From 58bac2c43ae6e29b06e7d103fd5ce89a6a48fe9c Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Wed, 24 Jan 2024 09:45:30 +0100 Subject: [PATCH 1/2] remove field_metadata.json dependency, pass as parser argument --- .gitignore | 3 +- package.json | 3 +- src/MetadataParser.ts | 26 +- src/Vcf.ts | 2 + src/VcfParser.ts | 14 +- src/VepMetadataParser.ts | 19 +- src/__tests__/MetadataParser.test.ts | 5 +- src/__tests__/VepMetadataParser.test.ts | 5 +- src/__tests__/field_metadata.json | 454 ++++++++++++++++++++++++ 9 files changed, 500 insertions(+), 31 deletions(-) create mode 100644 src/__tests__/field_metadata.json diff --git a/.gitignore b/.gitignore index 969bb5a..674056b 100644 --- a/.gitignore +++ b/.gitignore @@ -2,5 +2,4 @@ node_modules dist /.idea/ coverage -/.vscode/ -src/metadata/field_metadata.json \ No newline at end of file +/.vscode/ \ No newline at end of file diff --git a/package.json b/package.json index d6b7f80..0a543b6 100644 --- a/package.json +++ b/package.json @@ -1,9 +1,8 @@ { "name": "@molgenis/vip-report-vcf", - "version": "1.8.0", + "version": "2.0.0", "description": "TypeScript VCF library with support for both reading and writing", "scripts": { - "preinstall": "curl --no-progress-meter --location https://github.com/molgenis/vip-utils/releases/download/v1.4.6/field_metadata.json --create-dirs --output src/metadata/field_metadata.json", "build": "tsc --build", "format": "prettier --write src/**/*.ts", "lint": "eslint src/**/*.ts", diff --git a/src/MetadataParser.ts b/src/MetadataParser.ts index 9087ed3..1a85651 100644 --- a/src/MetadataParser.ts +++ b/src/MetadataParser.ts @@ -1,7 +1,6 @@ import { parseIntegerValueNonNull, parseStringValueNonNull } from "./ValueParser"; import { createVepInfoMetadata, isVepInfoMetadata } from "./VepMetadataParser"; -import metadataJson from "./metadata/field_metadata.json"; -import { Metadata, Field } from "./FieldMetadata"; +import { Field, NestedFields, NestedMetadatas } from "./FieldMetadata"; export type NumberType = "NUMBER" | "PER_ALT" | "PER_ALT_AND_REF" | "PER_GENOTYPE" | "OTHER"; @@ -103,13 +102,16 @@ export interface InfoMetadata extends FieldMetadata { } const REG_EXP_FORMAT = /##FORMAT=/; -export function parseFormatMetadata(token: string): FieldMetadata { +/** + * @param token VCF format header line + * @param meta VCF format metadata not stored in the VCF e.g. to describe categorical data + */ +export function parseFormatMetadata(token: string, meta?: NestedFields): FieldMetadata { const result = token.match(REG_EXP_FORMAT); if (result === null) { throw new Error(`invalid format metadata '${token}'`); } const identifier = parseStringValueNonNull(result[1]); - const meta = metadataJson as Metadata; let number: NumberMetadata; let type: ValueType; @@ -117,8 +119,8 @@ export function parseFormatMetadata(token: string): FieldMetadata { let required; let label, description: string | undefined; - if (meta.format !== undefined && meta.format[identifier] !== undefined) { - const fieldMetadata: Field = meta.format[identifier]; + if (meta !== undefined && meta[identifier] !== undefined) { + const fieldMetadata: Field = meta[identifier]; number = { type: fieldMetadata.numberType, count: fieldMetadata.numberCount, separator: fieldMetadata.separator }; type = fieldMetadata.type; required = fieldMetadata.required !