** dynamically generated cached sample lists on server launch, can also be ds-supplied.
-	each is a Set of sample integer id (non-gdc ds) or sample name (case uuid for gdc)
-	*/
-	yesSamples?: Set<string | number>
-	noSamples?: Set<string | number>
-}
-
-type DtAssayAvailabilityByOrigin = {
-	byOrigin: {
-		/** each key is an origin value or category */
-		[index: string]: DtAssayAvailabilityTerm
-	}
-}
-
-/** assay availability can be set up as below, during server init it will query by assay dictionary terms to populate yes/no samples for each dt
-or as in gdc, it is entirely setup ad-hoc
-*/
-type Mds3AssayAvailability = {
-	/** object of key-value pairs. keys are dt values */
-	byDt: {
-		/** each index is a dt value */
-		[index: number]: DtAssayAvailabilityByOrigin | DtAssayAvailabilityTerm
-	}
-	/** if true, ds will use both filter and filter0 to filter samples (this is a temp quick fix)
-	 */
-	useFilter0?: true
-}
-
-// mds legacy; delete when all are migrated to mds3
-type LegacyAssayAvailability = {
-	file?: string
-	assays?: {
-		id: string
-		name: string
-		type: string
-		values?: {
-			[index: string]: { label: string; color: string }
-		}
-	}[]
-}
-
-export type CumBurdenData = {
-	/** directory containing cumulative burden data */
-	dir: string
-	files: {
-		fit: string
-		surv: string
-		sample: string
-	}
-	/** subdirectory containing bootstrap data */
-	bootsubdir: string
-	db: {
-		/** db file created by separate repo, pcb/utils/create.sql */
-		file: string
-		/** sqlite connection */
-		connection?: any
-	}
-}
-
-//Shared with genome.ts
-export type Cohort = {
-	/** if present, means correlation volcano plot analysis is enabled */
-	correlationVolcano?: CorrelationVolcano
-	cumburden?: CumBurdenData
-	db?: FileObj
-	/** customize the default chart to open on mass ui when there's no charts. if
-	 * missing it opens dictionary ui */
-	defaultChartType?: string
-	massNav?: MassNav
-	matrixplots?: MatrixPlots
-	mutationset?: MutationSet[]
-	renamedChartTypes?: { singleCellPlot?: string; sampleScatter?: string }
-	/** if present, supplies premade scatter plots */
-	scatterplots?: Scatterplots
-	termdb: Termdb
-	hiddenTermIds?: string[]
-	boxplots?: BoxPlots
-}
-
-/** Customizations specific to the mass nav component */
-type MassNav = {
-	/** Customization for the tabs*/
-	tabs?: {
-		/** supported keys: about, charts, groups, filter
-		invalid key is ignored
-		when dslabel is too long to show in about tab middle row or to define alternative label, 
-		do .tabs:{about:{mid:'alt label'}} */
-		about?: MassNavAboutTabEntry
-		charts?: MassNavTabEntry
-		groups?: MassNavTabEntry
-		filter?: MassNavTabEntry
-	}
-	/** customize background color of active navigation tab */
-	activeColor?: string
-	/** customize background color of active navigation tab on hover */
-	activeColorHover?: string
-}
-
-type MassNavTabEntry = {
-	/** show in a specific order of tabs */
-	order?: number
-	/** label appearing in the top row in upper case */
-	top?: string
-	/** biggest label appearing in the middle row */
-	mid?: string
-	/** label appearing in the bottom row*/
-	btm?: string
-	/** if true, does not show the tab */
-	hide?: boolean
-}
-
-type MassNavAboutTabEntry = MassNavTabEntry & {
-	/** html string, can include links to other
-	 * pages (e.g., tutorials, google group) */
-	additionalInfo?: string
-	/** static html contents to show specifically in "about" tab subheader
-	 * maybe used for other tabs as well.
