From fff76932bceb24706a24554053c591e0ca5b2f82 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 12:51:11 -0500 Subject: [PATCH 01/63] Update tsconfig.json --- tsconfig.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tsconfig.json b/tsconfig.json index cfcccefa..b2ac7be2 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,7 +1,7 @@ { "compilerOptions": { "allowJs": true, - "checkJs": false, + "checkJs": true, "target": "es2020", "module": "es2020", "moduleResolution": "node", @@ -9,7 +9,8 @@ "esModuleInterop": true, "allowSyntheticDefaultImports": true, "downlevelIteration": true, - "typeRoots": ["./node_modules/@types", "./types"] + "typeRoots": ["./node_modules/@types", "./types"], + "noImplicitAny": true }, "include": ["src/**/*"], "exclude": ["node_modules", "dist"] From dd4e8b147717cc283e249c4119c1b374a5259bdc Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 13:51:30 -0500 Subject: [PATCH 02/63] First working TypeScript conversion This contains the needed config changes, package installs, and a conversion of the schema specs module. --- babel.config.js | 8 +- browser/src/schema/init.js | 2 +- browser/src/schema/loader.spec.js | 2 +- jest.config.js | 5 +- package-lock.json | 210 +++++++++++++++++++++- package.json | 7 +- spec_tests/jsonTests.spec.js | 7 +- src/schema/{specs.js => specs.ts} | 82 ++++----- tsconfig.json | 3 +- xml-transformer.js => xml-transformer.cjs | 0 10 files changed, 266 insertions(+), 60 deletions(-) rename src/schema/{specs.js => specs.ts} (61%) rename xml-transformer.js => xml-transformer.cjs (100%) diff --git a/babel.config.js b/babel.config.js index 67dc225e..f575b653 100644 --- a/babel.config.js +++ b/babel.config.js @@ -1,11 +1,11 @@ -module.exports = { +export default { presets: [ ['@babel/preset-env', { targets: { node: '22' - }, - modules: 'commonjs' - }] + } + }], + '@babel/preset-typescript' ], plugins: [] } diff --git a/browser/src/schema/init.js b/browser/src/schema/init.js index 92f7d66e..ce068fad 100644 --- a/browser/src/schema/init.js +++ b/browser/src/schema/init.js @@ -14,7 +14,7 @@ import PartneredSchemaMerger from '../../../src/schema/schemaMerger' import { Schema, Schemas } from '../../../src/schema/containers' import { IssueError } from '../../../src/issues/issues' import { splitStringTrimAndRemoveBlanks } from '../../../src/utils/string' -import { SchemasSpec } from '../../../src/schema/specs' +import { SchemasSpec } from '../../../src/schema/specs.js' /** * Build a single schema container object from an XML file. diff --git a/browser/src/schema/loader.spec.js b/browser/src/schema/loader.spec.js index 7eaabc02..d755a469 100644 --- a/browser/src/schema/loader.spec.js +++ b/browser/src/schema/loader.spec.js @@ -1,6 +1,6 @@ import { describe, it, expect } from 'vitest' import { loadSchema } from './loader.js' -import { SchemaSpec } from '../../../src/schema/specs.js' +import { SchemaSpec } from '../../../src/schema/specs.ts' describe('Browser Schema Loader', () => { it('should return undefined when loading a bundled schema in test environment', async () => { diff --git a/jest.config.js b/jest.config.js index d5fa2985..3df9caa8 100644 --- a/jest.config.js +++ b/jest.config.js @@ -1,8 +1,9 @@ -module.exports = { +export default { testEnvironment: 'node', transform: { - '\\.xml$': '/xml-transformer.js', + '\\.xml$': '/xml-transformer.cjs', '^.+\\.(js|jsx)$': 'babel-jest', + '^.+\\.(ts|tsx)$': 'babel-jest', }, transformIgnorePatterns: ['/node_modules/(?!unicode-name|semver)'], testPathIgnorePatterns: ['node_modules/', '/types/test.ts', '/browser/'], diff --git a/package-lock.json b/package-lock.json index 98255a1f..caa35566 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,16 +13,19 @@ "fast-xml-parser": "^5.2.5", "lodash": "^4.17.21", "pluralize": "^8.0.0", - "semver": "^7.6.0", + "semver": "^7.7.2", "unicode-name": "^1.0.2" }, "devDependencies": { "@babel/core": "^7.28.0", "@babel/preset-env": "^7.28.0", + "@babel/preset-typescript": "^7.27.1", "@eslint/eslintrc": "^3.2.0", "@eslint/js": "^9.18.0", "@jest/globals": "^30.0.0", + "@types/lodash": "^4.17.20", "@types/node": "^24.2.0", + "@types/semver": "^7.7.0", "babel-jest": "^30.0.5", "chai": "^4.3.6", "esbuild": "^0.25.0", @@ -39,6 +42,7 @@ "prettier": "^3.2.5", "pretty-quick": "^4.0.0", "ts-jest": "^29.4.0", + "ts-node": "^10.9.2", "tsx": "^4.20.3", "typedoc": "^0.28.0", "typescript": "^5.4.5" @@ -1623,6 +1627,26 @@ "@babel/core": "^7.0.0-0" } }, + "node_modules/@babel/plugin-transform-typescript": { + "version": "7.28.0", + "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typescript/-/plugin-transform-typescript-7.28.0.tgz", + "integrity": "sha512-4AEiDEBPIZvLQaWlc9liCavE0xRM0dNca41WtBeM3jgFptfUOSG9z0uteLhq6+3rq+WB6jIvUwKDTpXEHPJ2Vg==", + "dev": true, + "license": "MIT", + "dependencies": { + "@babel/helper-annotate-as-pure": "^7.27.3", + "@babel/helper-create-class-features-plugin": "^7.27.1", + "@babel/helper-plugin-utils": "^7.27.1", + "@babel/helper-skip-transparent-expression-wrappers": "^7.27.1", + "@babel/plugin-syntax-typescript": "^7.27.1" + }, + "engines": { + "node": ">=6.9.0" + }, + "peerDependencies": { + "@babel/core": "^7.0.0-0" + } + }, "node_modules/@babel/plugin-transform-unicode-escapes": { "version": "7.27.1", "resolved": "https://registry.npmjs.org/@babel/plugin-transform-unicode-escapes/-/plugin-transform-unicode-escapes-7.27.1.tgz", @@ -1800,6 +1824,26 @@ "@babel/core": "^7.0.0-0 || ^8.0.0-0 <8.0.0" } }, + "node_modules/@babel/preset-typescript": { + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.27.1.tgz", + "integrity": "sha512-l7WfQfX0WK4M0v2RudjuQK4u99BS6yLHYEmdtVPP7lKV013zr9DygFuWNlnbvQ9LR+LS0Egz/XAvGx5U9MX0fQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@babel/helper-plugin-utils": "^7.27.1", + "@babel/helper-validator-option": "^7.27.1", + "@babel/plugin-syntax-jsx": "^7.27.1", + "@babel/plugin-transform-modules-commonjs": "^7.27.1", + "@babel/plugin-transform-typescript": "^7.27.1" + }, + "engines": { + "node": ">=6.9.0" + }, + "peerDependencies": { + "@babel/core": "^7.0.0-0" + } + }, "node_modules/@babel/template": { "version": "7.27.2", "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.27.2.tgz", @@ -1855,6 +1899,30 @@ "dev": true, "license": "MIT" }, + "node_modules/@cspotcode/source-map-support": { + "version": "0.8.1", + "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz", + "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==", + "dev": true, + "license": "MIT", + "dependencies": { + "@jridgewell/trace-mapping": "0.3.9" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/@cspotcode/source-map-support/node_modules/@jridgewell/trace-mapping": { + "version": "0.3.9", + "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.9.tgz", + "integrity": "sha512-3Belt6tdc8bPgAtbcmdtNJlirVoTmEb5e2gC94PnkwEW9jI6CAHUeoG85tjWP5WquqfavoMtMwiG4P926ZKKuQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@jridgewell/resolve-uri": "^3.0.3", + "@jridgewell/sourcemap-codec": "^1.4.10" + } + }, "node_modules/@emnapi/core": { "version": "1.4.5", "resolved": "https://registry.npmjs.org/@emnapi/core/-/core-1.4.5.tgz", @@ -3201,6 +3269,34 @@ "@sinonjs/commons": "^3.0.1" } }, + "node_modules/@tsconfig/node10": { + "version": "1.0.11", + "resolved": "https://registry.npmjs.org/@tsconfig/node10/-/node10-1.0.11.tgz", + "integrity": "sha512-DcRjDCujK/kCk/cUe8Xz8ZSpm8mS3mNNpta+jGCA6USEDfktlNvm1+IuZ9eTcDbNk41BHwpHHeW+N1lKCz4zOw==", + "dev": true, + "license": "MIT" + }, + "node_modules/@tsconfig/node12": { + "version": "1.0.11", + "resolved": "https://registry.npmjs.org/@tsconfig/node12/-/node12-1.0.11.tgz", + "integrity": "sha512-cqefuRsh12pWyGsIoBKJA9luFu3mRxCA+ORZvA4ktLSzIuCUtWVxGIuXigEwO5/ywWFMZ2QEGKWvkZG1zDMTag==", + "dev": true, + "license": "MIT" + }, + "node_modules/@tsconfig/node14": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/@tsconfig/node14/-/node14-1.0.3.tgz", + "integrity": "sha512-ysT8mhdixWK6Hw3i1V2AeRqZ5WfXg1G43mqoYlM2nc6388Fq5jcXyr5mRsqViLx/GJYdoL0bfXD8nmF+Zn/Iow==", + "dev": true, + "license": "MIT" + }, + "node_modules/@tsconfig/node16": { + "version": "1.0.4", + "resolved": "https://registry.npmjs.org/@tsconfig/node16/-/node16-1.0.4.tgz", + "integrity": "sha512-vxhUy4J8lyeyinH7Azl1pdd43GJhZH/tP2weN8TntQblOY+A0XbT8DJk1/oCPuOOyg/Ja757rG0CgHcWC8OfMA==", + "dev": true, + "license": "MIT" + }, "node_modules/@tybys/wasm-util": { "version": "0.10.0", "resolved": "https://registry.npmjs.org/@tybys/wasm-util/-/wasm-util-0.10.0.tgz", @@ -3308,6 +3404,13 @@ "dev": true, "license": "MIT" }, + "node_modules/@types/lodash": { + "version": "4.17.20", + "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.17.20.tgz", + "integrity": "sha512-H3MHACvFUEiujabxhaI/ImO6gUrd8oOurg7LQtS7mbwIXA/cUqWrvBsaeJ23aZEPk1TAYkurjfMbSELfoCXlGA==", + "dev": true, + "license": "MIT" + }, "node_modules/@types/node": { "version": "24.2.1", "resolved": "https://registry.npmjs.org/@types/node/-/node-24.2.1.tgz", @@ -3318,6 +3421,13 @@ "undici-types": "~7.10.0" } }, + "node_modules/@types/semver": { + "version": "7.7.0", + "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.7.0.tgz", + "integrity": "sha512-k107IF4+Xr7UHjwDc7Cfd6PRQfbdkiRabXGRjo07b4WyPahFBZCZ1sE+BNxYIJPPg73UkfOsVOLwqVc/6ETrIA==", + "dev": true, + "license": "MIT" + }, "node_modules/@types/stack-utils": { "version": "2.0.3", "resolved": "https://registry.npmjs.org/@types/stack-utils/-/stack-utils-2.0.3.tgz", @@ -3648,6 +3758,19 @@ "acorn": "^6.0.0 || ^7.0.0 || ^8.0.0" } }, + "node_modules/acorn-walk": { + "version": "8.3.4", + "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-8.3.4.tgz", + "integrity": "sha512-ueEepnujpqee2o5aIYnvHU6C0A42MNdsIDeqy5BydrkuC5R1ZuUFnm27EeFJGoEHJQgn3uleRvmTXaJgfXbt4g==", + "dev": true, + "license": "MIT", + "dependencies": { + "acorn": "^8.11.0" + }, + "engines": { + "node": ">=0.4.0" + } + }, "node_modules/ajv": { "version": "6.12.6", "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz", @@ -3724,6 +3847,13 @@ "node": ">= 8" } }, + "node_modules/arg": { + "version": "4.1.3", + "resolved": "https://registry.npmjs.org/arg/-/arg-4.1.3.tgz", + "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==", + "dev": true, + "license": "MIT" + }, "node_modules/argparse": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz", @@ -4280,6 +4410,13 @@ "url": "https://opencollective.com/core-js" } }, + "node_modules/create-require": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/create-require/-/create-require-1.1.1.tgz", + "integrity": "sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==", + "dev": true, + "license": "MIT" + }, "node_modules/cross-spawn": { "version": "7.0.6", "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz", @@ -4368,6 +4505,16 @@ "node": ">=8" } }, + "node_modules/diff": { + "version": "4.0.2", + "resolved": "https://registry.npmjs.org/diff/-/diff-4.0.2.tgz", + "integrity": "sha512-58lmxKSA4BNyLz+HHMUzlOEpg09FV+ev6ZMe3vJihgdxzgcwZ8VoEEPmALCZG9LmqfVoNMMKpttIYTVG6uDY7A==", + "dev": true, + "license": "BSD-3-Clause", + "engines": { + "node": ">=0.3.1" + } + }, "node_modules/eastasianwidth": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/eastasianwidth/-/eastasianwidth-0.2.0.tgz", @@ -7597,6 +7744,50 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/ts-node": { + "version": "10.9.2", + "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.2.tgz", + "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "@cspotcode/source-map-support": "^0.8.0", + "@tsconfig/node10": "^1.0.7", + "@tsconfig/node12": "^1.0.7", + "@tsconfig/node14": "^1.0.0", + "@tsconfig/node16": "^1.0.2", + "acorn": "^8.4.1", + "acorn-walk": "^8.1.1", + "arg": "^4.1.0", + "create-require": "^1.1.0", + "diff": "^4.0.1", + "make-error": "^1.1.1", + "v8-compile-cache-lib": "^3.0.1", + "yn": "3.1.1" + }, + "bin": { + "ts-node": "dist/bin.js", + "ts-node-cwd": "dist/bin-cwd.js", + "ts-node-esm": "dist/bin-esm.js", + "ts-node-script": "dist/bin-script.js", + "ts-node-transpile-only": "dist/bin-transpile.js", + "ts-script": "dist/bin-script-deprecated.js" + }, + "peerDependencies": { + "@swc/core": ">=1.2.50", + "@swc/wasm": ">=1.2.50", + "@types/node": "*", + "typescript": ">=2.7" + }, + "peerDependenciesMeta": { + "@swc/core": { + "optional": true + }, + "@swc/wasm": { + "optional": true + } + } + }, "node_modules/tslib": { "version": "2.4.0", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.4.0.tgz", @@ -7888,6 +8079,13 @@ "punycode": "^2.1.0" } }, + "node_modules/v8-compile-cache-lib": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz", + "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==", + "dev": true, + "license": "MIT" + }, "node_modules/v8-to-istanbul": { "version": "9.3.0", "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-9.3.0.tgz", @@ -8159,6 +8357,16 @@ "node": ">=8" } }, + "node_modules/yn": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", + "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=6" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/package.json b/package.json index f5f53b0b..c8af698a 100644 --- a/package.json +++ b/package.json @@ -2,6 +2,7 @@ "name": "hed-validator", "version": "4.1.4", "description": "A JavaScript validator for HED (Hierarchical Event Descriptor) strings.", + "type": "module", "main": "./dist/commonjs/index.js", "types": "./types/index.d.ts", "exports": { @@ -48,16 +49,19 @@ "fast-xml-parser": "^5.2.5", "lodash": "^4.17.21", "pluralize": "^8.0.0", - "semver": "^7.6.0", + "semver": "^7.7.2", "unicode-name": "^1.0.2" }, "devDependencies": { "@babel/core": "^7.28.0", "@babel/preset-env": "^7.28.0", + "@babel/preset-typescript": "^7.27.1", "@eslint/eslintrc": "^3.2.0", "@eslint/js": "^9.18.0", "@jest/globals": "^30.0.0", + "@types/lodash": "^4.17.20", "@types/node": "^24.2.0", + "@types/semver": "^7.7.0", "babel-jest": "^30.0.5", "chai": "^4.3.6", "esbuild": "^0.25.0", @@ -74,6 +78,7 @@ "prettier": "^3.2.5", "pretty-quick": "^4.0.0", "ts-jest": "^29.4.0", + "ts-node": "^10.9.2", "tsx": "^4.20.3", "typedoc": "^0.28.0", "typescript": "^5.4.5" diff --git a/spec_tests/jsonTests.spec.js b/spec_tests/jsonTests.spec.js index 8c2c0266..ab413023 100644 --- a/spec_tests/jsonTests.spec.js +++ b/spec_tests/jsonTests.spec.js @@ -1,18 +1,19 @@ +import * as fs from 'node:fs' +import path from 'node:path' + import chai from 'chai' const assert = chai.assert -import { beforeAll, describe, afterAll } from '@jest/globals' +import { beforeAll, describe, afterAll } from '@jest/globals' import { BidsHedIssue } from '../src/bids/types/issues' import { buildSchemas } from '../src/schema/init' import { SchemaSpec, SchemasSpec } from '../src/schema/specs' import { Schemas } from '../src/schema/containers' -import path from 'node:path' import { BidsSidecar, BidsTsvFile } from '../src/bids' import { generateIssue, IssueError } from '../src/issues/issues' import { DefinitionManager } from '../src/parser/definitionManager' import parseTSV from '../src/bids/tsvParser' import { shouldRun } from '../tests/testHelpers/testUtilities' -const fs = require('node:fs') const skipMap = new Map() const runAll = true diff --git a/src/schema/specs.js b/src/schema/specs.ts similarity index 61% rename from src/schema/specs.js rename to src/schema/specs.ts index 5eaeae73..f2aa8a73 100644 --- a/src/schema/specs.js +++ b/src/schema/specs.ts @@ -9,37 +9,33 @@ import { IssueError } from '../issues/issues' export class SchemaSpec { /** * The prefix of this schema. - * @type {string} */ - prefix + prefix: string /** * The version of this schema. - * @type {string} */ - version + version: string /** * The library name of this schema. - * @type {string} */ - library + library: string /** * The local path for this schema. - * @type {string} */ - localPath + localPath: string /** * Constructor. * - * @param {string} prefix The prefix of this schema. - * @param {string} version The version of this schema. - * @param {string?} library The library name of this schema. - * @param {string?} localPath The local path for this schema. + * @param prefix The prefix of this schema. + * @param version The version of this schema. + * @param library The library name of this schema. + * @param localPath The local path for this schema. */ - constructor(prefix, version, library = '', localPath = '') { + constructor(prefix: string, version: string, library = '', localPath = '') { this.prefix = prefix this.version = version this.library = library @@ -48,10 +44,8 @@ export class SchemaSpec { /** * Compute the name for the bundled copy of this schema. - * - * @returns {string} */ - get localName() { + get localName(): string { if (!this.library) { return 'HED' + this.version } else { @@ -62,12 +56,12 @@ export class SchemaSpec { /** * Parse a single schema specification string into a SchemaSpec object. * - * @param {string} versionSpec A schema version specification string (e.g., "nickname:library_version"). - * @returns {SchemaSpec} A schema specification object with parsed nickname, library, and version. + * @param versionSpec A schema version specification string (e.g., "nickname:library_version"). + * @returns A schema specification object with parsed nickname, library, and version. * @throws {IssueError} If the schema specification format is invalid. * @public */ - static parseVersionSpec(versionSpec) { + static parseVersionSpec(versionSpec: string): SchemaSpec { const [nickname, schema] = SchemaSpec._splitPrefixAndSchema(versionSpec) const [library, version] = SchemaSpec._splitLibraryAndVersion(schema, versionSpec) return new SchemaSpec(nickname, version, library) @@ -76,25 +70,25 @@ export class SchemaSpec { /** * Split a schema version string into prefix (nickname) and schema parts using colon delimiter. * - * @param {string} prefixSchemaSpec The schema version string to split. - * @returns {string[]} An array with [nickname, schema] where nickname may be empty string. + * @param prefixSchemaSpec The schema version string to split. + * @returns An array with [nickname, schema] where nickname may be empty string. * @throws {IssueError} If the schema specification format is invalid. * @private */ - static _splitPrefixAndSchema(prefixSchemaSpec) { + static _splitPrefixAndSchema(prefixSchemaSpec: string): [string, string] { return SchemaSpec._splitVersionSegments(prefixSchemaSpec, prefixSchemaSpec, ':') } /** * Split a schema string into library and version parts using underscore delimiter. * - * @param {string} libraryVersionSpec The schema string to split (library_version format). - * @param {string} originalVersion The original version string for error reporting. - * @returns {string[]} An array with [library, version] where library may be empty string. + * @param libraryVersionSpec The schema string to split (library_version format). + * @param originalVersion The original version string for error reporting. + * @returns An array with [library, version] where library may be empty string. * @throws {IssueError} If the schema specification format is invalid or version is not valid semver. * @private */ - static _splitLibraryAndVersion(libraryVersionSpec, originalVersion) { + static _splitLibraryAndVersion(libraryVersionSpec: string, originalVersion: string): [string, string] { const [library, version] = SchemaSpec._splitVersionSegments(libraryVersionSpec, originalVersion, '_') if (!semver.valid(version)) { IssueError.generateAndThrow('invalidSchemaSpecification', { spec: originalVersion }) @@ -105,14 +99,14 @@ export class SchemaSpec { /** * Split a version string into two segments using the specified delimiter. * - * @param {string} versionSpec The version string to split. - * @param {string} originalVersion The original version string for error reporting. - * @param {string} splitCharacter The character to use as delimiter (':' or '_'). - * @returns {string[]} An array with [firstSegment, secondSegment] where firstSegment may be empty string. + * @param versionSpec The version string to split. + * @param originalVersion The original version string for error reporting. + * @param splitCharacter The character to use as delimiter (':' or '_'). + * @returns An array with [firstSegment, secondSegment] where firstSegment may be empty string. * @throws {IssueError} If the schema specification format is invalid or contains non-alphabetic characters in first segment. * @private */ - static _splitVersionSegments(versionSpec, originalVersion, splitCharacter) { + static _splitVersionSegments(versionSpec: string, originalVersion: string, splitCharacter: string): [string, string] { const alphabeticRegExp = new RegExp('^[a-zA-Z]+$') const versionSplit = versionSpec.split(splitCharacter) const secondSegment = versionSplit.pop() @@ -135,33 +129,29 @@ export class SchemasSpec { * The specification mapping data. * @type {Map} */ - data + data: Map /** * Constructor. */ constructor() { - this.data = new Map() + this.data = new Map() } /** - * Iterator over the specifications. - * - * @yields {Iterator} - [string, SchemaSpec[]] + * Iterate over the schema specifications. */ - *[Symbol.iterator]() { - for (const [prefix, schemaSpecs] of this.data.entries()) { - yield [prefix, schemaSpecs] - } + *[Symbol.iterator](): MapIterator<[string, SchemaSpec[]]> { + return this.data.entries() } /** * Add a schema to this specification. * - * @param {SchemaSpec} schemaSpec A schema specification. - * @returns {SchemasSpec| map} This object. + * @param schemaSpec A schema specification. + * @returns This object. */ - addSchemaSpec(schemaSpec) { + addSchemaSpec(schemaSpec: SchemaSpec): SchemasSpec { if (this.data.has(schemaSpec.prefix)) { this.data.get(schemaSpec.prefix).push(schemaSpec) } else { @@ -173,12 +163,12 @@ export class SchemasSpec { /** * Parse a HED version specification into a schemas specification object. * - * @param {string|string[]} versionSpecs The HED version specification, can be a single version string or array of version strings. - * @returns {SchemasSpec} A schemas specification object containing parsed schema specifications. + * @param versionSpecs The HED version specification, can be a single version string or array of version strings. + * @returns A schemas specification object containing parsed schema specifications. * @throws {IssueError} If any schema specification is invalid. * @public */ - static parseVersionSpecs(versionSpecs) { + static parseVersionSpecs(versionSpecs: string | string[]): SchemasSpec { const schemasSpec = new SchemasSpec() const processVersion = castArray(versionSpecs) if (processVersion.length === 0) { diff --git a/tsconfig.json b/tsconfig.json index b2ac7be2..c628ace5 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,7 +1,8 @@ { "compilerOptions": { + "outDir": "./built", "allowJs": true, - "checkJs": true, + "checkJs": false, "target": "es2020", "module": "es2020", "moduleResolution": "node", diff --git a/xml-transformer.js b/xml-transformer.cjs similarity index 100% rename from xml-transformer.js rename to xml-transformer.cjs From 9a239b3604c2c5bd78325f7371ed4e11550d706e Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 13:57:27 -0500 Subject: [PATCH 03/63] Enable CI on typescript branch --- .github/workflows/coverage.yml | 4 +++- .github/workflows/test-types.yml | 4 ++-- .github/workflows/tests.yml | 4 ++-- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index f77be134..12ae8ac5 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -2,7 +2,9 @@ name: Test coverage on: push: - branches: [main] + branches: [main, typescript] + pull_request: + branches: [main, typescript] permissions: contents: read diff --git a/.github/workflows/test-types.yml b/.github/workflows/test-types.yml index 4be066ff..2850bd5e 100644 --- a/.github/workflows/test-types.yml +++ b/.github/workflows/test-types.yml @@ -2,9 +2,9 @@ name: Test TypeScript Definitions on: push: - branches: [main] + branches: [main, typescript] pull_request: - branches: [main] + branches: [main, typescript] jobs: test-types: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index db2bc333..0a0c68eb 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -2,9 +2,9 @@ name: Tests on: push: - branches: [main] + branches: [main, typescript] pull_request: - branches: [main] + branches: [main, typescript] permissions: contents: read From 5d7401d25e79a501e49b96232be469b393c1afde Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 14:09:49 -0500 Subject: [PATCH 04/63] Fix linter errors --- src/schema/specs.ts | 53 +++++++++++++++++++++++++-------------------- 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/src/schema/specs.ts b/src/schema/specs.ts index f2aa8a73..baf0a233 100644 --- a/src/schema/specs.ts +++ b/src/schema/specs.ts @@ -10,22 +10,22 @@ export class SchemaSpec { /** * The prefix of this schema. */ - prefix: string + readonly prefix: string /** * The version of this schema. */ - version: string + readonly version: string /** * The library name of this schema. */ - library: string + readonly library: string /** * The local path for this schema. */ - localPath: string + readonly localPath: string /** * Constructor. @@ -45,7 +45,7 @@ export class SchemaSpec { /** * Compute the name for the bundled copy of this schema. */ - get localName(): string { + public get localName(): string { if (!this.library) { return 'HED' + this.version } else { @@ -59,9 +59,8 @@ export class SchemaSpec { * @param versionSpec A schema version specification string (e.g., "nickname:library_version"). * @returns A schema specification object with parsed nickname, library, and version. * @throws {IssueError} If the schema specification format is invalid. - * @public */ - static parseVersionSpec(versionSpec: string): SchemaSpec { + public static parseVersionSpec(versionSpec: string): SchemaSpec { const [nickname, schema] = SchemaSpec._splitPrefixAndSchema(versionSpec) const [library, version] = SchemaSpec._splitLibraryAndVersion(schema, versionSpec) return new SchemaSpec(nickname, version, library) @@ -73,9 +72,8 @@ export class SchemaSpec { * @param prefixSchemaSpec The schema version string to split. * @returns An array with [nickname, schema] where nickname may be empty string. * @throws {IssueError} If the schema specification format is invalid. - * @private */ - static _splitPrefixAndSchema(prefixSchemaSpec: string): [string, string] { + private static _splitPrefixAndSchema(prefixSchemaSpec: string): [string, string] { return SchemaSpec._splitVersionSegments(prefixSchemaSpec, prefixSchemaSpec, ':') } @@ -86,9 +84,8 @@ export class SchemaSpec { * @param originalVersion The original version string for error reporting. * @returns An array with [library, version] where library may be empty string. * @throws {IssueError} If the schema specification format is invalid or version is not valid semver. - * @private */ - static _splitLibraryAndVersion(libraryVersionSpec: string, originalVersion: string): [string, string] { + private static _splitLibraryAndVersion(libraryVersionSpec: string, originalVersion: string): [string, string] { const [library, version] = SchemaSpec._splitVersionSegments(libraryVersionSpec, originalVersion, '_') if (!semver.valid(version)) { IssueError.generateAndThrow('invalidSchemaSpecification', { spec: originalVersion }) @@ -104,10 +101,13 @@ export class SchemaSpec { * @param splitCharacter The character to use as delimiter (':' or '_'). * @returns An array with [firstSegment, secondSegment] where firstSegment may be empty string. * @throws {IssueError} If the schema specification format is invalid or contains non-alphabetic characters in first segment. - * @private */ - static _splitVersionSegments(versionSpec: string, originalVersion: string, splitCharacter: string): [string, string] { - const alphabeticRegExp = new RegExp('^[a-zA-Z]+$') + private static _splitVersionSegments( + versionSpec: string, + originalVersion: string, + splitCharacter: string, + ): [string, string] { + const alphabeticRegExp = /^[a-zA-Z]+$/ const versionSplit = versionSpec.split(splitCharacter) const secondSegment = versionSplit.pop() const firstSegment = versionSplit.pop() @@ -127,22 +127,28 @@ export class SchemaSpec { export class SchemasSpec { /** * The specification mapping data. - * @type {Map} */ - data: Map + #data: Map /** * Constructor. */ constructor() { - this.data = new Map() + this.#data = new Map() + } + + /** + * The specification mapping data. + */ + public get data(): Map { + return new Map(this.#data) } /** * Iterate over the schema specifications. */ *[Symbol.iterator](): MapIterator<[string, SchemaSpec[]]> { - return this.data.entries() + yield* this.#data.entries() } /** @@ -151,11 +157,11 @@ export class SchemasSpec { * @param schemaSpec A schema specification. * @returns This object. */ - addSchemaSpec(schemaSpec: SchemaSpec): SchemasSpec { - if (this.data.has(schemaSpec.prefix)) { - this.data.get(schemaSpec.prefix).push(schemaSpec) + public addSchemaSpec(schemaSpec: SchemaSpec): this { + if (this.#data.has(schemaSpec.prefix)) { + this.#data.get(schemaSpec.prefix).push(schemaSpec) } else { - this.data.set(schemaSpec.prefix, [schemaSpec]) + this.