@molgenis/vip-report-template 6.2.0 → 7.0.0

package/src/utils/config/config.ts

@@ -0,0 +1,182 @@
+import { VariantType } from "../variantType.ts";
+import {
+  Config,
+  ConfigJson,
+  ConfigJsonRecordsPerPage,
+  ConfigJsonSorts,
+  ConfigJsonVariant,
+  ConfigJsonVariantConsequence,
+  ConfigJsonVariants,
+  ConfigJsonVariantTypeFields,
+  ConfigJsonVariantTypeFilters,
+  ConfigRecordsPerPage,
+  ConfigSamplesCells,
+  ConfigVariant,
+  ConfigVariantConsequence,
+  ConfigVariants,
+  ConfigVip,
+  Describable,
+} from "../../types/config";
+import { initConfigFilters } from "./configFilters.ts";
+import { composeSample, MetadataContainer, SampleContainer } from "../api.ts";
+import { initConfigSorts } from "./configSorts.ts";
+import { initConfigCells } from "./configCells.ts";
+import { ConfigInvalidError } from "../error.ts";
+import { initConfigVip } from "./configVip.ts";
+
+export function initConfig(
+  config: ConfigJson,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): Config {
+  const configVip = initConfigVip(config.vip, metadata);
+
+  const configStaticVariants: ConfigJsonVariants = sample !== null ? config.sample_variants : config.variants;
+  const configVariants = initConfigVariants(configStaticVariants, configVip, variantType, metadata, sample);
+
+  const configStaticVariant: ConfigJsonVariant = sample !== null ? config.sample_variant : config.variant;
+  const configVariant = initConfigVariant(configStaticVariant, variantType, metadata, sample);
+
+  const configStaticVariantConsequence: ConfigJsonVariantConsequence =
+    sample !== null ? config.sample_variant_consequence : config.variant_consequence;
+  const configVariantConsequence = initConfigVariantConsequence(
+    configStaticVariantConsequence,
+    variantType,
+    metadata,
+    sample,
+  );
+
+  return {
+    vip: configVip,
+    variants: configVariants,
+    variant: configVariant,
+    variantConsequence: configVariantConsequence,
+  };
+}
+
+function initConfigVariants(
+  config: ConfigJsonVariants,
+  configVip: ConfigVip,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): ConfigVariants {
+  const cells = initConfigVariantsCells(config.cells, variantType, metadata, sample);
+  const filters = initConfigVariantsFilters(config.filters, configVip, variantType, metadata, sample);
+  const sorts = initConfigVariantsSorts(config.sorts, variantType, metadata);
+  const recordsPerPage = initConfigVariantsRecordsPerPage(config.recordsPerPage, variantType);
+  return {
+    cells,
+    filters,
+    sorts,
+    recordsPerPage,
+  };
+}
+
+function initConfigVariantsCellsSamples(
+  config: ConfigJsonVariantTypeFields,
+  sample: SampleContainer,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+): ConfigSamplesCells | undefined {
+  const samples: SampleContainer[] = [
+    sample,
+    ...[sample.paternalSample, sample.maternalSample, ...sample.otherPedigreeSamples]
+      .filter((sample) => sample !== null)
+      .map((sample) => composeSample(sample)),
+  ];
+
+  const cellsSamples: ConfigSamplesCells = {};
+  samples.forEach(
+    (sample) => (cellsSamples[sample.item.id] = initConfigVariantsCells(config, variantType, metadata, sample)),
+  );
+  return cellsSamples;
+}
+
+function initConfigVariant(
+  config: ConfigJsonVariant,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): ConfigVariant {
+  const cells = initConfigVariantsCells(config.cells, variantType, metadata, sample);
+  const cellsSamples =
+    sample && config.sample_cells
+      ? initConfigVariantsCellsSamples(config.sample_cells, sample, variantType, metadata)
+      : undefined;
+
+  return {
+    cells,
+    samplesCells: cellsSamples,
+  };
+}
+
+function initConfigVariantConsequence(
+  config: ConfigJsonVariantConsequence,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): ConfigVariantConsequence {
+  const cellsSamples =
+    sample && config.sample_cells
+      ? initConfigVariantsCellsSamples(config.sample_cells, sample, variantType, metadata)
+      : undefined;
+
+  return {
+    samplesCells: cellsSamples,
+  };
+}
+
+function initConfigVariantsCells(
+  config: ConfigJsonVariantTypeFields,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+) {
+  const configValue = config[variantType.id] || config["all"];
+  if (configValue === undefined) throw new ConfigInvalidError(`missing required property 'cells.${variantType.id}'`);
+  if (configValue.length === 0)
+    throw new ConfigInvalidError(`property 'cells.${variantType.id}' requires at least one value`);
+  return initConfigCells(configValue, variantType, metadata, sample);
+}
+
+function initConfigVariantsFilters(
+  config: ConfigJsonVariantTypeFilters | undefined,
+  configVip: ConfigVip,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+) {
+  const configValue = config && (config[variantType.id] || config["all"]);
+  return configValue ? initConfigFilters(configValue, configVip, metadata, sample) : [];
+}
+
+function initConfigVariantsSorts(
+  config: ConfigJsonSorts | undefined,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+) {
+  const configValue = config && (config[variantType.id] || config["all"]);
+  return configValue ? initConfigSorts(configValue, metadata) : [];
+}
+
+function initConfigVariantsRecordsPerPage(
+  config: ConfigJsonRecordsPerPage | undefined,
+  variantType: VariantType,
+): ConfigRecordsPerPage {
+  const configValue = config && (config[variantType.id] || config["all"]);
+  return configValue || [{ number: 10, selected: true }, { number: 20 }, { number: 50 }, { number: 100 }];
+}
+
+export function getLabel(config: Describable, defaultLabel: string): string {
+  return config.label !== undefined ? config.label : defaultLabel;
+}
+
+export function getDescription(config: Describable, defaultDescription?: string): string | null {
+  return config.description !== undefined
+    ? config.description
+    : defaultDescription !== undefined
+      ? defaultDescription
+      : null;
+}

