Fix: invalid gtdbtk json documents can't be parsed

package.json

@@ -19,6 +19,7 @@
     "datatables.net-bs5": "^1.13.6",
     "datatables.net-vue3": "^2.1.3",
     "igv": "^2.15.10",
+    "json5": "^2.2.3",
     "pako": "^2.1.0",
     "vue": "^3.2.45",
     "vue-chartjs": "^5.2.0",

src/BakrepApi.ts

@@ -8,6 +8,7 @@ import { DatasetSchema, type Dataset } from "./model/Dataset";
 import { GtdbtkResultSchema, type GtdbtkResult } from "./model/GtdbtkResult";
 import { MlstResultSchema, type MlstResult } from "./model/MlstResults";
 import type { SearchInfo, SearchRequest } from "./model/Search";
+import json5 from "json5";
 
 let baseurl: string = "http://localhost:8080";
 function initApi(url: string) {
@@ -33,7 +34,7 @@ class BakrepApiImpl implements BakrepApi {
 
   toJson(r: Response): Promise<any> {
     if (!r.ok) throw r.text().then((t) => Promise.reject(t));
-    return r.json();
+    return r.text().then(json5.parse);
   }
 
   getDataset(id: string): Promise<Dataset> {

src/model/GtdbtkResult.ts

@@ -12,7 +12,7 @@ const ClassfificationSchema = z.object({
 
 const GtdbtkResultSchema = z.object({
   classification: ClassfificationSchema,
-  fastani_reference: z.string(),
+  fastani_reference: z.union([z.string(), z.nan()]),
   classification_method: z.string(),
   warnings: z.string(),
 });