@molgenis/vip-report-template 5.2.0 → 5.2.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "5.2.0",
+  "version": "5.2.2",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "scripts": {
     "build": "vite build",
@@ -15,33 +15,33 @@
   },
   "license": "LGPL-3.0",
   "devDependencies": {
-    "@molgenis/vite-plugin-inline": "^1.0.11",
-    "@typescript-eslint/eslint-plugin": "^5.51.0",
-    "@typescript-eslint/parser": "^5.51.0",
-    "@vitest/coverage-c8": "^0.28.4",
+    "@molgenis/vite-plugin-inline": "^1.0.12",
+    "@typescript-eslint/eslint-plugin": "^5.58.0",
+    "@typescript-eslint/parser": "^5.58.0",
+    "@vitest/coverage-c8": "^0.30.1",
     "bulma": "^0.9.4",
-    "eslint": "^8.33.0",
-    "eslint-config-prettier": "^8.6.0",
+    "eslint": "^8.38.0",
+    "eslint-config-prettier": "^8.8.0",
     "eslint-plugin-prettier": "^4.2.1",
-    "eslint-plugin-solid": "^0.9.4",
+    "eslint-plugin-solid": "^0.12.1",
     "husky": "^8.0.3",
-    "jsdom": "^21.1.0",
-    "prettier": "^2.8.4",
-    "sass": "^1.58.0",
-    "typescript": "^4.9.5",
-    "vite": "^4.1.1",
-    "vite-plugin-solid": "^2.5.0",
-    "vitest": "^0.28.4"
+    "jsdom": "^21.1.1",
+    "prettier": "^2.8.7",
+    "sass": "^1.62.0",
+    "typescript": "^5.0.4",
+    "vite": "^4.2.1",
+    "vite-plugin-solid": "^2.7.0",
+    "vitest": "^0.30.1"
   },
   "dependencies": {
-    "@fortawesome/fontawesome-svg-core": "^6.3.0",
-    "@fortawesome/free-solid-svg-icons": "^6.3.0",
-    "@molgenis/vip-report-api": "^4.3.3",
-    "@molgenis/vip-report-vcf": "^1.3.4",
+    "@fortawesome/fontawesome-svg-core": "^6.4.0",
+    "@fortawesome/free-solid-svg-icons": "^6.4.0",
+    "@molgenis/vip-report-api": "^4.3.4",
+    "@molgenis/vip-report-vcf": "^1.3.5",
+    "@solidjs/router": "^0.8.2",
     "base64-js": "^1.5.1",
-    "igv": "^2.13.11",
-    "solid-app-router": "^0.4.2",
-    "solid-js": "^1.6.10"
+    "igv": "^2.15.3",
+    "solid-js": "^1.7.3"
   },
   "lint-staged": {
     "src/**/*.{tsx,ts}": [

package/src/App.tsx

@@ -1,5 +1,5 @@
 import { Component, ErrorBoundary, onMount } from "solid-js";
-import { Link, Route, Routes, useLocation, useNavigate } from "solid-app-router";
+import { Link, Route, Routes, useLocation, useNavigate } from "@solidjs/router";
 import { VariantsView } from "./views/Variants";
 import { Variant } from "./views/Variant";
 import VariantData from "./views/data/VariantData";

package/src/components/Breadcrumb.tsx

@@ -1,4 +1,4 @@
-import { Link } from "solid-app-router";
+import { Link } from "@solidjs/router";
 import { Component, For } from "solid-js";
 
 export type BreadCrumbItem = { href?: string; text: string };

package/src/components/DatasetDropdown.tsx

@@ -1,6 +1,6 @@
 import { Component, createSignal, For } from "solid-js";
 import api from "../Api";
-import { useNavigate } from "solid-app-router";
+import { useNavigate } from "@solidjs/router";
 import { useStore } from "../store";
 
 export const DatasetDropdown: Component = () => {

package/src/components/InfoCollapsablePane.tsx

@@ -6,7 +6,7 @@ import { ValueArray } from "@molgenis/vip-report-vcf/src/ValueParser";
 import { Info } from "./record/Info";
 import { FieldValue } from "./record/field/Field";
 import { isCsqInfo } from "../utils/csqUtils";
-import { Link, useLocation } from "solid-app-router";
+import { Link, useLocation } from "@solidjs/router";
 
 export const InfoCollapsablePane: Component<{
   fields: FieldMetadata[];