#data.set(schemaSpec.prefix, [schemaSpec]) } return this } @@ -166,9 +172,8 @@ export class SchemasSpec { * @param versionSpecs The HED version specification, can be a single version string or array of version strings. * @returns A schemas specification object containing parsed schema specifications. * @throws {IssueError} If any schema specification is invalid. - * @public */ - static parseVersionSpecs(versionSpecs: string | string[]): SchemasSpec { + public static parseVersionSpecs(versionSpecs: string | string[]): SchemasSpec { const schemasSpec = new SchemasSpec() const processVersion = castArray(versionSpecs) if (processVersion.length === 0) { From 23a0beb248dfb645d237f8fa6cbb5ee92c6560aa Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 14:14:06 -0500 Subject: [PATCH 05/63] Fix remaining linter error --- src/schema/specs.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/specs.ts b/src/schema/specs.ts index baf0a233..b3f50704 100644 --- a/src/schema/specs.ts +++ b/src/schema/specs.ts @@ -128,7 +128,7 @@ export class SchemasSpec { /** * The specification mapping data. */ - #data: Map + readonly #data: Map /** * Constructor. From 4d5e19b1cfa3c89acc902162ef1b9a1e574aefd0 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 15:27:20 -0500 Subject: [PATCH 06/63] Refactor/rename schema classes and port to TypeScript This commit refactors the Schema class hierarchy and prepends "Hed" to the Schema and Schemas class names. It also ports the containers and init modules in the schemas folder to TypeScript. --- browser/src/bids/BidsWebAccessor.js | 6 +- browser/src/bids/BidsWebAccessor.spec.js | 2 +- browser/src/schema/init.js | 16 +- browser/src/schema/loader.js | 4 +- browser/src/schema/loader.spec.js | 2 +- spec_tests/jsonTests.spec.js | 4 +- src/bids/datasetParser.js | 2 +- src/bids/types/dataset.js | 4 +- src/bids/types/file.js | 2 +- src/bids/types/issues.js | 2 +- src/bids/types/json.js | 8 +- src/bids/validator/sidecarValidator.js | 4 +- src/bids/validator/tsvValidator.js | 6 +- src/bids/validator/validator.js | 4 +- src/parser/definitionManager.js | 14 +- src/parser/eventManager.js | 2 +- src/parser/parsedHedTag.js | 6 +- src/parser/parser.js | 12 +- src/parser/splitter.js | 4 +- src/parser/tagConverter.js | 6 +- src/schema/containers.js | 146 ----------------- src/schema/containers.ts | 153 ++++++++++++++++++ src/schema/{init.js => init.ts} | 32 ++-- src/schema/schemaMerger.js | 6 +- .../definitionManagerCreationTests.spec.js | 2 +- tests/jsonTests/schemaBuildTests.spec.js | 4 +- tests/otherTests/dataset.spec.js | 8 +- tests/otherTests/issues.spec.js | 4 +- tests/otherTests/schema.spec.js | 6 +- types/index.d.ts | 44 +++-- types/test.ts | 18 +-- 31 files changed, 269 insertions(+), 264 deletions(-) delete mode 100644 src/schema/containers.js create mode 100644 src/schema/containers.ts rename src/schema/{init.js => init.ts} (63%) diff --git a/browser/src/bids/BidsWebAccessor.js b/browser/src/bids/BidsWebAccessor.js index c22c8f7c..f1ff82e9 100644 --- a/browser/src/bids/BidsWebAccessor.js +++ b/browser/src/bids/BidsWebAccessor.js @@ -1,6 +1,6 @@ -import { BidsFileAccessor } from '../../../src/bids/datasetParser.js' -import { buildSchemasFromVersion } from '../schema/init.js' -import { BidsHedIssue } from '../../../src/bids/types/issues.js' +import { BidsFileAccessor } from '../../../src/bids/datasetParser' +import { buildSchemasFromVersion } from '../schema/init' +import { BidsHedIssue } from '../../../src/bids/types/issues' /** * Build HED schemas from a dataset description for the browser environment. diff --git a/browser/src/bids/BidsWebAccessor.spec.js b/browser/src/bids/BidsWebAccessor.spec.js index 90af75e4..b7095aa5 100644 --- a/browser/src/bids/BidsWebAccessor.spec.js +++ b/browser/src/bids/BidsWebAccessor.spec.js @@ -1,5 +1,5 @@ import { describe, it, expect } from 'vitest' -import { BidsWebAccessor } from './BidsWebAccessor.js' +import { BidsWebAccessor } from './BidsWebAccessor' // Mock File object for BidsWebAccessor tests const MockFile = class { diff --git a/browser/src/schema/init.js b/browser/src/schema/init.js index ce068fad..f1700001 100644 --- a/browser/src/schema/init.js +++ b/browser/src/schema/init.js @@ -7,20 +7,20 @@ import zip from 'lodash/zip' import { loadSchema } from './loader' -import { setParent } from '../../../src/utils/xml.js' +import { setParent } from '../../../src/utils/xml' import SchemaParser from '../../../src/schema/parser' import PartneredSchemaMerger from '../../../src/schema/schemaMerger' -import { Schema, Schemas } from '../../../src/schema/containers' +import { Schema, HedSchemas } from '../../../src/schema/containers' import { IssueError } from '../../../src/issues/issues' import { splitStringTrimAndRemoveBlanks } from '../../../src/utils/string' -import { SchemasSpec } from '../../../src/schema/specs.js' +import { SchemasSpec } from '../../../src/schema/specs' /** * Build a single schema container object from an XML file. * * @param {Object} xmlData The schema's XML data - * @returns {Schema} The HED schema object. + * @returns {HedSchema} The HED schema object. */ const buildSchemaObject = function (xmlData) { const rootElement = xmlData.HED @@ -33,7 +33,7 @@ const buildSchemaObject = function (xmlData) { * Build a single merged schema container object from one or more XML files. * * @param {Object[]} xmlData The schemas' XML data. - * @returns {Schema} The HED schema object. + * @returns {HedSchema} The HED schema object. */ const buildSchemaObjects = function (xmlData) { const schemas = xmlData.map((data) => buildSchemaObject(data)) @@ -48,7 +48,7 @@ const buildSchemaObjects = function (xmlData) { * Build a schema collection object from a schema specification. * * @param {SchemasSpec} schemaSpecs The description of which schemas to use. - * @returns {Promise} The schema container object and any issues found. + * @returns {Promise} The schema container object and any issues found. */ export async function buildSchemas(schemaSpecs) { const schemaPrefixes = Array.from(schemaSpecs.data.keys()) @@ -62,14 +62,14 @@ export async function buildSchemas(schemaSpecs) { ) const schemaObjects = schemaXmlData.map(buildSchemaObjects) const schemas = new Map(zip(schemaPrefixes, schemaObjects)) - return new Schemas(schemas) + return new HedSchemas(schemas) } /** * Build HED schemas from a version specification string. * * @param {string} hedVersionString The HED version specification string (can contain comma-separated versions). - * @returns {Promise} A Promise that resolves to the built schemas. + * @returns {Promise} A Promise that resolves to the built schemas. * @throws {IssueError} If the schema specification is invalid or schemas cannot be built. */ export async function buildSchemasFromVersion(hedVersionString) { diff --git a/browser/src/schema/loader.js b/browser/src/schema/loader.js index 0216d270..8202662a 100644 --- a/browser/src/schema/loader.js +++ b/browser/src/schema/loader.js @@ -2,8 +2,8 @@ /* Imports */ import { IssueError } from '../../../src/issues/issues' -import { parseSchemaXML } from '../../../src/utils/xml.js' -import { schemaData } from './vite-importer.js' +import { parseSchemaXML } from '../../../src/utils/xml' +import { schemaData } from './vite-importer' /** * Load schema XML data from a schema version or path description. diff --git a/browser/src/schema/loader.spec.js b/browser/src/schema/loader.spec.js index d755a469..899b826b 100644 --- a/browser/src/schema/loader.spec.js +++ b/browser/src/schema/loader.spec.js @@ -1,5 +1,5 @@ import { describe, it, expect } from 'vitest' -import { loadSchema } from './loader.js' +import { loadSchema } from './loader' import { SchemaSpec } from '../../../src/schema/specs.ts' describe('Browser Schema Loader', () => { diff --git a/spec_tests/jsonTests.spec.js b/spec_tests/jsonTests.spec.js index ab413023..1a96f64a 100644 --- a/spec_tests/jsonTests.spec.js +++ b/spec_tests/jsonTests.spec.js @@ -8,7 +8,7 @@ import { beforeAll, describe, afterAll } from '@jest/globals' import { BidsHedIssue } from '../src/bids/types/issues' import { buildSchemas } from '../src/schema/init' import { SchemaSpec, SchemasSpec } from '../src/schema/specs' -import { Schemas } from '../src/schema/containers' +import { HedSchemas } from '../src/schema/containers' import { BidsSidecar, BidsTsvFile } from '../src/bids' import { generateIssue, IssueError } from '../src/issues/issues' import { DefinitionManager } from '../src/parser/definitionManager' @@ -332,7 +332,7 @@ describe('HED validation using JSON tests', () => { hedMap.set(prefix, schema) } } - return new Schemas(hedMap) + return new HedSchemas(hedMap) } beforeAll(async () => { diff --git a/src/bids/datasetParser.js b/src/bids/datasetParser.js index ec7d69bb..03d10ea4 100644 --- a/src/bids/datasetParser.js +++ b/src/bids/datasetParser.js @@ -12,7 +12,7 @@ import fsp from 'node:fs/promises' import path from 'node:path' -import { organizePaths } from '../utils/paths.js' +import { organizePaths } from '../utils/paths' import { generateIssue } from '../issues/issues' import { BidsHedIssue } from './types/issues' import { buildBidsSchemas } from './schema' diff --git a/src/bids/types/dataset.js b/src/bids/types/dataset.js index 51681c98..68bacb47 100644 --- a/src/bids/types/dataset.js +++ b/src/bids/types/dataset.js @@ -42,7 +42,7 @@ import path from 'node:path' * * @property {Map} sidecarMap Map of BIDS sidecar files that contain HED annotations. * @property {string|null} datasetRootDirectory The dataset's root directory as an absolute path (Node.js context). - * @property {Schemas} hedSchemas The HED schemas used to validate this dataset. + * @property {HedSchemas} hedSchemas The HED schemas used to validate this dataset. * @property {BidsFileAccessor} fileAccessor The BIDS file accessor. */ export class BidsDataset { @@ -61,7 +61,7 @@ export class BidsDataset { /** * The HED schemas used to validate this dataset. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas diff --git a/src/bids/types/file.js b/src/bids/types/file.js index 7adadcf0..5dafa278 100644 --- a/src/bids/types/file.js +++ b/src/bids/types/file.js @@ -39,7 +39,7 @@ export class BidsFile { /** * Validate this validator's tsv file. * - * @param {Schemas} schemas - The HED schemas used to validate this file. + * @param {HedSchemas} schemas - The HED schemas used to validate this file. * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file. */ validate(schemas) { diff --git a/src/bids/types/issues.js b/src/bids/types/issues.js index 4915a52b..20860fca 100644 --- a/src/bids/types/issues.js +++ b/src/bids/types/issues.js @@ -2,7 +2,7 @@ * Provides a wrapper for HED validation issues that is compatible with the BIDS validator. * @module issues */ -import { generateIssue, IssueError } from '../../issues/issues.js' +import { generateIssue, IssueError } from '../../issues/issues' /** * @typedef {import('../../issues/issues.js').Issue} Issue diff --git a/src/bids/types/json.js b/src/bids/types/json.js index 7525f1a8..b9fb93b7 100644 --- a/src/bids/types/json.js +++ b/src/bids/types/json.js @@ -131,7 +131,7 @@ export class BidsSidecar extends BidsJsonFile { * * The parsed strings are placed into {@link parsedHedData}. * - * @param {Schemas} hedSchemas - The HED schema collection. + * @param {HedSchemas} hedSchemas - The HED schema collection. * @param {boolean} fullValidation - True if full validation should be performed. * @returns {Array} [Issue[], Issue[]] Any errors and warnings found */ @@ -396,7 +396,7 @@ export class BidsSidecarKey { * * ###Note: This sets the parsedHedData as a side effect. * - * @param {Schemas} hedSchemas The HED schema collection. + * @param {HedSchemas} hedSchemas The HED schema collection. * @param {boolean} fullValidation True if full validation should be performed. * @returns {Array} - [Issue[], Issues[]] Errors and warnings that result from parsing. */ @@ -413,7 +413,7 @@ export class BidsSidecarKey { * ### Note: * The value strings cannot contain definitions. * - * @param {Schemas} hedSchemas - The HED schemas to use. + * @param {HedSchemas} hedSchemas - The HED schemas to use. * @param {boolean} fullValidation - True if full validation should be performed. * @returns {Array} - [Issue[], Issue[]] - Errors due for the value. * @private @@ -432,7 +432,7 @@ export class BidsSidecarKey { /** * Parse the categorical values associated with this key. - * @param {Schemas} hedSchemas - The HED schemas used to check against. + * @param {HedSchemas} hedSchemas - The HED schemas used to check against. * @param {boolean} fullValidation - True if full validation should be performed. * @returns {Array} - Array[Issue[], Issue[]] A list of error issues and warning issues. * @private diff --git a/src/bids/validator/sidecarValidator.js b/src/bids/validator/sidecarValidator.js index 0170a0c9..35fb2652 100644 --- a/src/bids/validator/sidecarValidator.js +++ b/src/bids/validator/sidecarValidator.js @@ -1,7 +1,7 @@ import { BidsHedIssue } from '../types/issues' import ParsedHedString from '../../parser/parsedHedString' import { generateIssue, IssueError, updateIssueParameters } from '../../issues/issues' -import { getCharacterCount } from '../../utils/string.js' +import { getCharacterCount } from '../../utils/string' import { BidsValidator } from './validator' /** @@ -18,7 +18,7 @@ export class BidsHedSidecarValidator extends BidsValidator { * Constructor for the BidsHedSidecarValidator. * * @param {BidsSidecar} sidecar - The BIDS sidecar being validated. - * @param {Schemas} hedSchemas - The schemas used for the sidecar validation. + * @param {HedSchemas} hedSchemas - The schemas used for the sidecar validation. */ constructor(sidecar, hedSchemas) { super(hedSchemas) diff --git a/src/bids/validator/tsvValidator.js b/src/bids/validator/tsvValidator.js index 3679d6ad..8d4073c4 100644 --- a/src/bids/validator/tsvValidator.js +++ b/src/bids/validator/tsvValidator.js @@ -28,7 +28,7 @@ export class BidsHedTsvValidator extends BidsValidator { * Constructor. * * @param {BidsTsvFile} tsvFile - The BIDS TSV file being validated. - * @param {Schemas} hedSchemas - The HED schemas used to validate the tsv file. + * @param {HedSchemas} hedSchemas - The HED schemas used to validate the tsv file. */ constructor(tsvFile, hedSchemas) { super(hedSchemas) @@ -285,7 +285,7 @@ export class BidsHedTsvParser { /** * The HED schema collection being parsed against. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas @@ -293,7 +293,7 @@ export class BidsHedTsvParser { * Constructor. * * @param {BidsTsvFile} tsvFile The BIDS TSV file being parsed. - * @param {Schemas} hedSchemas The HED schema collection being parsed against. + * @param {HedSchemas} hedSchemas The HED schema collection being parsed against. */ constructor(tsvFile, hedSchemas) { this.tsvFile = tsvFile diff --git a/src/bids/validator/validator.js b/src/bids/validator/validator.js index 0af0b144..0726d9e8 100644 --- a/src/bids/validator/validator.js +++ b/src/bids/validator/validator.js @@ -5,7 +5,7 @@ export class BidsValidator { /** * The HED schema collection being validated against. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas @@ -24,7 +24,7 @@ export class BidsValidator { /** * Constructor. * - * @param {Schemas} hedSchemas - The HED schemas used for validation. + * @param {HedSchemas} hedSchemas - The HED schemas used for validation. */ constructor(hedSchemas) { this.hedSchemas = hedSchemas // Will be set when the file is validated diff --git a/src/parser/definitionManager.js b/src/parser/definitionManager.js index a365ed7e..bf77d1b0 100644 --- a/src/parser/definitionManager.js +++ b/src/parser/definitionManager.js @@ -52,7 +52,7 @@ export class Definition { /** * Return the evaluated definition contents and any issues. * @param {ParsedHedTag} tag - The parsed HED tag whose details should be checked. - * @param {Schemas} hedSchema - The HED schemas used to validate against. + * @param {HedSchemas} hedSchema - The HED schemas used to validate against. * @param {boolean} placeholderAllowed - If true then placeholder is allowed in the def tag. * @returns {Array} - Returns [string, Issue[], Issue[]] containing the evaluated normalized definition string and any issues in the evaluation, */ @@ -110,7 +110,7 @@ export class Definition { * Create a list of Definition objects from a list of strings. * * @param {string} hedString - A string representing a definition. - * @param {Schemas} hedSchemas - The HED schemas to use in creation. + * @param {HedSchemas} hedSchemas - The HED schemas to use in creation. * @returns {Array} - Returns [Definition, Issue[], Issue[]] with the definition and any issues. */ static createDefinition(hedString, hedSchemas) { @@ -224,7 +224,7 @@ export class DefinitionManager { /** * Check the Def tags in a HED string for missing or incorrectly used Def tags. * @param {ParsedHedString} hedString - A parsed HED string to be checked. - * @param {Schemas} hedSchemas - Schemas to validate against. + * @param {HedSchemas} hedSchemas - Schemas to validate against. * @param {boolean} placeholderAllowed - If true then placeholder is allowed in the def tag. * @returns {Issue[]} - If there is no matching definition or definition applied incorrectly. */ @@ -243,7 +243,7 @@ export class DefinitionManager { /** * Check the Def tags in a HED string for missing or incorrectly used Def-expand tags. * @param {ParsedHedString} hedString - A parsed HED string to be checked. - * @param {Schemas} hedSchemas - Schemas to validate against. + * @param {HedSchemas} hedSchemas - Schemas to validate against. * @param {boolean} placeholderAllowed - If true then placeholder is allowed in the def tag. * @returns {Issue[]} - If there is no matching definition or definition applied incorrectly. */ @@ -263,7 +263,7 @@ export class DefinitionManager { /** * Evaluate the definition based on a parsed HED tag. * @param {ParsedHedTag} tag - The tag to evaluate against the definitions. - * @param {Schemas} hedSchemas - The schemas to be used to assist in the evaluation. + * @param {HedSchemas} hedSchemas - The schemas to be used to assist in the evaluation. * @param {boolean} placeholderAllowed - If true then placeholder is allowed in the def tag. * @returns {Array} - Returns [string, Issue[]] with definition contents for this tag and any issues. * @@ -282,7 +282,7 @@ export class DefinitionManager { /** * Recursively check for Def-expand groups in this group. * @param {ParsedHedGroup} topGroup - a top group in a HED string to be evaluated for Def-expand groups. - * @param {Schemas} hedSchemas - The HED schemas to used in the check. + * @param {HedSchemas} hedSchemas - The HED schemas to used in the check. * @param {boolean} placeholderAllowed - If true then placeholder is allowed in the def tag. * @returns {Issue[]} * @private @@ -342,7 +342,7 @@ export class DefinitionManager { * Create a list of Definition objects from a list of strings. * * @param {string[]} defStrings - A list of string definitions. - * @param {Schemas} hedSchemas - The HED schemas to use in creation. + * @param {HedSchemas} hedSchemas - The HED schemas to use in creation. * @returns {Array} - Returns [Definition[], Issue[]] with a definition list and any issues found. */ static createDefinitions(defStrings, hedSchemas) { diff --git a/src/parser/eventManager.js b/src/parser/eventManager.js index b89ce269..a119c009 100644 --- a/src/parser/eventManager.js +++ b/src/parser/eventManager.js @@ -1,5 +1,5 @@ import { generateIssue } from '../issues/issues' -import { BidsHedIssue } from '../bids/types/issues.js' +import { BidsHedIssue } from '../bids/types/issues' export class Event { /** diff --git a/src/parser/parsedHedTag.js b/src/parser/parsedHedTag.js index e57a6c1d..e2509537 100644 --- a/src/parser/parsedHedTag.js +++ b/src/parser/parsedHedTag.js @@ -25,7 +25,7 @@ export default class ParsedHedTag extends ParsedHedSubstring { /** * The HED schema this tag belongs to. - * @type {Schema} + * @type {HedSchema} */ schema @@ -70,7 +70,7 @@ export default class ParsedHedTag extends ParsedHedSubstring { * Constructor. * * @param {TagSpec} tagSpec The token for this tag. - * @param {Schemas} hedSchemas The collection of HED schemas. + * @param {HedSchemas} hedSchemas The collection of HED schemas. * @param {string} hedString The original HED string. * @throws {IssueError} If tag conversion or parsing fails. */ @@ -83,7 +83,7 @@ export default class ParsedHedTag extends ParsedHedSubstring { /** * Convert this tag to its various forms * - * @param {Schemas} hedSchemas The collection of HED schemas. + * @param {HedSchemas} hedSchemas The collection of HED schemas. * @param {string} hedString The original HED string. * @param {TagSpec} tagSpec The token for this tag. * @throws {IssueError} If tag conversion or parsing fails. diff --git a/src/parser/parser.js b/src/parser/parser.js index 7a0d4b57..104d7678 100644 --- a/src/parser/parser.js +++ b/src/parser/parser.js @@ -16,7 +16,7 @@ class HedStringParser { /** * The collection of HED schemas. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas @@ -36,7 +36,7 @@ class HedStringParser { * Constructor. * * @param {string|ParsedHedString} hedString - The HED string to be parsed. - * @param {Schemas} hedSchemas - The collection of HED schemas. + * @param {HedSchemas} hedSchemas - The collection of HED schemas. * @param {boolean} definitionsAllowed - True if definitions are allowed * @param {boolean} placeholdersAllowed - True if placeholders are allowed */ @@ -169,7 +169,7 @@ class HedStringParser { * Parse a list of HED strings. * * @param {string[]|ParsedHedString[]} hedStrings A list of HED strings. - * @param {Schemas} hedSchemas The collection of HED schemas. + * @param {HedSchemas} hedSchemas The collection of HED schemas. * @param {boolean} definitionsAllowed - True if definitions are allowed * @param {boolean} placeholdersAllowed - True if placeholders are allowed * @returns {Array} - [ParsedHedString[], Issue[], Issue[]] representing the parsed HED strings and any errors and warnings. @@ -203,7 +203,7 @@ class HedStringParser { * ###Note: now separates errors and warnings for easier handling. * * @param {string|ParsedHedString} hedString A (possibly already parsed) HED string. - * @param {Schemas} hedSchemas - The collection of HED schemas. + * @param {HedSchemas} hedSchemas - The collection of HED schemas. * @param {boolean} definitionsAllowed - True if definitions are allowed. * @param {boolean} placeholdersAllowed - True if placeholders are allowed. * @param {boolean} fullValidation - True if full validation is required. @@ -217,7 +217,7 @@ export function parseHedString(hedString, hedSchemas, definitionsAllowed, placeh * Parse a HED string in a standalone context. * * @param {string|ParsedHedString} hedString - A (possibly already parsed) HED string. - * @param {Schemas} hedSchemas - The collection of HED schemas. + * @param {HedSchemas} hedSchemas - The collection of HED schemas. * @param {DefinitionManager|null} defManager - The definition manager to use for parsing definitions. * @returns {Array} - [ParsedHedString, Issue[], Issue[]] representing the parsed HED string and any issues found. */ @@ -231,7 +231,7 @@ export function parseStandaloneString(hedString, hedSchemas, defManager = null) * ###Note: now separates errors and warnings for easier handling. * * @param {string[]|ParsedHedString[]} hedStrings - A list of HED strings. - * @param {Schemas} hedSchemas - The collection of HED schemas. + * @param {HedSchemas} hedSchemas - The collection of HED schemas. * @param {boolean} definitionsAllowed - True if definitions are allowed * @param {boolean} placeholdersAllowed - True if placeholders are allowed * @param {boolean} fullValidation - True if full validation is required. diff --git a/src/parser/splitter.js b/src/parser/splitter.js index 5844bca7..a8722b70 100644 --- a/src/parser/splitter.js +++ b/src/parser/splitter.js @@ -14,7 +14,7 @@ export default class HedStringSplitter { /** * The collection of HED schemas. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas @@ -28,7 +28,7 @@ export default class HedStringSplitter { * Constructor. * * @param {string} hedString The HED string to be split and parsed. - * @param {Schemas} hedSchemas The collection of HED schemas. + * @param {HedSchemas} hedSchemas The collection of HED schemas. */ constructor(hedString, hedSchemas) { this.hedString = hedString diff --git a/src/parser/tagConverter.js b/src/parser/tagConverter.js index 11a47fce..05a24534 100644 --- a/src/parser/tagConverter.js +++ b/src/parser/tagConverter.js @@ -4,7 +4,7 @@ import { ReservedChecker } from './reservedChecker' /** * @typedef {import('../schema/entries.js').SchemaTag} SchemaTag - * @typedef {import('../schema/containers.js').Schemas} Schemas + * @typedef {import('../schema/containers.ts').HedSchemas} Schemas * @typedef {import('./tokenizer.js').TagSpec} TagSpec */ @@ -38,7 +38,7 @@ export default class TagConverter { /** * A HED schema collection. - * @type {Schemas} + * @type {HedSchemas} */ hedSchemas @@ -64,7 +64,7 @@ export default class TagConverter { * Constructor. * * @param {TagSpec} tagSpec The tag specification to convert. - * @param {Schemas} hedSchemas The HED schema collection. + * @param {HedSchemas} hedSchemas The HED schema collection. */ constructor(tagSpec, hedSchemas) { this.hedSchemas = hedSchemas diff --git a/src/schema/containers.js b/src/schema/containers.js deleted file mode 100644 index 5d841039..00000000 --- a/src/schema/containers.js +++ /dev/null @@ -1,146 +0,0 @@ -import lt from 'semver/functions/lt' - -import { IssueError } from '../issues/issues' - -/** - * An imported HED 3 schema. - */ -export class Schema { - /** - * The HED schema version. - * @type {string} - */ - version - - /** - * The HED library schema name. - * @type {string} - */ - library - - /** - * This schema's prefix in the active schema set. - * @type {string} - */ - prefix - - /** - * The collection of schema entries. - * @type {SchemaEntries} - */ - entries - - /** - * The standard HED schema version this schema is linked to. - * @type {string} - */ - withStandard - - /** - * Constructor. - * - * @param {Object} xmlData The schema XML data. - * @param {SchemaEntries} entries A collection of schema entries. - */ - constructor(xmlData, entries) { - const rootElement = xmlData.HED - this.version = rootElement?.$?.version - this.library = rootElement?.$?.library ?? '' - - if (!this.library && this.version && lt(this.version, '8.0.0')) { - IssueError.generateAndThrow('deprecatedStandardSchemaVersion', { - version: this.version, - }) - } - - if (!this.library) { - this.withStandard = this.version - } else { - this.withStandard = xmlData.HED?.$?.withStandard - } - this.entries = entries - } -} - -/** - * An imported lazy partnered HED 3 schema. - */ -export class PartneredSchema extends Schema { - /** - * The actual HED 3 schemas underlying this partnered schema. - * @type {Schema[]} - */ - actualSchemas - - /** - * Constructor. - * - * @param {Schema[]} actualSchemas The actual HED 3 schemas underlying this partnered schema. - */ - constructor(actualSchemas) { - if (actualSchemas.length === 0) { - IssueError.generateAndThrowInternalError('A partnered schema set must contain at least one schema.') - } - super({}, actualSchemas[0].entries) - this.actualSchemas = actualSchemas - this.withStandard = actualSchemas[0].withStandard - this.library = undefined - } -} - -/** - * The collection of active HED schemas. - */ -export class Schemas { - /** - * The imported HED schemas. - * - * The empty string key ("") corresponds to the schema with no prefix, - * while other keys correspond to the respective prefixes. - * - * @type {Map} - */ - schemas - - /** - * Constructor. - * @param {Schema|Map} schemas The imported HED schemas. - */ - constructor(schemas) { - if (schemas instanceof Map) { - this.schemas = schemas - } else if (schemas instanceof Schema) { - this.schemas = new Map([['', schemas]]) - } else { - IssueError.generateAndThrowInternalError('Invalid type passed to Schemas constructor') - } - if (this.schemas) { - this._addPrefixesToSchemas() - } - } - - _addPrefixesToSchemas() { - for (const [prefix, schema] of this.schemas) { - schema.prefix = prefix - } - } - - /** - * Return the schema with the given prefix. - * - * @param {string} schemaName A prefix in the schema set. - * @returns {Schema} The schema object corresponding to that prefix. - */ - getSchema(schemaName) { - return this.schemas?.get(schemaName) - } - - /** - * The base schema, i.e. the schema with no prefix, if one is defined. - * - * @returns {Schema} - */ - get baseSchema() { - return this.getSchema('') - } -} diff --git a/src/schema/containers.ts b/src/schema/containers.ts new file mode 100644 index 00000000..6b411b2b --- /dev/null +++ b/src/schema/containers.ts @@ -0,0 +1,153 @@ +import lt from 'semver/functions/lt' + +import { IssueError } from '../issues/issues' +import { SchemaEntries } from './entries' + +type HedSchemaXMLObject = { HED: { $: { version: string; library?: string; withStandard?: string } } } + +export class HedSchema { + /** + * The collection of schema entries. + */ + readonly entries: SchemaEntries + + /** + * The standard HED schema version this schema is linked to. + */ + readonly withStandard: string + + /** + * This schema's prefix in the active schema set. + */ + prefix: string + + /** + * Constructor. + * + * @param entries A collection of schema entries. + * @param withStandard The standard HED schema version this schema is linked to. + */ + constructor(entries: SchemaEntries, withStandard: string) { + this.entries = entries + this.withStandard = withStandard + } +} + +/** + * An imported HED 3 schema. + */ +export class PrimarySchema extends HedSchema { + /** + * The HED schema version. + */ + readonly version: string + + /** + * The HED library schema name. + */ + readonly library: string + + /** + * Constructor. + * + * @param xmlData The schema XML data. + * @param entries A collection of schema entries. + */ + constructor(xmlData: HedSchemaXMLObject, entries: SchemaEntries) { + let withStandard + const rootElement = xmlData.HED + const library = rootElement.