@sjcrh/proteinpaint-types 2.102.0 → 2.105.0

package/dist/{chunk-Z2WFGV6V.js → chunk-IYDRVZXE.js}

@@ -22,7 +22,7 @@ var diffExpPayload = {
 var validDERequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && "number" === typeof input3.min_count && "number" === typeof input3.min_total_count && ("text" === input3.storage_type || "HDF5" === input3.storage_type) && (void 0 === input3.method || "string" === typeof input3.method) && true;
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && "number" === typeof input3.min_count && "number" === typeof input3.min_total_count && ("text" === input3.storage_type || "HDF5" === input3.storage_type) && (void 0 === input3.method || "string" === typeof input3.method) && true && (void 0 === input3.VarGenes || "number" === typeof input3.VarGenes);
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -52,7 +52,11 @@ var validDERequest = (input) => {
         path: _path2 + ".method",
         expected: "(string | undefined)",
         value: input3.method
-      }), true].every((flag) => flag);
+      }), true, void 0 === input3.VarGenes || "number" === typeof input3.VarGenes || $report(_exceptionable2, {
+        path: _path2 + ".VarGenes",
+        expected: "(number | undefined)",
+        value: input3.VarGenes
+      })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "DERequest",

package/dist/{chunk-CETMA2FU.js → chunk-OTFT3JZB.js}

@@ -54,7 +54,7 @@ var validGdcMafResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed;
-    const $io1 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (void 0 === input3.sample_types || Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id;
+    const $io1 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -62,19 +62,19 @@ var validGdcMafResponse = (input) => {
     ((input2, _path, _exceptionable = true) => {
       const $vo0 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
         path: _path2 + ".files",
-        expected: "Array<File>",
+        expected: "Array<GdcMafFile>",
         value: input3.files
       })) && input3.files.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
         path: _path2 + ".files[" + _index1 + "]",
-        expected: "File",
+        expected: "GdcMafFile",
         value: elem
       })) && $vo1(elem, _path2 + ".files[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
         path: _path2 + ".files[" + _index1 + "]",
-        expected: "File",
+        expected: "GdcMafFile",
         value: elem
       })).every((flag) => flag) || $report(_exceptionable2, {
         path: _path2 + ".files",
-        expected: "Array<File>",
+        expected: "Array<GdcMafFile>",
         value: input3.files
       }), "number" === typeof input3.filesTotal || $report(_exceptionable2, {
         path: _path2 + ".filesTotal",
@@ -101,9 +101,9 @@ var validGdcMafResponse = (input) => {
         path: _path2 + ".file_size",
         expected: "number",
         value: input3.file_size
-      }), void 0 === input3.sample_types || (Array.isArray(input3.sample_types) || $report(_exceptionable2, {
+      }), (Array.isArray(input3.sample_types) || $report(_exceptionable2, {
         path: _path2 + ".sample_types",
-        expected: "(Array<string> | undefined)",
+        expected: "Array<string>",
         value: input3.sample_types
       })) && input3.sample_types.map((elem, _index2) => "string" === typeof elem || $report(_exceptionable2, {
         path: _path2 + ".sample_types[" + _index2 + "]",
@@ -111,7 +111,7 @@ var validGdcMafResponse = (input) => {
         value: elem
       })).every((flag) => flag) || $report(_exceptionable2, {
         path: _path2 + ".sample_types",
-        expected: "(Array<string> | undefined)",
+        expected: "Array<string>",
         value: input3.sample_types
       }), "string" === typeof input3.project_id || $report(_exceptionable2, {
         path: _path2 + ".project_id",

package/dist/gdc.maf.js

@@ -2,7 +2,7 @@ import {
   gdcMafPayload,
   validGdcMafRequest,
   validGdcMafResponse
-} from "./chunk-CETMA2FU.js";
+} from "./chunk-OTFT3JZB.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   gdcMafPayload,