-	 * Will not render if cohort.termdb.selectCohort is present */
-	html?: string
-	/** declare data release. Shown with the server info */
-	dataRelease?: {
-		/** data release version */
-		version: string
-		/** link to data release page */
-		link: string
-	}
-	/** "active" items, shown as clickable buttons in about tab. click an item to launch a plot */
-	activeItems?: {
-		items: ActiveItem[]
-		// can add holderStyle to customize
-	}
-}
-
-type ActiveItem = {
-	/** string or html to show inside the button for the item, potentially allow to include <image> as logo */
-	title: string
-	/** plot object describing the plot to be launched */
-	plot: object
-}
-
-type Title = {
-	text: string
-	link?: string
-}
-
-type ViewMode = {
-	byAttribute?: string
-	byInfo?: string
-	inuse?: boolean
-}
-
-/*** types supporting Mds Dataset types ***/
-type BaseMds = {
-	genome?: string //Not declared in TermdbTest
-	assayAvailability?: Mds3AssayAvailability | LegacyAssayAvailability
-}
-
-export type Mds = BaseMds & {
-	// replaced by mds3!!!
-	isMds: boolean
-	about?: KeyVal[]
-	sampleAssayTrack?: FileObj
-	singlesamplemutationjson?: FileObj
-	cohort?: any
-	queries?: any
-	mutationAttribute?: any
-	version?: { label: string; link: string }
-	gene2mutcount?: any
-	locusAttribute?: any
-	alleleAttribute?: {
-		attributes: {
-			[attrName: string]: {
-				label: string
-				isnumeric: number
-				filter: number
-			}
-		}
-	}
-}
-
-type PreInitStatus = {
-	/**
-	 * status: 'OK' indicates a valid response
-	 *
-	 * status: 'recoverableError' may cause the server code to retry until the response is healthy,
-	 * depending on the server startup code flow
-	 *
-	 * other status will be considered fatal error
-	 * */
-	status: string
-	/** response message as related to the status */
-	message?: string
-	/** arbitrary response payload properties that is specific to a dataset */
-	[props: string]: any
-}
-
-export type PreInit = {
-	/**
-	  getStatus() is used to make sure that data sources are ready before starting to query data;
-		for example, wait on GDC API server to be healthy before starting to initialize, 
-		or wait for intermittent network errors to clear on a network mount; 
-		HTTP connection timeout errors or status 5xx are considered recoverable,
-		status 4xx are not considered recoverable (client-related request errors)
-	*/
-	getStatus: () => Promise<PreInitStatus>
-	/**
-	 * dev only, used to test preInit handling by simulating different
-	 * responses in a known sequence of steps that may edit the preInit
-	 * response
-	 */
-	test?: {
-		/** the current number of calls to preInit.getStatus() */
-		numCalls: number
-		/**
-		 * an arbitrary response payload property that is edited in mayEditResponse()
-		 * for example, this is used to simulate a stale or current GDC version
-		 * */
-		minor: number
-		/**
-		 * a callback to potentially edit the preInit.getStatus() response
-		 */
-		mayEditResponse: (response: any) => any
-	}
-}
-
-/** see details in termdb.server.init.ts
- */
-export type isSupportedChartCallbacks = {
-	[chartType: string]: (f: any) => boolean | undefined
-}
-
-export type Mds3 = BaseMds & {
-	/** set in initGenomesDs.js during launch, should use .genomename instead of .genome */
-	genomename?: string // use this
-	genome?: string // avoid using it
-	/** server-side genome obj to which this ds belongs to is attached here in initGenomesDs.js during launch, 
-	so this obj can be conveniently available to server side functions without having to introduce extra param
-	TODO apply Genome type
-	*/
-	genomeObj?: any
-	label?: Title
-	isMds3: boolean
-	loadWithoutBlocking?: boolean
-	preInit?: PreInit
-	init?: {
-		/** number of milliseconds to wait before calling th preInit.getStatus() again */
-		retryDelay?: number
-		/** maximum number of tries to complete initialization, including preInit.getStatus() before validation steps
-		 * and the nonblocking steps after validation. Before the retryMax is reached, errors are considered recoverable;