$.library ?? '' + const version = rootElement.$.version + + if (!library) { + withStandard = version + } else { + withStandard = xmlData.HED.$.withStandard + } + + super(entries, withStandard) + + if (!this.library && this.version && lt(this.version, '8.0.0')) { + IssueError.generateAndThrow('deprecatedStandardSchemaVersion', { + version: this.version, + }) + } + + this.library = library + this.version = version + } +} + +/** + * An imported lazy partnered HED 3 schema. + */ +export class PartneredSchema extends HedSchema { + /** + * The actual HED 3 schemas underlying this partnered schema. + */ + readonly actualSchemas: HedSchema[] + + /** + * Constructor. + * + * @param actualSchemas The actual HED 3 schemas underlying this partnered schema. + */ + constructor(actualSchemas: HedSchema[]) { + if (actualSchemas.length === 0) { + IssueError.generateAndThrowInternalError('A partnered schema set must contain at least one schema.') + } + super(actualSchemas[0].entries, actualSchemas[0].withStandard) + this.actualSchemas = actualSchemas + } +} + +/** + * The collection of active HED schemas. + */ +export class HedSchemas { + /** + * The imported HED schemas. + * + * The empty string key ("") corresponds to the schema with no prefix, + * while other keys correspond to the respective prefixes. + */ + readonly schemas: Map + + /** + * Constructor. + * @param schemas The imported HED schemas. + */ + constructor(schemas: Map | HedSchema) { + if (schemas instanceof Map) { + this.schemas = schemas + } else if (schemas instanceof HedSchema) { + this.schemas = new Map([['', schemas]]) + } + if (this.schemas) { + this.#addPrefixesToSchemas() + } + } + + #addPrefixesToSchemas() { + for (const [prefix, schema] of this.schemas) { + schema.prefix = prefix + } + } + + /** + * Return the schema with the given prefix. + * + * @param schemaName A prefix in the schema set. + * @returns The schema object corresponding to that prefix. + */ + public getSchema(schemaName: string): HedSchema | undefined { + return this.schemas?.get(schemaName) + } + + /** + * The base schema, i.e. the schema with no prefix, if one is defined. + */ + public get baseSchema(): HedSchema | undefined { + return this.getSchema('') + } +} diff --git a/src/schema/init.js b/src/schema/init.ts similarity index 63% rename from src/schema/init.js rename to src/schema/init.ts index c8fa4843..8218a07f 100644 --- a/src/schema/init.js +++ b/src/schema/init.ts @@ -5,31 +5,33 @@ import { setParent } from '../utils/xml' import SchemaParser from './parser' import PartneredSchemaMerger from './schemaMerger' -import { Schema, Schemas } from './containers' +import { HedSchema, PrimarySchema, HedSchemas } from './containers' import { IssueError } from '../issues/issues' import { splitStringTrimAndRemoveBlanks } from '../utils/string' import { SchemasSpec } from './specs' +type HedSchemaXMLObject = { HED: { $: { version: string; library?: string; withStandard?: string } } } + /** * Build a single schema container object from an XML file. * - * @param {Object} xmlData The schema's XML data - * @returns {Schema} The HED schema object. + * @param xmlData The schema's XML data + * @returns The HED schema object. */ -const buildSchemaObject = function (xmlData) { +function buildSchemaObject(xmlData: HedSchemaXMLObject): PrimarySchema { const rootElement = xmlData.HED setParent(rootElement, null) const schemaEntries = new SchemaParser(rootElement).parse() - return new Schema(xmlData, schemaEntries) + return new PrimarySchema(xmlData, schemaEntries) } /** * Build a single merged schema container object from one or more XML files. * - * @param {Object[]} xmlData The schemas' XML data. - * @returns {Schema} The HED schema object. + * @param xmlData The schemas' XML data. + * @returns The HED schema object. */ -const buildSchemaObjects = function (xmlData) { +function buildSchemaObjects(xmlData: HedSchemaXMLObject[]): HedSchema { const schemas = xmlData.map((data) => buildSchemaObject(data)) if (schemas.length === 1) { return schemas[0] @@ -41,10 +43,10 @@ const buildSchemaObjects = function (xmlData) { /** * Build a schema collection object from a schema specification. * - * @param {SchemasSpec} schemaSpecs The description of which schemas to use. - * @returns {Promise} The schema container object and any issues found. + * @param schemaSpecs The description of which schemas to use. + * @returns The schema container object and any issues found. */ -export async function buildSchemas(schemaSpecs) { +export async function buildSchemas(schemaSpecs: SchemasSpec): Promise { const schemaPrefixes = Array.from(schemaSpecs.data.keys()) /* Data format example: * [[xmlData, ...], [xmlData, xmlData, ...], ...] */ @@ -56,17 +58,17 @@ export async function buildSchemas(schemaSpecs) { ) const schemaObjects = schemaXmlData.map(buildSchemaObjects) const schemas = new Map(zip(schemaPrefixes, schemaObjects)) - return new Schemas(schemas) + return new HedSchemas(schemas) } /** * Build HED schemas from a version specification string. * - * @param {string} hedVersionString The HED version specification string (can contain comma-separated versions). - * @returns {Promise} A Promise that resolves to the built schemas. + * @param hedVersionString The HED version specification string (can contain comma-separated versions). + * @returns A Promise that resolves to the built schemas. * @throws {IssueError} If the schema specification is invalid or schemas cannot be built. */ -export async function buildSchemasFromVersion(hedVersionString) { +export async function buildSchemasFromVersion(hedVersionString?: string): Promise { hedVersionString ??= '' const hedVersionSpecStrings = splitStringTrimAndRemoveBlanks(hedVersionString, ',') const hedVersionSpecs = SchemasSpec.parseVersionSpecs(hedVersionSpecStrings) diff --git a/src/schema/schemaMerger.js b/src/schema/schemaMerger.js index cf00e07d..77144a3a 100644 --- a/src/schema/schemaMerger.js +++ b/src/schema/schemaMerger.js @@ -5,13 +5,13 @@ import { PartneredSchema } from './containers' export default class PartneredSchemaMerger { /** * The sources of data to be merged. - * @type {Schema[]} + * @type {HedSchema[]} */ sourceSchemas /** * The current source of data to be merged. - * @type {Schema} + * @type {HedSchema} */ currentSource @@ -24,7 +24,7 @@ export default class PartneredSchemaMerger { /** * Constructor. * - * @param {Schema[]} sourceSchemas The sources of data to be merged. + * @param {HedSchema[]} sourceSchemas The sources of data to be merged. */ constructor(sourceSchemas) { this.sourceSchemas = sourceSchemas diff --git a/tests/jsonTests/definitionManagerCreationTests.spec.js b/tests/jsonTests/definitionManagerCreationTests.spec.js index 670687f0..94c8fc51 100644 --- a/tests/jsonTests/definitionManagerCreationTests.spec.js +++ b/tests/jsonTests/definitionManagerCreationTests.spec.js @@ -6,7 +6,7 @@ import path from 'node:path' import { buildSchemas } from '../../src/schema/init' import { SchemaSpec, SchemasSpec } from '../../src/schema/specs' import { parseHedString } from '../../src/parser/parser' -import { definitionTestData } from '../jsonTestData/definitionManagerCreationTests.data' +import { definitionTestData } from '../jsonTestData/definitionManagerCreationTests.data.js' import { shouldRun } from '../testHelpers/testUtilities' import { Definition, DefinitionManager } from '../../src/parser/definitionManager' import { Issue } from '../../src/issues/issues' diff --git a/tests/jsonTests/schemaBuildTests.spec.js b/tests/jsonTests/schemaBuildTests.spec.js index e888cf42..6745b16e 100644 --- a/tests/jsonTests/schemaBuildTests.spec.js +++ b/tests/jsonTests/schemaBuildTests.spec.js @@ -7,7 +7,7 @@ import { BidsJsonFile } from '../../src/bids' import { shouldRun } from '../testHelpers/testUtilities' import { schemaBuildTestData } from '../jsonTestData/schemaBuildTests.data' -import { Schemas } from '../../src/schema/containers' +import { HedSchemas } from '../../src/schema/containers' // Ability to select individual tests to run const skipMap = new Map() @@ -31,7 +31,7 @@ describe('Schema build validation', () => { assert.strictEqual(caughtErrorString, expectedErrorString, header) if (expectedErrorCode === null) { - assert.instanceOf(schema, Schemas, header + caughtErrorString) + assert.instanceOf(schema, HedSchemas, header + caughtErrorString) } } diff --git a/tests/otherTests/dataset.spec.js b/tests/otherTests/dataset.spec.js index 012371c7..657bdae5 100644 --- a/tests/otherTests/dataset.spec.js +++ b/tests/otherTests/dataset.spec.js @@ -4,7 +4,7 @@ import fs from 'node:fs' import { toMatchIssue } from '../testHelpers/toMatchIssue' import { BidsDataset } from '../../src/bids/types/dataset' import { BidsDirectoryAccessor, BidsFileAccessor } from '../../src/bids/datasetParser' -import { Schemas } from '../../src/schema/containers' +import { HedSchemas } from '../../src/schema/containers' expect.extend({ toMatchIssue(receivedError, expectedCode, expectedParams) { @@ -28,7 +28,7 @@ describe('BidsDataset', () => { const [dataset, issues] = await BidsDataset.create(demoDataRoot, BidsDirectoryAccessor) expect(dataset).toBeInstanceOf(BidsDataset) expect(issues.length).toBe(0) - expect(dataset.hedSchemas).toBeInstanceOf(Schemas) + expect(dataset.hedSchemas).toBeInstanceOf(HedSchemas) expect(dataset.sidecarMap.size).toBe(9) }) @@ -51,7 +51,7 @@ describe('BidsDataset', () => { expect(issues).toEqual([]) expect(dataset.hedSchemas).toBeDefined() expect(dataset.hedSchemas).not.toBeNull() - expect(dataset.hedSchemas).toBeInstanceOf(Schemas) + expect(dataset.hedSchemas).toBeInstanceOf(HedSchemas) }) it('should throw "missingSchemaSpecification" if dataset_description.json is missing', async () => { @@ -133,7 +133,7 @@ describe('BidsDataset', () => { describe('validate', () => { it('should return an empty array if there are no validation issues', async () => { const [dataset, issues] = await BidsDataset.create(demoDataRoot, BidsDirectoryAccessor) - expect(dataset.hedSchemas).toBeInstanceOf(Schemas) + expect(dataset.hedSchemas).toBeInstanceOf(HedSchemas) expect(issues).toEqual([]) const tissues = await dataset.validate() diff --git a/tests/otherTests/issues.spec.js b/tests/otherTests/issues.spec.js index 4ee1df72..47f1d808 100644 --- a/tests/otherTests/issues.spec.js +++ b/tests/otherTests/issues.spec.js @@ -1,5 +1,5 @@ -import { BidsHedIssue } from '../../src/bids/types/issues.js' -import { Issue, IssueError, generateIssue } from '../../src/issues/issues.js' +import { BidsHedIssue } from '../../src/bids/types/issues' +import { Issue, IssueError, generateIssue } from '../../src/issues/issues' describe('BidsHedIssue', () => { describe('transformToBids', () => { diff --git a/tests/otherTests/schema.spec.js b/tests/otherTests/schema.spec.js index 336bc395..71657de6 100644 --- a/tests/otherTests/schema.spec.js +++ b/tests/otherTests/schema.spec.js @@ -7,9 +7,9 @@ import { PartneredSchema } from '../../src/schema/containers' import { buildSchemas, buildSchemasFromVersion } from '../../src/schema/init' import { SchemaSpec, SchemasSpec } from '../../src/schema/specs' import { buildSchemasSpec } from '../../src/bids/schema' -import { BidsJsonFile } from '../../src/bids/index.js' -import { IssueError } from '../../src/issues/issues.js' -import { getLocalSchemaVersions } from '../../src/schema/config.js' +import { BidsJsonFile } from '../../src/bids/index' +import { IssueError } from '../../src/issues/issues' +import { getLocalSchemaVersions } from '../../src/schema/config' describe('HED schemas', () => { describe('Schema loading', () => { diff --git a/types/index.d.ts b/types/index.d.ts index 6fc93e2b..2e7b45fc 100644 --- a/types/index.d.ts +++ b/types/index.d.ts @@ -8,7 +8,7 @@ export class BidsDataset { sidecarMap: Map /** The HED schemas used to validate this dataset */ - hedSchemas: Schemas | null + hedSchemas: HedSchemas | null /** Factory method to create a BidsDataset */ static create( @@ -38,7 +38,7 @@ export class BidsJsonFile { constructor(name: string, file: object | null, jsonData: Record) /** Validate this file against HED schemas */ - validate(schemas: Schemas | undefined): BidsHedIssue[] + validate(schemas: HedSchemas | undefined): BidsHedIssue[] /** Whether this file has any HED data */ get hasHedData(): boolean @@ -73,10 +73,10 @@ export class BidsSidecar extends BidsJsonFile { get hasHedData(): boolean /** Parse this sidecar's HED strings within the sidecar structure */ - parseSidecarKeys(hedSchemas: Schemas, fullValidation?: boolean): [Issue[], Issue[]] + parseSidecarKeys(hedSchemas: HedSchemas, fullValidation?: boolean): [Issue[], Issue[]] /** Validate this file against HED schemas */ - validate(schemas: Schemas | undefined): BidsHedIssue[] + validate(schemas: HedSchemas | undefined): BidsHedIssue[] /** The validator class used to validate this file */ get validatorClass(): any @@ -110,7 +110,7 @@ export class BidsTsvFile { get isTimelineFile(): boolean /** Validate this file against HED schemas */ - validate(schemas: Schemas | undefined): BidsHedIssue[] + validate(schemas: HedSchemas | undefined): BidsHedIssue[] /** The validator class used to validate this file */ get validatorClass(): any @@ -248,7 +248,7 @@ export class Definition { /** Evaluate the definition and return contents with any issues */ evaluateDefinition( tag: ParsedHedTag, - hedSchema: Schemas, + hedSchema: HedSchemas, placeholderAllowed: boolean, ): [string | null, Issue[], Issue[]] @@ -256,7 +256,7 @@ export class Definition { equivalent(other: Definition): boolean /** Create a definition from a HED string */ - static createDefinition(hedString: string, hedSchemas: Schemas): [Definition | null, Issue[], Issue[]] + static createDefinition(hedString: string, hedSchemas: HedSchemas): [Definition | null, Issue[], Issue[]] /** Factory method to create a Definition from a group */ static createDefinitionFromGroup(definitionGroup: ParsedHedGroup): [Definition | null, Issue[], Issue[]] @@ -275,10 +275,10 @@ export class DefinitionManager { addDefinition(definition: Definition): Issue[] /** Check Def tags in a HED string for missing or incorrectly used definitions */ - validateDefs(hedString: ParsedHedString, hedSchemas: Schemas, placeholderAllowed: boolean): Issue[] + validateDefs(hedString: ParsedHedString, hedSchemas: HedSchemas, placeholderAllowed: boolean): Issue[] /** Check Def-expand tags in a HED string for missing or incorrectly used definitions */ - validateDefExpands(hedString: ParsedHedString, hedSchemas: Schemas, placeholderAllowed: boolean): Issue[] + validateDefExpands(hedString: ParsedHedString, hedSchemas: HedSchemas, placeholderAllowed: boolean): Issue[] } // Parsed HED types (used by Definition) @@ -331,7 +331,7 @@ export class ParsedHedTag { /** The canonical form of the HED tag */ canonicalTag: string /** The HED schema this tag belongs to */ - schema: Schema + schema: HedSchema /** The schema's representation of this tag */ schemaTag: SchemaTag /** The tag value */ @@ -346,7 +346,7 @@ export class ParsedHedTag { _units: string /** Constructor for ParsedHedTag */ - constructor(tagSpec: TagSpec, hedSchemas: Schemas, hedString: string) + constructor(tagSpec: TagSpec, hedSchemas: HedSchemas, hedString: string) /** Format this tag nicely */ format(long?: boolean): string @@ -431,11 +431,7 @@ export class ParsedHedString { } // Schema types -export class Schema { - /** The HED schema version */ - version: string - /** The HED library schema name */ - library: string +export class HedSchema { /** This schema's prefix in the active schema set */ prefix: string /** The collection of schema entries */ @@ -602,17 +598,17 @@ export class SchemaTag extends SchemaEntryWithAttributes { parentHasAttribute(attributeName: string): boolean } -export class Schemas { +export class HedSchemas { /** The imported HED schemas */ - schemas: Map + schemas: Map - constructor(schemas: Schema | Map) + constructor(schemas: HedSchema | Map) /** Get schema by name */ - getSchema(name?: string): Schema + getSchema(name?: string): HedSchema | undefined /** The base schema, i.e. the schema with no prefix, if one is defined. */ - get baseSchema(): Schema + get baseSchema(): HedSchema | undefined } // Schema exports @@ -633,7 +629,7 @@ export function buildSchemasFromVersion(version: string): Promise */ export function parseHedString( hedString: string | ParsedHedString, - hedSchemas: Schemas, + hedSchemas: HedSchemas, definitionsAllowed: boolean, placeholdersAllowed: boolean, fullValidation: boolean, @@ -649,7 +645,7 @@ export function parseHedString( */ export function parseStandaloneString( hedString: string | ParsedHedString, - hedSchemas: Schemas, + hedSchemas: HedSchemas, defManager?: DefinitionManager | null, ): [ParsedHedString, Issue[], Issue[]] @@ -665,7 +661,7 @@ export function parseStandaloneString( */ export function parseHedStrings( hedStrings: (string | ParsedHedString)[], - hedSchemas: Schemas, + hedSchemas: HedSchemas, definitionsAllowed: boolean, placeholdersAllowed: boolean, fullValidation: boolean, diff --git a/types/test.ts b/types/test.ts index 1c450c74..ead0f9ad 100644 --- a/types/test.ts +++ b/types/test.ts @@ -25,7 +25,7 @@ import { ParsedHedColumnSplice, // Schema - Schema, + HedSchema, SchemaEntries, SchemaEntryManager, SchemaEntry, @@ -37,7 +37,7 @@ import { SchemaUnitModifier, SchemaValueClass, SchemaTag, - Schemas, + HedSchemas, // Parser functions parseStandaloneString, @@ -59,7 +59,7 @@ const fakePath = '/fake/path' const fakeFile: object = { name: 'fake.json', path: fakePath } const fakeHedString = 'Event' -async function testBids(schemas: Schemas) { +async function testBids(schemas: HedSchemas) { // BidsDataset const [dataset, bidsIssues] = await BidsDataset.create(fakePath, BidsDirectoryAccessor) if (dataset) { @@ -159,7 +159,7 @@ function testIssues() { } function testParser( - schemas: Schemas, + schemas: HedSchemas, parsedString: ParsedHedString, parsedTag: ParsedHedTag, parsedGroup: ParsedHedGroup, @@ -189,7 +189,7 @@ function testParser( // ParsedHedTag const tagSpec: TagSpec = { tag: 'tag', library: 'lib', start: 0, end: 3 } const parsedHedTag = new ParsedHedTag(tagSpec, schemas, fakeHedString) - const schema: Schema = parsedHedTag.schema + const schema: HedSchema = parsedHedTag.schema const schemaTag: SchemaTag = parsedHedTag.schemaTag console.log( parsedHedTag.originalTag, @@ -245,13 +245,13 @@ function testParser( parsedHedString.toString() } -function testSchemaTypes(schemas: Schemas) { - // Schema - const schema: Schema = schemas.getSchema('') +function testSchemaTypes(schemas: HedSchemas) { + // HedSchema + const schema: HedSchema = schemas.getSchema('') if (!schema) { return } - console.log(schema.version, schema.library, schema.prefix, schema.entries, schema.withStandard) + console.log(schema.prefix, schema.entries, schema.withStandard) // SchemaEntries const entries: SchemaEntries = schema.entries From 173a2b5929cad360612278ceef904b5184eabe8f Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 11 Aug 2025 17:23:53 -0500 Subject: [PATCH 07/63] Fix linter error --- tests/otherTests/schema.spec.js | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/otherTests/schema.spec.js b/tests/otherTests/schema.spec.js index 71657de6..9584ea9c 100644 --- a/tests/otherTests/schema.spec.js +++ b/tests/otherTests/schema.spec.js @@ -2,13 +2,12 @@ import chai from 'chai' const assert = chai.assert import { beforeAll, describe, it } from '@jest/globals' -import { generateIssue } from '../../src/issues/issues' +import { generateIssue, IssueError } from '../../src/issues/issues' import { PartneredSchema } from '../../src/schema/containers' import { buildSchemas, buildSchemasFromVersion } from '../../src/schema/init' import { SchemaSpec, SchemasSpec } from '../../src/schema/specs' import { buildSchemasSpec } from '../../src/bids/schema' import { BidsJsonFile } from '../../src/bids/index' -import { IssueError } from '../../src/issues/issues' import { getLocalSchemaVersions } from '../../src/schema/config' describe('HED schemas', () => { From adc15b6dadd5cc20b04552adf715f0343e61fae8 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 13 Aug 2025 05:26:52 -0500 Subject: [PATCH 08/63] Implement Copilot suggestions --- src/schema/containers.ts | 6 ++---- tests/jsonTests/definitionManagerCreationTests.spec.js | 5 +++-- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/src/schema/containers.ts b/src/schema/containers.ts index 6b411b2b..9e83a406 100644 --- a/src/schema/containers.ts +++ b/src/schema/containers.ts @@ -120,12 +120,10 @@ export class HedSchemas { constructor(schemas: Map | HedSchema) { if (schemas instanceof Map) { this.schemas = schemas - } else if (schemas instanceof HedSchema) { + } else { this.schemas = new Map([['', schemas]]) } - if (this.schemas) { - this.#addPrefixesToSchemas() - } + this.#addPrefixesToSchemas() } #addPrefixesToSchemas() { diff --git a/tests/jsonTests/definitionManagerCreationTests.spec.js b/tests/jsonTests/definitionManagerCreationTests.spec.js index 94c8fc51..9af4419e 100644 --- a/tests/jsonTests/definitionManagerCreationTests.spec.js +++ b/tests/jsonTests/definitionManagerCreationTests.spec.js @@ -1,12 +1,13 @@ +import path from 'node:path' + import chai from 'chai' const assert = chai.assert import { beforeAll, describe, afterAll } from '@jest/globals' -import path from 'node:path' import { buildSchemas } from '../../src/schema/init' import { SchemaSpec, SchemasSpec } from '../../src/schema/specs' import { parseHedString } from '../../src/parser/parser' -import { definitionTestData } from '../jsonTestData/definitionManagerCreationTests.data.js' +import { definitionTestData } from '../jsonTestData/definitionManagerCreationTests.data' import { shouldRun } from '../testHelpers/testUtilities' import { Definition, DefinitionManager } from '../../src/parser/definitionManager' import { Issue } from '../../src/issues/issues' From 4bd670a3836db19e5afe2b2536916ac0c51cfa59 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 13 Aug 2025 05:31:01 -0500 Subject: [PATCH 09/63] Test constants instead of yet-to-be-assigned object fields --- src/schema/containers.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/schema/containers.ts b/src/schema/containers.ts index 9e83a406..87b1fe25 100644 --- a/src/schema/containers.ts +++ b/src/schema/containers.ts @@ -67,9 +67,9 @@ export class PrimarySchema extends HedSchema { super(entries, withStandard) - if (!this.library && this.version && lt(this.version, '8.0.0')) { + if (!library && version && lt(version, '8.0.0')) { IssueError.generateAndThrow('deprecatedStandardSchemaVersion', { - version: this.version, + version, }) } From 99e2ac3e31d9fbc55a6e11536de5bbc676f3ff76 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 13 Aug 2025 06:49:24 -0500 Subject: [PATCH 10/63] Port schema merging and entries to TypeScript SchemaEntryManager._definitions being public is unsatisfactory and should be fixed later. --- package-lock.json | 8 + package.json | 1 + src/parser/tagConverter.js | 2 +- src/schema/containers.ts | 2 +- src/schema/{entries.js => entries.ts} | 409 ++++++++---------- .../{schemaMerger.js => schemaMerger.ts} | 62 ++- 6 files changed, 211 insertions(+), 273 deletions(-) rename src/schema/{entries.js => entries.ts} (60%) rename src/schema/{schemaMerger.js => schemaMerger.ts} (73%) diff --git a/package-lock.json b/package-lock.json index caa35566..a98f1971 100644 --- a/package-lock.json +++ b/package-lock.json @@ -25,6 +25,7 @@ "@jest/globals": "^30.0.0", "@types/lodash": "^4.17.20", "@types/node": "^24.2.0", + "@types/pluralize": "^0.0.33", "@types/semver": "^7.7.0", "babel-jest": "^30.0.5", "chai": "^4.3.6", @@ -3421,6 +3422,13 @@ "undici-types": "~7.10.0" } }, + "node_modules/@types/pluralize": { + "version": "0.0.33", + "resolved": "https://registry.npmjs.org/@types/pluralize/-/pluralize-0.0.33.tgz", + "integrity": "sha512-JOqsl+ZoCpP4e8TDke9W79FDcSgPAR0l6pixx2JHkhnRjvShyYiAYw2LVsnA7K08Y6DeOnaU6ujmENO4os/cYg==", + "dev": true, + "license": "MIT" + }, "node_modules/@types/semver": { "version": "7.7.0", "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.7.0.tgz", diff --git a/package.json b/package.json index c8af698a..62f396f2 100644 --- a/package.json +++ b/package.json @@ -61,6 +61,7 @@ "@jest/globals": "^30.0.0", "@types/lodash": "^4.17.20", "@types/node": "^24.2.0", + "@types/pluralize": "^0.0.33", "@types/semver": "^7.7.0", "babel-jest": "^30.0.5", "chai": "^4.3.6", diff --git a/src/parser/tagConverter.js b/src/parser/tagConverter.js index 05a24534..722d55d5 100644 --- a/src/parser/tagConverter.js +++ b/src/parser/tagConverter.js @@ -3,7 +3,7 @@ import { getTagSlashIndices } from '../utils/hedStrings' import { ReservedChecker } from './reservedChecker' /** - * @typedef {import('../schema/entries.js').SchemaTag} SchemaTag + * @typedef {import('../schema/entries.ts').SchemaTag} SchemaTag * @typedef {import('../schema/containers.ts').HedSchemas} Schemas * @typedef {import('./tokenizer.js').TagSpec} TagSpec */ diff --git a/src/schema/containers.ts b/src/schema/containers.ts index 87b1fe25..539da99e 100644 --- a/src/schema/containers.ts +++ b/src/schema/containers.ts @@ -126,7 +126,7 @@ export class HedSchemas { this.