package/src/components/SampleTable.tsx

@@ -1,4 +1,4 @@
-import { Link } from "solid-app-router";
+import { Link } from "@solidjs/router";
 import { Component, createMemo, For, Show } from "solid-js";
 import { Item, Phenotype, PhenotypicFeature, Sample } from "@molgenis/vip-report-api/src/Api";
 import { HpoTerm } from "./HpoTerm";

package/src/components/VariantInfoNestedTable.tsx

@@ -6,7 +6,7 @@ import { FieldHeader } from "./FieldHeader";
 import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
 import { Item } from "@molgenis/vip-report-api/src/Api";
 import { isCsqInfo } from "../utils/csqUtils";
-import { Link, useLocation } from "solid-app-router";
+import { Link, useLocation } from "@solidjs/router";
 
 function isNonEmptyNestedInfoItem(nestedInfoField: FieldMetadata, index: number, value: Value[] | Value[][]): boolean {
   const infoField = nestedInfoField.nested?.items[index];

package/src/components/VariantSampleTable.tsx

@@ -42,7 +42,7 @@ export const VariantSampleTable: Component<{
                           allelicBalance={
                             props.record.data.s[props.samples[i()].index]["VIAB"] as number | undefined | null
                           }
-                          readDepth={props.record.data.s[props.samples[i()].index]["DP"] as number | undefined}
+                          readDepth={props.record.data.s[props.samples[i()].index]["DP"] as number | undefined | null}
                         />
                       </td>
                     )}

package/src/components/VariantsSampleTable.tsx

@@ -2,7 +2,7 @@ import { Genotype, Metadata, Record } from "@molgenis/vip-report-vcf/src/Vcf";
 import { Ref } from "./record/Ref";
 import { Chrom } from "./record/Chrom";
 import { Pos } from "./record/Pos";
-import { Link } from "solid-app-router";
+import { Link } from "@solidjs/router";
 import { HtsFileMetadata, Item, Sample } from "@molgenis/vip-report-api/src/Api";
 import { GenotypeField } from "./record/format/GenotypeField";
 import { InfoCollapsablePane } from "./InfoCollapsablePane";
@@ -11,7 +11,6 @@ import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
 import { FieldHeader } from "./FieldHeader";
 import { Abbr } from "./Abbr";
 import { abbreviateHeader } from "../utils/field";
-import { ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
 
 export const VariantsSampleTable: Component<{
   item: Item<Sample>;

package/src/components/VariantsTable.tsx

@@ -9,7 +9,7 @@ import { Qual } from "./record/Qual";
 import { Filter } from "./record/Filter";
 import { Info } from "./record/Info";
 import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { Link } from "solid-app-router";
+import { Link } from "@solidjs/router";
 import { HtsFileMetadata, Item } from "@molgenis/vip-report-api/src/Api";
 import { FieldHeader } from "./FieldHeader";
 import { InfoCollapsablePane } from "./InfoCollapsablePane";

package/src/components/record/Format.tsx

@@ -13,7 +13,7 @@ export const Format: Component<{
   record: Item<Record>;
   isAbbreviate: boolean;
   allelicBalance: number | undefined | null;
-  readDepth: number | undefined;
+  readDepth: number | undefined | null;
 }> = (props) => {
   return (
     <Switch

package/src/components/record/format/GenotypeField.tsx

@@ -35,10 +35,10 @@ export const GenotypeField: Component<{
   altAlleles: (string | null)[];
   isAbbreviate: boolean;
   allelicBalance: number | undefined | null;
-  readDepth: number | undefined;
+  readDepth: number | undefined | null;
 }> = (props) => {
   const allelicImbalance: boolean = isAllelicImbalance(props.genotype, props.allelicBalance);
-  const lowReadDepth = props.readDepth !== undefined && props.readDepth < 20;
+  const lowReadDepth = props.readDepth !== undefined && props.readDepth !== null && props.readDepth < 20;
   return (
     <>
       <For each={props.genotype.a}>

package/src/components/record/info/Consequence.tsx

@@ -10,7 +10,7 @@ export const Consequence: Component<FieldProps> = (props) => {
       <span>{consequence()[0]}</span>
       {consequence().length > 1 && (
         <span>
-          , <Abbr title={consequence().slice(1).join(", ")} value="\u2026" />
+          , <Abbr title={consequence().slice(1).join(", ")} value={"\u2026"} />
         </span>
       )}
     </>

package/src/store/index.tsx

@@ -1,4 +1,4 @@
-import { hashIntegration, Router } from "solid-app-router";
+import { hashIntegration, Router } from "@solidjs/router";
 import { Context, createContext, ParentComponent, useContext } from "solid-js";
 import { createStore } from "solid-js/store";
 import { Item, Query, Sample, SortOrder } from "@molgenis/vip-report-api/src/Api";

