@molgenis/vip-report-template 7.1.2 → 8.0.0

package/src/mocks/config_vcf.json

@@ -465,6 +465,15 @@
           "type": "composed",
           "name": "locus"
         },
+        {
+          "type": "info",
+          "name": "CSQ/PICK",
+          "defaultValue": "true"
+        },
+        {
+          "type": "info",
+          "name": "n_object0/n_string1"
+        },
         {
           "type": "info",
           "name": "CSQ/SYMBOL"
@@ -493,7 +502,8 @@
         },
         {
           "type": "info",
-          "name": "CSQ/VKGL_CL"
+          "name": "CSQ/VKGL_CL",
+          "defaultValue": "LP,VUS"
         },
         {
           "type": "info",
@@ -532,6 +542,10 @@
           "name": "CSQ/HPO",
           "label": "Gene-phenotype association (HPO)"
         },
+        {
+          "type": "info",
+          "name": "CSQ/PICK"
+        },
         {
           "type": "info",
           "name": "CSQ/GADO_PD",

package/src/types/config.d.ts

@@ -73,27 +73,31 @@ export type ConfigJsonFieldItem =
 export type ConfigJsonFieldItemGroup = { type: "group"; fields: ConfigJsonFieldItem[] };
 export type ConfigJsonField = ConfigJsonFieldItem | ConfigJsonFieldItemGroup;
 
-export interface ConfigJsonFilterFixed extends Describable {
+export interface DescribableFilter extends Describable {
+  defaultValue?: string;
+}
+
+export interface ConfigJsonFilterFixed extends DescribableFilter {
   type: "fixed";
   name: "chrom" | "pos" | "id" | "ref" | "alt" | "qual" | "filter";
 }
 
-export interface ConfigJsonFilterInfo extends Describable {
+export interface ConfigJsonFilterInfo extends DescribableFilter {
   type: "info";
   name: string;
 }
 
-export interface ConfigJsonFilterFormat extends Describable {
+export interface ConfigJsonFilterFormat extends DescribableFilter {
   type: "format";
   name: string;
 }
 
-export interface ConfigJsonFilterGenotype extends Describable {
+export interface ConfigJsonFilterGenotype extends DescribableFilter {
   type: "genotype";
   name: string;
 }
 
-export interface ConfigJsonFilterComposed extends Describable {
+export interface ConfigJsonFilterComposed extends DescribableFilter {
   type: "composed";
   name: "allelicImbalance" | "deNovo" | "hpo" | "inheritanceMatch" | "locus" | "vipC" | "vipCS";
 }

package/src/types/configCells.d.ts

@@ -20,6 +20,7 @@ export type CellType =
 interface ConfigCellBase<T extends CellValue> {
   type: CellType;
   label: () => string;
+  parentLabel?: () => string;
   description: () => string | null;
   value: (record: Item<VcfRecord>, valueIndex: number) => T;
   valueCount: (record: Item<VcfRecord>) => number;

package/src/types/configFilter.d.ts

@@ -57,6 +57,7 @@ export type ConfigFilter =
 export interface ConfigFilterBase {
   type: FilterType;
   id: FilterId;
+  defaultValue?: string;
   label: () => string;
   description: () => string | null;
 }

package/src/types/configFilterComposed.d.ts

@@ -10,6 +10,7 @@ import { FieldMetadataWrapper } from "../utils/vcf.ts";
 
 export type ChromosomeId = string;
 export type FilterValueHpo = FilterValueCategorical;
+export type FilterValuePick = FilterValueCategorical;
 export type FilterValueLocus = { chromosome: ChromosomeId; start?: number; end?: number };
 export type FilterValueVipC = FilterValueCategorical;
 export type FilterValueVipCS = FilterValueCategorical;
@@ -23,10 +24,12 @@ export type ConfigFilterComposed =
   | ConfigFilterAllelicImbalance
   | ConfigFilterInheritanceMatch
   | ConfigFilterDeNovo
+  | ConfigFilterPick
   | ConfigFilterVipC
   | ConfigFilterVipCS;
 
 export type ConfigFilterHpo = ConfigFilterField;
+export type ConfigFilterPick = ConfigFilterField;
 
 export interface ConfigFilterAllelicImbalance extends ConfigFilterBase {
   sample: SampleContainer;