#addPrefixesToSchemas() } - #addPrefixesToSchemas() { + #addPrefixesToSchemas(): void { for (const [prefix, schema] of this.schemas) { schema.prefix = prefix } diff --git a/src/schema/entries.js b/src/schema/entries.ts similarity index 60% rename from src/schema/entries.js rename to src/schema/entries.ts index da2030be..8b2e0801 100644 --- a/src/schema/entries.js +++ b/src/schema/entries.ts @@ -3,6 +3,7 @@ pluralize.addUncountableRule('hertz') import { IssueError } from '../issues/issues' import Memoizer from '../utils/memoizer' +import SchemaParser from './parser' /** * SchemaEntries class @@ -10,45 +11,39 @@ import Memoizer from '../utils/memoizer' export class SchemaEntries extends Memoizer { /** * The schema's properties. - * @type {SchemaEntryManager} */ - properties + readonly properties: SchemaEntryManager /** * The schema's attributes. - * @type {SchemaEntryManager} */ - attributes + readonly attributes: SchemaEntryManager /** * The schema's value classes. - * @type {SchemaEntryManager} */ - valueClasses + readonly valueClasses: SchemaEntryManager /** * The schema's unit classes. - * @type {SchemaEntryManager} */ - unitClasses + readonly unitClasses: SchemaEntryManager /** * The schema's unit modifiers. - * @type {SchemaEntryManager} */ - unitModifiers + readonly unitModifiers: SchemaEntryManager /** * The schema's tags. - * @type {SchemaEntryManager} */ - tags + readonly tags: SchemaEntryManager /** * Constructor. - * @param {SchemaParser} schemaParser A constructed schema parser. + * @param schemaParser A constructed schema parser. */ - constructor(schemaParser) { + constructor(schemaParser: SchemaParser) { super() this.properties = new SchemaEntryManager(schemaParser.properties) this.attributes = new SchemaEntryManager(schemaParser.attributes) @@ -61,81 +56,71 @@ export class SchemaEntries extends Memoizer { /** * A manager of {@link SchemaEntry} objects. - * - * @template T */ -export class SchemaEntryManager extends Memoizer { +export class SchemaEntryManager extends Memoizer { /** * The definitions managed by this entry manager. - * @type {Map} */ - _definitions + readonly _definitions: Map /** * Constructor. * - * @param {Map} definitions A map of schema entry definitions. + * @param definitions A map of schema entry definitions. */ - constructor(definitions) { + constructor(definitions: Map) { super() this._definitions = definitions } /** * Iterator over the entry manager's entries. - * - * @template T - * @returns {IterableIterator} - [string, T] */ - [Symbol.iterator]() { + public [Symbol.iterator](): MapIterator<[string, T]> { return this._definitions.entries() } /** * Iterator over the entry manager's keys. - * - * @returns {IterableIterator} - [string] */ - keys() { + public keys(): MapIterator { return this._definitions.keys() } /** * Iterator over the entry manager's keys. - * - * @returns {IterableIterator} - [T] */ - values() { + public values(): MapIterator { return this._definitions.values() } /** * Determine whether the entry with the given name exists. * - * @param {string} name The name of the entry. - * @return {boolean} Whether the entry exists. + * @param name The name of the entry. + * @return Whether the entry exists. */ - hasEntry(name) { + public hasEntry(name: string): boolean { return this._definitions.has(name) } /** * Get the entry with the given name. * - * @param {string} name - The name of the entry to retrieve. - * @returns {T} - The entry with that name. + * @param name The name of the entry to retrieve. + * @returns The entry with that name. */ - getEntry(name) { + public getEntry(name: string): T { return this._definitions.get(name) } /** * Get a collection of entries with the given boolean attribute. * - * @param {string} booleanAttributeName - The name of boolean attribute to filter on. - * @returns {Map} - string->T representing a collection of entries with that attribute. + * @param booleanAttributeName The name of boolean attribute to filter on. + * @returns A subset of the managed collection with the given boolean attribute. */ - getEntriesWithBooleanAttribute(booleanAttributeName) { + public getEntriesWithBooleanAttribute(booleanAttributeName: string): Map { return this._memoize(booleanAttributeName, () => { return this.filter(([, v]) => { return v.hasBooleanAttribute(booleanAttributeName) @@ -146,33 +131,20 @@ export class SchemaEntryManager extends Memoizer { /** * Filter the map underlying this manager. * - * @param {function} fn - ([string, T]): boolean specifying the filtering function. - * @returns {Map} - string->T representing a collection of entries with that attribute. + * @param fn The filtering function. + * @returns A subset of the managed collection satisfying the filter. */ - filter(fn) { - return SchemaEntryManager._filterDefinitionMap(this._definitions, fn) - } - - /** - * Filter a definition map. - * - * @template T - * @param {Map} definitionMap The definition map. - * @param {function} fn - ([string, T]):boolean specifying the filtering function. - * @returns {Map} - string->T representing the filtered definitions. - * @protected - */ - static _filterDefinitionMap(definitionMap, fn) { - const pairArray = Array.from(definitionMap.entries()) + public filter(fn: (entry: [string, T]) => boolean): Map { + const pairArray = Array.from(this._definitions.entries()) return new Map(pairArray.filter((entry) => fn(entry))) } /** * The number of entries in this collection. * - * @returns {number} The number of entries in this collection. + * @returns The number of entries in this collection. */ - get length() { + public get length(): number { return this._definitions.size } } @@ -183,20 +155,18 @@ export class SchemaEntryManager extends Memoizer { export class SchemaEntry extends Memoizer { /** * The name of this schema entry. - * @type {string} */ - _name + private readonly _name: string - constructor(name) { + constructor(name: string) { super() this._name = name } /** * The name of this schema entry. - * @returns {string} */ - get name() { + public get name(): string { return this._name } @@ -205,16 +175,17 @@ export class SchemaEntry extends Memoizer { * * This method is a stub to be overridden in {@link SchemaEntryWithAttributes}. * - * @param {string} attributeName The attribute to check for. - * @returns {boolean} Whether this schema entry has this attribute. + * @param attributeName The attribute to check for. + * @returns Whether this schema entry has this attribute. */ // eslint-disable-next-line no-unused-vars - hasBooleanAttribute(attributeName) { + public hasBooleanAttribute(attributeName: string): boolean { return false } } // TODO: Switch back to class constant once upstream bug is fixed. +type SchemaPropertyType = 'categoryProperty' | 'typeProperty' | 'roleProperty' const categoryProperty = 'categoryProperty' const typeProperty = 'typeProperty' const roleProperty = 'roleProperty' @@ -225,36 +196,32 @@ const roleProperty = 'roleProperty' export class SchemaProperty extends SchemaEntry { /** * The type of the property. - * @type {string} */ - _propertyType + private readonly _propertyType: SchemaPropertyType - constructor(name, propertyType) { + constructor(name: string, propertyType: SchemaPropertyType) { super(name) this._propertyType = propertyType } /** * Whether this property describes a schema category. - * @returns {boolean} */ - get isCategoryProperty() { + public get isCategoryProperty(): boolean { return this._propertyType === categoryProperty } /** * Whether this property describes a data type. - * @returns {boolean} */ - get isTypeProperty() { + public get isTypeProperty(): boolean { return this._propertyType === typeProperty } /** * Whether this property describes a role. - * @returns {boolean} */ - get isRoleProperty() { + public get isRoleProperty(): boolean { return this._propertyType === roleProperty } } @@ -272,30 +239,27 @@ const stringProperty = new SchemaProperty('stringProperty', typeProperty) export class SchemaAttribute extends SchemaEntry { /** * The categories of elements this schema attribute applies to. - * @type {Set} */ - _categoryProperties + private readonly _categoryProperties: Set /** * The data type of this schema attribute. - * @type {SchemaProperty} */ - _typeProperty + private readonly _typeProperty: SchemaProperty /** * The set of role properties for this schema attribute. - * @type {Set} */ - _roleProperties + private readonly _roleProperties: Set /** * Constructor. * - * @param {string} name The name of the schema attribute. - * @param {SchemaProperty[]} properties The properties assigned to this schema attribute. + * @param name The name of the schema attribute. + * @param properties The properties assigned to this schema attribute. */ - constructor(name, properties) { - super(name, new Set(), new Map()) + constructor(name: string, properties: SchemaProperty[]) { + super(name) // Parse properties const categoryProperties = properties.filter((property) => property?.isCategoryProperty) @@ -307,9 +271,8 @@ export class SchemaAttribute extends SchemaEntry { /** * The categories of elements this schema attribute applies to. - * @returns {Set|SchemaProperty|undefined} */ - get categoryProperty() { + public get categoryProperty(): Set | SchemaProperty | undefined { switch (this._categoryProperties.size) { case 0: return undefined @@ -322,17 +285,15 @@ export class SchemaAttribute extends SchemaEntry { /** * The data type property of this schema attribute. - * @returns {SchemaProperty} */ - get typeProperty() { + public get typeProperty(): SchemaProperty { return this._typeProperty } /** * The set of role properties for this schema attribute. - * @returns {Set} */ - get roleProperties() { + public get roleProperties(): Set { return new Set(this._roleProperties) } } @@ -343,41 +304,28 @@ export class SchemaAttribute extends SchemaEntry { export class SchemaEntryWithAttributes extends SchemaEntry { /** * The set of boolean attributes this schema entry has. - * @type {Set} */ - booleanAttributes + readonly booleanAttributes: Set /** * The collection of value attributes this schema entry has. - * @type {Map} */ - valueAttributes + readonly valueAttributes: Map /** * The set of boolean attribute names this schema entry has. - * @type {Set} */ - booleanAttributeNames + readonly booleanAttributeNames: Set /** * The collection of value attribute names this schema entry has. - * @type {Map} */ - valueAttributeNames + readonly valueAttributeNames: Map - constructor(name, booleanAttributes, valueAttributes) { + constructor(name: string, booleanAttributes: Set, valueAttributes: Map) { super(name) this.booleanAttributes = booleanAttributes this.valueAttributes = valueAttributes - this._parseAttributeNames() - } - - /** - * Create aliases of the attribute collections keyed on their names. - * - * @private - */ - _parseAttributeNames() { this.booleanAttributeNames = new Set() for (const attribute of this.booleanAttributes) { this.booleanAttributeNames.add(attribute.name) @@ -390,43 +338,41 @@ export class SchemaEntryWithAttributes extends SchemaEntry { /** * Whether this schema entry has this attribute (by name). - * @param {string} attributeName The attribute to check for. - * @returns {boolean} Whether this schema entry has this attribute. + * @param attributeName The attribute to check for. + * @returns Whether this schema entry has this attribute. */ - hasAttribute(attributeName) { + public hasAttribute(attributeName: string): boolean { return this.booleanAttributeNames.has(attributeName) || this.valueAttributeNames.has(attributeName) } /** * Whether this schema entry has this boolean attribute (by name). - * @param {string} attributeName The attribute to check for. - * @returns {boolean} Whether this schema entry has this attribute. + * @param attributeName The attribute to check for. + * @returns Whether this schema entry has this attribute. */ - hasBooleanAttribute(attributeName) { + public hasBooleanAttribute(attributeName: string): boolean { return this.booleanAttributeNames.has(attributeName) } /** * Retrieve the value of a value attribute (by name) on this schema entry. - * @param {string} attributeName The attribute whose value should be returned. - * @param {boolean} alwaysReturnArray Whether to return a singleton array instead of a scalar value. - * @returns {*} The value of the attribute. + * @param attributeName The attribute whose value should be returned. + * @param alwaysReturnArray Whether to return a singleton array instead of a scalar value. + * @returns The value of the attribute. */ - getAttributeValue(attributeName, alwaysReturnArray = false) { + public getAttributeValue(attributeName: string, alwaysReturnArray = false): any { return SchemaEntryWithAttributes._getMapArrayValue(this.valueAttributeNames, attributeName, alwaysReturnArray) } /** * Return a map value, with a scalar being returned in lieu of a singleton array if alwaysReturnArray is false. * - * @template K,V - * @param {Map} map The map to search. - * @param {K} key A key in the map. - * @param {boolean} alwaysReturnArray Whether to return a singleton array instead of a scalar value. - * @returns {V|V[]} The value for the key in the passed map. - * @private + * @param map The map to search. + * @param key A key in the map. + * @param alwaysReturnArray Whether to return a singleton array instead of a scalar value. + * @returns The value for the key in the passed map. */ - static _getMapArrayValue(map, key, alwaysReturnArray) { + private static _getMapArrayValue(map: Map, key: K, alwaysReturnArray: boolean): V | V[] { const value = map.get(key) if (!alwaysReturnArray && Array.isArray(value) && value.length === 1) { return value[0] @@ -442,19 +388,23 @@ export class SchemaEntryWithAttributes extends SchemaEntry { export class SchemaUnit extends SchemaEntryWithAttributes { /** * The legal derivatives of this unit. - * @type {string[]} */ - _derivativeUnits + private readonly _derivativeUnits: string[] /** * Constructor. * - * @param {string} name The name of the unit. - * @param {Set} booleanAttributes This unit's boolean attributes. - * @param {Map} valueAttributes This unit's key-value attributes. - * @param {SchemaEntryManager} unitModifiers The collection of unit modifiers. - */ - constructor(name, booleanAttributes, valueAttributes, unitModifiers) { + * @param name The name of the unit. + * @param booleanAttributes This unit's boolean attributes. + * @param valueAttributes This unit's key-value attributes. + * @param unitModifiers The collection of unit modifiers. + */ + constructor( + name: string, + booleanAttributes: Set, + valueAttributes: Map, + unitModifiers: SchemaEntryManager, + ) { super(name, booleanAttributes, valueAttributes) this._derivativeUnits = [name] @@ -476,40 +426,40 @@ export class SchemaUnit extends SchemaEntryWithAttributes { } } - _pushPluralUnit() { + private _pushPluralUnit(): string | null { if (!this.isUnitSymbol) { - const pluralUnit = pluralize.plural(this._name) + const pluralUnit = pluralize.plural(this.name) this._derivativeUnits.push(pluralUnit) return pluralUnit } return null } - *derivativeUnits() { + public *derivativeUnits(): Generator { for (const unit of this._derivativeUnits) { yield unit } } - get isPrefixUnit() { + public get isPrefixUnit(): boolean { return this.hasAttribute('unitPrefix') } - get isSIUnit() { + public get isSIUnit(): boolean { return this.hasAttribute('SIUnit') } - get isUnitSymbol() { + public get isUnitSymbol(): boolean { return this.hasAttribute('unitSymbol') } /** * Determine if a value has this unit. * - * @param {string} value -- either the whole value or the part after a blank (if not a prefix unit) - * @returns {boolean} Whether the value has these units. + * @param value Either the whole value or the part after a blank (if not a prefix unit) + * @returns Whether the value has these units. */ - validateUnit(value) { + public validateUnit(value: string): boolean { if (value == null || value === '') { return false } @@ -534,42 +484,45 @@ export class SchemaUnitClass extends SchemaEntryWithAttributes { * The units for this unit class. * @type {Map} */ - _units + private readonly _units: Map /** * Constructor. * - * @param {string} name The name of this unit class. - * @param {Set} booleanAttributes The boolean attributes for this unit class. - * @param {Map} valueAttributes The value attributes for this unit class. - * @param {Map} units The units for this unit class. - */ - constructor(name, booleanAttributes, valueAttributes, units) { + * @param name The name of this unit class. + * @param booleanAttributes The boolean attributes for this unit class. + * @param valueAttributes The value attributes for this unit class. + * @param units The units for this unit class. + */ + constructor( + name: string, + booleanAttributes: Set, + valueAttributes: Map, + units: Map, + ) { super(name, booleanAttributes, valueAttributes) this._units = units } /** * Get the units for this unit class. - * @returns {Map} */ - get units() { + public get units(): Map { return new Map(this._units) } /** * Get the default unit for this unit class. - * @returns {SchemaUnit} */ - get defaultUnit() { + public get defaultUnit(): SchemaUnit { return this._units.get(this.getAttributeValue('defaultUnits')) } /** * Extracts the Unit class and remainder - * @returns {Array} [SchemaUnit, string, string] containing unit class, unit string, and value string + * @returns Unit class, unit string, and value string */ - extractUnit(value) { + public extractUnit(value: string): [SchemaUnit | null, string | null, string] { let actualUnit = null // The Unit class of the value let actualValueString = null // The actual value part of the value let actualUnitString = null @@ -610,11 +563,7 @@ export class SchemaUnitClass extends SchemaEntryWithAttributes { /** * SchemaUnitModifier class */ -export class SchemaUnitModifier extends SchemaEntryWithAttributes { - constructor(name, booleanAttributes, valueAttributes) { - super(name, booleanAttributes, valueAttributes) - } -} +export class SchemaUnitModifier extends SchemaEntryWithAttributes {} /** * SchemaValueClass class @@ -622,28 +571,30 @@ export class SchemaUnitModifier extends SchemaEntryWithAttributes { export class SchemaValueClass extends SchemaEntryWithAttributes { /** * The character class-based regular expression. - * @type {RegExp} - * @private */ - _charClassRegex + private readonly _charClassRegex: RegExp /** * The "word form"-based regular expression. - * @type {RegExp} - * @private */ - _wordRegex + private readonly _wordRegex: RegExp /** * Constructor. * - * @param {string} name The name of this value class. - * @param {Set} booleanAttributes The boolean attributes for this value class. - * @param {Map} valueAttributes The value attributes for this value class. - * @param {RegExp} charClassRegex The character class-based regular expression for this value class. - * @param {RegExp} wordRegex The "word form"-based regular expression for this value class. - */ - - constructor(name, booleanAttributes, valueAttributes, charClassRegex, wordRegex) { + * @param name The name of this value class. + * @param booleanAttributes The boolean attributes for this value class. + * @param valueAttributes The value attributes for this value class. + * @param charClassRegex The character class-based regular expression for this value class. + * @param wordRegex The "word form"-based regular expression for this value class. + */ + + constructor( + name: string, + booleanAttributes: Set, + valueAttributes: Map, + charClassRegex: RegExp, + wordRegex: RegExp, + ) { super(name, booleanAttributes, valueAttributes) this._charClassRegex = charClassRegex this._wordRegex = wordRegex @@ -652,10 +603,10 @@ export class SchemaValueClass extends SchemaEntryWithAttributes { /** * Determine if a value is valid according to this value class. * - * @param {string} value A HED value. - * @returns {boolean} Whether the value conforms to this value class. + * @param value A HED value. + * @returns Whether the value conforms to this value class. */ - validateValue(value) { + public validateValue(value: string): boolean { return this._wordRegex.test(value) && this._charClassRegex.test(value) } } @@ -666,42 +617,40 @@ export class SchemaValueClass extends SchemaEntryWithAttributes { export class SchemaTag extends SchemaEntryWithAttributes { /** * This tag's parent tag. - * @type {SchemaTag} - * @private */ - _parent + private _parent: SchemaTag /** * This tag's unit classes. - * @type {SchemaUnitClass[]} - * @private */ - _unitClasses + private readonly _unitClasses: SchemaUnitClass[] /** * This tag's value-classes - * @type {SchemaValueClass[]} - * @private */ - _valueClasses + private readonly _valueClasses: SchemaValueClass[] /** * This tag's value-taking child. - * @type {SchemaValueTag} - * @private */ - _valueTag + private _valueTag: SchemaValueTag /** * Constructor. * - * @param {string} name The name of this tag. - * @param {Set} booleanAttributes The boolean attributes for this tag. - * @param {Map} valueAttributes The value attributes for this tag. - * @param {SchemaUnitClass[]} unitClasses The unit classes for this tag. - * @param {SchemaValueClass[]} valueClasses The value classes for this tag. - */ - constructor(name, booleanAttributes, valueAttributes, unitClasses, valueClasses) { + * @param name The name of this tag. + * @param booleanAttributes The boolean attributes for this tag. + * @param valueAttributes The value attributes for this tag. + * @param unitClasses The unit classes for this tag. + * @param valueClasses The value classes for this tag. + */ + constructor( + name: string, + booleanAttributes: Set, + valueAttributes: Map, + unitClasses: SchemaUnitClass[], + valueClasses: SchemaValueClass[], + ) { super(name, booleanAttributes, valueAttributes) this._unitClasses = unitClasses ?? [] this._valueClasses = valueClasses ?? [] @@ -709,41 +658,37 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * This tag's unit classes. - * @type {SchemaUnitClass[]} */ - get unitClasses() { + public get unitClasses(): SchemaUnitClass[] { return this._unitClasses.slice() // The slice prevents modification } /** * Whether this tag has any unit classes. - * @returns {boolean} */ - get hasUnitClasses() { + public get hasUnitClasses(): boolean { return this._unitClasses.length !== 0 } /** * This tag's value classes. - * @type {SchemaValueClass[]} */ - get valueClasses() { + public get valueClasses(): SchemaValueClass[] { return this._valueClasses.slice() } /** * This tag's value-taking child tag. - * @returns {SchemaValueTag} */ - get valueTag() { + public get valueTag(): SchemaValueTag { return this._valueTag } /** * Set the tag's value-taking child tag. - * @param {SchemaValueTag} newValueTag The new value-taking child tag. + * @param newValueTag The new value-taking child tag. */ - set valueTag(newValueTag) { + public set valueTag(newValueTag: SchemaValueTag) { if (!this._isPrivateFieldSet(this._valueTag, 'value tag')) { this._valueTag = newValueTag } @@ -751,17 +696,16 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * This tag's parent tag. - * @type {SchemaTag} */ - get parent() { + public get parent(): SchemaTag { return this._parent } /** * Set the tag's parent tag. - * @param {SchemaTag} newParent The new parent tag. + * @param newParent The new parent tag. */ - set parent(newParent) { + public set parent(newParent: SchemaTag) { if (!this._isPrivateFieldSet(this._parent, 'parent')) { this._parent = newParent } @@ -770,13 +714,13 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * Throw an error if a private field is already set. * - * @param {*} field The field being set. - * @param {string} fieldName The name of the field (for error reporting). - * @return {boolean} Whether the field is set (never returns true). + * @param field The field being set. + * @param fieldName The name of the field (for error reporting). + * @return Whether the field is set (never returns true). * @throws {IssueError} If the field is already set. * @private */ - _isPrivateFieldSet(field, fieldName) { + private _isPrivateFieldSet(field: any, fieldName: string): boolean { if (field !== undefined) { IssueError.generateAndThrowInternalError( `Attempted to set ${fieldName} for schema tag ${this.longName} when it already has one.`, @@ -787,9 +731,8 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * Return all of this tag's ancestors. - * @returns {Array} */ - get ancestors() { + public get ancestors(): SchemaTag[] { return this._memoize('ancestors', () => { if (this.parent) { return [this.parent, ...this.parent.ancestors] @@ -800,9 +743,8 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * This tag's long name. - * @returns {string} */ - get longName() { + public get longName(): string { const nameParts = this.ancestors.map((parentTag) => parentTag.name) nameParts.reverse().push(this.name) return nameParts.join('/') @@ -811,10 +753,10 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * Extend this tag's short name. * - * @param {string} extension The extension. - * @returns {string} The extended short string. + * @param extension The extension. + * @returns The extended short string. */ - extend(extension) { + public extend(extension: string): string { if (extension) { return this.name + '/' + extension } else { @@ -825,10 +767,10 @@ export class SchemaTag extends SchemaEntryWithAttributes { /** * Extend this tag's long name. * - * @param {string} extension The extension. - * @returns {string} The extended long string. + * @param extension The extension. + * @returns The extended long string. */ - longExtend(extension) { + public longExtend(extension: string): string { if (extension) { return this.longName + '/' + extension } else { @@ -843,9 +785,8 @@ export class SchemaTag extends SchemaEntryWithAttributes { export class SchemaValueTag extends SchemaTag { /** * This tag's long name. - * @returns {string} */ - get longName() { + public get longName(): string { const nameParts = this.ancestors.map((parentTag) => parentTag.name) nameParts.reverse().push('#') return nameParts.join('/') @@ -854,20 +795,20 @@ export class SchemaValueTag extends SchemaTag { /** * Extend this tag's short name. * - * @param {string} extension The extension. - * @returns {string} The extended short string. + * @param extension The extension. + * @returns The extended short string. */ - extend(extension) { + public extend(extension: string): string { return this.parent.extend(extension) } /** * Extend this tag's long name. * - * @param {string} extension The extension. - * @returns {string} The extended long string. + * @param extension The extension. + * @returns The extended long string. */ - longExtend(extension) { + public longExtend(extension: string): string { return this.parent.longExtend(extension) } } diff --git a/src/schema/schemaMerger.js b/src/schema/schemaMerger.ts similarity index 73% rename from src/schema/schemaMerger.js rename to src/schema/schemaMerger.ts index 77144a3a..5fe36e05 100644 --- a/src/schema/schemaMerger.js +++ b/src/schema/schemaMerger.ts @@ -1,32 +1,29 @@ import { IssueError } from '../issues/issues' -import { SchemaTag, SchemaValueTag } from './entries' -import { PartneredSchema } from './containers' +import { SchemaAttribute, SchemaEntryManager, SchemaTag, SchemaValueTag } from './entries' +import { HedSchema, PartneredSchema } from './containers' export default class PartneredSchemaMerger { /** * The sources of data to be merged. - * @type {HedSchema[]} */ - sourceSchemas + sourceSchemas: HedSchema[] /** * The current source of data to be merged. - * @type {HedSchema} */ - currentSource + currentSource: HedSchema /** * The destination of data to be merged. - * @type {PartneredSchema} */ - destination + destination: PartneredSchema /** * Constructor. * - * @param {HedSchema[]} sourceSchemas The sources of data to be merged. + * @param sourceSchemas The sources of data to be merged. */ - constructor(sourceSchemas) { + constructor(sourceSchemas: HedSchema[]) { this.sourceSchemas = sourceSchemas this.destination = new PartneredSchema(sourceSchemas) this._validate() @@ -34,9 +31,8 @@ export default class PartneredSchemaMerger { /** * Pre-validate the partnered schemas. - * @private */ - _validate() { + private _validate(): void { for (const schema of this.sourceSchemas.slice(1)) { if (schema.withStandard !