@sjcrh/proteinpaint-types 2.178.0 → 2.179.0

package/dist/termdb.chat2.js

@@ -1,7 +1,7 @@
 import {
   validChatRequest,
   validChatResponse
-} from "./chunk-GAYJUXNZ.js";
+} from "./chunk-4J5BPYYR.js";
 import {
   ChatPayload
 } from "./chunk-FRXRNCDV.js";

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NRV6MPRM.js";
+} from "./chunk-E2O4N7OC.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-UWAVSKMD.js";
+} from "./chunk-7V7USAKJ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.dmr.js

@@ -2,7 +2,7 @@ import {
   TermdbDmrPayload,
   validTermdbDmrRequest,
   validTermdbDmrResponse
-} from "./chunk-CYQDO4FX.js";
+} from "./chunk-FQLGK65A.js";
 import "./chunk-YNHC5SXO.js";
 export {
   TermdbDmrPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-CX2Y673E.js";
+} from "./chunk-MKM4A5NU.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-YHKFJCXG.js";
+} from "./chunk-YI63CW7Y.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-HZEV7D5E.js";
+} from "./chunk-JTZQYNIT.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-UFYKXOY2.js";
+} from "./chunk-DUFHC6EI.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-FQYNRDHB.js";
+} from "./chunk-CC4IBTKW.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-PHRILOVX.js";
+} from "./chunk-RANWGPF7.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.178.0",
+  "version": "2.179.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -161,6 +161,17 @@ type AiApi = {
 	}
 }
 
+/** 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?: (twLst: any) => void
+}
+
 type SnvIndelFormat = {
 	[index: string]: {
 		/* has value for a non-GT field indicating the variant 
@@ -1460,12 +1471,6 @@ export type Termdb = {
 	}
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: (clientAuthResult: any) => boolean
-	/** ds-supplied async callback to build dictionary
-	argument: dataset object
-	sets termdb.q{}
-	no return
-	*/
-	buildDictionary?: (ds: any) => void
 	converSampleIds?: boolean
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
@@ -1567,7 +1572,8 @@ keep this setting here for reason of:
 		gdcapi?: true
 	}
 	/** Do not use a union here. */
-	dictionary?: GdcApi & AiApi
+	/** 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 }
@@ -2044,8 +2050,22 @@ export type Mds3 = BaseMds & {
 		}
 	}
 	// !!! TODO: improve these type definitions below !!!
-	getHostHeaders?: (q?: any) => any
 	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) => {
+		host: {
+			[apiStyle: string]: string
+		}
+		headers?: {
+			[field: string]: string
+		}
+	}
+	/** a dataset may track req.headers based on an abort signal and/or filter0 that was created for the req;
+	 * 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
 	}

package/src/filter.ts

@@ -18,19 +18,26 @@ Filter
 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[]
+	ranges: (NumericBin | { value: number; label?: string; name?: string })[]
 	// TODO: define uncomputable values object
-	values: {
+	values?: {
 		key: string
 		value: number
 		uncomputable: true
@@ -51,16 +58,37 @@ export type ConditionTvs = BaseTvs & {
 	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
 }
 
-type GeneVariantTvs = BaseTvs & {
+export type GeneVariantTvs = BaseTvs & {
 	term: DtTerm
-	values: { key: string; label: string; value: string }[]
+	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 & {
@@ -78,4 +106,5 @@ export type Filter = {
 	join: string
 	tag?: string // client-side only
 	lst: ({ type: 'tvs'; tvs: Tvs } | Filter)[]
+	$id?: string // Optional ID property
 }

package/src/routes/termdb.chat2.ts

@@ -115,7 +115,7 @@ export type plot_type = {
 	type: 'plot'
 	/** The type of plot to be displayed on the UI.
 	 *  Standard categories are listed; datasets may define additional custom categories. */
-	plot: 'summary' | 'dge' | 'survival' | 'matrix' | 'sampleScatter'
+	plot: 'summary' | 'dge' | 'survival' | 'matrix' | 'sampleScatter' | 'hierCluster'
 }
 
 export type resource_type = {
@@ -132,7 +132,7 @@ export type none_type = {
 export type QueryClassification = { type: 'plot' } | { type: 'notplot' }
 
 /** Specific plot type returned by classifyPlotType in plot.ts */
-export type PlotType = 'summary' | 'dge' | 'survival' | 'matrix' | 'samplescatter'
+export type PlotType = 'summary' | 'dge' | 'survival' | 'matrix' | 'samplescatter' | 'hiercluster'
 
 export type DEType = {
 	/** Name of group1 which is an array of filter terms */
@@ -148,6 +148,17 @@ export type MatrixType = {
 	terms?: string[]
 	/** Names of genes to include as gene variant rows in the matrix (e.g. "TP53", "KRAS", "NRAS") */
 	geneNames?: string[]
+	/** Names of gene sets containing ssGSEA enrichment scores */
+	genesetNames?: string[]
+	/** Optional simple filter terms to restrict the sample set */
+	simpleFilter?: FilterTerm[]
+}
+
+export type HierClusterType = {
+	/** Names of genes to include in the hierarchical clustering (e.g. "TP53", "KRAS", "BCR") */
+	geneNames?: string[]
+	/** Names of gene sets containing list of genes to be used for hierarchical clustering */
+	genesetNames?: string[]
 	/** Optional simple filter terms to restrict the sample set */
 	simpleFilter?: FilterTerm[]
 }

package/src/routes/termdb.dmr.ts

@@ -11,7 +11,10 @@ export type TermdbDmrRequest = {
 	chr: string
 	start: number
 	stop: number
-	// todo more params
+	/** optional regulatory domain annotations for the GP model */
+	annotations?: DmrAnnotation[]
+	/** max fraction of NaN per probe before dropping (default 0.5) */
+	nan_threshold?: number
 	filter?: Filter
 	__protected__?: any
 }
@@ -21,13 +24,25 @@ type Sample = {
 	sample: string
 }
 
+type DmrAnnotation = {
+	name: string
+	start: number
+	end: number
+	base_methylation?: number
+	length_scale_bp?: number
+}
+
 export type TermdbDmrSuccessResponse = {
 	status: 'ok'
 	dmrs: {
 		chr: string
 		start: number
 		stop: number
-		// todo more stats
+		width: number
+		max_delta_beta: number
+		/** hyper = group2 hypermethylated relative to group1; hypo = opposite */
+		direction: 'hyper' | 'hypo'
+		probability: number
 	}[]
 }
 

package/src/terms/termCollection.ts

@@ -7,7 +7,6 @@ export type CategoryKey = { key: string; shown: boolean }
 
 type BaseTermCollection = BaseTerm & {
 	name: string
-	collectionId?: string
 	type: 'termCollection'
 	/** list of term.ids that are available in this collection. this is used in request payload and server side */
 	termIds?: string[]
@@ -50,7 +49,6 @@ export type RawNumericTermCollection = {
 	type?: 'termCollection'
 	memberType?: 'numeric'
 	name?: string
-	collectionId?: string
 	termIds?: string[]
 	termlst?: BaseTerm[]
 	propsByTermId?: {
@@ -66,7 +64,6 @@ export type RawCategoricalTermCollection = {
 	type?: 'termCollection'
 	memberType?: 'categorical'
 	name?: string
-	collectionId?: string
 	termIds?: string[]
 	termlst?: BaseTerm[]
 	propsByTermId?: {