package/src/views/Sample.tsx

@@ -1,5 +1,5 @@
 import { Component, For, Show } from "solid-js";
-import { Link, useRouteData } from "solid-app-router";
+import { Link, useRouteData } from "@solidjs/router";
 import { Loader } from "../components/Loader";
 import { Breadcrumb } from "../components/Breadcrumb";
 import { SampleRouteData } from "./data/SampleData";

package/src/views/SampleVariant.tsx

@@ -1,5 +1,5 @@
 import { Component, createResource, For, Show } from "solid-js";
-import { useRouteData } from "solid-app-router";
+import { useRouteData } from "@solidjs/router";
 import { Loader } from "../components/Loader";
 import { GenomeBrowser } from "../components/GenomeBrowser";
 import { fetchPedigreeSamples, fetchRecordsMeta, getRecordLabel } from "../utils/ApiUtils";

package/src/views/SampleVariantConsequence.tsx

@@ -1,5 +1,5 @@
 import { Component, createResource, Show } from "solid-js";
-import { useRouteData } from "solid-app-router";
+import { useRouteData } from "@solidjs/router";
 import { Loader } from "../components/Loader";
 import {
   fetchDecisionTree,

package/src/views/SampleVariants.tsx

@@ -1,5 +1,5 @@
 import { Component, createMemo, createResource, Show } from "solid-js";
-import { useRouteData } from "solid-app-router";
+import { useRouteData } from "@solidjs/router";
 import { HtsFileMetadata, Item, Params, PhenotypicFeature, Sample, SortPath } from "@molgenis/vip-report-api/src/Api";
 import { Loader } from "../components/Loader";
 import { SearchBox } from "../components/SearchBox";

package/src/views/Variant.tsx

@@ -1,5 +1,5 @@
 import { Component, createResource, For, Show } from "solid-js";
-import { useRouteData } from "solid-app-router";
+import { useRouteData } from "@solidjs/router";
 import { GenomeBrowser } from "../components/GenomeBrowser";
 import { Loader } from "../components/Loader";
 import { Value } from "@molgenis/vip-report-vcf/src/ValueParser";

package/src/views/VariantConsequence.tsx

@@ -1,5 +1,5 @@
 import { Component, createResource, Show } from "solid-js";
-import { useRouteData } from "solid-app-router";
+import { useRouteData } from "@solidjs/router";
 import { Loader } from "../components/Loader";
 import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
 import { VariantTable } from "../components/VariantTable";

package/src/views/data/SampleData.tsx

@@ -1,5 +1,5 @@
 import { createResource, Resource } from "solid-js";
-import { RouteDataFuncArgs } from "solid-app-router/dist/types";
+import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
 import { EMPTY_SAMPLE_ITEM, fetchSampleById } from "../../utils/ApiUtils";
 import { Item, Sample } from "@molgenis/vip-report-api/src/Api";
 

package/src/views/data/SampleVariantConsequenceData.tsx

@@ -1,4 +1,4 @@
-import { RouteDataFuncArgs } from "solid-app-router/dist/types";
+import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
 import { SampleVariantRouteData } from "./SampleVariantData";
 
 export type SampleVariantConsequenceRouteData = { consequenceId: number } & SampleVariantRouteData;

package/src/views/data/SampleVariantData.tsx

@@ -1,5 +1,5 @@
 import { createResource, Resource } from "solid-js";
-import { RouteDataFuncArgs } from "solid-app-router/dist/types";
+import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
 import { fetchRecordById } from "../../utils/ApiUtils";
 import { SampleRouteData } from "./SampleData";
 import { Item } from "@molgenis/vip-report-api/src/Api";

package/src/views/data/VariantConsequenceData.tsx

@@ -1,4 +1,4 @@
-import { RouteDataFuncArgs } from "solid-app-router/dist/types";
+import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
 import { VariantRouteData } from "./VariantData";
 
 export type VariantConsequenceRouteData = { consequenceId: number } & VariantRouteData;

package/src/views/data/VariantData.tsx

@@ -1,5 +1,5 @@
 import { createResource, Resource } from "solid-js";
-import { RouteDataFuncArgs } from "solid-app-router/dist/types";
+import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
 import { EMPTY_RECORD_ITEM, fetchRecordById } from "../../utils/ApiUtils";
 import { Item } from "@molgenis/vip-report-api/src/Api";
 import { Record } from "@molgenis/vip-report-vcf/src/Vcf";