@molgenis/vip-report-template 6.1.1 → 7.0.0

package/src/index.tsx

@@ -7,33 +7,38 @@ import App from "./App";
 import { dom, library } from "@fortawesome/fontawesome-svg-core";
 import {
   faAngleDown,
+  faAngleRight,
   faAngleUp,
   faCircleExclamation,
-  faCircleXmark,
   faCircleInfo,
   faCircleQuestion,
+  faCircleXmark,
   faDownload,
   faExternalLink,
   faHome,
+  faInfo,
   faSearch,
 } from "@fortawesome/free-solid-svg-icons";
 import { Provider } from "./store";
-import { ErrorBoundary } from "solid-js";
-import { Error } from "./components/Error";
+import { createSignal, ErrorBoundary, Show } from "solid-js";
 import { HashRouter, Route } from "@solidjs/router";
 import { Home } from "./views/Home";
 import { Samples } from "./views/Samples";
 import { Sample } from "./views/Sample";
-import { SampleVariantsView } from "./views/SampleVariants";
-import { SampleVariantView } from "./views/SampleVariant";
-import { SampleVariantConsequenceView } from "./views/SampleVariantConsequence";
-import { VariantsView } from "./views/Variants";
+import { SampleVariant } from "./views/SampleVariant";
+import { SampleVariantConsequence } from "./views/SampleVariantConsequence";
+import { VariantsRedirect } from "./views/VariantsRedirect.tsx";
 import { Variant } from "./views/Variant";
 import { VariantConsequence } from "./views/VariantConsequence";
 import { Help } from "./views/Help";
+import { SampleVariants } from "./views/SampleVariants.tsx";
+import { SampleVariantsRedirect } from "./views/SampleVariantsRedirect.tsx";
+import { Variants } from "./views/Variants.tsx";
+import { ErrorNotification } from "./components/ErrorNotification.tsx";
 
 library.add(
   faAngleDown,
+  faAngleRight,
   faAngleUp,
   faCircleExclamation,
   faCircleXmark,
@@ -42,6 +47,7 @@ library.add(
   faDownload,
   faExternalLink,
   faHome,
+  faInfo,
   faSearch,
 );
 
@@ -50,16 +56,29 @@ function processIcons() {
   dom.watch();
 }
 
-if (document.readyState === "complete") {
+// process icons if document state is "complete" or "interactive", list for event if "loading"
+if (document.readyState !== "loading") {
   processIcons();
 } else {
   window.addEventListener("DOMContentLoaded", processIcons);
 }
 
+const [error, setError] = createSignal<unknown>();
+window.addEventListener("error", function () {
+  setError({ message: "An unexpected error occurred" });
+});
+
+window.addEventListener("unhandledrejection", function () {
+  setError({ message: "An unexpected error occurred" });
+});
+
 render(
   () => (
     <Provider>
-      <ErrorBoundary fallback={(err) => <Error error={err as unknown} />}>
+      <Show when={error() !== undefined}>
+        <ErrorNotification error={error()} />
+      </Show>
+      <ErrorBoundary fallback={(err) => <ErrorNotification error={err} />}>
         <HashRouter root={App}>
           <Route path="/" component={Home} />
           <Route path="/samples">
@@ -67,22 +86,32 @@ render(
             <Route path="/:sampleId">
               <Route path="/" component={Sample} />
               <Route path="/variants">
-                <Route path="/" component={SampleVariantsView} />
-                <Route path="/:variantId">
-                  <Route path="/" component={SampleVariantView} />
-                  <Route path="/consequences">
-                    <Route path="/:consequenceId" component={SampleVariantConsequenceView} />
+                <Route path="/" component={SampleVariantsRedirect} />
+                <Route path="/:variantType">
+                  <Route path="/" component={SampleVariants} />
+                  <Route path="/variant">
+                    <Route path="/:variantId">
+                      <Route path="/" component={SampleVariant} />
+                      <Route path="/consequences">
+                        <Route path="/:consequenceId" component={SampleVariantConsequence} />
+                      </Route>
+                    </Route>
                   </Route>
                 </Route>
               </Route>
             </Route>
           </Route>
           <Route path="/variants">
-            <Route path="/" component={VariantsView} />
-            <Route path="/:variantId">
-              <Route path="/" component={Variant} />
-              <Route path="/consequences">
-                <Route path="/:consequenceId" component={VariantConsequence} />
+            <Route path="/" component={VariantsRedirect} />
+            <Route path="/:variantType">
+              <Route path="/" component={Variants} />
+              <Route path="/variant">
+                <Route path="/:variantId">
+                  <Route path="/" component={Variant} />
+                  <Route path="/consequences">
+                    <Route path="/:consequenceId" component={VariantConsequence} />
+                  </Route>
+                </Route>
               </Route>
             </Route>
           </Route>