== undefined ? fieldMetadata.required : false; @@ -146,7 +148,11 @@ export function parseFormatMetadata(token: string): FieldMetadata { const REG_EXP_INFO = /##INFO=/; -export function parseInfoMetadata(token: string): InfoMetadata { +/** + * @param token VCF info header line + * @param meta VCF info metadata not stored in the VCF e.g. to describe nested data from VEP + */ +export function parseInfoMetadata(token: string, meta?: NestedMetadatas): InfoMetadata { const result = token.match(REG_EXP_INFO); if (result === null) { throw new Error(`invalid info metadata '${token}'`); @@ -168,17 +174,17 @@ export function parseInfoMetadata(token: string): InfoMetadata { infoMetadata.version = version; } - const nested = createNestedInfoMetadata(infoMetadata); + const nested = createNestedInfoMetadata(infoMetadata, meta); if (nested != null) { infoMetadata.nested = nested; } return infoMetadata; } -function createNestedInfoMetadata(infoMetadata: InfoMetadata): NestedFieldMetadata | null { +function createNestedInfoMetadata(infoMetadata: InfoMetadata, meta?: NestedMetadatas): NestedFieldMetadata | null { let nestedInfoMetadata: NestedFieldMetadata | null; if (isVepInfoMetadata(infoMetadata)) { - nestedInfoMetadata = createVepInfoMetadata(infoMetadata); + nestedInfoMetadata = createVepInfoMetadata(infoMetadata, meta); } else { nestedInfoMetadata = null; } diff --git a/src/Vcf.ts b/src/Vcf.ts index 8c2a43b..5ce66cd 100644 --- a/src/Vcf.ts +++ b/src/Vcf.ts @@ -1,6 +1,7 @@ // this is .ts instead of .d.ts file to work around https://github.com/TypeStrong/ts-loader/issues/1036 import { FormatMetadataContainer, Genotype, RecordSample } from "./SampleDataParser"; import { FieldMetadataContainer, InfoContainer } from "./VcfParser"; +import { Metadata as ExternalMetadata } from "./FieldMetadata"; export type { FormatMetadataContainer, Genotype, RecordSample }; @@ -9,6 +10,7 @@ export interface Metadata { info: FieldMetadataContainer; format: FormatMetadataContainer; samples: string[]; + external?: ExternalMetadata; } export interface Container { diff --git a/src/VcfParser.ts b/src/VcfParser.ts index 719eb2b..d9ce8a5 100644 --- a/src/VcfParser.ts +++ b/src/VcfParser.ts @@ -12,6 +12,7 @@ import { FieldMetadata, parseFormatMetadata, parseInfoMetadata } from "./Metadat import { parseValue } from "./DataParser"; import { FormatMetadataContainer, parseRecordSample, RecordSample } from "./SampleDataParser"; import { Metadata, Record } from "./Vcf"; +import { Metadata as ExternalMetadata } from "./FieldMetadata"; const viabFormatMeta: FieldMetadata = { id: "VIAB", @@ -33,8 +34,12 @@ export interface InfoContainer { [index: string]: Value | ValueArray; } -export function parseVcf(vcf: string): Container { - const container = { +/** + * @param vcf VCF file contents + * @param meta additional VCF metadata e.g. to describe categorical or nested data + */ +export function parseVcf(vcf: string, meta?: ExternalMetadata): Container { + const container: Container = { metadata: { lines: [], info: {}, @@ -43,6 +48,7 @@ export function parseVcf(vcf: string): Container { }, data: [], }; + if (meta) container.metadata.external = meta; for (const line of vcf.split(/\r?\n/)) { if (line.length !== 0) { @@ -69,10 +75,10 @@ function parseLine(line: string, vcf: Container) { function parseMetadataLine(line: string, metadata: Metadata) { if (line.startsWith("##INFO")) { - const infoMetadata = parseInfoMetadata(line); + const infoMetadata = parseInfoMetadata(line, metadata.external?.info); metadata.info[infoMetadata.id] = infoMetadata; } else if (line.startsWith("##FORMAT")) { - const formatMetadata = parseFormatMetadata(line); + const formatMetadata = parseFormatMetadata(line, metadata.external?.format); metadata.format[formatMetadata.id] = formatMetadata; if (formatMetadata.id === "AD") { metadata.format["VIAB"] = viabFormatMeta; diff --git a/src/VepMetadataParser.ts b/src/VepMetadataParser.ts index e11be5d..2cb6b2a 100644 --- a/src/VepMetadataParser.ts +++ b/src/VepMetadataParser.ts @@ -1,6 +1,5 @@ import { InfoMetadata, NestedFieldMetadata, NumberMetadata, NumberType, ValueType } from "./MetadataParser"; -import metadataJson from "./metadata/field_metadata.json"; -import { Metadata, Field, NestedMetadata } from "./FieldMetadata"; +import { Field, NestedMetadata, NestedMetadatas } from "./FieldMetadata"; const REG_EXP_VEP = /Consequence annotations from Ensembl VEP. Format: (.