@sjcrh/proteinpaint-types 2.157.1-0 → 2.159.0

package/dist/{chunk-UGYLBYUU.js → chunk-5L4VF3ZL.js}

@@ -74,7 +74,15 @@ var validTermdbSingleSampleMutationResponse = (input) => {
         return Array.isArray(value) && value.every((elem) => "object" === typeof elem && null !== elem && $io5(elem));
       return true;
     });
-    const $io5 = (input3) => (void 0 === input3.nameHtml || "string" === typeof input3.nameHtml) && (void 0 === input3.name || "string" === typeof input3.name) && (void 0 === input3.inuse || "boolean" === typeof input3.inuse) && (Array.isArray(input3.mlst) && input3.mlst.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io2(elem)));
+    const $io5 = (input3) => (void 0 === input3.nameHtml || "string" === typeof input3.nameHtml) && (void 0 === input3.name || "string" === typeof input3.name) && (void 0 === input3.inuse || "boolean" === typeof input3.inuse) && (Array.isArray(input3.mlst) && input3.mlst.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io2(elem))) && (void 0 === input3.attrs || "object" === typeof input3.attrs && null !== input3.attrs && false === Array.isArray(input3.attrs) && $io6(input3.attrs));
+    const $io6 = (input3) => Object.keys(input3).every((key) => {
+      const value = input3[key];
+      if (void 0 === value)
+        return true;
+      if (RegExp(/(.*)/).test(key))
+        return "string" === typeof value;
+      return true;
+    });
     const $iu0 = (input3) => (() => {
       if (void 0 !== input3.status)
         return $io0(input3);
@@ -200,7 +208,27 @@ var validTermdbSingleSampleMutationResponse = (input) => {
         path: _path2 + ".mlst",
         expected: "Array<object>",
         value: input3.mlst
+      }), void 0 === input3.attrs || ("object" === typeof input3.attrs && null !== input3.attrs && false === Array.isArray(input3.attrs) || $report(_exceptionable2, {
+        path: _path2 + ".attrs",
+        expected: "(__type.o3 | undefined)",
+        value: input3.attrs
+      })) && $vo6(input3.attrs, _path2 + ".attrs", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".attrs",
+        expected: "(__type.o3 | undefined)",
+        value: input3.attrs
       })].every((flag) => flag);
+      const $vo6 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
+        const value = input3[key];
+        if (void 0 === value)
+          return true;
+        if (RegExp(/(.*)/).test(key))
+          return "string" === typeof value || $report(_exceptionable2, {
+            path: _path2 + $join(key),
+            expected: "string",
+            value
+          });
+        return true;
+      }).every((flag) => flag)].every((flag) => flag);
       const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
         if (void 0 !== input3.status)
           return $vo0(input3, _path2, _exceptionable2);

package/dist/{chunk-WCF7WIJY.js → chunk-D37D752M.js}

@@ -20,7 +20,7 @@ var GRIN2Payload = {
 var validGRIN2Request = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions)) && (void 0 === input3.svOptions || "object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) && $io4(input3.svOptions)) && (void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow);
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.qValueThreshold || "number" === typeof input3.qValueThreshold) && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions)) && (void 0 === input3.svOptions || "object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) && $io4(input3.svOptions)) && (void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow);
     const $io1 = (input3) => (void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth) && (void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount) && (void 0 === input3.consequences || Array.isArray(input3.consequences) && input3.consequences.every((elem) => "string" === typeof elem)) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
     const $io2 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.maxSegLength || "number" === typeof input3.maxSegLength) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
     const $io3 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
@@ -54,6 +54,10 @@ var validGRIN2Request = (input) => {
         path: _path2 + ".pngDotRadius",
         expected: "(number | undefined)",
         value: input3.pngDotRadius
+      }), true, void 0 === input3.qValueThreshold || "number" === typeof input3.qValueThreshold || $report(_exceptionable2, {
+        path: _path2 + ".qValueThreshold",
+        expected: "(number | undefined)",
+        value: input3.qValueThreshold
       }), true, void 0 === input3.snvindelOptions || ("object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) || $report(_exceptionable2, {
         path: _path2 + ".snvindelOptions",
         expected: "(__type | undefined)",

package/dist/grin2.js

@@ -2,7 +2,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-WCF7WIJY.js";
+} from "./chunk-D37D752M.js";
 import "./chunk-YNHC5SXO.js";
 export {
   GRIN2Payload,

package/dist/index.js

@@ -47,7 +47,7 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-UGYLBYUU.js";
+} from "./chunk-5L4VF3ZL.js";
 import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
@@ -217,7 +217,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-WCF7WIJY.js";
+} from "./chunk-D37D752M.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,

package/dist/termdb.singleSampleMutation.js

@@ -2,7 +2,7 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-UGYLBYUU.js";
+} from "./chunk-5L4VF3ZL.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleSampleMutationPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.157.1-0",
+  "version": "2.159.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1380,24 +1380,23 @@ export type Termdb = {
 	 * in order to minimize the ease of extracting identifiable information from aggregate data
 	 * in server response
 	 *
-	 * returns: {minSampleSize, canAccess}, see below
+	 * returns: {minSize, canAccess}, see below
 	 */
 	checkAccessToSampleData?: (
 		/** req.query as processed through app middleware (pre-parsed, may have req.body props, __protectec__, etc) */
 		q: any,
 		data: {
-			/** the number of samples with matching data from one or more queried terms */
-			sampleCount: number
-			/** option to specify sample names that is accessible to the current user,
-			 * not using sample ID since portal embedder and token generator does not
-			 * know the internal sample ID-to-name mapping */
-			sampleNames?: string[]
+			/** the number of samples or sites with matching data from one or more queried terms */
+			count: number
+			/** option to specify sample names or sites that are accessible to the current user,
+			 */
+			names?: string[]
 		}
 	) => {
-		/** the required minimum sample size for the current user,
+		/** the required minimum size for the current user to access certain data,
 		 * may be dependent on login status or other context
 		 * */
-		minSampleSize: number
+		minSize: number
 		/** whether downstreadm backend code can proceed */
 		canAccess: boolean
 	}
@@ -1562,6 +1561,7 @@ keep this setting here for reason of:
 	}
 	//terms  are shown in the dictionary based on term and user role.
 	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
+	hiddenIds?: string[]
 	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
 }
 

package/src/routes/grin2.ts

@@ -29,6 +29,12 @@ export type GRIN2Request = {
 	/** Radius of the PNG rendered dots (default: 2) */
 	pngDotRadius?: number
 
+	/** Lesion type colors */
+	lesionTypeColors?: any
+
+	/** Threshold for q-values to be included as interactive dots */
+	qValueThreshold?: number
+
 	/** Filter from existing PP infrastructure */
 	filter?: any // Filter object passed to get_samples(filter, ds)
 

package/src/routes/termdb.singleSampleMutation.ts

@@ -14,7 +14,7 @@ type ValidResponse = {
 	mlst: object[]
 	/** total number of items for each dt, useful to indicate snvindel limited to 10k for a hypermutator */
 	dt2total?: { dt: number; total: number }[]
-	/** this declares alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
+	/** declares presence of alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
 	key: dt value
 	value: array of objects, each is a distinct set of data points for this dt
 		on ui, selecting an object will allow to show this data in disco plot
@@ -30,6 +30,10 @@ type ValidResponse = {
 			inuse?: boolean
 			/** required list of events from this data */
 			mlst: object[]
+			/** optional info about this source */
+			attrs?: {
+				[index: string]: string
+			}
 		}[]
 	}
 }