package/src/mocks/GRCh37/decisionTree.json

@@ -2,14 +2,13 @@
   "rootNode": "filter",
   "nodes": {
     "filter": {
+      "label": "filter",
       "type": "BOOL",
       "description": "All filters passed",
       "query": {
         "field": "FILTER",
         "operator": "==",
-        "value": [
-          "PASS"
-        ]
+        "value": ["PASS"]
       },
       "outcomeTrue": {
         "nextNode": "vkgl"
@@ -22,6 +21,7 @@
       }
     },
     "spliceAI": {
+      "label": "spliceAI",
       "type": "BOOL_MULTI",
       "fields": [
         "INFO/CSQ/SpliceAI_pred_DS_AG",
@@ -67,6 +67,7 @@
       }
     },
     "vkgl": {
+      "label": "VKGL",
       "type": "CATEGORICAL",
       "description": "VKGL classification",
       "field": "INFO/CSQ/VKGL_CL",
@@ -92,6 +93,7 @@
       }
     },
     "annotSV": {
+      "label": "AnnotSV",
       "type": "CATEGORICAL",
       "description": "VKGL classification",
       "field": "INFO/CSQ/ASV_ACMG_class",
@@ -117,12 +119,10 @@
       }
     },
     "gnomad": {
+      "label": "GnomAD",
       "type": "BOOL_MULTI",
       "description": "gnomAD_AF < 0.02 && gnomAD_HN < 5",
-      "fields": [
-        "INFO/CSQ/gnomAD_AF",
-        "INFO/CSQ/gnomAD_HN"
-      ],
+      "fields": ["INFO/CSQ/gnomAD_AF", "INFO/CSQ/gnomAD_HN"],
       "outcomes": [
         {
           "operator": "OR",
@@ -151,6 +151,7 @@
       }
     },
     "effect": {
+      "label": "Effect",
       "type": "BOOL",
       "description": "Consequence contains 'missense'",
       "query": {
@@ -169,10 +170,9 @@
       }
     },
     "clinVar": {
+      "label": "ClinVar",
       "type": "BOOL_MULTI",
-      "fields": [
-        "INFO/CSQ/CLIN_SIG"
-      ],
+      "fields": ["INFO/CSQ/CLIN_SIG"],
       "outcomes": [
         {
           "queries": [
@@ -195,10 +195,7 @@
             {
               "field": "INFO/CSQ/CLIN_SIG",
               "operator": "contains_any",
-              "value": [
-                "likely_benign",
-                "benign"
-              ]
+              "value": ["likely_benign", "benign"]
             }
           ],
           "outcomeTrue": {
@@ -210,10 +207,7 @@
             {
               "field": "INFO/CSQ/CLIN_SIG",
               "operator": "contains_any",
-              "value": [
-                "likely_pathogenic",
-                "pathogenic"
-              ]
+              "value": ["likely_pathogenic", "pathogenic"]
             }
           ],
           "outcomeTrue": {
@@ -229,6 +223,7 @@
       }
     },
     "sift": {
+      "label": "SIFT",
       "description": "SIFT qualitative prediction",
       "type": "BOOL",
       "query": {
@@ -247,11 +242,10 @@
       }
     },
     "polyphen": {
+      "label": "PolyPhen",
       "description": "PolyPhen qualitative prediction",
       "type": "BOOL_MULTI",
-      "fields": [
-        "INFO/CSQ/PolyPhen"
-      ],
+      "fields": ["INFO/CSQ/PolyPhen"],
       "outcomes": [
         {
           "queries": [
@@ -304,6 +298,7 @@
       }
     },
     "impact": {
+      "label": "IMPACT",
       "type": "CATEGORICAL",
       "description": "IMPACT rating",
       "field": "INFO/CSQ/IMPACT",
@@ -325,28 +320,34 @@
         "nextNode": "exit_vus"
       }
     },
-    "exit_lq": {
+    "exit_rm": {
+      "label": "Remove",
       "description": "Low quality variants.",
       "type": "LEAF",
       "class": "LQ"
     },
     "exit_b": {
+      "label": "Benign",
       "type": "LEAF",
       "class": "B"
     },
     "exit_lb": {
+      "label": "Likely Benign",
       "type": "LEAF",
       "class": "LB"
     },
     "exit_vus": {
+      "label": "Unknown Significance",
       "type": "LEAF",
       "class": "VUS"
     },
     "exit_lp": {
+      "label": "Likely Pathogenic",
       "type": "LEAF",
       "class": "LP"
     },
     "exit_p": {
+      "label": "Pathogenic",
       "type": "LEAF",
       "class": "P"
     }