+)/; @@ -8,14 +7,14 @@ export function isVepInfoMetadata(infoMetadata: InfoMetadata): boolean { return infoMetadata.description !== undefined && REG_EXP_VEP.test(infoMetadata.description); } -export function createVepInfoMetadata(infoMetadata: InfoMetadata): NestedFieldMetadata { +export function createVepInfoMetadata(infoMetadata: InfoMetadata, meta?: NestedMetadatas): NestedFieldMetadata { return { separator: "|", - items: parseVepInfoMetadataArray(infoMetadata), + items: parseVepInfoMetadataArray(infoMetadata, meta), }; } -function parseVepInfoMetadataArray(infoMetadata: InfoMetadata): InfoMetadata[] { +function parseVepInfoMetadataArray(infoMetadata: InfoMetadata, meta?: NestedMetadatas): InfoMetadata[] { const token = infoMetadata.description; const result = token ? token.match(REG_EXP_VEP) : null; if (result === null) { @@ -23,10 +22,10 @@ function parseVepInfoMetadataArray(infoMetadata: InfoMetadata): InfoMetadata[] { } const tokens = result[1].split("|"); - return tokens.map((part) => parseVepInfoMetadata(infoMetadata, part)); + return tokens.map((part) => parseVepInfoMetadata(infoMetadata, part, meta)); } -function parseVepInfoMetadata(infoMetadata: InfoMetadata, token: string): InfoMetadata { +function parseVepInfoMetadata(infoMetadata: InfoMetadata, token: string, meta?: NestedMetadatas): InfoMetadata { let numberType: NumberType; let numberCount; let separator: string | undefined; @@ -35,10 +34,8 @@ function parseVepInfoMetadata(infoMetadata: InfoMetadata, token: string): InfoMe let required; let label, description: string | undefined; - const meta = metadataJson as Metadata; - const nestedMetadata: NestedMetadata = meta.info["CSQ"]; - const nestedFields = nestedMetadata.nestedFields; - const fieldMetadata: Field = nestedFields[token]; + const nestedMetadata: NestedMetadata | undefined = meta ? meta["CSQ"] : undefined; + const fieldMetadata: Field | undefined = nestedMetadata?.nestedFields[token]; if (fieldMetadata !== undefined) { numberType = fieldMetadata.numberType; diff --git a/src/__tests__/MetadataParser.test.ts b/src/__tests__/MetadataParser.test.ts index 6a02fdf..1e6d583 100644 --- a/src/__tests__/MetadataParser.test.ts +++ b/src/__tests__/MetadataParser.test.ts @@ -6,6 +6,8 @@ import { parseValueType, } from "../MetadataParser"; import { expect, test } from "vitest"; +import metadataJson from "./field_metadata.json"; +import { Metadata } from "../FieldMetadata"; test("parse number metadata - A", () => { expect(parseNumberMetadata("A")).toStrictEqual({ type: "PER_ALT", separator: "," }); @@ -66,9 +68,10 @@ test("parse format metadata", () => { }); test("parse format metadata from json", () => { + const meta = metadataJson as Metadata; const token = '##FORMAT='; - expect(parseFormatMetadata(token)).toStrictEqual({ + expect(parseFormatMetadata(token, meta.format)).toStrictEqual({ id: "VI", number: { type: "OTHER", count: undefined, separator: "," }, type: "CATEGORICAL", diff --git a/src/__tests__/VepMetadataParser.test.ts b/src/__tests__/VepMetadataParser.test.ts index 10c04c3..14ba163 100644 --- a/src/__tests__/VepMetadataParser.test.ts +++ b/src/__tests__/VepMetadataParser.test.ts @@ -1,6 +1,8 @@ import { createVepInfoMetadata, isVepInfoMetadata } from "../VepMetadataParser"; import { InfoMetadata } from "../MetadataParser"; import { expect, test } from "vitest"; +import metadataJson from "./field_metadata.json"; +import { Metadata } from "../FieldMetadata"; const vepInfoMetadata: InfoMetadata = { id: "CSQ", @@ -40,7 +42,8 @@ test("is vep info metadata - false", () => { }); test("create vep metadata", () => { - expect(createVepInfoMetadata(vepInfoMetadata)).toStrictEqual({ + const meta = metadataJson as Metadata; + expect(createVepInfoMetadata(vepInfoMetadata, meta.info)).toStrictEqual({ separator: "|", items: [ { diff --git a/src/__tests__/field_metadata.json b/src/__tests__/field_metadata.json new file mode 100644 index 0000000..316f0a5 --- /dev/null +++ b/src/__tests__/field_metadata.json @@ -0,0 +1,454 @@ +{ + "format": { + "VI": { + "label": "Inheritance", + "description": "An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD, YL, MT", + "numberType": "OTHER", + "separator": ",", + "type": "CATEGORICAL", + "categories": [ + "AD", + "AD_IP", + "AR", + "AR_C", + "XLD", + "XLR", + "YL", + "MT" + ] + } + }, + "info": { + "CSQ": { + "nestedFields": { + "ALLELE_NUM": { + "label": "Allele Nr.", + "description": "Allele nr within the VCF file.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "INTEGER" + }, + "ALPHSCORE": { + "label": "AlphScore", + "description": "AlphScore pathogenicity score for missense variants", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "CAPICE_CL": { + "label": "CAPICE", + "description": "CAPICE classification", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "B", + "LB", + "VUS", + "LP", + "P" + ] + }, + "CAPICE_SC": { + "label": "CAPICE", + "description": "CAPICE pathogenicity score", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "cDNA_position": { + "label": "cDNA pos", + "description": "Position within the cDNA.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "CDS_position": { + "label": "CDS pos", + "description": "Position within the coding sequence.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "CLIN_SIG": { + "label": "ClinVar", + "description": "ClinVar classification(s)", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "clinVar": { + "label": "ClinVar ID", + "description": "ClinVar Variation ID", + "numberType": "OTHER", + "type": "INTEGER" + }, + "clinVar_CLNID": { + "label": "ClinVar ID", + "description": "ClinVar Variation ID", + "numberType": "OTHER", + "type": "INTEGER" + }, + "clinVar_CLNSIG": { + "label": "ClinVar variant", + "description": "Clinical significance for this single variant", + "numberType": "OTHER", + "separator": "/", + "type": "CATEGORICAL", + "categories": [ + "Benign", + "Likely_benign", + "Uncertain_significance", + "Likely_pathogenic", + "Pathogenic", + "Conflicting_interpretations_of_pathogenicity" + ] + }, + "clinVar_CLNSIGINCL": { + "label": "ClinVar variant combination", + "description": "Clinical significance for a haplotype or genotype that includes this variant", + "numberType": "OTHER", + "separator": "&", + "type": "CATEGORICAL", + "categories": [ + "Benign", + "Likely_benign", + "Uncertain_significance", + "Likely_pathogenic", + "Pathogenic", + "Conflicting_interpretations_of_pathogenicity" + ] + }, + "clinVar_CLNREVSTAT": { + "label": "ClinVar status", + "description": "ClinVar review status", + "numberType": "OTHER", + "separator": "&", + "type": "CATEGORICAL", + "categories": [ + "practice_guideline", + "reviewed_by_expert_panel", + "criteria_provided", + "_multiple_submitters", + "_no_conflicts", + "_single_submitter", + "_conflicting_interpretations", + "no_assertion_criteria_provided", + "no_assertion_provided" + ] + }, + "Consequence": { + "label": "Effect", + "description": "Effect(s) described as Sequence Ontology