@sjcrh/proteinpaint-types 2.118.3-2 → 2.119.0

package/dist/{chunk-3QALQGW4.js → chunk-3C26VWPU.js}

@@ -75,7 +75,7 @@ var validDEResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.sample_size1 && "number" === typeof input3.sample_size2 && "string" === typeof input3.method && (void 0 === input3.images || Array.isArray(input3.images) && input3.images.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
-    const $io1 = (input3) => "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change && "string" === typeof input3.gene_name && "string" === typeof input3.gene_symbol;
+    const $io1 = (input3) => "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change && "string" === typeof input3.gene_id && "string" === typeof input3.gene_name;
     const $io2 = (input3) => "string" === typeof input3.src && "number" === typeof input3.size && "string" === typeof input3.key;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
@@ -139,14 +139,14 @@ var validDEResponse = (input) => {
         path: _path2 + ".fold_change",
         expected: "number",
         value: input3.fold_change
+      }), "string" === typeof input3.gene_id || $report(_exceptionable2, {
+        path: _path2 + ".gene_id",
+        expected: "string",
+        value: input3.gene_id
       }), "string" === typeof input3.gene_name || $report(_exceptionable2, {
         path: _path2 + ".gene_name",
         expected: "string",
         value: input3.gene_name
-      }), "string" === typeof input3.gene_symbol || $report(_exceptionable2, {
-        path: _path2 + ".gene_symbol",
-        expected: "string",
-        value: input3.gene_symbol
       })].every((flag) => flag);
       const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.src || $report(_exceptionable2, {
         path: _path2 + ".src",

package/dist/{chunk-W4JULXYD.js → chunk-HURSYPTO.js}

@@ -65,7 +65,7 @@ var validSampleWSImagesResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
     const $io0 = (input3) => Array.isArray(input3.sampleWSImages) && input3.sampleWSImages.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
-    const $io1 = (input3) => "string" === typeof input3.filename && "string" === typeof input3.metadata;
+    const $io1 = (input3) => "string" === typeof input3.filename && (void 0 === input3.overlays || Array.isArray(input3.overlays) && input3.overlays.every((elem) => "string" === typeof elem)) && "string" === typeof input3.metadata;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -92,6 +92,18 @@ var validSampleWSImagesResponse = (input) => {
         path: _path2 + ".filename",
         expected: "string",
         value: input3.filename
+      }), void 0 === input3.overlays || (Array.isArray(input3.overlays) || $report(_exceptionable2, {
+        path: _path2 + ".overlays",
+        expected: "(Array<string> | undefined)",
+        value: input3.overlays
+      })) && input3.overlays.map((elem, _index2) => "string" === typeof elem || $report(_exceptionable2, {
+        path: _path2 + ".overlays[" + _index2 + "]",
+        expected: "string",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".overlays",
+        expected: "(Array<string> | undefined)",
+        value: input3.overlays
       }), "string" === typeof input3.metadata || $report(_exceptionable2, {
         path: _path2 + ".metadata",
         expected: "string",

package/dist/index.js

@@ -82,7 +82,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-3QALQGW4.js";
+} from "./chunk-3C26VWPU.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
@@ -147,7 +147,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-W4JULXYD.js";
+} from "./chunk-HURSYPTO.js";
 import {
   snpPayload,
   validSnpRequest,

package/dist/samplewsimages.js

@@ -2,7 +2,7 @@ import {
   sampleWSImagesPayload,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse
-} from "./chunk-W4JULXYD.js";
+} from "./chunk-HURSYPTO.js";
 import "./chunk-CNSSF43V.js";
 export {
   sampleWSImagesPayload,

package/dist/termdb.DE.js

@@ -2,7 +2,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-3QALQGW4.js";
+} from "./chunk-3C26VWPU.js";
 import "./chunk-CNSSF43V.js";
 export {
   diffExpPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.118.3-2",
+  "version": "2.119.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -580,14 +580,22 @@ type CnvSegment = {
 	/** 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
 	*/
-	/** if value>0, skip if value<this cutoff, set to a large value e.g. 100 for not filtering */
 	cnvGainCutoff?: number
-	/** if value<0, skip if value>this cutoff, set to a large negative value e.g. -100 for not filtering */
+	/*
+	- 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
 	 */
@@ -930,10 +938,14 @@ export type WSImages = {
 	*/
 	imageBySampleFolder: string
 
+	annotationsColor?: Array<number>
+
 	/** 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 */
+	getWSIAnnotations?: (sampleName: string, wsiImage: string) => Promise<string[]>
 }
 
 /*** types supporting Termdb ***/
@@ -1310,6 +1322,8 @@ keep this setting here for reason of:
 		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

package/src/routes/samplewsimages.ts

@@ -13,6 +13,7 @@ export type SampleWSImagesResponse = {
 
 export type WSImage = {
 	filename: string
+	overlays?: Array<string>
 	metadata: string
 }
 

package/src/routes/termdb.DE.ts

@@ -70,8 +70,8 @@ export type DataEntry = {
 	adjusted_p_value: number
 	original_p_value: number
 	fold_change: number
+	gene_id: string
 	gene_name: string
-	gene_symbol: string
 }
 
 export type DEImage = {