@sjcrh/proteinpaint-types 2.95.0 → 2.96.1

package/dist/{chunk-BY2JABTF.js → chunk-RIJYASPK.js}

@@ -21,7 +21,7 @@ var boxplotPayload = {
 var validBoxPlotRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && true && true;
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.orderByMedian && true && true && true;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -35,6 +35,10 @@ var validBoxPlotRequest = (input) => {
         path: _path2 + ".dslabel",
         expected: "string",
         value: input3.dslabel
+      }), "boolean" === typeof input3.orderByMedian || $report(_exceptionable2, {
+        path: _path2 + ".orderByMedian",
+        expected: "boolean",
+        value: input3.orderByMedian
       }), true, true, true].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",

package/dist/index.js

@@ -132,7 +132,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-BY2JABTF.js";
+} from "./chunk-RIJYASPK.js";
 import {
   gdcTopMutatedGenePayload,
   validGdcTopMutatedGeneRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-BY2JABTF.js";
+} from "./chunk-RIJYASPK.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   boxplotPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.95.0",
+  "version": "2.96.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -243,6 +243,72 @@ type Population = {
 	sets: PopulationINFOset[]
 }
 
+/** 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
+*/
+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
@@ -269,7 +335,7 @@ so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig canno
 	}
 	allowSNPs?: boolean
 	vcfid4skewerName?: boolean
-	details?: any
+	details?: SnvindelComputeDetails
 }
 
 type SvFusion = {
@@ -517,32 +583,30 @@ export type SingleCellGeneExpressionGdc = {
 
 export type SingleCellSamplesNative = {
 	src: 'native'
-
-	/** 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
-firstColumnName allow to change name of 1st column from "Sample" to different, e.g. "Case" for gdc
-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
-*/
+	/** kept to prevent tsc err */
 	firstColumnName?: string
-
-	/** do not use for native ds! gdc-only property. kept as optional to avoid tsc err */
-	experimentColumns?: string
-
-	/** any other columns to be added to sample table. each is a term id */
+	/** any columns to be added to sample table. each is a term id */
 	sampleColumns?: { termid: string }[]
-
-	/** dynamically added getter */
+	/** used on client but not on ds */
+	experimentColumns?: { label: string }[]
 	get?: (q: any) => any
 }
 
 export type SingleCellSamplesGdc = {
 	src: 'gdcapi'
-	get?: (q: any) => any
 	/** if missing refer to the samples as 'sample', this provides override e.g. 'case' */
+	/** 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
+firstColumnName allow to change name of 1st column from "Sample" to different, e.g. "Case" for gdc
+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
+*/
 	firstColumnName?: string
+	/** same as SingleCellSamplesNative */
 	sampleColumns?: { termid: string }[]
+	/** used on client but not on ds */
 	experimentColumns?: { label: string }[]
+	get?: (q: any) => any
 }
 
 export type SingleCellDataGdc = {
@@ -881,6 +945,10 @@ type SortPriorityEntry = {
 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 (months, years, etc) displayed in the x-axis of survival plot */
+	timeUnit?: string
+	/** the customized x-axis tick values of survival plot */
+	xTickValues?: number[]
 }
 
 type MatrixSettings = {
@@ -944,6 +1012,8 @@ type NumericDictTermCluster = {
 	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 Survival = {
@@ -960,6 +1030,16 @@ type MatrixPlotsEntry = {
 	getConfig?: (f: any) => void
 }
 
+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 MatrixPlots = {
 	plots: MatrixPlotsEntry[]
 }
@@ -1211,9 +1291,6 @@ export type Cohort = {
 
 /** Customizations specific to the mass nav component */
 type MassNav = {
-	/** optional title of this ds, if missing use ds.label. shown on mass nav header.
-	 * use blank string to not to show a label*/
-	title?: Title
 	/** Customization for the tabs*/
 	tabs?: {
 		/** supported keys: about, charts, groups, filter

package/src/routes/termdb.boxplot.ts

@@ -1,11 +1,14 @@
 import type { RoutePayload } from './routeApi.js'
 
+/**Args set in Termdb vocab and from mass box plot */
 export type BoxPlotRequest = {
 	/** Args set in TermVocab */
 	/** term1 or term */
 	tw: any
 	genome: string
 	dslabel: string
+	/** sort plots by median value */
+	orderByMedian: boolean
 	/** term2 */
 	overlayTw?: any
 	filter: any