@molgenis/vip-report-template 7.1.1 → 7.1.2

package/.travis.yml

@@ -1,6 +1,8 @@
 os: linux
 dist: jammy
 language: node_js
+env:
+  - COREPACK_INTEGRITY_KEYS=0 # workaround for https://github.com/nodejs/corepack/issues/627
 node_js:
   - 22
 branches:

package/package.json

@@ -1,38 +1,38 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "7.1.1",
+  "version": "7.1.2",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "license": "LGPL-3.0",
   "devDependencies": {
-    "@molgenis/vite-plugin-inline": "^1.0.27",
+    "@molgenis/vite-plugin-inline": "^1.0.29",
     "@types/async-lock": "^1.4.2",
-    "@types/node": "^22.9.3",
-    "@vitest/coverage-v8": "^2.1.5",
+    "@types/node": "^22.13.4",
+    "@vitest/coverage-v8": "^3.0.5",
     "async-lock": "^1.4.1",
-    "bulma": "^1.0.2",
-    "eslint": "^9.15.0",
-    "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-solid": "^0.14.4",
+    "bulma": "^1.0.3",
+    "eslint": "^9.20.1",
+    "eslint-config-prettier": "^10.0.1",
+    "eslint-plugin-solid": "^0.14.5",
     "husky": "^9.1.7",
-    "jsdom": "^25.0.1",
-    "prettier": "^3.3.3",
-    "sass": "^1.81.0",
-    "typescript": "^5.6.3",
-    "typescript-eslint": "^8.15.0",
-    "vite": "^5.4.11",
-    "vite-plugin-solid": "^2.10.2",
-    "vitest": "^2.1.5"
+    "jsdom": "^26.0.0",
+    "prettier": "^3.5.1",
+    "sass": "^1.85.0",
+    "typescript": "^5.7.3",
+    "typescript-eslint": "^8.24.0",
+    "vite": "^6.1.0",
+    "vite-plugin-solid": "^2.11.1",
+    "vitest": "^3.0.5"
   },
   "dependencies": {
-    "@fortawesome/fontawesome-svg-core": "^6.7.1",
-    "@fortawesome/free-solid-svg-icons": "^6.7.1",
-    "@molgenis/vip-report-api": "^6.2.2",
-    "@molgenis/vip-report-vcf": "^3.1.0",
-    "@solidjs/router": "^0.15.1",
+    "@fortawesome/fontawesome-svg-core": "^6.7.2",
+    "@fortawesome/free-solid-svg-icons": "^6.7.2",
+    "@molgenis/vip-report-api": "^6.2.3",
+    "@molgenis/vip-report-vcf": "^3.1.1",
+    "@solidjs/router": "^0.15.3",
     "ajv": "^8.17.1",
     "base64-js": "^1.5.1",
-    "igv": "^3.1.0",
-    "solid-js": "^1.9.3"
+    "igv": "^3.1.4",
+    "solid-js": "^1.9.4"
   },
   "lint-staged": {
     "src/**/*.{tsx,ts}": [

package/src/components/SearchBox.tsx

@@ -1,4 +1,5 @@
 import { Component, createEffect, createSignal } from "solid-js";
+import { removeZeroWidthAndTrim } from "../utils/utils.ts";
 
 export const SearchBox: Component<{ value?: string | null; onInput: (value: string) => void }> = (props) => {
   const [value, setValue] = createSignal("");
@@ -16,7 +17,7 @@ export const SearchBox: Component<{ value?: string | null; onInput: (value: stri
           class="input"
           type="text"
           value={value()}
-          onInput={(e) => setValue((e.target as HTMLInputElement).value)}
+          onInput={(e) => setValue(removeZeroWidthAndTrim((e.target as HTMLInputElement).value))}
           onKeyUp={(e) => {
             if (e.code === "Enter") {
               props.onInput(value());

package/src/components/form/Input.tsx

@@ -1,4 +1,5 @@
 import { Component } from "solid-js";
+import { removeZeroWidthAndTrim } from "../../utils/utils.ts";
 
 export type InputValue = string;
 export type InputChangeEvent = { value: InputValue };
@@ -13,7 +14,9 @@ export const Input: Component<InputProps> = (props) => {
       type="text"
       {...(props.value ? { value: props.value } : {})}
       placeholder={props.placeholder}
-      onInput={(event) => props.onValueChange({ value: (event.target as HTMLInputElement).value })}
+      onInput={(event) =>
+        props.onValueChange({ value: removeZeroWidthAndTrim((event.target as HTMLInputElement).value) })
+      }
     />
   );
 };

