@molgenis/vip-report-template 5.5.5 → 5.7.0

package/src/views/SampleVariants.tsx

@@ -158,9 +158,24 @@ export const SampleVariants: Component<{
       actions.setSampleVariantsFilterQuery(
         props.sample,
         {
-          selector: selectorGq,
-          operator: ">=",
-          args: 20,
+          operator: "or",
+          args: [
+            {
+              selector: selectorGq,
+              operator: ">=",
+              args: 20,
+            },
+            {
+              selector: selectorGq,
+              operator: "==",
+              args: null,
+            },
+            {
+              selector: selectorGq,
+              operator: "==",
+              args: undefined,
+            },
+          ],
         },
         selectorKey(selectorGq),
       );
@@ -173,6 +188,19 @@ export const SampleVariants: Component<{
         selectorKey(["s", props.sample.data.index, ...selector(viabField)]),
       );
     }
+    const viField = props.recordsMeta.format?.VI;
+    if (viField) {
+      const selectorVi = sampleSelector(props.sample, viField);
+      actions.setSampleVariantsFilterQuery(
+        props.sample,
+        {
+          selector: selectorVi,
+          operator: "has_any",
+          args: ["AD", "AR", "AR_C", "XLD", "XLR"],
+        },
+        selectorKey(selectorVi),
+      );
+    }
   }
 
   if (getStateVariants()?.sort === undefined) {
@@ -213,12 +241,31 @@ export const SampleVariants: Component<{
 
   const formatFields = createMemo(() => {
     const formatFieldMap = props.recordsMeta.format;
-    const includedFields = ["VIM", "VID", "GQ", "VIAB", "GT", "DP"];
+    const includedFields = ["VIM", "VID", "VI", "GQ", "VIAB", "GT", "DP"];
     return formatFieldMap
       ? includedFields.map((fieldId) => formatFieldMap[fieldId]).filter((field) => field !== undefined)
       : [];
   });
 
+  const filterInfoFields = createMemo(() => {
+    const csqNestedFields = props.recordsMeta.info.CSQ?.nested?.items;
+    const includedFields = [];
+    const additionalCsqFieldsIds = ["IncompletePenetrance"];
+    const filterInfoFieldsIds = ["SVTYPE"];
+    const additionalCsqFields = csqNestedFields
+      ? (additionalCsqFieldsIds
+          .map((fieldId) => csqNestedFields.find((field) => field.id === fieldId))
+          .filter((field) => field !== undefined) as FieldMetadata[])
+      : [];
+    const filterInfoFields = filterInfoFieldsIds
+      .map((fieldId) => props.recordsMeta.info[fieldId])
+      .filter((field) => field !== undefined);
+    includedFields.push(...infoFields());
+    includedFields.push(...additionalCsqFields);
+    includedFields.push(...filterInfoFields);
+    return includedFields;
+  });
+
   const page = () => getStateVariants()?.page;
   const pageSize = () => getStateVariants()?.pageSize;
   const searchQuery = () => getStateVariants()?.searchQuery;
@@ -269,7 +316,7 @@ export const SampleVariants: Component<{
       <div class="column is-1-fullhd is-2">
         <SearchBox value={searchQuery()} onInput={onSearchChange} />
         <Filters
-          fields={infoFields()}
+          fields={filterInfoFields()}
           samplesFields={[{ sample: props.sample, fields: formatFields() }]}
           queries={filterQueries()}
           onChange={onFilterChange}

package/src/views/data/SampleData.tsx

@@ -3,9 +3,11 @@ 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";
 
+export type SampleParams = { sampleId: string };
 export type SampleRouteData = { sample: Resource<Item<Sample>> };
 
 export default function SampleData({ params }: RouteDataFuncArgs): SampleRouteData {
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
   const [sample] = createResource(() => params.sampleId, fetchSampleById, { initialValue: EMPTY_SAMPLE_ITEM });
   return { sample };
 }

package/src/views/data/SampleVariantConsequenceData.tsx

@@ -7,6 +7,7 @@ export default function SampleVariantConsequenceData({
   params,
   data,
 }: RouteDataFuncArgs): SampleVariantConsequenceRouteData {
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access, @typescript-eslint/no-unsafe-argument
   const consequenceId: number = parseInt(params.consequenceId);
   return { ...(data as SampleVariantRouteData), consequenceId };
 }

package/src/views/data/SampleVariantData.tsx

@@ -8,6 +8,7 @@ import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
 export type SampleVariantRouteData = SampleRouteData & { variant: Resource<Item<Record> | undefined> };
 
 export default function SampleVariantData({ params, data }: RouteDataFuncArgs): SampleVariantRouteData {
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
   const [variant] = createResource(() => params.variantId, fetchRecordById);
   return { ...(data as SampleRouteData), variant };
 }

package/src/views/data/VariantConsequenceData.tsx

@@ -4,6 +4,7 @@ import { VariantRouteData } from "./VariantData";
 export type VariantConsequenceRouteData = { consequenceId: number } & VariantRouteData;
 
 export default function VariantConsequenceData({ params, data }: RouteDataFuncArgs): VariantConsequenceRouteData {
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access, @typescript-eslint/no-unsafe-argument
   const consequenceId: number = parseInt(params.consequenceId);
   return { ...(data as VariantRouteData), consequenceId };
 }

package/src/views/data/VariantData.tsx

@@ -7,6 +7,7 @@ import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
 export type VariantRouteData = { variant: Resource<Item<Record>> };
 
 export default function VariantData({ params }: RouteDataFuncArgs): VariantRouteData {
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
   const [variant] = createResource(() => params.variantId, fetchRecordById, { initialValue: EMPTY_RECORD_ITEM });
   return { variant };
 }

package/tsconfig.json

@@ -3,7 +3,7 @@
     "strict": true,
     "target": "ESNext",
     "module": "ESNext",
-    "moduleResolution": "node",
+    "moduleResolution": "bundler",
     "allowSyntheticDefaultImports": true,
     "esModuleInterop": true,
     "jsx": "preserve",

package/{vite.config.ts → vite.config.mts}

@@ -1,6 +1,6 @@
 import { defineConfig } from "vitest/config";
 import solidPlugin from "vite-plugin-solid";
-import inlinePlugin from "@molgenis/vite-plugin-inline/src/vite-plugin-inline.js";
+import inlinePlugin from "@molgenis/vite-plugin-inline";
 
 export default defineConfig({
   plugins: [solidPlugin(), inlinePlugin()],
@@ -12,7 +12,7 @@ export default defineConfig({
     polyfillDynamicImport: false,
     // inline plugin build options
     rollupOptions: {
-      input: ["./index.html", "@molgenis/vite-plugin-inline/src/loader.ts"],
+      input: ["./index.html", "./node_modules/@molgenis/vite-plugin-inline/dist/loader.js"],
       output: {
         manualChunks: undefined,
       },