@molgenis/vip-report-template 7.0.2 → 7.0.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "7.0.2",
+  "version": "7.0.3",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "license": "LGPL-3.0",
   "devDependencies": {

package/src/components/RecordsTable.tsx

@@ -49,7 +49,7 @@ export const RecordsTableHeaderCells: Component<{ fieldConfigs: ConfigCells }> =
   );
 };
 
-const RecordsTableHeaderCell: Component<{
+export const RecordsTableHeaderCell: Component<{
   fieldConfig: ConfigCellItem;
 }> = (props) => {
   const label = () => props.fieldConfig.label();

package/src/components/VariantConsequenceContainer.tsx

@@ -43,7 +43,7 @@ export const VariantConsequenceContainer: Component<{
         <div class="column is-4">
           <div>
             <h1 class="title is-5">Info</h1>
-            <VariantInfoTable infoMetadataContainer={props.metadata.records.info} infoContainer={props.record.data.n} />
+            <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
           </div>
           <div class="mt-3">
             <h1 class="title is-5">Consequence</h1>

package/src/components/VariantContainer.tsx

@@ -34,18 +34,10 @@ export const VariantContainer: Component<{
           <h1 class="title is-5">Record</h1>
           <VariantTable variant={props.record.data} />
         </div>
-        <Show
-          when={
-            Object.values(props.metadata.records.info).filter(
-              (info) => !info.nested && props.record.data.n[info.id] !== undefined,
-            ).length > 0
-          }
-        >
-          <div class="column is-3">
-            <h1 class="title is-5">Info</h1>
-            <VariantInfoTable infoMetadataContainer={props.metadata.records.info} infoContainer={props.record.data.n} />
-          </div>
-        </Show>
+        <div class="column is-3">
+          <h1 class="title is-5">Info</h1>
+          <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
+        </div>
         <Show when={config().variant.samplesCells}>
           {(samplesCells) => (
             <div class="column">

package/src/components/VariantInfoTable.tsx

@@ -1,27 +1,38 @@
 import { Component, For } from "solid-js";
-import { FieldMetadataContainer, InfoContainer } from "@molgenis/vip-report-vcf";
-import { FieldInfo } from "./field/info/FieldInfo.tsx";
+import { VcfRecord } from "@molgenis/vip-report-vcf";
 import { Table } from "./Table.tsx";
+import { Item } from "@molgenis/vip-report-api";
+import { RecordsTableCell, RecordsTableHeaderCell } from "./RecordsTable.tsx";
+import { initConfigCells } from "../utils/config/configCells.ts";
+import { MetadataContainer } from "../utils/api.ts";
+import { VariantType } from "../utils/variantType.ts";
 
 export const VariantInfoTable: Component<{
-  infoMetadataContainer: FieldMetadataContainer;
-  infoContainer: InfoContainer;
+  variantType: VariantType;
+  metadata: MetadataContainer;
+  record: Item<VcfRecord>;
 }> = (props) => {
-  const fieldMetadatas = () =>
-    Object.values(props.infoMetadataContainer).filter(
-      (info) => !info.nested && props.infoContainer[info.id] !== undefined,
-    );
+  const configCells = () =>
+    initConfigCells(
+      [
+        {
+          type: "info",
+          name: "((?!CSQ).)*",
+        },
+      ],
+      props.variantType,
+      props.metadata,
+      null,
+    ).filter((configCell) => configCell.type !== "group");
 
   return (
-    <Table>
+    <Table borderless={true}>
       <tbody>
-        <For each={fieldMetadatas()}>
-          {(fieldMetadata) => (
+        <For each={configCells()}>
+          {(fieldConfig) => (
             <tr>
-              <td>{fieldMetadata.id}</td>
-              <td>
-                <FieldInfo metadata={fieldMetadata} value={props.infoContainer[fieldMetadata.id]} />
-              </td>
+              <RecordsTableHeaderCell fieldConfig={fieldConfig} />
+              <RecordsTableCell fieldConfig={fieldConfig} record={props.record} />
             </tr>
           )}
         </For>

package/src/mocks/GRCh37/field_metadata.json

@@ -180,7 +180,7 @@
           "label": "ClinVar",
           "description": "Clinical significance for this single variant",
           "numberType": "OTHER",
-          "separator": "/",
+          "separator": "&",
           "type": "CATEGORICAL",
           "categories": {
             "Benign": {
@@ -765,8 +765,8 @@
     "STR_STATUS": {
       "label": "STR status",
       "description": "Repeat expansion status as decided by Stranger",
-      "numberType": "NUMBER",
-      "numberCount": 1,
+      "numberType": "PER_ALT",
+      "separator": ",",
       "type": "CATEGORICAL",
       "categories": {
         "normal": {

package/src/mocks/GRCh38/field_metadata.json

@@ -203,9 +203,13 @@
               "label": "P",
               "description": "Pathogenic"
             },
-            "Conflicting_interpretations_of_pathogenicity": {
+            "Conflicting_classifications_of_pathogenicity": {
               "label": "Conflict",
-              "description": "Conflicting interpretations of pathogenicity"
+              "description": "Conflicting classifications of pathogenicity"
+            },
+            "Other": {
+              "label": "Other",
+              "description": "Classifications that do not match the common categorical values."
             }
           }
         },
@@ -236,9 +240,9 @@
               "label": "P",
               "description": "Pathogenic"
             },
-            "Conflicting_interpretations_of_pathogenicity": {
+            "Conflicting_classifications_of_pathogenicity": {
               "label": "Conflict",
-              "description": "Conflicting interpretations of pathogenicity"
+              "description": "Conflicting classifications of pathogenicity"
             }
           }
         },
@@ -273,8 +277,8 @@
               "label": "Single submitter",
               "description": "There is a single submitted record with a classification"
             },
-            "_conflicting_interpretations": {
-              "label": "Conflicting_interpretations",
+            "_conflicting_classifications": {
+              "label": "Conflicting_classifications",
               "description": "There are conflicting classifications"
             },
             "no_assertion_criteria_provided": {
@@ -283,6 +287,15 @@
             },
             "no_assertion_provided": {
               "label": "No assertion provided"
+            },
+            "no_classification_for_the_single_variant": {
+              "label": "No classification for the single variant"
+            },
+            "no_classification_provided": {
+              "label": "No classification provided"
+            },
+            "no_classifications_from_unflagged_records": {
+              "label": "No classifications from unflagged records"
             }
           }
         },
@@ -765,8 +778,8 @@
     "STR_STATUS": {
       "label": "STR status",
       "description": "Repeat expansion status as decided by Stranger",
-      "numberType": "NUMBER",
-      "numberCount": 1,
+      "numberType": "PER_ALT",
+      "separator": ",",
       "type": "CATEGORICAL",
       "categories": {
         "normal": {