@sjcrh/proteinpaint-types 2.126.0 → 2.128.0

package/dist/{chunk-NWEXA2YB.js → chunk-B2DJ3H7H.js}

@@ -7,7 +7,7 @@ import {
 var import_typia = __toESM(require_lib(), 1);
 
 // src/routes/gdc.grin2.ts
-var gdcGRIN2Payload = {
+var gdcGRIN2listPayload = {
   request: {
     typeId: "GdcGRIN2listRequest"
   },
@@ -260,7 +260,7 @@ var validRunGRIN2Request = (input) => {
 var validRunGRIN2Response = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.imagestring || "string" === typeof input3.imagestring) && true && true;
+    const $io0 = (input3) => ("success" === input3.status || "error" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && true && true;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -274,10 +274,10 @@ var validRunGRIN2Response = (input) => {
         path: _path2 + ".error",
         expected: "(string | undefined)",
         value: input3.error
-      }), void 0 === input3.imagestring || "string" === typeof input3.imagestring || $report(_exceptionable2, {
-        path: _path2 + ".imagestring",
+      }), void 0 === input3.pngImg || "string" === typeof input3.pngImg || $report(_exceptionable2, {
+        path: _path2 + ".pngImg",
         expected: "(string | undefined)",
-        value: input3.imagestring
+        value: input3.pngImg
       }), true, true].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
@@ -299,7 +299,7 @@ var validRunGRIN2Response = (input) => {
 };
 
 export {
-  gdcGRIN2Payload,
+  gdcGRIN2listPayload,
   runGRIN2Payload,
   validGdcGRIN2listRequest,
   validGdcGRIN2listResponse,

package/dist/{chunk-A3XJW6BZ.js → chunk-XZAH6P4D.js}

@@ -21,7 +21,7 @@ var genesetEnrichmentPayload = {
 var validGenesetEnrichmentRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem) && (Array.isArray(input3.fold_change) && input3.fold_change.every((elem) => "number" === typeof elem)) && "boolean" === typeof input3.filter_non_coding_genes && "string" === typeof input3.genome && "string" === typeof input3.geneSetGroup && (void 0 === input3.geneset_name || "string" === typeof input3.geneset_name) && (void 0 === input3.pickle_file || "string" === typeof input3.pickle_file) && "number" === typeof input3.num_permutations && ("blitzgsea" === input3.method || "cerno" === input3.method);
+    const $io0 = (input3) => Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem) && (Array.isArray(input3.fold_change) && input3.fold_change.every((elem) => "number" === typeof elem)) && "boolean" === typeof input3.filter_non_coding_genes && "string" === typeof input3.genome && "string" === typeof input3.geneSetGroup && (void 0 === input3.geneset_name || "string" === typeof input3.geneset_name) && (void 0 === input3.pickle_file || "string" === typeof input3.pickle_file) && "number" === typeof input3.num_permutations;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -75,10 +75,6 @@ var validGenesetEnrichmentRequest = (input) => {
         path: _path2 + ".num_permutations",
         expected: "number",
         value: input3.num_permutations
-      }), "blitzgsea" === input3.method || "cerno" === input3.method || $report(_exceptionable2, {
-        path: _path2 + ".method",
-        expected: '("blitzgsea" | "cerno")',
-        value: input3.method
       })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",

package/dist/gdc.grin2.js

@@ -1,14 +1,14 @@
 import {
-  gdcGRIN2Payload,
+  gdcGRIN2listPayload,
   runGRIN2Payload,
   validGdcGRIN2listRequest,
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-NWEXA2YB.js";
+} from "./chunk-B2DJ3H7H.js";
 import "./chunk-CNSSF43V.js";
 export {
-  gdcGRIN2Payload,
+  gdcGRIN2listPayload,
   runGRIN2Payload,
   validGdcGRIN2listRequest,
   validGdcGRIN2listResponse,

package/dist/genesetEnrichment.js

@@ -2,7 +2,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-A3XJW6BZ.js";
+} from "./chunk-XZAH6P4D.js";
 import "./chunk-CNSSF43V.js";
 export {
   genesetEnrichmentPayload,

package/dist/index.js

@@ -169,13 +169,13 @@ import {
   validDZImagesResponse
 } from "./chunk-XT2IWGYK.js";
 import {
-  gdcGRIN2Payload,
+  gdcGRIN2listPayload,
   runGRIN2Payload,
   validGdcGRIN2listRequest,
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-NWEXA2YB.js";
+} from "./chunk-B2DJ3H7H.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,
@@ -195,7 +195,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-A3XJW6BZ.js";
+} from "./chunk-XZAH6P4D.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
@@ -257,7 +257,7 @@ export {
   diffExpPayload,
   dsDataPayload,
   dzImagesPayload,
-  gdcGRIN2Payload,
+  gdcGRIN2listPayload,
   gdcMafPayload,
   geneLookupPayload,
   genesetEnrichmentPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.126.0",
+  "version": "2.128.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1929,12 +1929,6 @@ export type PreInit = {
 	retryDelay?: number
 	/** maximum number of times to call preInit.getStatus() before giving up */
 	retryMax?: number
-	/**
-	 * optional callback to send notifications of pre-init errors
-	 * for St. Jude, this may reuse code that post to Slack channel;
-	 * in dev and other portals, this may use custom callbacks
-	 * */
-	errorCallback?: (response: PreInitStatus) => void
 	/**
 	 * dev only, used to test preInit handling by simulating different
 	 * responses in a known sequence of steps that may edit the preInit
@@ -1971,8 +1965,19 @@ export type Mds3 = BaseMds & {
 		retryDelay?: number
 		/** maximum number of times to call preInit.getStatus() before giving up */
 		retryMax?: number
+		/** server-computed cumulative count of the attempted init retries */
+		currentRetry?: number
+		/**
+		 * optional callback to send notifications of pre-init errors
+		 * for St. Jude, this may reuse code that post to Slack channel;
+		 * in dev and other portals, this may use custom callbacks
+		 * */
+		errorCallback?: (response: PreInitStatus) => void
 	}
-	initErrorCallback?: (a: any) => void
+	/** optional callback to invoke non-blocking code after dataset query validation in mds3.init.js;
+	 * for GDC, this callback is created after buildDictionary in initGdc.js
+	 **/
+	initNonblocking?: (a: any) => void
 	viewModes?: ViewMode[]
 	dsinfo?: KeyVal[]
 	queries?: Mds3Queries

package/src/routes/gdc.grin2.ts

@@ -73,7 +73,7 @@ export type RunGRIN2Response = {
 	/** Error message if status is 'error' */
 	error?: string
 	/** Path to the generated image if status is 'success' */
-	imagestring?: string
+	pngImg?: string
 	/** Download status */
 	download?: any
 	/** Table of top genes indentified by analysis */
@@ -82,7 +82,7 @@ export type RunGRIN2Response = {
 /**
  * Route payload definitions for type checking
  */
-export const gdcGRIN2Payload: RoutePayload = {
+export const gdcGRIN2listPayload: RoutePayload = {
 	request: {
 		typeId: 'GdcGRIN2listRequest'
 	},

package/src/routes/genesetEnrichment.ts

@@ -17,8 +17,6 @@ export type GenesetEnrichmentRequest = {
 	pickle_file?: string
 	/** Number of permutations to be carried out for GSEA analysis */
 	num_permutations: number
-	/** Method used for GSEA blitzgsea/cerno */
-	method: 'blitzgsea' | 'cerno'
 }
 
 type pathway_attributes = {