package/src/utils/api.ts

@@ -2,26 +2,23 @@ import {
   AppMetadata,
   Cram,
   DecisionTree,
-  HtsFileMetadata,
   Item,
-  Json,
   PagedItems,
   Params,
   PhenotypicFeature,
   Query,
+  RecordParams,
   Sample,
-  WindowApiClient,
 } from "@molgenis/vip-report-api";
 import { isSampleFather, isSampleMother } from "./sample.ts";
-import { NestedFieldMetadata, Value, VcfMetadata, VcfRecord } from "@molgenis/vip-report-vcf";
-import { createRecordSort } from "./query/sort.ts";
-import { createFieldMap, FieldMap, isNumerical } from "./vcf.ts";
-import { compareCsq, compareCsqDefault } from "./csq.ts";
+import { InfoOrder, VcfMetadata, VcfRecord } from "@molgenis/vip-report-vcf";
+import { createFieldMap, FieldMap } from "./vcf.ts";
 import { VariantTypeId } from "./variantType.ts";
 import { MockApiClient } from "../mocks/MockApiClient.ts";
 import { ConfigJson } from "../types/config";
 import { RuntimeError } from "./error.ts";
 import { validateConfig } from "./config/configValidator.ts";
+import { WindowApiClientFactory } from "@molgenis/vip-report-api";
 
 export type VcfMetadataContainer = VcfMetadata & {
   fieldMap: FieldMap;
@@ -31,7 +28,6 @@ export type VcfMetadataContainer = VcfMetadata & {
  */
 export type MetadataContainer = {
   app: AppMetadata;
-  htsFile: HtsFileMetadata;
   records: VcfMetadataContainer;
   variantTypeIds: Set<VariantTypeId>;
 };
@@ -50,7 +46,7 @@ export type SampleContainer = {
 
 // lazy import MockApiClient to ensure that it is excluded from the build artifact
 const api = import.meta.env.PROD
-  ? new WindowApiClient()
+  ? await (async () => await WindowApiClientFactory.create())()
   : await (async () => {
       const module = await import("../mocks/MockApiClient.ts");
       return new module.MockApiClient();
@@ -58,7 +54,7 @@ const api = import.meta.env.PROD
 
 export async function fetchConfig(): Promise<ConfigJson> {
   console.log("Api.fetchConfig");
-  const config: Json = await api.getConfig();
+  const config = await api.getConfig();
   if (config === null) throw new RuntimeError("no config provided");
   return validateConfig(config);
 }
@@ -89,9 +85,8 @@ export async function fetchSamples(params: Params): Promise<PagedItems<SampleCon
  */
 export async function fetchMetadata(): Promise<MetadataContainer> {
   console.log("Api.fetchMetadata");
-  const [appMetadata, htsFileMetadata, recordsMetadata, variantTypeIds] = await Promise.all([
+  const [appMetadata, recordsMetadata, variantTypeIds] = await Promise.all([
     api.getAppMetadata(),
-    api.getHtsFileMetadata(),
     api.getRecordsMeta(),
     fetchVariantTypeIdsQuery(),
   ]);
@@ -99,7 +94,7 @@ export async function fetchMetadata(): Promise<MetadataContainer> {
   // precompute field map
   const fieldMap = createFieldMap(recordsMetadata);
 
-  return { app: appMetadata, htsFile: htsFileMetadata, records: { ...recordsMetadata, fieldMap }, variantTypeIds };
+  return { app: appMetadata, records: { ...recordsMetadata, fieldMap }, variantTypeIds };
 }
 
 /**
@@ -118,48 +113,25 @@ export async function fetchSampleById(sampleId: number): Promise<SampleContainer
   return composeSample(sample, phenotypicFeatures, pedigreeSamples, variantTypeIds);
 }
 
-export async function fetchRecordById(id: number): Promise<Item<VcfRecord>> {
+export async function fetchRecordById(id: number, samples?: Item<Sample>[]): Promise<Item<VcfRecord>> {
   console.log("Api.fetchRecordById", id);
-  return api.getRecordById(id);
+  const sampleIds = samples?.map((sample) => sample.id) ?? [];
+  return api.getRecordById(id, sampleIds);
 }
 
-export async function fetchRecords(params: Params): Promise<PagedItems<VcfRecord>> {
+export async function fetchRecords(params: RecordParams): Promise<PagedItems<VcfRecord>> {
   console.log("Api.fetchRecords", JSON.stringify(params));
-  const [recordsMeta, records] = await Promise.all([api.getRecordsMeta(), api.getRecords(params)]);
-  if (recordsMeta.info.CSQ === undefined) {
-    return records;
-  }
+  return api.getRecords(params);
+}
 