== this.destination.withStandard) { IssueError.generateAndThrow('differentWithStandard', { @@ -50,9 +46,9 @@ export default class PartneredSchemaMerger { /** * Merge the lazy partnered schemas. * - * @returns {PartneredSchema} The merged partnered schema. + * @returns The merged partnered schema. */ - mergeSchemas() { + public mergeSchemas(): PartneredSchema { for (const additionalSchema of this.sourceSchemas.slice(1)) { this.currentSource = additionalSchema this._mergeData() @@ -62,35 +58,29 @@ export default class PartneredSchemaMerger { /** * The source schema's tag collection. - * - * @return {SchemaEntryManager} */ - get sourceTags() { + get sourceTags(): SchemaEntryManager { return this.currentSource.entries.tags } /** * The destination schema's tag collection. - * - * @returns {SchemaEntryManager} */ - get destinationTags() { + get destinationTags(): SchemaEntryManager { return this.destination.entries.tags } /** * Merge two lazy partnered schemas. - * @private */ - _mergeData() { + private _mergeData(): void { this._mergeTags() } /** * Merge the tags from two lazy partnered schemas. - * @private */ - _mergeTags() { + private _mergeTags(): void { for (const tag of this.sourceTags.values()) { this._mergeTag(tag) } @@ -99,10 +89,9 @@ export default class PartneredSchemaMerger { /** * Merge a tag from one schema to another. * - * @param {SchemaTag} tag The tag to copy. - * @private + * @param tag The tag to copy. */ - _mergeTag(tag) { + private _mergeTag(tag: SchemaTag): void { if (!tag.getAttributeValue('inLibrary')) { return } @@ -126,12 +115,11 @@ export default class PartneredSchemaMerger { /** * Copy a tag from one schema to another. * - * @param {SchemaTag} tag The tag to copy. - * @private + * @param tag The tag to copy. */ - _copyTagToSchema(tag) { - const booleanAttributes = new Set() - const valueAttributes = new Map() + private _copyTagToSchema(tag: SchemaTag): void { + const booleanAttributes = new Set() + const valueAttributes = new Map() for (const attribute of tag.booleanAttributes) { booleanAttributes.add(this.destination.entries.attributes.getEntry(attribute.name) ?? attribute) @@ -140,18 +128,18 @@ export default class PartneredSchemaMerger { valueAttributes.set(this.destination.entries.attributes.getEntry(key.name) ?? key, value) } - /** - * @type {SchemaUnitClass[]} - */ const unitClasses = tag.unitClasses.map( (unitClass) => this.destination.entries.unitClasses.getEntry(unitClass.name) ?? unitClass, ) + const valueClasses = tag.valueClasses.map( + (valueClass) => this.destination.entries.valueClasses.getEntry(valueClass.name) ?? valueClass, + ) let newTag if (tag instanceof SchemaValueTag) { - newTag = new SchemaValueTag(tag.name, booleanAttributes, valueAttributes, unitClasses) + newTag = new SchemaValueTag(tag.name, booleanAttributes, valueAttributes, unitClasses, valueClasses) } else { - newTag = new SchemaTag(tag.name, booleanAttributes, valueAttributes, unitClasses) + newTag = new SchemaTag(tag.name, booleanAttributes, valueAttributes, unitClasses, valueClasses) } const destinationParentTag = this.destinationTags.getEntry(tag.parent?.name?.toLowerCase()) if (destinationParentTag) { From cfdeb92ccf42606c4abdbe4743bfb5f95ac33256 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 13 Aug 2025 07:46:14 -0500 Subject: [PATCH 11/63] Remove full property modeling Schema properties have changed significantly over the 8.x schema series, and continuing the partial modeling of them is no longer worthwhile. --- src/schema/entries.ts | 103 +++++------------------------------------- src/schema/parser.js | 34 +++----------- 2 files changed, 19 insertions(+), 118 deletions(-) diff --git a/src/schema/entries.ts b/src/schema/entries.ts index 8b2e0801..a7a0a53b 100644 --- a/src/schema/entries.ts +++ b/src/schema/entries.ts @@ -184,73 +184,19 @@ export class SchemaEntry extends Memoizer { } } -// TODO: Switch back to class constant once upstream bug is fixed. -type SchemaPropertyType = 'categoryProperty' | 'typeProperty' | 'roleProperty' -const categoryProperty = 'categoryProperty' -const typeProperty = 'typeProperty' -const roleProperty = 'roleProperty' - /** * A schema property. */ -export class SchemaProperty extends SchemaEntry { - /** - * The type of the property. - */ - private readonly _propertyType: SchemaPropertyType - - constructor(name: string, propertyType: SchemaPropertyType) { - super(name) - this._propertyType = propertyType - } - - /** - * Whether this property describes a schema category. - */ - public get isCategoryProperty(): boolean { - return this._propertyType === categoryProperty - } - - /** - * Whether this property describes a data type. - */ - public get isTypeProperty(): boolean { - return this._propertyType === typeProperty - } - - /** - * Whether this property describes a role. - */ - public get isRoleProperty(): boolean { - return this._propertyType === roleProperty - } -} - -// Pseudo-properties - -// TODO: Switch back to class constant once upstream bug is fixed. -export const nodeProperty = new SchemaProperty('nodeProperty', categoryProperty) -export const schemaAttributeProperty = new SchemaProperty('schemaAttributeProperty', categoryProperty) -const stringProperty = new SchemaProperty('stringProperty', typeProperty) +export class SchemaProperty extends SchemaEntry {} /** * A schema attribute. */ export class SchemaAttribute extends SchemaEntry { /** - * The categories of elements this schema attribute applies to. - */ - private readonly _categoryProperties: Set - - /** - * The data type of this schema attribute. + * The properties assigned to this schema attribute. */ - private readonly _typeProperty: SchemaProperty - - /** - * The set of role properties for this schema attribute. - */ - private readonly _roleProperties: Set + readonly _properties: Set /** * Constructor. @@ -258,43 +204,16 @@ export class SchemaAttribute extends SchemaEntry { * @param name The name of the schema attribute. * @param properties The properties assigned to this schema attribute. */ - constructor(name: string, properties: SchemaProperty[]) { + constructor(name: string, properties: Set) { super(name) - - // Parse properties - const categoryProperties = properties.filter((property) => property?.isCategoryProperty) - this._categoryProperties = categoryProperties.length === 0 ? new Set([nodeProperty]) : new Set(categoryProperties) - const typeProperties = properties.filter((property) => property?.isTypeProperty) - this._typeProperty = typeProperties.length === 0 ? stringProperty : typeProperties[0] - this._roleProperties = new Set(properties.filter((property) => property?.isRoleProperty)) - } - - /** - * The categories of elements this schema attribute applies to. - */ - public get categoryProperty(): Set | SchemaProperty | undefined { - switch (this._categoryProperties.size) { - case 0: - return undefined - case 1: - return Array.from(this._categoryProperties)[0] - default: - return this._categoryProperties - } - } - - /** - * The data type property of this schema attribute. - */ - public get typeProperty(): SchemaProperty { - return this._typeProperty + this._properties = properties } /** - * The set of role properties for this schema attribute. + * The collection of properties for this schema attribute. */ - public get roleProperties(): Set { - return new Set(this._roleProperties) + public get properties(): Set { + return new Set(this._properties) } } @@ -746,7 +665,8 @@ export class SchemaTag extends SchemaEntryWithAttributes { */ public get longName(): string { const nameParts = this.ancestors.map((parentTag) => parentTag.name) - nameParts.reverse().push(this.name) + nameParts.reverse() + nameParts.push(this.name) return nameParts.join('/') } @@ -788,7 +708,8 @@ export class SchemaValueTag extends SchemaTag { */ public get longName(): string { const nameParts = this.ancestors.map((parentTag) => parentTag.name) - nameParts.reverse().push('#') + nameParts.reverse() + nameParts.push('#') return nameParts.join('/') } diff --git a/src/schema/parser.js b/src/schema/parser.js index 8143dbfd..61788ecc 100644 --- a/src/schema/parser.js +++ b/src/schema/parser.js @@ -142,32 +142,12 @@ export default class SchemaParser { return new Map(zip(tagElements, tags)) } - // Rewrite starts here. - parseProperties() { const propertyDefinitions = this._getDefinitionElements('property') this.properties = new Map() for (const definition of propertyDefinitions) { const propertyName = SchemaParser.getElementTagName(definition) - if (this._versionDefinitions.categoryProperties?.has(propertyName)) { - this.properties.set( - propertyName, - // TODO: Switch back to class constant once upstream bug is fixed. - new SchemaProperty(propertyName, 'categoryProperty'), - ) - } else if (this._versionDefinitions.typeProperties?.has(propertyName)) { - this.properties.set( - propertyName, - // TODO: Switch back to class constant once upstream bug is fixed. - new SchemaProperty(propertyName, 'typeProperty'), - ) - } else if (this._versionDefinitions.roleProperties?.has(propertyName)) { - this.properties.set( - propertyName, - // TODO: Switch back to class constant once upstream bug is fixed. - new SchemaProperty(propertyName, 'roleProperty'), - ) - } + this.properties.set(propertyName, new SchemaProperty(propertyName)) } this._addCustomProperties() } @@ -179,7 +159,7 @@ export default class SchemaParser { const attributeName = SchemaParser.getElementTagName(definition) const propertyElements = definition.property ?? [] const properties = propertyElements.map((element) => this.properties.get(SchemaParser.getElementTagName(element))) - this.attributes.set(attributeName, new SchemaAttribute(attributeName, properties)) + this.attributes.set(attributeName, new SchemaAttribute(attributeName, new Set(properties))) } this._addCustomAttributes() } @@ -370,11 +350,11 @@ export default class SchemaParser { if (semver.lt(this.rootElement.$.version, '8.3.0')) { filteredAttributeArray = attributeArray.filter((attribute) => - attribute.roleProperties.has(this.properties.get('isInheritedProperty')), + attribute.properties.has(this.properties.get('isInheritedProperty')), ) } else { filteredAttributeArray = attributeArray.filter( - (attribute) => !attribute.roleProperties.has(this.properties.get('annotationProperty')), + (attribute) => !attribute.properties.has(this.properties.get('annotationProperty')), ) } @@ -484,17 +464,17 @@ export default class SchemaParser { const isInheritedProperty = this.properties.get('isInheritedProperty') const extensionAllowedAttribute = this.attributes.get('extensionAllowed') if (this.rootElement.$.library === undefined && semver.lt(this.rootElement.$.version, '8.2.0')) { - extensionAllowedAttribute._roleProperties.add(isInheritedProperty) + extensionAllowedAttribute._properties.add(isInheritedProperty) } const inLibraryAttribute = this.attributes.get('inLibrary') if (inLibraryAttribute && semver.lt(this.rootElement.$.version, '8.3.0')) { - inLibraryAttribute._roleProperties.add(isInheritedProperty) + inLibraryAttribute._properties.add(isInheritedProperty) } } _addCustomProperties() { if (this.rootElement.$.library === undefined && semver.lt(this.rootElement.$.version, '8.2.0')) { - const recursiveProperty = new SchemaProperty('isInheritedProperty', 'roleProperty') + const recursiveProperty = new SchemaProperty('isInheritedProperty') this.properties.set('isInheritedProperty', recursiveProperty) } } From d3f6f2c9e77d3f71bb00e4931b407c9998b0342d Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Thu, 21 Aug 2025 15:53:57 -0500 Subject: [PATCH 12/63] Modify tag manager field instead of definition map --- src/schema/entries.ts | 11 +++++++++-- src/schema/schemaMerger.ts | 20 ++++++++++---------- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/src/schema/entries.ts b/src/schema/entries.ts index a7a0a53b..2244d7ed 100644 --- a/src/schema/entries.ts +++ b/src/schema/entries.ts @@ -37,7 +37,7 @@ export class SchemaEntries extends Memoizer { /** * The schema's tags. */ - readonly tags: SchemaEntryManager + tags: SchemaEntryManager /** * Constructor. @@ -61,7 +61,7 @@ export class SchemaEntryManager extends Memoizer { /** * The definitions managed by this entry manager. */ - readonly _definitions: Map + private readonly _definitions: Map /** * Constructor. @@ -73,6 +73,13 @@ export class SchemaEntryManager extends Memoizer { this._definitions = definitions } + /** + * Return a copy of the managed definition map. + */ + public get definitions(): Map { + return new Map(this._definitions) + } + /** * Iterator over the entry manager's entries. */ diff --git a/src/schema/schemaMerger.ts b/src/schema/schemaMerger.ts index 5fe36e05..87691068 100644 --- a/src/schema/schemaMerger.ts +++ b/src/schema/schemaMerger.ts @@ -18,6 +18,11 @@ export default class PartneredSchemaMerger { */ destination: PartneredSchema + /** + * The tag definitions of the partnered schema + */ + destinationTagDefinitions: Map + /** * Constructor. * @@ -26,6 +31,7 @@ export default class PartneredSchemaMerger { constructor(sourceSchemas: HedSchema[]) { this.sourceSchemas = sourceSchemas this.destination = new PartneredSchema(sourceSchemas) + this.destinationTagDefinitions = this.destination.entries.tags.definitions this._validate() } @@ -63,13 +69,6 @@ export default class PartneredSchemaMerger { return this.currentSource.entries.tags } - /** - * The destination schema's tag collection. - */ - get destinationTags(): SchemaEntryManager { - return this.destination.entries.tags - } - /** * Merge two lazy partnered schemas. */ @@ -84,6 +83,7 @@ export default class PartneredSchemaMerger { for (const tag of this.sourceTags.values()) { this._mergeTag(tag) } + this.destination.entries.tags = new SchemaEntryManager(this.destinationTagDefinitions) } /** @@ -97,7 +97,7 @@ export default class PartneredSchemaMerger { } const shortName = tag.name - if (this.destinationTags.hasEntry(shortName.toLowerCase())) { + if (this.destinationTagDefinitions.has(shortName.toLowerCase())) { IssueError.generateAndThrow('lazyPartneredSchemasShareTag', { tag: shortName }) } @@ -141,7 +141,7 @@ export default class PartneredSchemaMerger { } else { newTag = new SchemaTag(tag.name, booleanAttributes, valueAttributes, unitClasses, valueClasses) } - const destinationParentTag = this.destinationTags.getEntry(tag.parent?.name?.toLowerCase()) + const destinationParentTag = this.destinationTagDefinitions.get(tag.parent?.name?.toLowerCase()) if (destinationParentTag) { newTag.parent = destinationParentTag if (newTag instanceof SchemaValueTag) { @@ -149,6 +149,6 @@ export default class PartneredSchemaMerger { } } - this.destinationTags._definitions.set(newTag.name.toLowerCase(), newTag) + this.destinationTagDefinitions.set(newTag.name.toLowerCase(), newTag) } } From c9bd26166c6ef9a27c8572f8fa906c099503e0fe Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Thu, 21 Aug 2025 18:30:47 -0500 Subject: [PATCH 13/63] Port schema parser to TypeScript Also create new type module for XML schema data --- src/schema/containers.ts | 3 +- src/schema/init.ts | 3 +- src/schema/{parser.js => parser.ts} | 292 +++++++++++++++++----------- src/schema/xmlType.ts | 34 ++++ tsconfig.json | 7 +- 5 files changed, 221 insertions(+), 118 deletions(-) rename src/schema/{parser.js => parser.ts} (56%) create mode 100644 src/schema/xmlType.ts diff --git a/src/schema/containers.ts b/src/schema/containers.ts index 539da99e..764e937b 100644 --- a/src/schema/containers.ts +++ b/src/schema/containers.ts @@ -2,8 +2,7 @@ import lt from 'semver/functions/lt' import { IssueError } from '../issues/issues' import { SchemaEntries } from './entries' - -type HedSchemaXMLObject = { HED: { $: { version: string; library?: string; withStandard?: string } } } +import { HedSchemaXMLObject } from './xmlType' export class HedSchema { /** diff --git a/src/schema/init.ts b/src/schema/init.ts index 8218a07f..2f434c4a 100644 --- a/src/schema/init.ts +++ b/src/schema/init.ts @@ -9,8 +9,7 @@ import { HedSchema, PrimarySchema, HedSchemas } from './containers' import { IssueError } from '../issues/issues' import { splitStringTrimAndRemoveBlanks } from '../utils/string' import { SchemasSpec } from './specs' - -type HedSchemaXMLObject = { HED: { $: { version: string; library?: string; withStandard?: string } } } +import { HedSchemaXMLObject } from './xmlType' /** * Build a single schema container object from an XML file. diff --git a/src/schema/parser.js b/src/schema/parser.ts similarity index 56% rename from src/schema/parser.js rename to src/schema/parser.ts index 61788ecc..0c93cbad 100644 --- a/src/schema/parser.js +++ b/src/schema/parser.ts @@ -1,4 +1,3 @@ -import Set from 'core-js-pure/actual/set' import flattenDeep from 'lodash/flattenDeep' import zip from 'lodash/zip' import semver from 'semver' @@ -17,57 +16,70 @@ import { } from './entries' import { IssueError } from '../issues/issues' -import classRegex from '../data/json/classRegex.json' +import { DefinitionElement, HedSchemaRootElement, NamedElement, NodeElement } from './xmlType' -const lc = (str) => str.toLowerCase() +interface ClassRegex { + char_regex: { + [key: string]: string + } + class_chars: { + [key: string]: string[] + } + class_words: { + [key: string]: string + } +} + +import * as _classRegex from '../data/json/classRegex.json' +const classRegex: ClassRegex = _classRegex + +const lc = (str: string) => str.toLowerCase() export default class SchemaParser { /** * The root XML element. - * @type {Object} */ - rootElement + rootElement: HedSchemaRootElement - /** - * @type {Map} - */ - properties + properties: Map - /** - * @type {Map} - */ - attributes + attributes: Map /** * The schema's value classes. - * @type {SchemaEntryManager} */ - valueClasses + valueClasses: SchemaEntryManager /** * The schema's unit classes. - * @type {SchemaEntryManager} */ - unitClasses + unitClasses: SchemaEntryManager /** * The schema's unit modifiers. - * @type {SchemaEntryManager} */ - unitModifiers + unitModifiers: SchemaEntryManager /** * The schema's tags. - * @type {SchemaEntryManager} */ - tags + tags: SchemaEntryManager + + /** + * Version-specific definitions. + */ + private _versionDefinitions: { + typeProperties: Set + categoryProperties: Set + roleProperties: Set + } /** * Constructor. * * @param {Object} rootElement The root XML element. */ - constructor(rootElement) { + constructor(rootElement: HedSchemaRootElement) { this.rootElement = rootElement this._versionDefinitions = { typeProperties: new Set(['boolProperty']), @@ -84,12 +96,12 @@ export default class SchemaParser { } } - parse() { + public parse(): SchemaEntries { this.populateDictionaries() return new SchemaEntries(this) } - populateDictionaries() { + private populateDictionaries(): void { this.parseProperties() this.parseAttributes() this.parseUnitModifiers() @@ -98,7 +110,7 @@ export default class SchemaParser { this.parseTags() } - getAllChildTags(parentElement, excludeTakeValueTags = true) { + private getAllChildTags(parentElement: NodeElement, excludeTakeValueTags = true): NodeElement[] { if (excludeTakeValueTags && SchemaParser.getElementTagName(parentElement) === '#') { return [] } @@ -107,11 +119,13 @@ export default class SchemaParser { childTags.push(parentElement) } const tagElementChildren = parentElement.node ?? [] - childTags.push(...flattenDeep(tagElementChildren.map((child) => this.getAllChildTags(child, excludeTakeValueTags)))) + childTags.push( + ...flattenDeep(tagElementChildren.map((child: NodeElement) => this.getAllChildTags(child, excludeTakeValueTags))), + ) return childTags } - static getParentTagName(tagElement) { + private static getParentTagName(tagElement: NodeElement): string { const parentTagElement = tagElement.$parent if (parentTagElement?.$parent) { return SchemaParser.getElementTagName(parentTagElement) @@ -123,28 +137,30 @@ export default class SchemaParser { /** * Extract the name of an XML element. * - * @param {Object} element An XML element. - * @returns {string} The name of the element. + * @param element An XML element. + * @returns The name of the element. */ - static getElementTagName(element) { + private static getElementTagName(element: NamedElement): string { return element.name._ } /** * Retrieve all the tags in the schema. * - * @returns {Map} The tag names and XML elements. + * @returns The tag names and XML elements. */ - getAllTags() { + private getAllTags(): Map { const nodeRoot = this.rootElement.schema - const tagElements = this.getAllChildTags(nodeRoot, false) - const tags = tagElements.map((element) => SchemaParser.getElementTagName(element)) + const tagElements = [] + const tagElementChildren = nodeRoot.node + tagElements.push(...flattenDeep(tagElementChildren.map((child: NodeElement) => this.getAllChildTags(child, false)))) + const tags = tagElements.map((element: NodeElement) => SchemaParser.getElementTagName(element)) return new Map(zip(tagElements, tags)) } - parseProperties() { - const propertyDefinitions = this._getDefinitionElements('property') - this.properties = new Map() + private parseProperties(): void { + const propertyDefinitions = this.rootElement.propertyDefinitions.propertyDefinition + this.properties = new Map() for (const definition of propertyDefinitions) { const propertyName = SchemaParser.getElementTagName(definition) this.properties.set(propertyName, new SchemaProperty(propertyName)) @@ -152,19 +168,21 @@ export default class SchemaParser { this._addCustomProperties() } - parseAttributes() { - const attributeDefinitions = this._getDefinitionElements('schemaAttribute') - this.attributes = new Map() + private parseAttributes() { + const attributeDefinitions = this.rootElement.schemaAttributeDefinitions.schemaAttributeDefinition + this.attributes = new Map() for (const definition of attributeDefinitions) { const attributeName = SchemaParser.getElementTagName(definition) const propertyElements = definition.property ?? [] - const properties = propertyElements.map((element) => this.properties.get(SchemaParser.getElementTagName(element))) + const properties = propertyElements.map((element: NamedElement) => + this.properties.get(SchemaParser.getElementTagName(element)), + ) this.attributes.set(attributeName, new SchemaAttribute(attributeName, new Set(properties))) } this._addCustomAttributes() } - _getValueClassChars(name) { + private _getValueClassChars(name: string): RegExp { let classChars if (Array.isArray(classRegex.class_chars[name]) && classRegex.class_chars[name].length > 0) { classChars = @@ -175,12 +193,13 @@ export default class SchemaParser { return new RegExp(classChars) } - parseValueClasses() { - const valueClasses = new Map() - const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions('valueClass') + private parseValueClasses() { + const valueClasses = new Map() + const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions( + this.rootElement.valueClassDefinitions.valueClassDefinition, + ) for (const [name, valueAttributes] of valueAttributeDefinitions) { const booleanAttributes = booleanAttributeDefinitions.get(name) - //valueClasses.set(name, new SchemaValueClass(name, booleanAttributes, valueAttributes)) const charRegex = this._getValueClassChars(name) const wordRegex = new RegExp(classRegex.class_words[name] ?? '^.+$') valueClasses.set(name, new SchemaValueClass(name, booleanAttributes, valueAttributes, charRegex, wordRegex)) @@ -188,9 +207,11 @@ export default class SchemaParser { this.valueClasses = new SchemaEntryManager(valueClasses) } - parseUnitModifiers() { - const unitModifiers = new Map() - const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions('unitModifier') + private parseUnitModifiers() { + const unitModifiers = new Map() + const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions( + this.rootElement.unitModifierDefinitions.unitModifierDefinition, + ) for (const [name, valueAttributes] of valueAttributeDefinitions) { const booleanAttributes = booleanAttributeDefinitions.get(name) unitModifiers.set(name, new SchemaUnitModifier(name, booleanAttributes, valueAttributes)) @@ -198,9 +219,11 @@ export default class SchemaParser { this.unitModifiers = new SchemaEntryManager(unitModifiers) } - parseUnitClasses() { - const unitClasses = new Map() - const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions('unitClass') + private parseUnitClasses(): void { + const unitClasses = new Map() + const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions( + this.rootElement.unitClassDefinitions.unitClassDefinition, + ) const unitClassUnits = this.parseUnits() for (const [name, valueAttributes] of valueAttributeDefinitions) { @@ -210,13 +233,13 @@ export default class SchemaParser { this.unitClasses = new SchemaEntryManager(unitClasses) } - parseUnits() { - const unitClassUnits = new Map() - const unitClassElements = this._getDefinitionElements('unitClass') + private parseUnits(): Map> { + const unitClassUnits = new Map>() + const unitClassElements = this.rootElement.unitClassDefinitions.unitClassDefinition const unitModifiers = this.unitModifiers for (const element of unitClassElements) { const elementName = SchemaParser.getElementTagName(element) - const units = new Map() + const units = new Map() unitClassUnits.set(elementName, units) if (element.unit === undefined) { continue @@ -238,21 +261,23 @@ export default class SchemaParser { /** * Parse the schema's tags. */ - parseTags() { + private parseTags(): void { const tags = this.getAllTags() const shortTags = this._getShortTags(tags) const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseAttributeElements( tags.keys(), - (element) => shortTags.get(element), + (element: NodeElement) => shortTags.get(element), ) const tagUnitClassDefinitions = this._processTagUnitClasses(shortTags, valueAttributeDefinitions) + const tagValueClassDefinitions = this._processTagValueClasses(shortTags, valueAttributeDefinitions) this._processRecursiveAttributes(shortTags, booleanAttributeDefinitions) const tagEntries = this._createSchemaTags( booleanAttributeDefinitions, valueAttributeDefinitions, tagUnitClassDefinitions, + tagValueClassDefinitions, ) this._injectTagFields(tags, shortTags, tagEntries) @@ -263,12 +288,11 @@ export default class SchemaParser { /** * Generate the map from tag elements to shortened tag names. * - * @param {Map} tags The map from tag elements to tag strings. - * @returns {Map} The map from tag elements to shortened tag names. - * @private + * @param tags The map from tag elements to tag strings. + * @returns The map from tag elements to shortened tag names. */ - _getShortTags(tags) { - const shortTags = new Map() + private _getShortTags(tags: Map): Map { + const shortTags = new Map() for (const tagElement of tags.keys()) { const shortKey = SchemaParser.getElementTagName(tagElement) === '#' @@ -282,21 +306,23 @@ export default class SchemaParser { /** * Process unit classes in tags. * - * @param {Map} shortTags The map from tag elements to shortened tag names. - * @param {Map>} valueAttributeDefinitions The map from shortened tag names to their value schema attributes. - * @returns {Map} The map from shortened tag names to their unit classes. - * @private + * @param shortTags The map from tag elements to shortened tag names. + * @param valueAttributeDefinitions The map from shortened tag names to their value schema attributes. + * @returns The map from shortened tag names to their unit classes. */ - _processTagUnitClasses(shortTags, valueAttributeDefinitions) { + private _processTagUnitClasses( + shortTags: Map, + valueAttributeDefinitions: Map>, + ): Map { const tagUnitClassAttribute = this.attributes.get('unitClass') - const tagUnitClassDefinitions = new Map() + const tagUnitClassDefinitions = new Map() for (const tagName of shortTags.values()) { const valueAttributes = valueAttributeDefinitions.get(tagName) if (valueAttributes.has(tagUnitClassAttribute)) { tagUnitClassDefinitions.set( tagName, - valueAttributes.get(tagUnitClassAttribute).map((unitClassName) => { + valueAttributes.get(tagUnitClassAttribute).map((unitClassName: string) => { return this.unitClasses.getEntry(unitClassName) }), ) @@ -307,14 +333,46 @@ export default class SchemaParser { return tagUnitClassDefinitions } + /** + * Process value classes in tags. + * + * @param shortTags The map from tag elements to shortened tag names. + * @param valueAttributeDefinitions The map from shortened tag names to their value schema attributes. + * @returns The map from shortened tag names to their value classes. + */ + private _processTagValueClasses( + shortTags: Map, + valueAttributeDefinitions: Map>, + ): Map { + const tagValueClassAttribute = this.attributes.get('valueClass') + const tagValueClassDefinitions = new Map() + + for (const tagName of shortTags.values()) { + const valueAttributes = valueAttributeDefinitions.get(tagName) + if (valueAttributes.has(tagValueClassAttribute)) { + tagValueClassDefinitions.set( + tagName, + valueAttributes.get(tagValueClassAttribute).map((valueClassName: string) => { + return this.valueClasses.getEntry(valueClassName) + }), + ) + // valueAttributes.delete(tagValueClassAttribute) + } + } + + return tagValueClassDefinitions + } + /** * Process recursive schema attributes. * - * @param {Map} shortTags The map from tag elements to shortened tag names. - * @param {Map>} booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. Passed by reference. - * @private + * @param shortTags The map from tag elements to shortened tag names. + * @param booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. Passed by reference. */ - _processRecursiveAttributes(shortTags, booleanAttributeDefinitions) { + private _processRecursiveAttributes( + shortTags: Map, + booleanAttributeDefinitions: Map>, + ): void { const recursiveAttributeMap = this._generateRecursiveAttributeMap(shortTags, booleanAttributeDefinitions) for (const [tagElement, recursiveAttributes] of recursiveAttributeMap) { @@ -329,13 +387,15 @@ export default class SchemaParser { /** * Generate a map from tags to their recursive attributes. * - * @param {Map} shortTags The map from tag elements to shortened tag names. - * @param {Map>} booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. Passed by reference. - * @private + * @param shortTags The map from tag elements to shortened tag names. + * @param booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. Passed by reference. */ - _generateRecursiveAttributeMap(shortTags, booleanAttributeDefinitions) { + private _generateRecursiveAttributeMap( + shortTags: Map, + booleanAttributeDefinitions: Map>, + ): Map> { const recursiveAttributes = this._getRecursiveAttributes() - const recursiveAttributeMap = new Map() + const recursiveAttributeMap = new Map>() for (const [tagElement, tagName] of shortTags) { recursiveAttributeMap.set(tagElement, booleanAttributeDefinitions.get(tagName)?.intersection(recursiveAttributes)) @@ -344,7 +404,7 @@ export default class SchemaParser { return recursiveAttributeMap } - _getRecursiveAttributes() { + private _getRecursiveAttributes(): Set { const attributeArray = Array.from(this.attributes.values()) let filteredAttributeArray @@ -364,15 +424,20 @@ export default class SchemaParser { /** * Create the {@link SchemaTag} objects. * - * @param {Map>} booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. - * @param {Map>} valueAttributeDefinitions The map from shortened tag names to their value schema attributes. - * @param {Map} tagUnitClassDefinitions The map from shortened tag names to their unit classes. - * @returns {Map} The map from lowercase shortened tag names to their tag objects. - * @private + * @param booleanAttributeDefinitions The map from shortened tag names to their boolean schema attributes. + * @param valueAttributeDefinitions The map from shortened tag names to their value schema attributes. + * @param tagUnitClassDefinitions The map from shortened tag names to their unit classes. + * @param tagValueClassDefinitions The map from shortened tag names to their value classes. + * @returns The map from lowercase shortened tag names to their tag objects. */ - _createSchemaTags(booleanAttributeDefinitions, valueAttributeDefinitions, tagUnitClassDefinitions) { + private _createSchemaTags( + booleanAttributeDefinitions: Map>, + valueAttributeDefinitions: Map>, + tagUnitClassDefinitions: Map, + tagValueClassDefinitions: Map, + ): Map { const tagTakesValueAttribute = this.attributes.get('takesValue') - const tagEntries = new Map() + const tagEntries = new Map() for (const [name, valueAttributes] of valueAttributeDefinitions) { if (tagEntries.has(name)) { @@ -381,11 +446,15 @@ export default class SchemaParser { const booleanAttributes = booleanAttributeDefinitions.get(name) const unitClasses = tagUnitClassDefinitions.get(name) + const valueClasses = tagValueClassDefinitions.get(name) if (booleanAttributes.has(tagTakesValueAttribute)) { - tagEntries.set(lc(name), new SchemaValueTag(name, booleanAttributes, valueAttributes, unitClasses)) + tagEntries.set( + lc(name), + new SchemaValueTag(name, booleanAttributes, valueAttributes, unitClasses, valueClasses), + ) } else { - tagEntries.set(lc(name), new SchemaTag(name, booleanAttributes, valueAttributes, unitClasses)) + tagEntries.set(lc(name), new SchemaTag(name, booleanAttributes, valueAttributes, unitClasses, valueClasses)) } } @@ -395,12 +464,15 @@ export default class SchemaParser { /** * Inject special tag fields into the {@link SchemaTag} objects. * - * @param {Map} tags The map from tag elements to tag strings. - * @param {Map} shortTags The map from tag elements to shortened tag names. - * @param {Map} tagEntries The map from shortened tag names to tag objects. - * @private + * @param tags The map from tag elements to tag strings. + * @param shortTags The map from tag elements to shortened tag names. + * @param tagEntries The map from shortened tag names to tag objects. */ - _injectTagFields(tags, shortTags, tagEntries) { + private _injectTagFields( + tags: Map, + shortTags: Map, + tagEntries: Map, + ): void { for (const tagElement of tags.keys()) { const tagName = shortTags.get(tagElement) const parentTagName = shortTags.get(tagElement.