package/dist/index.js

@@ -82,7 +82,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-Z2WFGV6V.js";
+} from "./chunk-IYDRVZXE.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
@@ -152,7 +152,7 @@ import {
   gdcMafPayload,
   validGdcMafRequest,
   validGdcMafResponse
-} from "./chunk-CETMA2FU.js";
+} from "./chunk-OTFT3JZB.js";
 import {
   GdcMafPayload,
   validGdcMafBuildRequest,

package/dist/termdb.DE.js

@@ -2,7 +2,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-Z2WFGV6V.js";
+} from "./chunk-IYDRVZXE.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   diffExpPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.102.0",
+  "version": "2.105.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -338,8 +338,19 @@ so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig canno
 }
 
 type SvFusion = {
-	byrange: {
-		/** file paths for sv fusion data */
+	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
 	}
 }
@@ -583,11 +594,10 @@ export type SingleCellSamples = {
 	/** 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
+	- 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
 	*/
-	firstColumnName?: string
 	/** any columns to be added to sample table. each is a term id */
 	sampleColumns?: { termid: string }[]
 	/** used on client but not on ds */
@@ -597,6 +607,8 @@ export type SingleCellSamples = {
 	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
 }
 
 export type SingleCellDataGdc = {
@@ -924,7 +936,7 @@ type CorrelationVolcano = {
 	}
 }
 
-type MatrixSettingsControlLabels = {
+type UiLabels = {
 	samples?: string
 	sample?: string
 	Samples?: string
@@ -993,7 +1005,7 @@ type MatrixSettings = {
 	svgCanvasSwitch?: number
 	cellEncoding?: string
 	cellbg?: string
-	controlLabels?: MatrixSettingsControlLabels
+	controlLabels?: UiLabels
 	sortSamplesBy?: string
 	sortPriority?: SortPriorityEntry[]
 	ignoreCnvValues?: boolean
@@ -1171,7 +1183,6 @@ keep this setting here for reason of:
 - mds3.variant2samples consider this setting, allows to handle other datasets of same issue
   */
 	useLower?: boolean
-
 	matrix?: Matrix
 	numericDictTermCluster?: NumericDictTermCluster
 	survival?: Survival

package/src/routes/gdc.maf.ts

@@ -3,7 +3,7 @@ import type { RoutePayload } from './routeApi.js'
 
 // an object representing gdc maf file, to be shown on client table
 
-export type File = {
+export type GdcMafFile = {
 	/** A string representing the file's UUID (Universally Unique Identifier) , can be accessed via https://api.gdc.cancer.gov/data/<uuid>*/
 	id: string
 	/** A string representing a submitter ID for the case associated with this file */
@@ -12,8 +12,8 @@ export type File = {
 	case_uuid: string
 	/** An integer as the byte size of this file, compressed */
 	file_size: number
-	/** Array of strings, each is a sample type, for all samples involved in generating the maf file */
-	sample_types?: string[]
+	/** Array of strings, each is 'tumor descriptor+tissue type', for all samples involved in generating the maf file */
+	sample_types: string[]
 	/** A string representing the type of workflow used to generate or process this file */
 	//workflow_type: string
 	/** A string as the project id of the case */
@@ -34,7 +34,7 @@ export type GdcMafRequest = {
 
 export type GdcMafResponse = {
 	/** List of file objects passing filter and to be displayed on client */
-	files: File[]
+	files: GdcMafFile[]
 	/** Total number of files found by API (in case bigger than files.length) */
 	filesTotal: number
 	/** Maximum total size of maf files allowed, for indicating on ui while selecting files */

package/src/routes/termdb.DE.ts

@@ -17,6 +17,8 @@ export type DERequest = {
 	method?: string
 	/** Term for confounding variable (if present) */
 	tw?: any
+	/** Number of variable genes (defined only for parametric DE methods) */
+	VarGenes?: number
 }
 
 export type ExpressionInput = {
@@ -38,6 +40,8 @@ export type ExpressionInput = {
 	conf1?: any[]
 	/** Type of the confounding variable (categorical/float) */
 	conf1_type?: 'categorical' | 'float'
+	/** Number of variable genes to be included for DE analysis (optional) */
+	VarGenes?: number
 }
 
 export type DEResponse = {