term(s)", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "Existing_variation": { + "label": "Ex. var.", + "description": "Existing variation.", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "Feature_type": { + "label": "Feature Type.", + "description": "The VEP feature type", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "Transcript", + "RegulatoryFeature", + "MotifFeature" + ], + "required": true + }, + "FLAGS": { + "label": "Flags", + "description": "Flags", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "GADO_PD": { + "label": "GADO_PD", + "description": "The GADO prediction for the relation between the HPO terms of the proband(s) and the gene, HC: high confidence, LC: low confidence.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "LC", + "HC" + ] + }, + "GADO_SC": { + "label": "GADO_SC", + "description": "The combined prioritization GADO Z-score over the HPO of the proband(s) terms for this case.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "gnomAD_AF": { + "label": "gnomAD AF", + "description": "gnomAD allele frequency", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "gnomAD_COV": { + "label": "gnomAD COV", + "description": "gnomAD coverage (percent of individuals in gnomAD source)", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "gnomAD_FAF95": { + "label": "gnomAD FAF95", + "description": "gnomAD filter allele frequency (95% confidence)", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "gnomAD_FAF99": { + "label": "gnomAD FAF99", + "description": "gnomAD filter allele frequency (99% confidence)", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "gnomAD_HN": { + "label": "gnomAD HN", + "description": "gnomAD number of homozygotes", + "numberType": "NUMBER", + "numberCount": 1, + "type": "INTEGER" + }, + "gnomAD_SRC": { + "label": "gnomAD SRC", + "description": "gnomAD source (E=exomes, G=genomes, T=total)", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "E", + "G", + "T" + ] + }, + "gnomAD_QC": { + "label": "gnomAD QC", + "description": "gnomAD quality control filters that failed", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "HGNC_ID": { + "label": "HGNC ID", + "description": "The HGNC gene ID", + "numberType": "NUMBER", + "numberCount": 1, + "type": "INTEGER" + }, + "HGVSc": { + "label": "HGVS C", + "description": "HGVS nomenclature: coding DNA reference sequence", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "HGVSp": { + "label": "HGVS P", + "description": "HGVS nomenclature: protein reference sequence", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "HPO": { + "label": "HPO", + "description": "Human phenotype ontology matches.", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "IMPACT": { + "label": "Impact", + "description": "The Impact as predicted by VEP", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "LOW", + "MODERATE", + "HIGH", + "MODIFIER" + ], + "required": true + }, + "IncompletePenetrance": { + "label": "Gene: Inc.Pen.", + "description": "The gene is associated with Incomplete Penetrance (1:true)", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "InheritanceModesGene": { + "label": "Inh.Pat.", + "description": "Inheritance pattern", + "numberType": "OTHER", + "separator": "&", + "type": "STRING" + }, + "ncER": { + "label": "ncER", + "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "PHENO": { + "label": "Pheno", + "description": "Phenotype match.", + "numberType": "OTHER", + "separator": "&", + "type": "INTEGER" + }, + "PICK": { + "label": "PICK", + "description": "Boolean indicating if this is the VEP picked transcript.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "INTEGER" + }, + "PolyPhen": { + "label": "PolyPhen", + "description": "PolyPhen score.