$parent) @@ -415,20 +487,18 @@ export default class SchemaParser { } } - _parseDefinitions(category) { - const definitionElements = this._getDefinitionElements(category) + private _parseDefinitions( + definitionElements: Iterable, + ): [Map>, Map>] { return this._parseAttributeElements(definitionElements, SchemaParser.getElementTagName) } - _getDefinitionElements(category) { - const categoryTagName = category + 'Definition' - const categoryParentTagName = categoryTagName + 's' - return this.rootElement[categoryParentTagName][categoryTagName] - } - - _parseAttributeElements(elements, namer) { - const booleanAttributeDefinitions = new Map() - const valueAttributeDefinitions = new Map() + private _parseAttributeElements( + elements: Iterable, + namer: (element: NamedElement) => string, + ): [Map>, Map>] { + const booleanAttributeDefinitions = new Map>() + const valueAttributeDefinitions = new Map>() for (const element of elements) { const [booleanAttributes, valueAttributes] = this._parseAttributeElement(element) @@ -441,9 +511,9 @@ export default class SchemaParser { return [booleanAttributeDefinitions, valueAttributeDefinitions] } - _parseAttributeElement(element) { - const booleanAttributes = new Set() - const valueAttributes = new Map() + private _parseAttributeElement(element: DefinitionElement): [Set, Map] { + const booleanAttributes = new Set() + const valueAttributes = new Map() const tagAttributes = element.attribute ?? [] @@ -453,14 +523,14 @@ export default class SchemaParser { booleanAttributes.add(this.attributes.get(attributeName)) continue } - const values = tagAttribute.value.map((value) => value._) + const values = tagAttribute.value.map((value: any) => value._) valueAttributes.set(this.attributes.get(attributeName), values) } return [booleanAttributes, valueAttributes] } - _addCustomAttributes() { + private _addCustomAttributes(): void { const isInheritedProperty = this.properties.get('isInheritedProperty') const extensionAllowedAttribute = this.attributes.get('extensionAllowed') if (this.rootElement.$.library === undefined && semver.lt(this.rootElement.$.version, '8.2.0')) { @@ -472,7 +542,7 @@ export default class SchemaParser { } } - _addCustomProperties() { + private _addCustomProperties(): void { if (this.rootElement.$.library === undefined && semver.lt(this.rootElement.$.version, '8.2.0')) { const recursiveProperty = new SchemaProperty('isInheritedProperty') this.properties.set('isInheritedProperty', recursiveProperty) diff --git a/src/schema/xmlType.ts b/src/schema/xmlType.ts new file mode 100644 index 00000000..dbc024b4 --- /dev/null +++ b/src/schema/xmlType.ts @@ -0,0 +1,34 @@ +export type NamedElement = { name: { _: string } } +type AttributeElement = NamedElement & { value?: { _: any }[] } +export type DefinitionElement = NamedElement & { attribute?: AttributeElement[] } +export type NodeElement = DefinitionElement & { node?: NodeElement[]; $parent?: NodeElement | null } +type UnitElement = DefinitionElement +type UnitClassElement = DefinitionElement & { unit: UnitElement[] } +type UnitModifierElement = DefinitionElement +type ValueClassElement = DefinitionElement +type SchemaAttributeElement = NamedElement & { property: AttributeElement[] } +type PropertyElement = NamedElement + +export type HedSchemaRootElement = { + $: { version: string; library?: string; withStandard?: string } + schema: { node: NodeElement[] } + unitClassDefinitions: { + unitClassDefinition: UnitClassElement[] + } + unitModifierDefinitions: { + unitModifierDefinition: UnitModifierElement[] + } + valueClassDefinitions: { + valueClassDefinition: ValueClassElement[] + } + schemaAttributeDefinitions: { + schemaAttributeDefinition: SchemaAttributeElement[] + } + propertyDefinitions: { + propertyDefinition: PropertyElement[] + } +} + +export type HedSchemaXMLObject = { + HED: HedSchemaRootElement +} diff --git a/tsconfig.json b/tsconfig.json index c628ace5..a61bba52 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -3,15 +3,16 @@ "outDir": "./built", "allowJs": true, "checkJs": false, - "target": "es2020", - "module": "es2020", + "target": "esnext", + "module": "esnext", "moduleResolution": "node", "skipLibCheck": true, "esModuleInterop": true, "allowSyntheticDefaultImports": true, "downlevelIteration": true, "typeRoots": ["./node_modules/@types", "./types"], - "noImplicitAny": true + "noImplicitAny": true, + "resolveJsonModule": true }, "include": ["src/**/*"], "exclude": ["node_modules", "dist"] From 9285f211475b47bc36266fe7b11c8031615724ef Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 27 Aug 2025 12:14:50 -0500 Subject: [PATCH 14/63] Fixing linter and other issues --- src/schema/entries.ts | 54 +++++++++++++++++++------------------- src/schema/parser.ts | 35 +++++++++++------------- src/schema/schemaMerger.ts | 6 ++--- src/schema/xmlType.ts | 15 +++++------ 4 files changed, 52 insertions(+), 58 deletions(-) diff --git a/src/schema/entries.ts b/src/schema/entries.ts index 2244d7ed..b1232c52 100644 --- a/src/schema/entries.ts +++ b/src/schema/entries.ts @@ -236,7 +236,7 @@ export class SchemaEntryWithAttributes extends SchemaEntry { /** * The collection of value attributes this schema entry has. */ - readonly valueAttributes: Map + readonly valueAttributes: Map /** * The set of boolean attribute names this schema entry has. @@ -246,9 +246,9 @@ export class SchemaEntryWithAttributes extends SchemaEntry { /** * The collection of value attribute names this schema entry has. */ - readonly valueAttributeNames: Map + readonly valueAttributeNames: Map - constructor(name: string, booleanAttributes: Set, valueAttributes: Map) { + constructor(name: string, booleanAttributes: Set, valueAttributes: Map) { super(name) this.booleanAttributes = booleanAttributes this.valueAttributes = valueAttributes @@ -281,30 +281,30 @@ export class SchemaEntryWithAttributes extends SchemaEntry { } /** - * Retrieve the value of a value attribute (by name) on this schema entry. + * Retrieve a single value of a value attribute (by name) on this schema entry, throwing an error if more than one value exists. * @param attributeName The attribute whose value should be returned. - * @param alwaysReturnArray Whether to return a singleton array instead of a scalar value. * @returns The value of the attribute. + * @throws {IssueError} If the attribute has more than one value. */ - public getAttributeValue(attributeName: string, alwaysReturnArray = false): any { - return SchemaEntryWithAttributes._getMapArrayValue(this.valueAttributeNames, attributeName, alwaysReturnArray) + public getSingleAttributeValue(attributeName: string): string | undefined { + const attributeValues = this.valueAttributeNames.get(attributeName) + if (attributeValues === undefined) { + return undefined + } else if (attributeValues.length > 1) { + IssueError.generateAndThrowInternalError( + `More than one value exists for attribute ${attributeName}, when only one value was expected.`, + ) + } + return attributeValues[0] } /** - * Return a map value, with a scalar being returned in lieu of a singleton array if alwaysReturnArray is false. - * - * @param map The map to search. - * @param key A key in the map. - * @param alwaysReturnArray Whether to return a singleton array instead of a scalar value. - * @returns The value for the key in the passed map. - */ - private static _getMapArrayValue(map: Map, key: K, alwaysReturnArray: boolean): V | V[] { - const value = map.get(key) - if (!alwaysReturnArray && Array.isArray(value) && value.length === 1) { - return value[0] - } else { - return value - } + * Retrieve all values of a value attribute (by name) on this schema entry. + * @param attributeName The attribute whose value should be returned. + * @returns The values of the attribute. + */ + public getAttributeValues(attributeName: string): string[] | undefined { + return this.valueAttributeNames.get(attributeName) } } @@ -328,7 +328,7 @@ export class SchemaUnit extends SchemaEntryWithAttributes { constructor( name: string, booleanAttributes: Set, - valueAttributes: Map, + valueAttributes: Map, unitModifiers: SchemaEntryManager, ) { super(name, booleanAttributes, valueAttributes) @@ -423,7 +423,7 @@ export class SchemaUnitClass extends SchemaEntryWithAttributes { constructor( name: string, booleanAttributes: Set, - valueAttributes: Map, + valueAttributes: Map, units: Map, ) { super(name, booleanAttributes, valueAttributes) @@ -440,8 +440,8 @@ export class SchemaUnitClass extends SchemaEntryWithAttributes { /** * Get the default unit for this unit class. */ - public get defaultUnit(): SchemaUnit { - return this._units.get(this.getAttributeValue('defaultUnits')) + public get defaultUnit(): SchemaUnit | undefined { + return this._units.get(this.getSingleAttributeValue('defaultUnits')) } /** @@ -517,7 +517,7 @@ export class SchemaValueClass extends SchemaEntryWithAttributes { constructor( name: string, booleanAttributes: Set, - valueAttributes: Map, + valueAttributes: Map, charClassRegex: RegExp, wordRegex: RegExp, ) { @@ -573,7 +573,7 @@ export class SchemaTag extends SchemaEntryWithAttributes { constructor( name: string, booleanAttributes: Set, - valueAttributes: Map, + valueAttributes: Map, unitClasses: SchemaUnitClass[], valueClasses: SchemaValueClass[], ) { diff --git a/src/schema/parser.ts b/src/schema/parser.ts index 0c93cbad..9c03dbb0 100644 --- a/src/schema/parser.ts +++ b/src/schema/parser.ts @@ -119,9 +119,7 @@ export default class SchemaParser { childTags.push(parentElement) } const tagElementChildren = parentElement.node ?? [] - childTags.push( - ...flattenDeep(tagElementChildren.map((child: NodeElement) => this.getAllChildTags(child, excludeTakeValueTags))), - ) + childTags.push(...flattenDeep(tagElementChildren.map((child) => this.getAllChildTags(child, excludeTakeValueTags)))) return childTags } @@ -153,8 +151,8 @@ export default class SchemaParser { const nodeRoot = this.rootElement.schema const tagElements = [] const tagElementChildren = nodeRoot.node - tagElements.push(...flattenDeep(tagElementChildren.map((child: NodeElement) => this.getAllChildTags(child, false)))) - const tags = tagElements.map((element: NodeElement) => SchemaParser.getElementTagName(element)) + tagElements.push(...flattenDeep(tagElementChildren.map((child) => this.getAllChildTags(child, false)))) + const tags = tagElements.map((element) => SchemaParser.getElementTagName(element)) return new Map(zip(tagElements, tags)) } @@ -174,9 +172,7 @@ export default class SchemaParser { for (const definition of attributeDefinitions) { const attributeName = SchemaParser.getElementTagName(definition) const propertyElements = definition.property ?? [] - const properties = propertyElements.map((element: NamedElement) => - this.properties.get(SchemaParser.getElementTagName(element)), - ) + const properties = propertyElements.map((element) => this.properties.get(SchemaParser.getElementTagName(element))) this.attributes.set(attributeName, new SchemaAttribute(attributeName, new Set(properties))) } this._addCustomAttributes() @@ -312,7 +308,7 @@ export default class SchemaParser { */ private _processTagUnitClasses( shortTags: Map, - valueAttributeDefinitions: Map>, + valueAttributeDefinitions: Map>, ): Map { const tagUnitClassAttribute = this.attributes.get('unitClass') const tagUnitClassDefinitions = new Map() @@ -322,7 +318,7 @@ export default class SchemaParser { if (valueAttributes.has(tagUnitClassAttribute)) { tagUnitClassDefinitions.set( tagName, - valueAttributes.get(tagUnitClassAttribute).map((unitClassName: string) => { + valueAttributes.get(tagUnitClassAttribute).map((unitClassName) => { return this.unitClasses.getEntry(unitClassName) }), ) @@ -342,7 +338,7 @@ export default class SchemaParser { */ private _processTagValueClasses( shortTags: Map, - valueAttributeDefinitions: Map>, + valueAttributeDefinitions: Map>, ): Map { const tagValueClassAttribute = this.attributes.get('valueClass') const tagValueClassDefinitions = new Map() @@ -352,10 +348,11 @@ export default class SchemaParser { if (valueAttributes.has(tagValueClassAttribute)) { tagValueClassDefinitions.set( tagName, - valueAttributes.get(tagValueClassAttribute).map((valueClassName: string) => { + valueAttributes.get(tagValueClassAttribute).map((valueClassName) => { return this.valueClasses.getEntry(valueClassName) }), ) + // TODO: Uncomment once value validation uses value classes. // valueAttributes.delete(tagValueClassAttribute) } } @@ -432,7 +429,7 @@ export default class SchemaParser { */ private _createSchemaTags( booleanAttributeDefinitions: Map>, - valueAttributeDefinitions: Map>, + valueAttributeDefinitions: Map>, tagUnitClassDefinitions: Map, tagValueClassDefinitions: Map, ): Map { @@ -489,16 +486,16 @@ export default class SchemaParser { private _parseDefinitions( definitionElements: Iterable, - ): [Map>, Map>] { + ): [Map>, Map>] { return this._parseAttributeElements(definitionElements, SchemaParser.getElementTagName) } private _parseAttributeElements( elements: Iterable, namer: (element: NamedElement) => string, - ): [Map>, Map>] { + ): [Map>, Map>] { const booleanAttributeDefinitions = new Map>() - const valueAttributeDefinitions = new Map>() + const valueAttributeDefinitions = new Map>() for (const element of elements) { const [booleanAttributes, valueAttributes] = this._parseAttributeElement(element) @@ -511,9 +508,9 @@ export default class SchemaParser { return [booleanAttributeDefinitions, valueAttributeDefinitions] } - private _parseAttributeElement(element: DefinitionElement): [Set, Map] { + private _parseAttributeElement(element: DefinitionElement): [Set, Map] { const booleanAttributes = new Set() - const valueAttributes = new Map() + const valueAttributes = new Map() const tagAttributes = element.attribute ?? [] @@ -523,7 +520,7 @@ export default class SchemaParser { booleanAttributes.add(this.attributes.get(attributeName)) continue } - const values = tagAttribute.value.map((value: any) => value._) + const values = tagAttribute.value.map((value) => value._.toString()) valueAttributes.set(this.attributes.get(attributeName), values) } diff --git a/src/schema/schemaMerger.ts b/src/schema/schemaMerger.ts index 87691068..c2b8a929 100644 --- a/src/schema/schemaMerger.ts +++ b/src/schema/schemaMerger.ts @@ -92,7 +92,7 @@ export default class PartneredSchemaMerger { * @param tag The tag to copy. */ private _mergeTag(tag: SchemaTag): void { - if (!tag.getAttributeValue('inLibrary')) { + if (!tag.getAttributeValues('inLibrary')) { return } @@ -101,10 +101,10 @@ export default class PartneredSchemaMerger { IssueError.generateAndThrow('lazyPartneredSchemasShareTag', { tag: shortName }) } - const rootedTagShortName = tag.getAttributeValue('rooted') + const rootedTagShortName = tag.getSingleAttributeValue('rooted') if (rootedTagShortName) { const parentTag = tag.parent - if (parentTag?.name?.toLowerCase() !== rootedTagShortName?.toLowerCase()) { + if (parentTag?.name?.toLowerCase() !== rootedTagShortName.toLowerCase()) { IssueError.generateAndThrowInternalError(`Node ${shortName} is improperly rooted.`) } } diff --git a/src/schema/xmlType.ts b/src/schema/xmlType.ts index dbc024b4..b5de6569 100644 --- a/src/schema/xmlType.ts +++ b/src/schema/xmlType.ts @@ -1,13 +1,10 @@ export type NamedElement = { name: { _: string } } -type AttributeElement = NamedElement & { value?: { _: any }[] } +export type AttributeValue = string | number +export type AttributeElement = NamedElement & { value?: { _: AttributeValue }[] } export type DefinitionElement = NamedElement & { attribute?: AttributeElement[] } export type NodeElement = DefinitionElement & { node?: NodeElement[]; $parent?: NodeElement | null } -type UnitElement = DefinitionElement -type UnitClassElement = DefinitionElement & { unit: UnitElement[] } -type UnitModifierElement = DefinitionElement -type ValueClassElement = DefinitionElement +type UnitClassElement = DefinitionElement & { unit: DefinitionElement[] } type SchemaAttributeElement = NamedElement & { property: AttributeElement[] } -type PropertyElement = NamedElement export type HedSchemaRootElement = { $: { version: string; library?: string; withStandard?: string } @@ -16,16 +13,16 @@ export type HedSchemaRootElement = { unitClassDefinition: UnitClassElement[] } unitModifierDefinitions: { - unitModifierDefinition: UnitModifierElement[] + unitModifierDefinition: DefinitionElement[] } valueClassDefinitions: { - valueClassDefinition: ValueClassElement[] + valueClassDefinition: DefinitionElement[] } schemaAttributeDefinitions: { schemaAttributeDefinition: SchemaAttributeElement[] } propertyDefinitions: { - propertyDefinition: PropertyElement[] + propertyDefinition: NamedElement[] } } From d3f0eedc50be54fd085efdd153932ea6f2ecf077 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 27 Aug 2025 14:20:27 -0500 Subject: [PATCH 15/63] Mark versionDefinitions as read-only --- src/schema/parser.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/parser.ts b/src/schema/parser.ts index 9c03dbb0..0356bdb8 100644 --- a/src/schema/parser.ts +++ b/src/schema/parser.ts @@ -68,7 +68,7 @@ export default class SchemaParser { /** * Version-specific definitions. */ - private _versionDefinitions: { + private readonly _versionDefinitions: { typeProperties: Set categoryProperties: Set roleProperties: Set From fe487e03904ea344e5db924350a3d7f7e8d477de Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Sat, 6 Sep 2025 12:36:15 -0500 Subject: [PATCH 16/63] Port XML loading code to TypeScript Also reorder functions in a couple of already-ported modules. --- browser/src/schema/init.js | 6 +-- browser/src/schema/loader.js | 2 +- src/schema/init.ts | 56 ++++++++++------------ src/schema/{loader.js => loader.ts} | 54 +++++++++++---------- src/schema/parser.ts | 16 +++---- src/utils/{xml.js => xml.ts} | 74 +++++++++++++++-------------- 6 files changed, 102 insertions(+), 106 deletions(-) rename src/schema/{loader.js => loader.ts} (62%) rename src/utils/{xml.js => xml.ts} (55%) diff --git a/browser/src/schema/init.js b/browser/src/schema/init.js index f1700001..ec6ec277 100644 --- a/browser/src/schema/init.js +++ b/browser/src/schema/init.js @@ -7,8 +7,6 @@ import zip from 'lodash/zip' import { loadSchema } from './loader' -import { setParent } from '../../../src/utils/xml' - import SchemaParser from '../../../src/schema/parser' import PartneredSchemaMerger from '../../../src/schema/schemaMerger' import { Schema, HedSchemas } from '../../../src/schema/containers' @@ -23,9 +21,7 @@ import { SchemasSpec } from '../../../src/schema/specs' * @returns {HedSchema} The HED schema object. */ const buildSchemaObject = function (xmlData) { - const rootElement = xmlData.HED - setParent(rootElement, null) - const schemaEntries = new SchemaParser(rootElement).parse() + const schemaEntries = new SchemaParser(xmlData.HED).parse() return new Schema(xmlData, schemaEntries) } diff --git a/browser/src/schema/loader.js b/browser/src/schema/loader.js index 8202662a..8d07adfc 100644 --- a/browser/src/schema/loader.js +++ b/browser/src/schema/loader.js @@ -2,7 +2,7 @@ /* Imports */ import { IssueError } from '../../../src/issues/issues' -import { parseSchemaXML } from '../../../src/utils/xml' +import parseSchemaXML from '../../../src/utils/xml.js' import { schemaData } from './vite-importer' /** diff --git a/src/schema/init.ts b/src/schema/init.ts index 2f434c4a..9057f146 100644 --- a/src/schema/init.ts +++ b/src/schema/init.ts @@ -1,8 +1,6 @@ import zip from 'lodash/zip' import loadSchema from './loader' -import { setParent } from '../utils/xml' - import SchemaParser from './parser' import PartneredSchemaMerger from './schemaMerger' import { HedSchema, PrimarySchema, HedSchemas } from './containers' @@ -11,34 +9,6 @@ import { splitStringTrimAndRemoveBlanks } from '../utils/string' import { SchemasSpec } from './specs' import { HedSchemaXMLObject } from './xmlType' -/** - * Build a single schema container object from an XML file. - * - * @param xmlData The schema's XML data - * @returns The HED schema object. - */ -function buildSchemaObject(xmlData: HedSchemaXMLObject): PrimarySchema { - const rootElement = xmlData.HED - setParent(rootElement, null) - const schemaEntries = new SchemaParser(rootElement).parse() - return new PrimarySchema(xmlData, schemaEntries) -} - -/** - * Build a single merged schema container object from one or more XML files. - * - * @param xmlData The schemas' XML data. - * @returns The HED schema object. - */ -function buildSchemaObjects(xmlData: HedSchemaXMLObject[]): HedSchema { - const schemas = xmlData.map((data) => buildSchemaObject(data)) - if (schemas.length === 1) { - return schemas[0] - } - const partneredSchemaMerger = new PartneredSchemaMerger(schemas) - return partneredSchemaMerger.mergeSchemas() -} - /** * Build a schema collection object from a schema specification. * @@ -73,3 +43,29 @@ export async function buildSchemasFromVersion(hedVersionString?: string): Promis const hedVersionSpecs = SchemasSpec.parseVersionSpecs(hedVersionSpecStrings) return buildSchemas(hedVersionSpecs) } + +/** + * Build a single merged schema container object from one or more XML files. + * + * @param xmlData The schemas' XML data. + * @returns The HED schema object. + */ +function buildSchemaObjects(xmlData: HedSchemaXMLObject[]): HedSchema { + const schemas = xmlData.map((data) => buildSchemaObject(data)) + if (schemas.length === 1) { + return schemas[0] + } + const partneredSchemaMerger = new PartneredSchemaMerger(schemas) + return partneredSchemaMerger.mergeSchemas() +} + +/** + * Build a single schema container object from an XML file. + * + * @param xmlData The schema's XML data + * @returns The HED schema object. + */ +function buildSchemaObject(xmlData: HedSchemaXMLObject): PrimarySchema { + const schemaEntries = new SchemaParser(xmlData.HED).parse() + return new PrimarySchema(xmlData, schemaEntries) +} diff --git a/src/schema/loader.js b/src/schema/loader.ts similarity index 62% rename from src/schema/loader.js rename to src/schema/loader.ts index 0628fdfb..975cad30 100644 --- a/src/schema/loader.js +++ b/src/schema/loader.ts @@ -3,18 +3,20 @@ /* Imports */ import * as files from '../utils/files' import { IssueError } from '../issues/issues' -import { parseSchemaXML } from '../utils/xml' +import parseSchemaXML from '../utils/xml' import { localSchemaMap, localSchemaNames } from './config' // Changed from localSchemaList +import { SchemaSpec } from './specs' +import { HedSchemaXMLObject } from './xmlType' /** * Load schema XML data from a schema version or path description. * - * @param {SchemaSpec} schemaDef The description of which schema to use. - * @returns {Promise} The schema XML data. + * @param schemaDef The description of which schema to use. + * @returns The schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -export default async function loadSchema(schemaDef = null) { +export default async function loadSchema(schemaDef: SchemaSpec): Promise { const xmlData = await loadPromise(schemaDef) if (xmlData === null) { IssueError.generateAndThrow('invalidSchemaSpecification', { spec: JSON.stringify(schemaDef) }) @@ -25,14 +27,12 @@ export default async function loadSchema(schemaDef = null) { /** * Choose the schema Promise from a schema version or path description. * - * @param {SchemaSpec} schemaDef The description of which schema to use. - * @returns {Promise} The schema XML data. + * @param schemaDef The description of which schema to use. + * @returns The schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -async function loadPromise(schemaDef) { - if (schemaDef === null) { - return null - } else if (schemaDef.localPath) { +async function loadPromise(schemaDef: SchemaSpec): Promise { + if (schemaDef.localPath) { return loadLocalSchema(schemaDef.localPath) } else if (localSchemaNames.includes(schemaDef.localName)) { // Changed condition @@ -45,12 +45,12 @@ async function loadPromise(schemaDef) { /** * Load schema XML data from the HED GitHub repository. * - * @param {SchemaSpec} schemaDef The standard schema version to load. - * @returns {Promise} The schema XML data. + * @param schemaDef The standard schema version to load. + * @returns The schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -function loadRemoteSchema(schemaDef) { - let url +async function loadRemoteSchema(schemaDef: SchemaSpec): Promise { + let url: string if (schemaDef.library) { url = `https://raw.githubusercontent.com/hed-standard/hed-schemas/refs/heads/main/library_schemas/${schemaDef.library}/hedxml/HED_${schemaDef.library}_${schemaDef.version}.xml` } else { @@ -62,22 +62,22 @@ function loadRemoteSchema(schemaDef) { /** * Load schema XML data from a local file. * - * @param {string} path The path to the schema XML data. - * @returns {Promise} The schema XML data. + * @param path The path to the schema XML data. + * @returns The schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -function loadLocalSchema(path) { +async function loadLocalSchema(path: string): Promise { return loadSchemaFile(files.readFile(path), 'localSchemaLoadFailed', { path: path }) } /** * Load schema XML data from a bundled file. * - * @param {SchemaSpec} schemaDef The description of which schema to use. - * @returns {Promise} The schema XML data. + * @param schemaDef The description of which schema to use. + * @returns The schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -async function loadBundledSchema(schemaDef) { +async function loadBundledSchema(schemaDef: SchemaSpec): Promise { try { return parseSchemaXML(localSchemaMap.get(schemaDef.localName)) } catch (error) { @@ -89,13 +89,17 @@ async function loadBundledSchema(schemaDef) { /** * Actually load the schema XML file. * - * @param {Promise} xmlDataPromise The Promise containing the unparsed XML data. - * @param {string} issueCode The issue code. - * @param {Object} issueArgs The issue arguments passed from the calling function. - * @returns {Promise} The parsed schema XML data. + * @param xmlDataPromise The Promise containing the unparsed XML data. + * @param issueCode The issue code. + * @param issueArgs The issue arguments passed from the calling function. + * @returns The parsed schema XML data. * @throws {IssueError} If the schema could not be loaded. */ -async function loadSchemaFile(xmlDataPromise, issueCode, issueArgs) { +async function loadSchemaFile( + xmlDataPromise: Promise, + issueCode: string, + issueArgs: Record, +): Promise { try { const data = await xmlDataPromise return parseSchemaXML(data) diff --git a/src/schema/parser.ts b/src/schema/parser.ts index 0356bdb8..f9b3edf3 100644 --- a/src/schema/parser.ts +++ b/src/schema/parser.ts @@ -114,13 +114,11 @@ export default class SchemaParser { if (excludeTakeValueTags && SchemaParser.getElementTagName(parentElement) === '#') { return [] } - const childTags = [] - if (parentElement.