-  const orders = createRecordSort(recordsMeta, params.sort).orders.filter(
-    (order) =>
-      order.field.parent?.id === "CSQ" &&
-      isNumerical(order.field) &&
-      order.field.number.type === "NUMBER" &&
-      order.field.number.count === 1,
-  );
-
-  const fieldMetas = (recordsMeta.info.CSQ.nested as NestedFieldMetadata).items;
-  const consequenceIndex = fieldMetas.findIndex((item) => item.id === "Consequence");
-  const pickIndex = fieldMetas.findIndex((item) => item.id === "PICK");
-
-  for (const record of records.items) {
-    const csqArray = record.data.n.CSQ as Value[][] | undefined;
-    if (csqArray) {
-      csqArray.sort((aValue, bValue) => {
-        for (const order of orders) {
-          const compareValue = compareCsq(aValue, bValue, order.field, order.direction);
-          if (compareValue !== 0) return compareValue;
-        }
-        return compareCsqDefault(aValue, bValue, pickIndex, consequenceIndex);
-      });
-    }
-  }
-  return records;
+export async function fetchInfoOrder(): Promise<InfoOrder> {
+  console.log("Api.fetchInfoOrder");
+  return api.getInfoOrder();
 }
 
 export async function fetchSampleProbandIds(): Promise<number[]> {
   console.log("Api.fetchSampleProbandIds");
-  const query: Query = { selector: ["proband"], operator: "==", args: true };
+  const query: Query = { selector: ["sample", "proband"], operator: "==", args: true };
   const samplePagedItems = await api.getSamples({ query, page: 0, size: Number.MAX_SAFE_INTEGER });
   return samplePagedItems.items.map((sampleItem) => sampleItem.id);
 }
@@ -232,8 +204,8 @@ async function fetchPedigreeSamples(sample: Item<Sample>): Promise<PagedItems<Sa
     query: {
       operator: "and",
       args: [
-        { selector: ["person", "individualId"], operator: "!=", args: sample.data.person.individualId },
-        { selector: ["person", "familyId"], operator: "==", args: sample.data.person.familyId },
+        { selector: ["sample", "individualId"], operator: "!=", args: sample.data.person.individualId },
+        { selector: ["sample", "familyId"], operator: "==", args: sample.data.person.familyId },
       ],
     },
     size: Number.MAX_SAFE_INTEGER,
@@ -242,7 +214,7 @@ async function fetchPedigreeSamples(sample: Item<Sample>): Promise<PagedItems<Sa
 
 async function fetchPhenotypicFeatures(sample: Item<Sample>): Promise<PhenotypicFeature[]> {
   const phenotypes = await api.getPhenotypes({
-    query: { selector: ["subject", "id"], operator: "==", args: sample.data.person.individualId },
+    query: { selector: ["sample", "individualId"], operator: "==", args: sample.data.person.individualId },
     size: Number.MAX_SAFE_INTEGER,
   });
   return phenotypes.items.map((item) => item.data).flatMap((phenotype) => phenotype.phenotypicFeaturesList);

package/src/utils/config/configCellsComposed.ts

@@ -425,7 +425,7 @@ function createConfigFieldCustomVipCS(
       ];
       return {
         vipCS: vipCS[valueIndex]!,
-        vipPS: vipPS && vipPS[valueIndex]!.split("&"),
+        vipPS: vipPS && vipPS.length > 0 && vipPS[valueIndex] !== undefined ? vipPS[valueIndex].split("&") : undefined,
       };
     },
   };

package/src/utils/config/configCellsField.ts

@@ -27,6 +27,8 @@ function createConfigFieldInfo(configStatic: ConfigJsonFieldInfo, field: FieldMe
   return {
     type: "info",
     field,
+    parentLabel: () =>
+      field.parent !== undefined ? getLabel(configStatic, field.parent.label || field.parent.id) : "",
     label: () => getLabel(configStatic, field.label || field.id),
     description: () => getDescription(configStatic, field.description),
     valueCount: (record: Item<VcfRecord>) => getInfoValueCount(record, field),

package/src/utils/config/configFiltersComposed.ts

@@ -78,6 +78,7 @@ function createConfigFilterHpo(
     label: () => getLabel(configStatic, fieldCsqHpo.label || "HPO"),
     description: () => getDescription(configStatic, filterField.description),
     field: filterField,
+    defaultValue: configStatic.defaultValue,
   };
 }
 
@@ -91,6 +92,7 @@ function createConfigFilterLocus(
     label: () => getLabel(configStatic, "Locus"),
     description: () => getDescription(configStatic),
     chromosomes: parseContigIds(metadata.records),
+    defaultValue: configStatic.defaultValue,
   };
 }
 