package/src/utils/config/configCells.ts

@@ -0,0 +1,74 @@
+import { ConfigCell, ConfigCellGroup, ConfigCellItem } from "../../types/configCells";
+import { initConfigCellComposed } from "./configCellsComposed.ts";
+import { ConfigCells, ConfigJsonField, ConfigJsonFieldItem, ConfigJsonFieldItemGroup } from "../../types/config";
+import { VariantType } from "../variantType.ts";
+import { MetadataContainer, SampleContainer } from "../api.ts";
+import { initConfigCellFixed } from "./configCellsFixed.ts";
+import { initConfigCellGenotype, initConfigCellInfo } from "./configCellsField.ts";
+
+import { ConfigInvalidError } from "../error.ts";
+
+export function initConfigCells(
+  configs: ConfigJsonField[],
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): ConfigCells {
+  const configCells: (ConfigCell | null)[] = configs.flatMap((configStaticField) => {
+    let configCells: (ConfigCell | null)[];
+    if (configStaticField.type === "group") {
+      configCells = [
+        initConfigCellItemGroup(configStaticField as ConfigJsonFieldItemGroup, variantType, metadata, sample),
+      ];
+    } else {
+      configCells = initConfigCellItem(configStaticField as ConfigJsonFieldItem, variantType, metadata, sample);
+    }
+    return configCells;
+  });
+  return configCells.filter((configCell) => configCell !== null);
+}
+
+function initConfigCellItemGroup(
+  config: ConfigJsonFieldItemGroup,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+) {
+  const configFields = initConfigCells(config.fields, variantType, metadata, sample) as ConfigCellItem[];
+
+  let fieldConfig: ConfigCellGroup | null;
+  if (configFields.length === 0) {
+    fieldConfig = null;
+  } else {
+    fieldConfig = { type: "group", fieldConfigs: configFields };
+  }
+  return fieldConfig;
+}
+
+function initConfigCellItem(
+  config: ConfigJsonFieldItem,
+  variantType: VariantType,
+  metadata: MetadataContainer,
+  sample: SampleContainer | null,
+): ConfigCell[] {
+  const type = config.type;
+
+  let configFields: (ConfigCell | null)[];
+  switch (type) {
+    case "fixed":
+      configFields = [initConfigCellFixed(config)];
+      break;
+    case "info":
+      configFields = initConfigCellInfo(config, metadata.records);
+      break;
+    case "format":
+      throw new ConfigInvalidError(`unsupported field type '${type}', did you mean to use 'genotype'?`);
+    case "genotype":
+      configFields = sample ? initConfigCellGenotype(config, metadata.records, sample) : [];
+      break;
+    case "composed":
+      configFields = [initConfigCellComposed(config, variantType, metadata, sample)];
+      break;
+  }
+  return configFields.filter((configField) => configField !== null);
+}