$parent) { - childTags.push(parentElement) - } + const childTags = [parentElement] const tagElementChildren = parentElement.node ?? [] - childTags.push(...flattenDeep(tagElementChildren.map((child) => this.getAllChildTags(child, excludeTakeValueTags)))) - return childTags + return childTags.concat( + flattenDeep(tagElementChildren.map((child) => this.getAllChildTags(child, excludeTakeValueTags))), + ) } private static getParentTagName(tagElement: NodeElement): string { @@ -166,7 +164,7 @@ export default class SchemaParser { this._addCustomProperties() } - private parseAttributes() { + private parseAttributes(): void { const attributeDefinitions = this.rootElement.schemaAttributeDefinitions.schemaAttributeDefinition this.attributes = new Map() for (const definition of attributeDefinitions) { @@ -189,7 +187,7 @@ export default class SchemaParser { return new RegExp(classChars) } - private parseValueClasses() { + private parseValueClasses(): void { const valueClasses = new Map() const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions( this.rootElement.valueClassDefinitions.valueClassDefinition, @@ -203,7 +201,7 @@ export default class SchemaParser { this.valueClasses = new SchemaEntryManager(valueClasses) } - private parseUnitModifiers() { + private parseUnitModifiers(): void { const unitModifiers = new Map() const [booleanAttributeDefinitions, valueAttributeDefinitions] = this._parseDefinitions( this.rootElement.unitModifierDefinitions.unitModifierDefinition, diff --git a/src/utils/xml.js b/src/utils/xml.ts similarity index 55% rename from src/utils/xml.js rename to src/utils/xml.ts index 8dc05764..cf2df5d1 100644 --- a/src/utils/xml.js +++ b/src/utils/xml.ts @@ -1,45 +1,14 @@ import { XMLParser } from 'fast-xml-parser' -/** - * Recursively set a field on each node of the tree pointing to the node's parent. - * - * @param {Object} node The child node. - * @param {Object} parent The parent node. - */ -const setNodeParent = function (node, parent) { - // Assume that we've already run this function if so. - if ('$parent' in node) { - return - } - node.$parent = parent - const childNodes = node.node ?? [] - for (const child of childNodes) { - setNodeParent(child, node) - } -} - -/** - * Handle top level of parent-setting recursion before passing to setNodeParent. - * - * @param {Object} node The child node. - * @param {Object} parent The parent node. - */ -export const setParent = function (node, parent) { - if (node.schema) { - node.$parent = null - setNodeParent(node.schema, null) - } else { - setNodeParent(node, parent) - } -} +import { HedSchemaXMLObject, HedSchemaRootElement, NodeElement } from '../schema/xmlType' /** * Parse the schema XML data. * - * @param {string} data The XML data. - * @returns {Promise} The schema XML data. + * @param data The XML data. + * @returns The schema XML data. */ -export async function parseSchemaXML(data) { +export default function parseSchemaXML(data: string): HedSchemaXMLObject { const alwaysArray = new Set(['node', 'property', 'attribute', 'value', 'unit']) const parser = new XMLParser({ ignoreAttributes: false, @@ -53,5 +22,38 @@ export async function parseSchemaXML(data) { return alwaysArray.has(name) }, }) - return parser.parse(data) + + const xmlData = parser.parse(data) as HedSchemaXMLObject + setParent(xmlData.HED) + return xmlData +} + +/** + * Handle top level of parent-setting recursion before passing to setNodeParent. + * + * @param rootElement The root element of the XML tree. + */ +function setParent(rootElement: HedSchemaRootElement): void { + const childNodes = rootElement.schema.node ?? [] + for (const child of childNodes) { + setNodeParent(child, null) + } +} + +/** + * Recursively set a field on each node of the tree pointing to the node's parent. + * + * @param node The child node. + * @param parent The parent node. + */ +function setNodeParent(node: NodeElement, parent: NodeElement | null): void { + // Assume that we've already run this function if so. + if ('$parent' in node) { + return + } + node.$parent = parent + const childNodes = node.node ?? [] + for (const child of childNodes) { + setNodeParent(child, node) + } } From 1f71bc052bd9a97d8bd9c46d3a1a017be0e02ef2 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Sat, 6 Sep 2025 14:57:08 -0500 Subject: [PATCH 17/63] Reformat two config files --- babel.config.js | 18 ++++++++++-------- jest.config.js | 6 +----- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/babel.config.js b/babel.config.js index f575b653..49218f78 100644 --- a/babel.config.js +++ b/babel.config.js @@ -1,12 +1,14 @@ export default { presets: [ - ['@babel/preset-env', { - targets: { - node: '22' - } - }], - '@babel/preset-typescript' + [ + '@babel/preset-env', + { + targets: { + node: '22', + }, + }, + ], + '@babel/preset-typescript', ], - plugins: [] + plugins: [], } - diff --git a/jest.config.js b/jest.config.js index 3df9caa8..a7987139 100644 --- a/jest.config.js +++ b/jest.config.js @@ -10,11 +10,7 @@ export default { moduleNameMapper: { '\\.(css|less|scss|sass)$': 'identity-obj-proxy', }, - collectCoverageFrom: [ - 'src/**/*.js', - '!src/**/*.spec.js', - '!src/**/*.test.js', - ], + collectCoverageFrom: ['src/**/*.js', '!src/**/*.spec.js', '!src/**/*.test.js'], coveragePathIgnorePatterns: [ '/node_modules/', '/tests/', From 9f0fcce2431d676c9b37ea0ce08f8e77fd400248 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Sat, 6 Sep 2025 15:30:55 -0500 Subject: [PATCH 18/63] Port schema config module to TypeScript Also freeze bundled schema lists for safety. --- src/schema/{config.js => config.ts} | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) rename src/schema/{config.js => config.ts} (55%) diff --git a/src/schema/config.js b/src/schema/config.ts similarity index 55% rename from src/schema/config.js rename to src/schema/config.ts index 93bfc5e8..b1ab1df1 100644 --- a/src/schema/config.js +++ b/src/schema/config.ts @@ -5,7 +5,7 @@ // The actual loading mechanism is handled by the schema loader, // which may use an application-provided loader for browser environments // or a Node.js fs-based loader for server-side/test environments. -export const localSchemaNames = [ +const _localSchemaNames = [ 'HED8.0.0', 'HED8.1.0', 'HED8.2.0', @@ -18,23 +18,36 @@ export const localSchemaNames = [ 'HED_score_2.1.0', // Add other bundled schema base names here if needed ] +/** + * This list defines the base names of HED XML schema files that are considered "bundled" with the library. + * The actual loading mechanism is handled by the schema loader, which may use an application-provided loader + * for browser environments or a Node.js fs-based loader for server-side/test environments. + */ +export const localSchemaNames = Object.freeze(_localSchemaNames) -let schemaMap +let _localSchemaMap // @ts-ignore __VITE_ENV__ is defined by Vite in browser builds if (typeof __VITE_ENV__ !== 'undefined' && __VITE_ENV__) { // In the browser, this map is not used. The loader uses import.meta.glob. - schemaMap = new Map() + _localSchemaMap = new Map() } else { // For Node.js, pre-load the schemas. - schemaMap = new Map( + _localSchemaMap = new Map( localSchemaNames.map((localSchema) => [localSchema, require(`../data/schemas/${localSchema}.xml`)]), ) } -export const localSchemaMap = schemaMap +/** + * A mapping from the bundled schema names to their XML data (as strings). + */ +export const localSchemaMap = Object.freeze(_localSchemaMap) -export const getLocalSchemaVersions = function () { - // Return a copy of the local schema names to avoid external modifications +/** + * Return a copy of the bundled schema names without the "HED" prefix. + * + * @returns The list of unprefixed bundled schema names. + */ +export function getLocalSchemaVersions(): string[] { return localSchemaNames.map((name) => name.replace(/^HED_?/, '')) } From 733d18689d72b05b755720a615cd6d005684d18b Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 10:00:43 -0500 Subject: [PATCH 19/63] Fix issue with Qlty config --- .qlty/qlty.toml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.qlty/qlty.toml b/.qlty/qlty.toml index b80f9057..3c6bdc71 100644 --- a/.qlty/qlty.toml +++ b/.qlty/qlty.toml @@ -17,9 +17,6 @@ exclude_patterns = [ "docs/", "dist/", "**/node_modules/", - "**/*.yml", - "**/*.yaml", - "**/*.json", "**/.gitignore", "**/README*", "**/LICENSE", From 6c772e806ee24fb653428e5f7595d4706716e895 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Sat, 6 Sep 2025 18:31:51 -0500 Subject: [PATCH 20/63] Port array utiilty function to TypeScript This was a multi-hour adventure, eventually solved by AI. --- src/parser/splitter.js | 2 +- src/utils/array.js | 19 ------------------- src/utils/array.ts | 21 +++++++++++++++++++++ 3 files changed, 22 insertions(+), 20 deletions(-) delete mode 100644 src/utils/array.js create mode 100644 src/utils/array.ts diff --git a/src/parser/splitter.js b/src/parser/splitter.js index 9496239d..702ee830 100644 --- a/src/parser/splitter.js +++ b/src/parser/splitter.js @@ -69,7 +69,7 @@ export default class HedStringSplitter { _createParsedTags(tagSpecs, groupSpecs) { // Create tags from specifications this.issues = [] - const parsedTags = recursiveMap((tagSpec) => this._createParsedTag(tagSpec), tagSpecs) + const parsedTags = recursiveMap(tagSpecs, (tagSpec) => this._createParsedTag(tagSpec)) // Create groups from the parsed tags const parsedTagsWithGroups = this._createParsedGroups(parsedTags, groupSpecs.children) diff --git a/src/utils/array.js b/src/utils/array.js deleted file mode 100644 index 67aab8dd..00000000 --- a/src/utils/array.js +++ /dev/null @@ -1,19 +0,0 @@ -/** This module holds the sidecar validator class. - * @module - */ - -/** - * Apply a function recursively to an array. - * - * @template T,U - * @param {function(T): U} fn The function to apply. - * @param {T[]} array The array to map. - * @returns {U[]} The mapped array. - */ -export function recursiveMap(fn, array) { - if (Array.isArray(array)) { - return array.map((element) => recursiveMap(fn, element)) - } else { - return fn(array) - } -} diff --git a/src/utils/array.ts b/src/utils/array.ts new file mode 100644 index 00000000..02031506 --- /dev/null +++ b/src/utils/array.ts @@ -0,0 +1,21 @@ +/** + * Array utility functions. + * @module + */ + +type NestedArray = T | NestedArray[] + +/** + * Apply a function recursively to an array. + * + * @param array The array to map. + * @param fn The function to apply. + * @returns The mapped array. + */ +export function recursiveMap(array: NestedArray, fn: (element: T) => U): NestedArray { + if (Array.isArray(array)) { + return array.map((element) => recursiveMap(element, fn)) + } else { + return fn(array) + } +} From 7d491d96888fb6349a5757de2dcaf1daa922667b Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 20 Oct 2025 11:37:38 -0500 Subject: [PATCH 21/63] Delete memoizer class Future cases of memoization will be handled by private instance fields. --- src/schema/entries.ts | 32 +++++++++++++++---------------- src/utils/memoizer.js | 44 ------------------------------------------- 2 files changed, 15 insertions(+), 61 deletions(-) delete mode 100644 src/utils/memoizer.js diff --git a/src/schema/entries.ts b/src/schema/entries.ts index 28563a29..7817f812 100644 --- a/src/schema/entries.ts +++ b/src/schema/entries.ts @@ -5,13 +5,12 @@ import pluralize from 'pluralize' pluralize.addUncountableRule('hertz') import { IssueError } from '../issues/issues' -import Memoizer from '../utils/memoizer' import SchemaParser from './parser' /** * SchemaEntries class */ -export class SchemaEntries extends Memoizer { +export class SchemaEntries { /** * The schema's properties. */ @@ -47,7 +46,6 @@ export class SchemaEntries extends Memoizer { * @param schemaParser A constructed schema parser. */ constructor(schemaParser: SchemaParser) { - super() this.properties = new SchemaEntryManager(schemaParser.properties) this.attributes = new SchemaEntryManager(schemaParser.attributes) this.valueClasses = schemaParser.valueClasses @@ -60,7 +58,7 @@ export class SchemaEntries extends Memoizer { /** * A manager of {@link SchemaEntry} objects. */ -export class SchemaEntryManager extends Memoizer { +export class SchemaEntryManager { /** * The definitions managed by this entry manager. */ @@ -72,7 +70,6 @@ export class SchemaEntryManager extends Memoizer { * @param definitions A map of schema entry definitions. */ constructor(definitions: Map) { - super() this._definitions = definitions } @@ -131,10 +128,8 @@ export class SchemaEntryManager extends Memoizer { * @returns A subset of the managed collection with the given boolean attribute. */ public getEntriesWithBooleanAttribute(booleanAttributeName: string): Map { - return this._memoize(booleanAttributeName, () => { - return this.filter(([, v]) => { - return v.hasBooleanAttribute(booleanAttributeName) - }) + return this.filter(([, v]) => { + return v.hasBooleanAttribute(booleanAttributeName) }) } @@ -162,14 +157,13 @@ export class SchemaEntryManager extends Memoizer { /** * SchemaEntry class */ -export class SchemaEntry extends Memoizer { +export class SchemaEntry { /** * The name of this schema entry. */ private readonly _name: string constructor(name: string) { - super() this._name = name } @@ -564,6 +558,11 @@ export class SchemaTag extends SchemaEntryWithAttributes { */ private _valueTag: SchemaValueTag + /** + * This tag's ancestor tags. + */ + #ancestors: SchemaTag[] + /** * Constructor. * @@ -662,12 +661,11 @@ export class SchemaTag extends SchemaEntryWithAttributes { * Return all of this tag's ancestors. */ public get ancestors(): SchemaTag[] { - return this._memoize('ancestors', () => { - if (this.parent) { - return [this.parent, ...this.parent.ancestors] - } - return [] - }) + if (this.#ancestors !== undefined) { + return this.#ancestors + } + this.#ancestors = this.parent ? [this.parent, ...this.parent.ancestors] : [] + return this.#ancestors } /** diff --git a/src/utils/memoizer.js b/src/utils/memoizer.js deleted file mode 100644 index ba7db9d4..00000000 --- a/src/utils/memoizer.js +++ /dev/null @@ -1,44 +0,0 @@ -/** Memoizer class. **/ - -import { IssueError } from '../issues/issues' - -/** - * Superclass for property memoization until we can get away with private fields. - */ -export default class Memoizer { - /** - * Map containing memoized properties (string --> any). - * - * @type {Map} - * @private - */ - _memoizedProperties - - /** - * Constructor. - */ - constructor() { - this._memoizedProperties = new Map() - } - - /** - * Memoize a property. - * - * @template T - * @param {string} propertyName The property name. - * @param {function() : T} valueComputer A function to compute the property's value. - * @returns {T} The computed value. - * @protected - */ - _memoize(propertyName, valueComputer) { - if (!propertyName) { - IssueError.generateAndThrowInternalError('Invalid property name in Memoizer subclass.') - } - if (this._memoizedProperties.has(propertyName)) { - return this._memoizedProperties.get(propertyName) - } - const value = valueComputer() - this._memoizedProperties.set(propertyName, value) - return value - } -} From ddfd26e2921d2580132128afe78dfbfa4356eaa2 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Mon, 20 Oct 2025 11:44:10 -0500 Subject: [PATCH 22/63] Port two easy utility modules to TypeScript --- src/utils/{files.js => files.ts} | 12 ++++++------ src/utils/{hedStrings.js => hedStrings.ts} | 7 ++++++- 2 files changed, 12 insertions(+), 7 deletions(-) rename src/utils/{files.js => files.ts} (74%) rename src/utils/{hedStrings.js => hedStrings.ts} (59%) diff --git a/src/utils/files.js b/src/utils/files.ts similarity index 74% rename from src/utils/files.js rename to src/utils/files.ts index fc14e94c..8fec449f 100644 --- a/src/utils/files.js +++ b/src/utils/files.ts @@ -8,11 +8,11 @@ import { IssueError } from '../issues/issues' /** * Read a local file. * - * @param {string} fileName The file path. - * @returns {Promise} A promise with the file contents. + * @param fileName The file path. + * @returns A promise with the file contents. * @throws {IssueError} If the file read failed or if called in a browser environment. */ -export async function readFile(fileName) { +export async function readFile(fileName: string): Promise { try { const stringBuffer = await readFilePromise(fileName, 'utf8') return stringBuffer.toString() @@ -24,11 +24,11 @@ export async function readFile(fileName) { /** * Read a remote file using HTTPS. * - * @param {string} url The remote URL. - * @returns {Promise} A promise with the file contents. + * @param url The remote URL. + * @returns A promise with the file contents. * @throws {IssueError} If the network read failed. */ -export async function readHTTPSFile(url) { +export async function readHTTPSFile(url: string): Promise { const response = await fetch(url) if (!response.ok) { IssueError.generateAndThrow('networkReadError', { diff --git a/src/utils/hedStrings.js b/src/utils/hedStrings.ts similarity index 59% rename from src/utils/hedStrings.js rename to src/utils/hedStrings.ts index f48673f3..908e07d3 100644 --- a/src/utils/hedStrings.js +++ b/src/utils/hedStrings.ts @@ -1,7 +1,12 @@ +/** + * HED string-related utility functions. + * @module + */ + /** * Get the indices of all slashes in a HED tag. */ -export const getTagSlashIndices = function (tag) { +export function getTagSlashIndices(tag: string): number[] { const indices = [] let i = -1 while ((i = tag.indexOf('/', i + 1)) >= 0) { From 4558294812185e4296731fad6d1fc804f3775ef0 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 22 Oct 2025 06:12:40 -0500 Subject: [PATCH 23/63] Port string utilities and HED issue code to TypeScript --- src/bids/types/issues.js | 2 +- src/issues/data.js | 507 --------------------------- src/issues/data.ts | 517 ++++++++++++++++++++++++++++ src/issues/{issues.js => issues.ts} | 146 ++++---- src/utils/string.js | 49 --- src/utils/string.ts | 58 ++++ 6 files changed, 661 insertions(+), 618 deletions(-) delete mode 100644 src/issues/data.js create mode 100644 src/issues/data.ts rename src/issues/{issues.js => issues.ts} (56%) delete mode 100644 src/utils/string.js create mode 100644 src/utils/string.ts diff --git a/src/bids/types/issues.js b/src/bids/types/issues.js index 3903671d..baec8dfe 100644 --- a/src/bids/types/issues.js +++ b/src/bids/types/issues.js @@ -5,7 +5,7 @@ import { generateIssue, IssueError } from '../../issues/issues' /** - * @typedef {import('../../issues/issues.js').Issue} Issue + * @typedef {import('../../issues/issues.ts').Issue} Issue */ /** diff --git a/src/issues/data.js b/src/issues/data.js deleted file mode 100644 index 44a410f1..00000000 --- a/src/issues/data.js +++ /dev/null @@ -1,507 +0,0 @@ -/** This module contains the templates for the issues. - * @module issues/data - */ - -import { stringTemplate } from '../utils/string' - -export default { - // Syntax issues - parentheses: { - hedCode: 'PARENTHESES_MISMATCH', - level: 'error', - message: stringTemplate`Number of opening and closing parentheses are unequal. ${'opening'} opening parentheses. ${'closing'} closing parentheses.`, - }, - unopenedParenthesis: { - hedCode: 'PARENTHESES_MISMATCH', - level: 'error', - message: stringTemplate`Closing parenthesis at index ${'index'} of string "${'string'}" does not have a corresponding opening parenthesis.`, - }, - unclosedParenthesis: { - hedCode: 'PARENTHESES_MISMATCH', - level: 'error', - message: stringTemplate`Opening parenthesis at index ${'index'} of string "${'string'}" does not have a corresponding closing parenthesis.`, - }, - commaMissing: { - hedCode: 'COMMA_MISSING', - level: 'error', - message: stringTemplate`Comma missing at position ${'index'} of string "${'string'}". ${'msg'}`, - }, - deprecatedTag: { - hedCode: 'ELEMENT_DEPRECATED', - level: 'warning', - message: stringTemplate`Tags "${'tags'} in "${'string'} are deprecated. Please see tag description for instructions on replacement.".`, - }, - duplicateTag: { - hedCode: 'TAG_EXPRESSION_REPEATED', - level: 'error', - message: stringTemplate`Duplicate tags - "${'tags'} in "${'string'}".`, - }, - extendedTag: { - hedCode: 'TAG_EXTENDED', - level: 'warning', - message: stringTemplate`Tag extensions found for ${'tags'} in "${'string'}".`, - }, - invalidCharacter: { - hedCode: 'CHARACTER_INVALID', - level: 'error', - message: stringTemplate`Invalid character "${'character'}" at index ${'index'} of string "${'string'}".`, - }, - // Common semantic validation issues - invalidTag: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Invalid tag - "${'tag'}". ${'msg'}`, - }, - extraSlash: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Tag has extra slash at index ${'index'} of string "${'string'}".`, - }, - extraBlank: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Tag has extra blank at index ${'index'} of string "${'string'}".`, - }, - extraCommaOrInvalid: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Either "${'previousTag'}" contains a comma when it should not or "${'tag'}" is not a valid tag.`, - }, - invalidTagPrefix: { - hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', - level: 'error', - message: stringTemplate`Either tag prefix at index ${'index'} contains non-alphabetic characters or does not have an associated schema. ${'msg'}`, - }, - multipleUniqueTags: { - hedCode: 'TAG_NOT_UNIQUE', - level: 'error', - message: stringTemplate`Multiple unique "${'tag'}" tags in "${'string'}".`, - }, - childRequired: { - hedCode: 'TAG_REQUIRES_CHILD', - level: 'error', - message: stringTemplate`Descendant tag required - "${'tag'}". ${'msg'}`, - }, - valueRequired: { - hedCode: 'TAG_REQUIRES_CHILD', - level: 'error', - message: stringTemplate`Tag "${'tag'}" requires a value.`, - }, - childForbidden: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Child tag or value not allowed - "${'tag'}".`, - }, - requiredPrefixMissing: { - hedCode: 'REQUIRED_TAG_MISSING', - level: 'warning', - message: stringTemplate`Tag with prefix "${'tagPrefix'}" is required.`, - }, - unitClassInvalidUnit: { - hedCode: 'UNITS_INVALID', - level: 'error', - message: stringTemplate`Invalid unit - "${'tag'}".`, - }, - invalidValue: { - hedCode: 'VALUE_INVALID', - level: 'error', - message: stringTemplate`Invalid placeholder value for tag "${'tag'}". ${'msg'}`, - }, - invalidPlaceholderContext: { - hedCode: 'PLACEHOLDER_INVALID', - level: 'error', - message: stringTemplate`"${'string'}" has "#" placeholders, which are not allowed in this context.`, - }, - invalidSidecarPlaceholder: { - hedCode: 'PLACEHOLDER_INVALID', - level: 'error', - message: stringTemplate`"${'string'}" of sidecar key "${'sidecarKey'}" has an invalid # placeholder.`, - }, - // HED 3-specific validation issues - invalidPlaceholder: { - hedCode: 'PLACEHOLDER_INVALID', - level: 'error', - message: stringTemplate`Invalid # placeholder - "${'tag'}".`, - }, - missingPlaceholder: { - hedCode: 'PLACEHOLDER_INVALID', - level: 'error', - message: stringTemplate`HED value string "${'string'}" is missing a required # placeholder for sidecar key "${'sidecarKey'}".`, - }, - extraPlaceholder: { - hedCode: 'PLACEHOLDER_INVALID', - level: 'error', - message: stringTemplate`HED value string "${'string'}" has too many placeholders in sidecar key "${'sidecarKey'}".`, - }, - invalidPlaceholderInDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Invalid placeholder or missing placeholder in definition - "${'definition'}". ${'msg'}`, - }, - invalidDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Invalid definition - "${'definition'}". ${'msg'}`, - }, - invalidDefinitionManager: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Invalid definition manager "${'defManager'}", usually because invalid external definitions were provided to a sidecar or tsv.`, - }, - nestedDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Illegal nested definition in tag group for definition "${'definition'}".`, - }, - missingDefinitionForDef: { - hedCode: 'DEF_INVALID', - level: 'error', - message: stringTemplate`Def tag found for definition name "${'definition'}" does not correspond to an existing definition.`, - }, - missingDefinitionForDefExpand: { - hedCode: 'DEF_EXPAND_INVALID', - level: 'error', - message: stringTemplate`Def-expand tag found for definition name "${'definition'}" does not correspond to an existing definition.`, - }, - invalidDefinitionGroupStructure: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`The Definition or Def-expand tag "${'tag'} in "${'tagGroup'}" has multiple top tags or more than one top group.`, - }, - invalidDefinitionForbidden: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`The Definition or Def-expand tag "${'tag'} in "${'tagGroup'}" has other definition-related tags in subgroups.`, - }, - defExpandContentsInvalid: { - hedCode: 'DEF_EXPAND_INVALID', - level: 'error', - message: stringTemplate`Def-expand contents "${'contents'}" disagree with evaluated definition "${'contentsDef'}".`, - }, - duplicateDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Definition "${'definition'}" is declared multiple times. This instance's tag group is "${'tagGroup'}".`, - }, - conflictingDefinitions: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Definition "${'definition1'}" and "${'definition2'}' conflict.`, - }, - duplicateDefinitionNames: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Definition "${'definition1'}" and "${'definition2'}" have same name but are not equivalent.`, - }, - multipleTagGroupsInDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Multiple inner tag groups found in definition "${'definition'}".`, - }, - illegalDefinitionGroupTag: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Illegal tag "${'tag'}" in tag group for definition "${'definition'}".`, - }, - illegalDefinitionContext: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Definition "${'definition'}" was found in string "${'string'}" in a context where definitions are not allowed.`, - }, - illegalInExclusiveContext: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`"${'tag'}" can only appear in groups with other definitions but "${'string'}" has other types of groups or tags.`, - }, - inactiveOnset: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`${'tag'} found for inactive onset with definition name and value "${'definition'}".`, - }, - temporalWithoutInnerGroup: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`${'tag'} found without an included inner top-level tag group. This instance's tag group is "${'tagGroup'}".`, - }, - temporalWithWrongNumberDefs: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`${'tag'} found in tag group "${'tagGroup'}" with the wrong number of Def tags and Def-expand groups.`, - }, - temporalWithoutDefinition: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`${'tag'} found in tag group "${'tagGroup'}" without an included definition.`, - }, - extraTagsInTemporal: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`Extra top-level tags or tag groups found in onset, inset, or offset group "${'tagGroup'}" with definition "${'definition'}".`, - }, - temporalTagInNonTemporalContext: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`HED event string "${'string'}" has temporal tags on line(s) [${'tsvline'}] in a tsv file without an onset time.`, - }, - duplicateTemporal: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`HED event string "${'string'}" has onset/offset/inset tags with duplicated definition "${'definition'}".`, - }, - multipleTemporalTags: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`HED event string "${'string'}" has multiple temporal tags ${'tags'} in the same group.`, - }, - multipleRequiresDefTags: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`HED event string "${'string'}" has multiple temporal tags ${'tags'} that require a definition in the same group.`, - }, - simultaneousDuplicateEvents: { - hedCode: 'TEMPORAL_TAG_ERROR', - level: 'error', - message: stringTemplate`Temporal tag group "${'tagGroup1'}" at ${'onset1'} line ${'tsvLine1'} is simultaneous with "${'tagGroup2'}" at ${'onset2'} line ${'tsvLine2'}.`, - }, - missingTagGroup: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag(s) "${'tag'}" must appear in a tag group.`, - }, - invalidTagGroup: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`"${'tagGroup'}" has invalid group tags or invalid number of subgroups.`, - }, - forbiddenSubgroupTags: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag "${'tag'}" in "${'string'}" cannot have tags "${'tagList'}" in a subgroup.`, - }, - invalidTopLevelTagGroupTag: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag "${'tag'}" is only allowed inside of a top-level tag group, but is not at top level in "${'string'}".`, - }, - invalidGroupTags: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tags "${'tags'}" in "${'string'}" cannot be in a subgroups together.`, - }, - invalidGroupTopTags: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tags "${'tags'}" cannot be at the same level in group "${'string'}".`, - }, - tooManyGroupTopTags: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Group "${'string'}" has too many or too few tags or Def-expand groups at the top level.`, - }, - multipleTopLevelTagGroupTags: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag "${'tag'}" found in top-level tag group where "${'otherTag'}" was already defined.`, - }, - invalidNumberOfSubgroups: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`The tag "${'tag'} is in a "${'string'} with too many or too few subgroups.`, - }, - invalidTopLevelTag: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag(s) "${'tag'}" should be in a top group in "${'string'}".