@molgenis/vip-report-template 7.0.0 → 7.0.2

package/.travis.yml

@@ -22,7 +22,7 @@ script:
   - pnpm run coverage
   - pnpm run build
 before_deploy:
-  - mv dist/index.html dist/vip-report-template.html
+  - cp dist/index.html dist/vip-report-template.html
 deploy:
   - provider: script
     script: bash scripts/deploy_npm_registry.sh

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "7.0.0",
+  "version": "7.0.2",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "license": "LGPL-3.0",
   "devDependencies": {

package/src/components/VariantsContainerHeader.tsx

@@ -34,7 +34,7 @@ export const VariantsContainerHeader: Component<{
       const sampleMother = props.sample.maternalSample;
       const sampleOtherFamilyMembers = props.sample.otherPedigreeSamples;
 
-      if (!(sampleFather === undefined && sampleMother === undefined && sampleOtherFamilyMembers.length === 0)) {
+      if (!(sampleFather === null && sampleMother === null && sampleOtherFamilyMembers.length === 0)) {
         const tokens: string[] = [];
         if (sampleMother !== null) {
           tokens.push(`mother (${getTitleAffectedStatusLabel(sampleMother)})`);

package/src/components/field/composed/FieldGenotypeStr.tsx

@@ -1,6 +1,7 @@
 import { Component, Show } from "solid-js";
 import { Allele } from "../../Allele";
 import { CellValueGenotype } from "../../../types/configCellComposed";
+import { FieldGenotypeSnvSv } from "./FieldGenotypeSnvSv.tsx";
 
 export const FieldGenotypeStr: Component<{
   value: CellValueGenotype;
@@ -12,7 +13,7 @@ export const FieldGenotypeStr: Component<{
     props.value.repeatUnitMatch !== undefined;
 
   return (
-    <Show when={showGenotype()}>
+    <Show when={showGenotype()} fallback={<FieldGenotypeSnvSv value={props.value} />}>
       <abbr title={`display repeat unit familiar to clinician: ${props.value.displayRepeatUnit!}`}>
         <Allele value={props.value.repeatUnitValue!} isAbbreviate={false} />
         <sub>n</sub>

package/src/types/config.d.ts

@@ -185,6 +185,6 @@ export type ConfigVariantConsequence = {
 export type ConfigVipParams = ConfigJsonVipParams;
 
 export type ConfigVip = {
-  filter_field: FieldMetadataWrapper;
+  filter_field: FieldMetadataWrapper | null;
   params: ConfigVipParams;
 };

package/src/utils/config/configVip.ts

@@ -7,13 +7,7 @@ export function initConfigVip(config: ConfigJsonVip, metadata: MetadataContainer
   const filterField = config.filter_field;
   const fieldMetadata = getSampleField(metadata.records, filterField.name);
 
-  if (fieldMetadata === undefined) {
-    throw new ConfigInvalidPropertyValueError(
-      "vip.filter_field.name",
-      filterField.name,
-      "does not exist in vcf metadata",
-    );
-  } else if (fieldMetadata.type !== "CATEGORICAL") {
+  if (fieldMetadata && fieldMetadata.type !== "CATEGORICAL") {
     throw new ConfigInvalidPropertyValueError(
       "vip.filter_field.name",
       filterField.name,
@@ -21,5 +15,5 @@ export function initConfigVip(config: ConfigJsonVip, metadata: MetadataContainer
     );
   }
 
-  return { filter_field: fieldMetadata, params: config.params };
+  return { filter_field: fieldMetadata || null, params: config.params };
 }

package/src/utils/query/query.ts

@@ -23,7 +23,9 @@ export function createQuery(
 
   if (sample !== null) {
     const querySample = createQuerySample(config.vip, sample);
-    queryParts.push(querySample);
+    if (querySample !== null) {
+      queryParts.push(querySample);
+    }
   }
 
   const queryFilters = createQueryFilters(config.variants.filters, filterValues);

package/src/utils/query/querySample.ts

@@ -5,10 +5,13 @@ import { ConfigVip } from "../../types/config";
 import { FilterValueCategorical } from "../../types/configFilter";
 import { createQueryFilterFieldCategorical } from "./queryFilterField.ts";
 
-export function createQuerySample(config: ConfigVip, sample: SampleContainer): Query {
+export function createQuerySample(config: ConfigVip, sample: SampleContainer): Query | null {
+  const filterField = config.filter_field;
+  if (filterField === null) return null;
+
   const filterValues = getFilterValues(config);
-  const selector = createSelectorSample(sample, config.filter_field);
-  return createQueryFilterFieldCategorical(selector, config.filter_field, filterValues);
+  const selector = createSelectorSample(sample, filterField);
+  return createQueryFilterFieldCategorical(selector, filterField, filterValues);
 }
 
 function getFilterValues(config: ConfigVip): FilterValueCategorical {

package/tests/utils/config/configVip.test.ts

@@ -44,10 +44,10 @@ describe("config vip", () => {
     test("init metadata unavailable", () => {
       vi.mocked(getSampleField).mockReturnValue(undefined);
 
-      expect(() => initConfigVip(config, metadata as MetadataContainer)).toThrowError(
-        /^config invalid: property 'vip.filter_field.name' value 'f' does not exist in vcf metadata$/,
-      );
-      expect(getSampleField).toHaveBeenCalledWith(vcfMetadata, "f");
+      expect(initConfigVip(config, metadata as MetadataContainer)).toStrictEqual({
+        filter_field: null,
+        params,
+      });
     });
   });
 });

package/tests/utils/query/querySample.test.ts

@@ -41,5 +41,12 @@ describe("query sample", () => {
         "__null",
       ]);
     });
+
+    test("create without filter field", () => {
+      const classes = "VUS,LP,P";
+      const config = { filter_field: null, params: { vcf: { filter_samples: { classes } } } } as ConfigVip;
+      const sample = { item: { data: { index: 1 } } } as SampleContainer;
+      expect(createQuerySample(config, sample)).toStrictEqual(null);
+    });
   });
 });