@molgenis/vip-report-template 6.1.1 → 7.0.0

package/src/utils/query.ts

@@ -1,154 +0,0 @@
-import {
-  Item,
-  Query,
-  QueryClause,
-  QueryOperator,
-  Sample,
-  Selector,
-  SelectorPart,
-  SortPath,
-} from "@molgenis/vip-report-api/src/Api";
-import { Metadata } from "@molgenis/vip-report-vcf/src/Vcf";
-import { FieldMetadata, InfoMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { FilterQueries } from "../store";
-
-export function createSampleQuery(
-  sample: Item<Sample>,
-  search: string | undefined,
-  filters: FilterQueries | undefined,
-  metadata: Metadata,
-): Query | null {
-  const genotypeSelector: Selector = ["s", sample.data.index, "GT", "t"];
-  const sampleQuery: Query = {
-    operator: "and",
-    args: [
-      { selector: genotypeSelector, operator: "!=", args: "hom_r" },
-      { selector: genotypeSelector, operator: "!=", args: "miss" },
-    ],
-  };
-  const searchFilterQuery = createQuery(search, filters, metadata);
-  const query: Query =
-    searchFilterQuery !== null ? { operator: "and", args: [sampleQuery, searchFilterQuery] } : sampleQuery;
-  return query;
-}
-
-export function createQuery(
-  search: string | undefined,
-  filters: FilterQueries | undefined,
-  metadata: Metadata,
-): Query | null {
-  let query: Query | null;
-
-  const searchQuery = search !== undefined ? createSearchQuery(search, metadata) : null;
-  const filterQuery = filters !== undefined ? createFilterQuery(filters) : null;
-  if (searchQuery !== null) {
-    query = filterQuery !== null ? { operator: "and", args: [searchQuery, filterQuery] } : searchQuery;
-  } else {
-    query = filterQuery !== null ? filterQuery : null;
-  }
-  return query;
-}
-
-export function createSearchQuery(search: string, metadata: Metadata): Query | null {
-  const parts: Query[] = [];
-  for (const infoKey in metadata.info) {
-    const infoMeta = metadata.info[infoKey];
-    parts.push(...createSearchQueryClausesInfo(search, infoMeta, ["n", infoMeta.id]));
-  }
-  return parts.length == 0 ? null : parts.length === 1 ? parts[0] : { operator: "or", args: parts };
-}
-
-function createSearchQueryClausesInfo(search: string, infoMetadata: InfoMetadata, selector: string[]): Query[] {
-  const clauses: Query[] = [];
-  if (infoMetadata.nested) {
-    for (let i = 0; i < infoMetadata.nested.items.length; ++i) {
-      clauses.push(
-        ...createSearchQueryClausesInfo(search, infoMetadata.nested.items[i], [...selector, "*", i.toString()]),
-      );
-    }
-  } else {
-    switch (infoMetadata.type) {
-      case "CATEGORICAL":
-      case "CHARACTER":
-      case "STRING": {
-        const nested = selector.find((item) => item === "*") !== undefined;
-        let operator: QueryOperator, args;
-        if (infoMetadata.number.count && infoMetadata.number.count === 1) {
-          operator = nested ? "~=_any" : "~=";
-          args = nested ? [search] : search;
-        } else {
-          operator = nested ? "any_~=_any" : "~=_any";
-          args = [search];
-        }
-        clauses.push({ selector, operator, args });
-        break;
-      }
-      default:
-        break;
-    }
-  }
-  return clauses;
-}
-
-function createFilterQuery(queries: FilterQueries): Query | null {
-  const queryClauses = Object.values(queries).filter((query) => query !== undefined) as QueryClause[];
-  if (queryClauses.length === 0) return null;
-  return queryClauses.length === 1 ? queryClauses[0] : { operator: "and", args: queryClauses };
-}
-
-export function selector(field: FieldMetadata): SelectorPart[] {
-  const selector: Selector = [];
-  let currentField: FieldMetadata | undefined = field;
-  do {
-    if (currentField.parent && currentField.parent.nested) {
-      const items = currentField.parent.nested.items;
-      let i;
-      for (i = 0; i < items.length; ++i) {
-        if (items[i].id === currentField.id) {
-          break;
-        }
-      }
-      selector.push(i);
-      if (currentField.parent.number.count !== 1) {
-        selector.push("*");
-      }
-    } else {
-      selector.push(currentField.id);
-    }
-    currentField = currentField.parent;
-  } while (currentField);
-  selector.reverse();
-  return selector;
-}
-
-export function infoSelector(field: FieldMetadata) {
-  return ["n", ...selector(field)];
-}
-
-export function sampleSelector(sample: Item<Sample>, field: FieldMetadata) {
-  return ["s", sample.data.index, ...selector(field)];
-}
-
-export function selectorKey(selector: Selector): string {
-  return Array.isArray(selector) ? selector.join("/") : selector.toString();
-}
-
-export function infoFieldKey(field: FieldMetadata): string {
-  return selectorKey(infoSelector(field));
-}
-
-export function sampleFieldKey(sample: Item<Sample>, field: FieldMetadata): string {
-  return selectorKey(sampleSelector(sample, field));
-}
-
-export function sampleCustomKey(sample: Item<Sample>, key: string): string {
-  return selectorKey(["s", sample.data.index, key]);
-}
-
-function sortPath(field: FieldMetadata): SortPath {
-  return selector(field).filter((part) => part !== "*");
-}
-
-export function infoSortPath(field: FieldMetadata): SortPath {
-  return ["n", ...sortPath(field)];
-}

package/src/utils/viewUtils.ts

@@ -1,32 +0,0 @@
-import { Value, ValueArray } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
-import { Sample } from "@molgenis/vip-report-api/src/Api";
-import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-
-export function getSpecificConsequence(csqs: ValueArray, rowIndex: number): ValueArray {
-  if (rowIndex < 0) {
-    throw new Error("Consequences index must be 0 or higher.");
-  }
-  return csqs.length >= rowIndex ? (csqs[rowIndex] as ValueArray) : [];
-}
-
-export function getConsequenceLabel(csq: ValueArray, rowIndex: number, csqMetadataArray: FieldMetadata[]) {
-  const csqIndex = csqMetadataArray.findIndex((csqMetadata) => csqMetadata.id === "Consequence");
-  const csqValues: ValueArray = getSpecificConsequence(csq, rowIndex);
-  const csqValue: Value = csqValues[csqIndex];
-  return csqValue;
-}
-
-export function getRecordSamples(record: Record, sample: Sample, pedigreeSamples: Sample[]) {
-  return [record.s[sample.index], ...pedigreeSamples.map((pedigreeSample) => record.s[pedigreeSample.index])];
-}
-
-export function getHeaderValue(key: string, lines: string[]): string | null {
-  const token = `##${key}=`;
-  for (const line of lines) {
-    if (line.startsWith(token)) {
-      return line.substring(token.length);
-    }
-  }
-  return null;
-}