@@ -110,6 +112,7 @@ function createConfigFilterAllelicImbalance(
     description: () => getDescription(configStatic, fieldViab.description),
     genotypeField: fieldGenotype,
     viabField: fieldViab,
+    defaultValue: configStatic.defaultValue,
     sample: sample,
   };
 }
@@ -129,6 +132,7 @@ function createConfigFilterInheritanceMatch(
     label: () => getLabel(configStatic, vimField.label || "VIM"),
     description: () => getDescription(configStatic, vimField.description),
     vimField: { ...vimField, required: true },
+    defaultValue: configStatic.defaultValue,
     sample: sample,
   };
 }
@@ -148,6 +152,7 @@ function createConfigFilterDeNovo(
     label: () => configStatic.label || vidField.label || "VID",
     description: () => configStatic.description || vidField.description || null,
     vidField: { ...vidField, required: true },
+    defaultValue: configStatic.defaultValue,
     sample: sample,
   };
 }
@@ -176,6 +181,7 @@ function createConfigFilterVipC(
     label: () => getLabel(configStatic, vipCField.label || "VIPC"),
     description: () => getDescription(configStatic, vipCField.description),
     field: { ...vipCField, categories: treeCategories },
+    defaultValue: configStatic.defaultValue,
   };
 }
 
@@ -203,6 +209,7 @@ function createConfigFilterVipCS(
     label: () => getLabel(configStatic, vipCSField.label || "VIPC_S"),
     description: () => getDescription(configStatic, vipCSField.description),
     field: { ...vipCSField, categories: treeCategories, required: true },
+    defaultValue: configStatic.defaultValue,
     sample,
   };
 }

package/src/utils/config/configFiltersField.ts

@@ -1,4 +1,4 @@
-import { ConfigJsonFieldGenotype, ConfigJsonFieldInfo } from "../../types/config";
+import { ConfigJsonFieldGenotype, ConfigJsonFieldInfo, ConfigJsonFilterInfo } from "../../types/config";
 import { ConfigFilterField, ConfigFilterFormat } from "../../types/configFilter";
 import { SampleContainer, VcfMetadataContainer } from "../api.ts";
 import { FieldMetadataWrapper, getInfoFieldsRegex, getSampleFieldsRegex } from "../vcf.ts";
@@ -29,8 +29,9 @@ export function initConfigFiltersGenotype(
     .map((field) => createConfigFilterGenotype(config, field, sample));
 }
 
-function createConfigFilterInfo(config: ConfigJsonFieldInfo, field: FieldMetadataWrapper): ConfigFilterField {
+function createConfigFilterInfo(config: ConfigJsonFilterInfo, field: FieldMetadataWrapper): ConfigFilterField {
   return {
+    defaultValue: config.defaultValue,
     type: "info",
     id: field.id,
     label: () => getLabel(config, field.label || field.id),

package/src/utils/config/configFiltersFixed.ts

@@ -48,6 +48,7 @@ function createConfigFilterChrom(config: ConfigJsonFilterFixed): ConfigFilterChr
     id: "chrom",
     label: () => getLabel(config, "Chromosome"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -57,6 +58,7 @@ function createConfigFilterPos(config: ConfigJsonFilterFixed): ConfigFilterPos {
     id: "pos",
     label: () => getLabel(config, "Position"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -66,6 +68,7 @@ function createConfigFilterId(config: ConfigJsonFilterFixed): ConfigFilterId {
     id: "id",
     label: () => getLabel(config, "Identifiers"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -75,6 +78,7 @@ function createConfigFilterRef(config: ConfigJsonFilterFixed): ConfigFilterRef {
     id: "ref",
     label: () => getLabel(config, "Reference"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -84,6 +88,7 @@ function createConfigFilterAlt(config: ConfigJsonFilterFixed): ConfigFilterAlt {
     id: "alt",
     label: () => getLabel(config, "Alt"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -93,6 +98,7 @@ function createConfigFilterQual(config: ConfigJsonFilterFixed): ConfigFilterQual
     id: "qual",
     label: () => getLabel(config, "Quality"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }
 
@@ -102,5 +108,6 @@ function createConfigFilterFilter(config: ConfigJsonFilterFixed): ConfigFilterFi
     id: "filter",
     label: () => getLabel(config, "Filter"),
     description: () => getDescription(config),
+    defaultValue: config.defaultValue,
   };
 }