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "Protein_position": { + "label": "Protein pos", + "description": "Position within the protein.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "PUBMED": { + "label": "PubMed", + "description": "PubMed citations", + "numberType": "OTHER", + "separator": "&", + "type": "INTEGER" + }, + "SIFT": { + "label": "SIFT", + "description": "SIFT score.", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "SOMATIC": { + "label": "Somatic", + "description": "Somatic.", + "numberType": "OTHER", + "separator": "&", + "type": "INTEGER" + }, + "SpliceAI_pred_DS_AG": { + "label": "SpliceAI AG", + "description": "SpliceAI Delta score (acceptor gain).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "SpliceAI_pred_DS_AL": { + "label": "SpliceAI AL", + "description": "SpliceAI Delta score (acceptor loss).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "SpliceAI_pred_DS_DG": { + "label": "SpliceAI DG", + "description": "SpliceAI Delta score (donor gain).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "SpliceAI_pred_DS_DL": { + "label": "SpliceAI DL", + "description": "SpliceAI Delta score (donor loss).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "FLOAT" + }, + "STRAND": { + "label": "Strand", + "description": "The strand of the gene (0=- 1=+).", + "numberType": "NUMBER", + "numberCount": 1, + "type": "INTEGER" + }, + "SYMBOL": { + "label": "Gene", + "description": "Gene symbol", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "VIPC": { + "label": "VIP", + "description": "VIP classification", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING", + "required": true + }, + "VIPL": { + "label": "VIP labels", + "description": "VIP decision tree labels", + "numberType": "NUMBER", + "numberCount": 1, + "type": "STRING" + }, + "VIPP": { + "label": "VIP path", + "description": "VIP decision tree path", + "numberType": "OTHER", + "separator": "&", + "type": "STRING", + "required": true + }, + "VKGL_CL": { + "label": "VKGL", + "description": "VKGL consensus classification", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "B", + "LB", + "VUS", + "LP", + "P" + ] + }, + "VKGL_UMCG": { + "label": "MVL", + "description": "UMCG managed variant list classification", + "numberType": "NUMBER", + "numberCount": 1, + "type": "CATEGORICAL", + "categories": [ + "B", + "LB", + "VUS", + "LP", + "P" + ] + } + } + } + } +} From b3b190b233ce0bbcb68ebd40c6e5d881bc61243c Mon Sep 17 00:00:00 2001 From: dennishendriksen Date: Thu, 25 Jan 2024 14:51:42 +0100 Subject: [PATCH 2/2] bump dependencies --- package.json | 18 +- pnpm-lock.yaml | 843 +++++++++++++++++++++---------------------------- 2 files changed, 363 insertions(+), 498 deletions(-) diff --git a/package.json b/package.json index 0a543b6..93e05b7 100644 --- a/package.json +++ b/package.json @@ -30,15 +30,15 @@ "access": "public" }, "devDependencies": { - "@typescript-eslint/eslint-plugin": "^6.13.2", - "@typescript-eslint/parser": "^6.13.2", - "@vitest/coverage-v8": "^1.0.1", - "eslint": "^8.55.0", + "@typescript-eslint/eslint-plugin": "^6.19.1", + "@typescript-eslint/parser": "^6.19.1", + "@vitest/coverage-v8": "^1.2.1", + "eslint": "^8.56.0", "eslint-config-prettier": "^9.1.0", - "eslint-plugin-prettier": "^5.0.1", - "husky": "^8.0.3", - "prettier": "^3.1.0", - "typescript": "^5.3.2", - "vitest": "^1.0.1" + "eslint-plugin-prettier": "^5.1.3", + "husky": "^9.0.3", + "prettier": "^3.2.4", + "typescript": "^5.3.3", + "vitest": "^1.2.1" } } diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 7af2387..6ca46c6 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -6,35 +6,35 @@ settings: devDependencies: '@typescript-eslint/eslint-plugin': - specifier: ^6.13.2 - version: 6.13.2(@typescript-eslint/parser@6.13.2)(eslint@8.55.0)(typescript@5.3.2) + specifier: ^6.19.1 + version: 6.19.1(@typescript-eslint/parser@6.19.1)(eslint@8.56.0)(typescript@5.3.3) '@typescript-eslint/parser': - specifier: ^6.13.2 - version: 6.13.2(eslint@8.55.0)(typescript@5.3.2) + specifier: ^6.19.1 + version: 6.19.1(eslint@8.56.0)(typescript@5.3.3) '@vitest/coverage-v8': - specifier: ^1.0.1 - version: 1.0.1(vitest@1.0.1) + specifier: ^1.2.1 + version: 1.2.1(vitest@1.2.1) eslint: - specifier: ^8.55.0 - version: 8.55.0 + specifier: ^8.56.0 + version: 8.56.0 eslint-config-prettier: specifier: ^9.1.0 - version: 9.1.0(eslint@8.55.0) + version: 9.1.0(eslint@8.56.0) eslint-plugin-prettier: - specifier: ^5.0.1 - version: 5.0.1(eslint-config-prettier@9.1.0)(eslint@8.55.0)(prettier@3.1.0) + specifier: ^5.1.3 + version: 5.1.3(eslint-config-prettier@9.1.0)(eslint@8.56.0)(prettier@3.2.4) husky: - specifier: ^8.0.3 - version: 8.0.3 + specifier: ^9.0.3 + version: 9.0.3 prettier: - specifier: ^3.1.0 - version: 3.1.0 + specifier: ^3.2.4 + version: 3.2.4 typescript: - specifier: ^5.3.2 - version: 5.3.2 + specifier: ^5.3.3 + version: 5.3.3 vitest: - specifier: ^1.0.1 - version: 1.0.1 + specifier: ^1.2.1 + version: 1.2.1 packages: @@ -48,7 +48,7 @@ packages: engines: {node: '>=6.0.0'} dependencies: '@jridgewell/gen-mapping': 0.3.3 - '@jridgewell/trace-mapping': 0.3.20 + '@jridgewell/trace-mapping': 0.3.22 dev: true /@babel/helper-string-parser@7.23.4: @@ -61,16 +61,16 @@ packages: engines: {node: '>=6.9.0'} dev: true - /@babel/parser@7.23.5: - resolution: {integrity: 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packages: dev: true optional: true - /@esbuild/android-x64@0.19.8: - resolution: {integrity: sha512-rdqqYfRIn4jWOp+lzQttYMa2Xar3OK9Yt2fhOhzFXqg0rVWEfSclJvZq5fZslnz6ypHvVf3CT7qyf0A5pM682A==} + /@esbuild/android-x64@0.19.12: + resolution: {integrity: sha512-3k7ZoUW6Q6YqhdhIaq/WZ7HwBpnFBlW905Fa4s4qWJyiNOgT1dOqDiVAQFwBH7gBRZr17gLrlFCRzF6jFh7Kew==} engines: {node: '>=12'} cpu: [x64] os: [android] @@ -109,8 +118,8 @@ packages: dev: true optional: true - /@esbuild/darwin-arm64@0.19.8: - resolution: {integrity: sha512-RQw9DemMbIq35Bprbboyf8SmOr4UXsRVxJ97LgB55VKKeJOOdvsIPy0nFyF2l8U+h4PtBx/1kRf0BelOYCiQcw==} + /@esbuild/darwin-arm64@0.19.12: + resolution: {integrity: sha512-B6IeSgZgtEzGC42jsI+YYu9Z3HKRxp8ZT3cqhvliEHovq8HSX2YX8lNocDn79gCKJXOSaEot9MVYky7AKjCs8g==} engines: {node: '>=12'} cpu: [arm64] os: [darwin] @@ -118,8 +127,8 @@ packages: dev: true optional: true - /@esbuild/darwin-x64@0.19.8: - resolution: {integrity: 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dev: true optional: true - /@esbuild/linux-ia32@0.19.8: - resolution: {integrity: sha512-1a8suQiFJmZz1khm/rDglOc8lavtzEMRo0v6WhPgxkrjcU0LkHj+TwBrALwoz/OtMExvsqbbMI0ChyelKabSvQ==} + /@esbuild/linux-ia32@0.19.12: + resolution: {integrity: sha512-Thsa42rrP1+UIGaWz47uydHSBOgTUnwBwNq59khgIwktK6x60Hivfbux9iNR0eHCHzOLjLMLfUMLCypBkZXMHA==} engines: {node: '>=12'} cpu: [ia32] os: [linux] @@ -172,8 +181,8 @@ packages: dev: true optional: true - /@esbuild/linux-loong64@0.19.8: - resolution: {integrity: sha512-fHZWS2JJxnXt1uYJsDv9+b60WCc2RlvVAy1F76qOLtXRO+H4mjt3Tr6MJ5l7Q78X8KgCFudnTuiQRBhULUyBKQ==} + /@esbuild/linux-loong64@0.19.12: + resolution: {integrity: sha512-LiXdXA0s3IqRRjm6rV6XaWATScKAXjI4R4LoDlvO7+yQqFdlr1Bax62sRwkVvRIrwXxvtYEHHI4dm50jAXkuAA==} engines: {node: '>=12'} cpu: [loong64] os: [linux] @@ -181,8 +190,8 @@ packages: dev: true optional: true - /@esbuild/linux-mips64el@0.19.8: - resolution: {integrity: 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