@sjcrh/proteinpaint-types 2.112.0 → 2.113.0

package/dist/index.js

@@ -97,7 +97,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NPVDG36X.js";
+} from "./chunk-OJWYCYKF.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-NPVDG36X.js";
+} from "./chunk-OJWYCYKF.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.112.0",
+  "version": "2.113.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -92,12 +92,17 @@ type bcfMafFile = {
 	maffile: string
 }
 
-type SnvindelByRange = {
-	/** if true, served from gdc. no other parameters TODO change to src='gdc/native' */
-	gdcapi?: boolean
+type SnvindelByIsoform = {
+	/** if true, served from gdc. no other parameters */
+	gdcapi?: true
+	/** getter function to retrieve data. dynamically added or ds-supplied */
+	get?: (f: any) => void
+}
 
+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 */
@@ -106,8 +111,8 @@ type SnvindelByRange = {
 	bcfMafFile?: bcfMafFile
 	/** allow to apply special configurations to certain INFO fields of the bcf file */
 	infoFields?: InfoFieldEntry[]
-	/** if true, bcf or chr2bcf uses string sample name in header. to be used during this migrating so the code can deal with old files with integer sample ids and new ones; TODO once all datasets are migrated, delete the flag */
-	tempflag_sampleNameInVcfHeader?: boolean
+	/** getter function to retrieve data. dynamically added or ds-supplied */
+	get?: (f: any) => void
 }
 
 type URLEntry = {
@@ -243,7 +248,6 @@ type Population = {
 }
 
 /** primarily for prebuilding germline genetic association for survivorship portal
-accessible to client via termdb.js?for=mds3queryDetails
 part of state of genomeBrowser plot
 allowing for user modification
 */
@@ -311,12 +315,10 @@ type SnvindelComputeGroup_info = {
 /** a data type under ds.queries{} */
 type SnvIndelQuery = {
 	forTrack?: boolean
-	/** allow to query data by either isoform or range
-	 * isoform query is only used for gdc api
-	 */
-	byisoform?: GdcApi
+	/** 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
+	byrange?: SnvindelByRange
 
 	infoUrl?: URLEntry[]
 	skewerRim?: SkewerRim
@@ -334,7 +336,12 @@ so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig canno
 	}
 	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 = {
@@ -718,6 +725,7 @@ type SCImages = {
 	label: string
 }
 
+/** genome browser LD track */
 type LdQuery = {
 	/** each track obj defines a ld track */
 	tracks: {
@@ -725,8 +733,6 @@ type LdQuery = {
 		name: string
 		/** relative path of ld .gz file */
 		file: string
-		/** dynamically added full path */
-		file0?: string
 		/** dynamically added */
 		nochr?: boolean
 		/** if to show by default */
@@ -785,6 +791,9 @@ type Mds3Queries = {
 	snvindel?: SnvIndelQuery
 	svfusion?: SvFusion
 	cnv?: CnvSegment
+	trackLst?: TrackLst
+	ld?: LdQuery
+	defaultCoord?: string
 	singleSampleMutation?: SingleSampleMutationQuery
 	NIdata?: NIdataQuery
 	geneExpression?: GeneExpressionQuery
@@ -799,15 +808,12 @@ type Mds3Queries = {
 		src: 'native' | 'gdc'
 		file: string
 	}
-	trackLst?: TrackLst
 	singleCell?: SingleCellQuery
 	geneCnv?: {
 		bygene?: {
 			gdcapi: true
 		}
 	}
-	defaultCoord?: string
-	ld?: LdQuery
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
 	/** depreciated. replaced by WSImages */

package/src/routes/termdb.DE.ts

@@ -46,6 +46,10 @@ export type ExpressionInput = {
 	conf2_mode?: 'continuous' | 'discrete'
 	/** Number of variable genes to be included for DE analysis (optional) */
 	VarGenes?: number
+	/** The methodology used for differential gene expression: wilcoxon, edgeR and limma */
+	DE_method: 'wilcoxon' | 'limma' | 'edgeR'
+	/** Cutoff for when mds plot will be generated for edgeR and limma test */
+	mds_cutoff: number
 }
 
 export type DEResponse = {

package/src/routes/termdb.cluster.ts

@@ -82,8 +82,13 @@ export type ValidResponse = {
 	byTermId: { [index: string]: any }
 	/**  */
 	bySampleId: { [index: string]: any }
-	/** list of term names that are excluded from analysis for lacking any numerical data */
-	removedHierClusterTerms?: string[]
+	/** list of term names that are excluded from analysis, one reason per set, for client display */
+	removedHierClusterTerms?: {
+		/** reason for skipping */
+		text: string
+		/** list of skipped item names */
+		lst: string[]
+	}[]
 }
 
 //response of just 1 gene, thus unable to do clustering

package/src/termsetting.ts

@@ -84,8 +84,8 @@ type BaseTermSettingOpts = {
 	 * before the pill name is truncated. */
 	abbrCutoff?: number
 	activeCohort?: number
-	/** tw.term.ids */
-	disable_terms?: string[]
+	/** array of term objects to show in the tree but not clickable */
+	disable_terms?: Term[]
 	// This is not used anywhere.
 	// Ok to remove?
 	handler: Handler
@@ -165,7 +165,7 @@ export type TermSettingInstance = {
 	clickNoPillDiv?: any
 	dom: InstanceDom
 	doNotHideTipInMain?: boolean
-	disable_terms?: string[]
+	disable_terms?: Term[]
 	durations: { exit: number }
 	filter?: Filter
 	handler?: Handler