-		 * errors when retryMax is reached will be fatal. */
-		retryMax?: number
-		/** option to trigger mds3InitNonblocking() on this dataset */
-		hasNonblockingSteps?: boolean
-		/** server-computed cumulative count of the attempted init retries */
-		currentRetry?: number
-		/**
-		 * optional callback to send notifications of pre-init errors
-		 * for St. Jude, this may reuse code that post to Slack channel;
-		 * in dev and other portals, this may use custom callbacks
-		 * */
-		errorCallback?: (response: PreInitStatus) => void
-	}
-	/** optional callback to invoke non-blocking code after dataset query validation in mds3.init.js;
-	 * for GDC, this callback is created after buildDictionary in initGdc.js
-	 **/
-	initNonblocking?: (a: any) => void
-	viewModes?: ViewMode[]
-	dsinfo?: KeyVal[]
-	queries?: Mds3Queries
-	cohort?: Cohort
-	isSupportedChartOverride?: isSupportedChartCallbacks
-	// TODO FIXME nest termdb under cohort
-	termdb?: Termdb
-	validate_filter0?: (f: any) => void
-	ssm2canonicalisoform?: GdcApi
-	variant2samples?: Variant2Samples
-	scatterplots?: Scatterplots
-	/** disables switching to genomic mode for the protein view mds3 tk of this ds
-	works by preventing block gmmode menu from showing "genomic" option
-	is only passed via mds3 adhoc ds copy, but not termdbConfig
-	for lack of a better place to put this attribute, as it's not appropriate to put in queries.snvindel{}
-	as snvindel is optional so even a cnv-only ds can disable genomic mode
-	*/
-	noGenomicMode4lollipopTk?: true
-	/** if ds.queries{} exists, server launch adds this convenient getter to wrap multiple queries data types
-	 */
-	mayGetGeneVariantData?: (f: any) => void
-	/** optional key-value pairs to pass to genomic queries getter when called in mayGetGeneVariantData() 
-	- only used in mayGetGeneVariantData! not in mds3.load.js
-	- for now only passed to snvindel.*.get and not yet other data types; add when needed
-	the param contents will be assessed by ds specific getter
-	this is serverside only, not passed to termdbConfig
-	*/
-	mayGetGeneVariantDataParam?: {
-		[key: string]: any
-		/** this flag determines whether geneVariant data is filtered during post-processing
-		normally, geneVariant data is filtered during data query
-		but the filter structure used by gdc is not compatible with
-		geneVariant data filtering, so this flag is used to filter
-		data during post-processing */
-		postProcessDtFilter?: boolean
-	}
-	demoJwtInput?: {
-		[role: string]: {
-			datasets?: string[]
-			/** unstructured json object */
-			clientAuthResult?: object
-			// below will be assigned by /demoToken route handler if not specified
-			iat?: number // jwt issued at time, unix time in seconds
-			exp?: number // jwt expiration, unix time in seconds
-			email?: string
-		}
-	}
-	// !!! TODO: improve these type definitions below !!!
-	serverconfigFeatures?: any
-	/** a dataset may supply custom URL host and headers to use when making external API requests, such as for GDC */
-	getHostHeaders?: (
-		q?: any,
-		overrides?: { [key: string]: string }
-	) => {
-		host: {
-			[apiStyle: string]: string
-		}
-		headers?: {
-			[field: string]: string
-		}
-	}
-	/** a dataset may track req.headers based on a req.query, abort signal, and/or filter0;
-	 * this tracking is necessary since the req.headers is not necessarily passed through all to downstream code
-	 * when processing external API-based dataset data, such as for GDC, but req.query.__abortSignal and filter0
-	 * both much more likely to be passed as-is and make it to when `getHostHeaders()` is called */
-	trackReqHeaders?: (req: any, res: any) => void
-	/** a dataset may supply additional information to include in the `/healthcheck` response payload, nested under byDataset[dslabel][genome] = {} property */
-	getHealth?: (ds: any) => {
-		[key: string]: any
-	}
-}
-
-export type Mds3WithCohort = Mds3 & {
-	cohort: Cohort
-}