package/src/mocks/GRCh38/decisionTreeStr.json

@@ -58,7 +58,7 @@
       "query": {
         "field": "INFO/CSQ/Consequence",
         "operator": "contains_any",
-        "value": ["upstream_gene_variant","downstream_gene_variant"]
+        "value": ["upstream_gene_variant", "downstream_gene_variant"]
       },
       "outcomeTrue": {
         "nextNode": "exit_rm"
@@ -119,9 +119,7 @@
       "query": {
         "field": "FILTER",
         "operator": "==",
-        "value": [
-          "PASS"
-        ]
+        "value": ["PASS"]
       },
       "outcomeTrue": {
         "nextNode": "vkgl"
@@ -166,9 +164,7 @@
       "label": "ClinVar",
       "description": "ClinVar classification",
       "type": "BOOL_MULTI",
-      "fields": [
-        "INFO/CSQ/clinVar_CLNSIG"
-      ],
+      "fields": ["INFO/CSQ/clinVar_CLNSIG"],
       "outcomes": [
         {
           "description": "Conflict",
@@ -176,7 +172,7 @@
             {
               "field": "INFO/CSQ/clinVar_CLNSIG",
               "operator": "contains_any",
-              "value": [ "Conflicting_interpretations_of_pathogenicity" ]
+              "value": ["Conflicting_interpretations_of_pathogenicity"]
             }
           ],
           "outcomeTrue": {
@@ -189,7 +185,7 @@
             {
               "field": "INFO/CSQ/clinVar_CLNSIG",
               "operator": "contains_any",
-              "value": [ "Likely_pathogenic", "Pathogenic" ]
+              "value": ["Likely_pathogenic", "Pathogenic"]
             }
           ],
           "outcomeTrue": {
@@ -202,7 +198,7 @@
             {
               "field": "INFO/CSQ/clinVar_CLNSIG",
               "operator": "contains_any",
-              "value": [ "Uncertain_significance" ]
+              "value": ["Uncertain_significance"]
             }
           ],
           "outcomeTrue": {
@@ -215,7 +211,7 @@
             {
               "field": "INFO/CSQ/clinVar_CLNSIG",
               "operator": "contains_any",
-              "value": [ "Likely_benign", "Benign" ]
+              "value": ["Likely_benign", "Benign"]
             }
           ],
           "outcomeTrue": {
@@ -357,10 +353,7 @@
       "label": "",
       "description": "gnomAD",
       "type": "BOOL_MULTI",
-      "fields": [
-        "INFO/CSQ/gnomAD_FAF99",
-        "INFO/CSQ/gnomAD_HN"
-      ],
+      "fields": ["INFO/CSQ/gnomAD_FAF99", "INFO/CSQ/gnomAD_HN"],
       "outcomes": [
         {
           "description": "Filtering allele Frequency (99% confidence) >= 0.02 or Number of Homozygotes > 5",

package/src/mocks/GRCh38/sampleTree.json

@@ -59,7 +59,7 @@
       "query": {
         "field": "FORMAT/VI",
         "operator": "contains_none",
-        "value": ["AR","AD","XLR","XLD","YL","MT","AR_C"]
+        "value": ["AR", "AD", "XLR", "XLD", "YL", "MT", "AR_C"]
       },
       "outcomeTrue": {
         "nextNode": "vid_IP"
@@ -172,4 +172,4 @@
       "class": "U4"
     }
   }
-}
+}

package/src/utils/utils.ts

@@ -65,3 +65,15 @@ export function validateIntervalInput(
     return `Input 'to' (${right}) for filter '${id}' should have a higher value than the 'from' input (${left}).`;
   }
 }
+
+/**
+ * Remove zero-width space Unicode characters from a string and trim
+ *
+ * U+200B zero-width space.
+ * U+200C zero-width non-joiner.
+ * U+200D zero-width joiner.
+ * U+FEFF zero-width non-breaking space.
+ */
+export function removeZeroWidthAndTrim(stringToTrim: string): string {
+  return stringToTrim.replace(/[\u200B-\u200D\uFEFF]/g, "").trim();
+}

package/tests/utils/utils.test.ts

@@ -7,6 +7,7 @@ import {
   href,
   isPositiveInteger,
   parseId,
+  removeZeroWidthAndTrim,
   validateIntervalInput,
 } from "../../src/utils/utils.ts";
 
@@ -117,4 +118,14 @@ describe("utils", () => {
       );
     });
   });
+
+  describe("zeroWidthTrim", () => {
+    test("string with zero-width unicode characters and space", () => {
+      expect(removeZeroWidthAndTrim("\u200Bb\u200Cc\u200Dd\uFEFF ")).toStrictEqual("bcd");
+    });
+
+    test("string without zero-width unicode characters", () => {
+      expect(removeZeroWidthAndTrim("bcd")).toStrictEqual("bcd");
+    });
+  });
 });