`, - }, - invalidGroupTag: { - hedCode: 'TAG_GROUP_ERROR', - level: 'error', - message: stringTemplate`Tag(s) "${'tag'}" should be in a group in "${'string'}".`, - }, - // Tag conversion issues - invalidParentNode: { - hedCode: 'TAG_EXTENSION_INVALID', - level: 'error', - message: stringTemplate`"${'tag'}" does not have "${'parentTag'}" as its parent in the schema. ${'msg'}`, - }, - invalidExtension: { - hedCode: 'TAG_EXTENSION_INVALID', - level: 'error', - message: stringTemplate`"${'tag'}" appears as an extension of "${'parentTag'}". ${'msg'}`, - }, - emptyTagFound: { - hedCode: 'TAG_EMPTY', - level: 'error', - message: stringTemplate`Empty tag at index ${'index'} cannot be converted.`, - }, - invalidTagString: { - hedCode: 'TAG_INVALID', - level: 'error', - message: stringTemplate`Tag string is null or undefined.`, - }, - duplicateTagsInSchema: { - hedCode: 'SCHEMA_DUPLICATE_NODE', - level: 'error', - message: stringTemplate`Source HED schema is invalid as it contains duplicate tags.`, - }, - // Curly brace issues - unopenedCurlyBrace: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Closing curly brace at index ${'index'} of string "${'string'}" does not have a corresponding opening curly brace. ${'msg'}`, - }, - unclosedCurlyBrace: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Opening curly brace at index ${'index'} of string "${'string'}" does not have a corresponding closing curly brace. ${'msg'}`, - }, - nestedCurlyBrace: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Opening curly brace at index ${'index'} of string "${'string'}" when curly brace expression is already open.`, - }, - emptyCurlyBrace: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Curly brace expression of string "${'string'}" is empty. ${'msg'}`, - }, - curlyBracesInDefinition: { - hedCode: 'DEFINITION_INVALID', - level: 'error', - message: stringTemplate`Illegal curly brace expression "${'sidecarKey'}" found in HED string containing definition "${'definition'}".`, - }, - curlyBracesInHedColumn: { - hedCode: 'CHARACTER_INVALID', - level: 'error', - message: stringTemplate`Curly brace expression "${'string'}" found in the HED column of a TSV file.`, - }, - curlyBracesNotAllowed: { - hedCode: 'CHARACTER_INVALID', - level: 'error', - message: stringTemplate`Curly brace expression not allowed in "${'string'}".`, - }, - recursiveCurlyBraces: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Sidecar key "${'sidecarKey'}", which has curly braces, is illegally referred to by a string using curly braces.`, - }, - recursiveCurlyBracesWithKey: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Sidecar key "${'sidecarKey'}", which has curly braces, is referred to by sidecar key "${'referrer'}", which also has curly braces.`, - }, - undefinedCurlyBraces: { - hedCode: 'SIDECAR_BRACES_INVALID', - level: 'error', - message: stringTemplate`Sidecar key "${'sidecarKey'}", used in curly braces, is not mapped to a defined column.`, - }, - // Schema issues - invalidSchemaSpecification: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`The supplied HED schema specification is invalid. Specification: ${'spec'}.`, - }, - missingSchemaSpecification: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`No valid HED schema specification was supplied.`, - }, - bundledSchemaLoadFailed: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`Could not load HED schema for spec "${'spec'}" from bundled copy - "${'error'}".`, - }, - localSchemaLoadFailed: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`Could not load HED schema from path "${'path'}" - "${'error'}".`, - }, - remoteSchemaLoadFailed: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`Could not load HED schema "${'spec'}" from remote repository - "${'error'}".`, - }, - unmatchedBaseSchema: { - hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', - level: 'error', - message: stringTemplate`Tag "${'tag'}" is declared to use a base schema in the dataset's schema listing, but no such schema was defined.`, - }, - unmatchedLibrarySchema: { - hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', - level: 'error', - message: stringTemplate`Tag "${'tag'}" is declared to use a library schema nicknamed "${'library'}" in the dataset's schema listing, but no such schema was found.`, - }, - differentWithStandard: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`Could not merge lazy partnered schemas with different "withStandard" values: "${'first'}" and "${'second'}".`, - }, - lazyPartneredSchemasShareTag: { - hedCode: 'SCHEMA_LOAD_FAILED', - level: 'error', - message: stringTemplate`Lazy partnered schemas are incompatible because they share the short tag "${'tag'}". These schemas require different prefixes.`, - }, - deprecatedStandardSchemaVersion: { - hedCode: 'VERSION_DEPRECATED', - level: 'error', - message: stringTemplate`HED standard schema version ${'version'} is deprecated. Please upgrade to a newer version.`, - }, - // BIDS issues - sidecarKeyMissing: { - hedCode: 'SIDECAR_KEY_MISSING', - level: 'warning', - message: stringTemplate`Values "${'values'}" appear for sidecar key "${'sidecarKey'}" of file "${'file'}", but were not defined in any associated sidecar.`, - }, - hedUsedAsSpliceButNoTsvHed: { - hedCode: 'SIDECAR_KEY_MISSING', - level: 'warning', - message: stringTemplate`Key "{HED}" was referenced in sidecar for file "${'file'}", but this file does not have a HED column.`, - }, - illegalSidecarHedType: { - hedCode: 'SIDECAR_INVALID', - level: 'error', - message: stringTemplate`The HED data for sidecar key "${'sidecarKey'}" of file "${'filePath'}" is not either a key-value dictionary or a string.`, - }, - illegalSidecarHedKey: { - hedCode: 'SIDECAR_INVALID', - level: 'error', - message: stringTemplate`The string 'HED' or 'n/a' was illegally used as a top-level sidecar key.`, - }, - illegalSidecarData: { - hedCode: 'SIDECAR_INVALID', - level: 'error', - message: stringTemplate`The data associated with sidecar key "${'sidecarKey'}" cannot be parsed.`, - }, - illegalSidecarHedCategoricalValue: { - hedCode: 'SIDECAR_INVALID', - level: 'error', - message: stringTemplate`The string 'HED' or 'n/a' was illegally used as a sidecar categorical value for sidecar key "${'sidecarKey'}" in sidecar "${'filePath'}".`, - }, - illegalSidecarHedDeepKey: { - hedCode: 'SIDECAR_INVALID', - level: 'error', - message: stringTemplate`An illegal "HED" appeared as a key below level 2 in a sidecar entry with top-level key "${'sidecarKey'}".`, - }, - // Internal errors - internalError: { - hedCode: 'INTERNAL_ERROR', - level: 'error', - message: stringTemplate`Internal error - message: "${'message'}".`, - }, - networkReadError: { - hedCode: 'INTERNAL_ERROR', - level: 'error', - message: stringTemplate`I/O error when reading from network - server responded to URL "${'url'}" with HTTP status code ${'statusCode'} ${'statusText'}.`, - }, - fileReadError: { - hedCode: 'INTERNAL_ERROR', - level: 'error', - message: stringTemplate`I/O error when reading file or directory "${'fileName'}" - message: "${'message'}".`, - }, - genericError: { - hedCode: 'INTERNAL_ERROR', - level: 'error', - message: (parameters) => - `Unknown HED error "${parameters.internalCode}" - parameters: "${JSON.stringify(parameters)}".`, - }, -} diff --git a/src/issues/data.ts b/src/issues/data.ts new file mode 100644 index 00000000..bf2015bc --- /dev/null +++ b/src/issues/data.ts @@ -0,0 +1,517 @@ +/** This module contains the templates for the issues. + * @module issues/data + */ + +import { issueMessageTemplate, IssueMessageTemplateString } from '../utils/string' + +export type IssueLevel = 'error' | 'warning' + +type IssueType = { + hedCode: string + level: IssueLevel + message: IssueMessageTemplateString +} + +const issueData: Record = { + // Syntax issues + parentheses: { + hedCode: 'PARENTHESES_MISMATCH', + level: 'error', + message: issueMessageTemplate`Number of opening and closing parentheses are unequal. ${'opening'} opening parentheses. ${'closing'} closing parentheses.`, + }, + unopenedParenthesis: { + hedCode: 'PARENTHESES_MISMATCH', + level: 'error', + message: issueMessageTemplate`Closing parenthesis at index ${'index'} of string "${'string'}" does not have a corresponding opening parenthesis.`, + }, + unclosedParenthesis: { + hedCode: 'PARENTHESES_MISMATCH', + level: 'error', + message: issueMessageTemplate`Opening parenthesis at index ${'index'} of string "${'string'}" does not have a corresponding closing parenthesis.`, + }, + commaMissing: { + hedCode: 'COMMA_MISSING', + level: 'error', + message: issueMessageTemplate`Comma missing at position ${'index'} of string "${'string'}". ${'msg'}`, + }, + deprecatedTag: { + hedCode: 'ELEMENT_DEPRECATED', + level: 'warning', + message: issueMessageTemplate`Tags "${'tags'} in "${'string'} are deprecated. Please see tag description for instructions on replacement.".`, + }, + duplicateTag: { + hedCode: 'TAG_EXPRESSION_REPEATED', + level: 'error', + message: issueMessageTemplate`Duplicate tags - "${'tags'} in "${'string'}".`, + }, + extendedTag: { + hedCode: 'TAG_EXTENDED', + level: 'warning', + message: issueMessageTemplate`Tag extensions found for ${'tags'} in "${'string'}".`, + }, + invalidCharacter: { + hedCode: 'CHARACTER_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid character "${'character'}" at index ${'index'} of string "${'string'}".`, + }, + // Common semantic validation issues + invalidTag: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid tag - "${'tag'}". ${'msg'}`, + }, + extraSlash: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Tag has extra slash at index ${'index'} of string "${'string'}".`, + }, + extraBlank: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Tag has extra blank at index ${'index'} of string "${'string'}".`, + }, + extraCommaOrInvalid: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Either "${'previousTag'}" contains a comma when it should not or "${'tag'}" is not a valid tag.`, + }, + invalidTagPrefix: { + hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', + level: 'error', + message: issueMessageTemplate`Either tag prefix at index ${'index'} contains non-alphabetic characters or does not have an associated schema. ${'msg'}`, + }, + multipleUniqueTags: { + hedCode: 'TAG_NOT_UNIQUE', + level: 'error', + message: issueMessageTemplate`Multiple unique "${'tag'}" tags in "${'string'}".`, + }, + childRequired: { + hedCode: 'TAG_REQUIRES_CHILD', + level: 'error', + message: issueMessageTemplate`Descendant tag required - "${'tag'}". ${'msg'}`, + }, + valueRequired: { + hedCode: 'TAG_REQUIRES_CHILD', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" requires a value.`, + }, + childForbidden: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Child tag or value not allowed - "${'tag'}".`, + }, + requiredPrefixMissing: { + hedCode: 'REQUIRED_TAG_MISSING', + level: 'warning', + message: issueMessageTemplate`Tag with prefix "${'tagPrefix'}" is required.`, + }, + unitClassInvalidUnit: { + hedCode: 'UNITS_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid unit - "${'tag'}".`, + }, + invalidValue: { + hedCode: 'VALUE_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid placeholder value for tag "${'tag'}". ${'msg'}`, + }, + invalidPlaceholderContext: { + hedCode: 'PLACEHOLDER_INVALID', + level: 'error', + message: issueMessageTemplate`"${'string'}" has "#" placeholders, which are not allowed in this context.`, + }, + invalidSidecarPlaceholder: { + hedCode: 'PLACEHOLDER_INVALID', + level: 'error', + message: issueMessageTemplate`"${'string'}" of sidecar key "${'sidecarKey'}" has an invalid # placeholder.`, + }, + // HED 3-specific validation issues + invalidPlaceholder: { + hedCode: 'PLACEHOLDER_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid # placeholder - "${'tag'}".`, + }, + missingPlaceholder: { + hedCode: 'PLACEHOLDER_INVALID', + level: 'error', + message: issueMessageTemplate`HED value string "${'string'}" is missing a required # placeholder for sidecar key "${'sidecarKey'}".`, + }, + extraPlaceholder: { + hedCode: 'PLACEHOLDER_INVALID', + level: 'error', + message: issueMessageTemplate`HED value string "${'string'}" has too many placeholders in sidecar key "${'sidecarKey'}".`, + }, + invalidPlaceholderInDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid placeholder or missing placeholder in definition - "${'definition'}". ${'msg'}`, + }, + invalidDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid definition - "${'definition'}". ${'msg'}`, + }, + invalidDefinitionManager: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Invalid definition manager "${'defManager'}", usually because invalid external definitions were provided to a sidecar or tsv.`, + }, + nestedDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Illegal nested definition in tag group for definition "${'definition'}".`, + }, + missingDefinitionForDef: { + hedCode: 'DEF_INVALID', + level: 'error', + message: issueMessageTemplate`Def tag found for definition name "${'definition'}" does not correspond to an existing definition.`, + }, + missingDefinitionForDefExpand: { + hedCode: 'DEF_EXPAND_INVALID', + level: 'error', + message: issueMessageTemplate`Def-expand tag found for definition name "${'definition'}" does not correspond to an existing definition.`, + }, + invalidDefinitionGroupStructure: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`The Definition or Def-expand tag "${'tag'} in "${'tagGroup'}" has multiple top tags or more than one top group.`, + }, + invalidDefinitionForbidden: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`The Definition or Def-expand tag "${'tag'} in "${'tagGroup'}" has other definition-related tags in subgroups.`, + }, + defExpandContentsInvalid: { + hedCode: 'DEF_EXPAND_INVALID', + level: 'error', + message: issueMessageTemplate`Def-expand contents "${'contents'}" disagree with evaluated definition "${'contentsDef'}".`, + }, + duplicateDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Definition "${'definition'}" is declared multiple times. This instance's tag group is "${'tagGroup'}".`, + }, + conflictingDefinitions: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Definition "${'definition1'}" and "${'definition2'}' conflict.`, + }, + duplicateDefinitionNames: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Definition "${'definition1'}" and "${'definition2'}" have same name but are not equivalent.`, + }, + multipleTagGroupsInDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Multiple inner tag groups found in definition "${'definition'}".`, + }, + illegalDefinitionGroupTag: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Illegal tag "${'tag'}" in tag group for definition "${'definition'}".`, + }, + illegalDefinitionContext: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Definition "${'definition'}" was found in string "${'string'}" in a context where definitions are not allowed.`, + }, + illegalInExclusiveContext: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`"${'tag'}" can only appear in groups with other definitions but "${'string'}" has other types of groups or tags.`, + }, + inactiveOnset: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`${'tag'} found for inactive onset with definition name and value "${'definition'}".`, + }, + temporalWithoutInnerGroup: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`${'tag'} found without an included inner top-level tag group. This instance's tag group is "${'tagGroup'}".`, + }, + temporalWithWrongNumberDefs: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`${'tag'} found in tag group "${'tagGroup'}" with the wrong number of Def tags and Def-expand groups.`, + }, + temporalWithoutDefinition: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`${'tag'} found in tag group "${'tagGroup'}" without an included definition.`, + }, + extraTagsInTemporal: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`Extra top-level tags or tag groups found in onset, inset, or offset group "${'tagGroup'}" with definition "${'definition'}".`, + }, + temporalTagInNonTemporalContext: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`HED event string "${'string'}" has temporal tags on line(s) [${'tsvline'}] in a tsv file without an onset time.`, + }, + duplicateTemporal: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`HED event string "${'string'}" has onset/offset/inset tags with duplicated definition "${'definition'}".`, + }, + multipleTemporalTags: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`HED event string "${'string'}" has multiple temporal tags ${'tags'} in the same group.`, + }, + multipleRequiresDefTags: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`HED event string "${'string'}" has multiple temporal tags ${'tags'} that require a definition in the same group.`, + }, + simultaneousDuplicateEvents: { + hedCode: 'TEMPORAL_TAG_ERROR', + level: 'error', + message: issueMessageTemplate`Temporal tag group "${'tagGroup1'}" at ${'onset1'} line ${'tsvLine1'} is simultaneous with "${'tagGroup2'}" at ${'onset2'} line ${'tsvLine2'}.`, + }, + missingTagGroup: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag(s) "${'tag'}" must appear in a tag group.`, + }, + invalidTagGroup: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`"${'tagGroup'}" has invalid group tags or invalid number of subgroups.`, + }, + forbiddenSubgroupTags: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" in "${'string'}" cannot have tags "${'tagList'}" in a subgroup.`, + }, + invalidTopLevelTagGroupTag: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" is only allowed inside of a top-level tag group, but is not at top level in "${'string'}".`, + }, + invalidGroupTags: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tags "${'tags'}" in "${'string'}" cannot be in a subgroups together.`, + }, + invalidGroupTopTags: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tags "${'tags'}" cannot be at the same level in group "${'string'}".`, + }, + tooManyGroupTopTags: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Group "${'string'}" has too many or too few tags or Def-expand groups at the top level.`, + }, + multipleTopLevelTagGroupTags: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" found in top-level tag group where "${'otherTag'}" was already defined.`, + }, + invalidNumberOfSubgroups: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`The tag "${'tag'} is in a "${'string'} with too many or too few subgroups.`, + }, + invalidTopLevelTag: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag(s) "${'tag'}" should be in a top group in "${'string'}".`, + }, + invalidGroupTag: { + hedCode: 'TAG_GROUP_ERROR', + level: 'error', + message: issueMessageTemplate`Tag(s) "${'tag'}" should be in a group in "${'string'}".`, + }, + // Tag conversion issues + invalidParentNode: { + hedCode: 'TAG_EXTENSION_INVALID', + level: 'error', + message: issueMessageTemplate`"${'tag'}" does not have "${'parentTag'}" as its parent in the schema. ${'msg'}`, + }, + invalidExtension: { + hedCode: 'TAG_EXTENSION_INVALID', + level: 'error', + message: issueMessageTemplate`"${'tag'}" appears as an extension of "${'parentTag'}". ${'msg'}`, + }, + emptyTagFound: { + hedCode: 'TAG_EMPTY', + level: 'error', + message: issueMessageTemplate`Empty tag at index ${'index'} cannot be converted.`, + }, + invalidTagString: { + hedCode: 'TAG_INVALID', + level: 'error', + message: issueMessageTemplate`Tag string is null or undefined.`, + }, + duplicateTagsInSchema: { + hedCode: 'SCHEMA_DUPLICATE_NODE', + level: 'error', + message: issueMessageTemplate`Source HED schema is invalid as it contains duplicate tags.`, + }, + // Curly brace issues + unopenedCurlyBrace: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Closing curly brace at index ${'index'} of string "${'string'}" does not have a corresponding opening curly brace. ${'msg'}`, + }, + unclosedCurlyBrace: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Opening curly brace at index ${'index'} of string "${'string'}" does not have a corresponding closing curly brace. ${'msg'}`, + }, + nestedCurlyBrace: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Opening curly brace at index ${'index'} of string "${'string'}" when curly brace expression is already open.`, + }, + emptyCurlyBrace: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Curly brace expression of string "${'string'}" is empty. ${'msg'}`, + }, + curlyBracesInDefinition: { + hedCode: 'DEFINITION_INVALID', + level: 'error', + message: issueMessageTemplate`Illegal curly brace expression "${'sidecarKey'}" found in HED string containing definition "${'definition'}".`, + }, + curlyBracesInHedColumn: { + hedCode: 'CHARACTER_INVALID', + level: 'error', + message: issueMessageTemplate`Curly brace expression "${'string'}" found in the HED column of a TSV file.`, + }, + curlyBracesNotAllowed: { + hedCode: 'CHARACTER_INVALID', + level: 'error', + message: issueMessageTemplate`Curly brace expression not allowed in "${'string'}".`, + }, + recursiveCurlyBraces: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Sidecar key "${'sidecarKey'}", which has curly braces, is illegally referred to by a string using curly braces.`, + }, + recursiveCurlyBracesWithKey: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Sidecar key "${'sidecarKey'}", which has curly braces, is referred to by sidecar key "${'referrer'}", which also has curly braces.`, + }, + undefinedCurlyBraces: { + hedCode: 'SIDECAR_BRACES_INVALID', + level: 'error', + message: issueMessageTemplate`Sidecar key "${'sidecarKey'}", used in curly braces, is not mapped to a defined column.`, + }, + // Schema issues + invalidSchemaSpecification: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`The supplied HED schema specification is invalid. Specification: ${'spec'}.`, + }, + missingSchemaSpecification: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`No valid HED schema specification was supplied.`, + }, + bundledSchemaLoadFailed: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`Could not load HED schema for spec "${'spec'}" from bundled copy - "${'error'}".`, + }, + localSchemaLoadFailed: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`Could not load HED schema from path "${'path'}" - "${'error'}".`, + }, + remoteSchemaLoadFailed: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`Could not load HED schema "${'spec'}" from remote repository - "${'error'}".`, + }, + unmatchedBaseSchema: { + hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" is declared to use a base schema in the dataset's schema listing, but no such schema was defined.`, + }, + unmatchedLibrarySchema: { + hedCode: 'TAG_NAMESPACE_PREFIX_INVALID', + level: 'error', + message: issueMessageTemplate`Tag "${'tag'}" is declared to use a library schema nicknamed "${'library'}" in the dataset's schema listing, but no such schema was found.`, + }, + differentWithStandard: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`Could not merge lazy partnered schemas with different "withStandard" values: "${'first'}" and "${'second'}".`, + }, + lazyPartneredSchemasShareTag: { + hedCode: 'SCHEMA_LOAD_FAILED', + level: 'error', + message: issueMessageTemplate`Lazy partnered schemas are incompatible because they share the short tag "${'tag'}". These schemas require different prefixes.`, + }, + deprecatedStandardSchemaVersion: { + hedCode: 'VERSION_DEPRECATED', + level: 'error', + message: issueMessageTemplate`HED standard schema version ${'version'} is deprecated. Please upgrade to a newer version.`, + }, + // BIDS issues + sidecarKeyMissing: { + hedCode: 'SIDECAR_KEY_MISSING', + level: 'warning', + message: issueMessageTemplate`Values "${'values'}" appear for sidecar key "${'sidecarKey'}" of file "${'file'}", but were not defined in any associated sidecar.`, + }, + hedUsedAsSpliceButNoTsvHed: { + hedCode: 'SIDECAR_KEY_MISSING', + level: 'warning', + message: issueMessageTemplate`Key "{HED}" was referenced in sidecar for file "${'file'}", but this file does not have a HED column.`, + }, + illegalSidecarHedType: { + hedCode: 'SIDECAR_INVALID', + level: 'error', + message: issueMessageTemplate`The HED data for sidecar key "${'sidecarKey'}" of file "${'filePath'}" is not either a key-value dictionary or a string.`, + }, + illegalSidecarHedKey: { + hedCode: 'SIDECAR_INVALID', + level: 'error', + message: issueMessageTemplate`The string 'HED' or 'n/a' was illegally used as a top-level sidecar key.`, + }, + illegalSidecarData: { + hedCode: 'SIDECAR_INVALID', + level: 'error', + message: issueMessageTemplate`The data associated with sidecar key "${'sidecarKey'}" cannot be parsed.`, + }, + illegalSidecarHedCategoricalValue: { + hedCode: 'SIDECAR_INVALID', + level: 'error', + message: issueMessageTemplate`The string 'HED' or 'n/a' was illegally used as a sidecar categorical value for sidecar key "${'sidecarKey'}" in sidecar "${'filePath'}".`, + }, + illegalSidecarHedDeepKey: { + hedCode: 'SIDECAR_INVALID', + level: 'error', + message: issueMessageTemplate`An illegal "HED" appeared as a key below level 2 in a sidecar entry with top-level key "${'sidecarKey'}".`, + }, + // Internal errors + internalError: { + hedCode: 'INTERNAL_ERROR', + level: 'error', + message: issueMessageTemplate`Internal error - message: "${'message'}".`, + }, + networkReadError: { + hedCode: 'INTERNAL_ERROR', + level: 'error', + message: issueMessageTemplate`I/O error when reading from network - server responded to URL "${'url'}" with HTTP status code ${'statusCode'} ${'statusText'}.`, + }, + fileReadError: { + hedCode: 'INTERNAL_ERROR', + level: 'error', + message: issueMessageTemplate`I/O error when reading file or directory "${'fileName'}" - message: "${'message'}".`, + }, + genericError: { + hedCode: 'INTERNAL_ERROR', + level: 'error', + message: (parameters) => + `Unknown HED error "${parameters.internalCode}" - parameters: "${JSON.stringify(parameters)}".`, + }, +} + +export default issueData diff --git a/src/issues/issues.js b/src/issues/issues.ts similarity index 56% rename from src/issues/issues.js rename to src/issues/issues.ts index 6d7e3899..f8b8f6f1 100644 --- a/src/issues/issues.js +++ b/src/issues/issues.ts @@ -1,24 +1,22 @@ /** This module holds the issue classes. * @module issues/issues */ -import mapValues from 'lodash/mapValues' -import issueData from './data' +import issueData, { IssueLevel } from './data' export class IssueError extends Error { /** * The associated HED issue. - * @type {import('./issues.js').Issue} */ - issue + issue: Issue /** * Constructor. * - * @param {Issue} issue The associated HED issue. - * @param {...*} params Extra parameters (to be forwarded to the {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Error | Error} constructor). + * @param issue The associated HED issue. + * @param params Extra parameters (to be forwarded to the {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Error | Error} constructor). */ - constructor(issue, ...params) { + constructor(issue: Issue, ...params: any[]) { // Pass remaining arguments (including vendor specific ones) to parent constructor super(issue.message, ...params) @@ -36,21 +34,21 @@ export class IssueError extends Error { /** * Generate a new {@link Issue} object and immediately throw it as an {@link IssueError}. * - * @param {string} internalCode The internal error code. - * @param {Object?} parameters The error string parameters. + * @param internalCode The internal error code. + * @param parameters The error string parameters. * @throws {IssueError} Corresponding to the generated {@link Issue}. */ - static generateAndThrow(internalCode, parameters = {}) { + static generateAndThrow(internalCode: string, parameters: Record = {}) { throw new IssueError(generateIssue(internalCode, parameters)) } /** * Generate a new {@link Issue} object for an internal error and immediately throw it as an {@link IssueError}. * - * @param {string} message A message describing the internal error. + * @param message A message describing the internal error. * @throws {IssueError} Corresponding to the generated internal error {@link Issue}. */ - static generateAndThrowInternalError(message = 'Unknown internal error') { + static generateAndThrowInternalError(message: string = 'Unknown internal error') { IssueError.generateAndThrow('internalError', { message: message }) } } @@ -68,43 +66,43 @@ export class Issue { /** * The internal error code. - * @type {string} */ - internalCode + internalCode: string /** * The HED 3 error code. - * @type {string} */ - hedCode + hedCode: string /** * The issue level (error or warning). - * @type {string} */ - level + level: IssueLevel /** * The detailed error message. - * @type {string} */ - message + message: string /** - * The parameters to the error message template. Object with string and map parameters. - * @type {Object} + * The bounds of this issue. */ - parameters + _bounds: [number, number] + + /** + * The parameters to the error message template. + */ + _parameters: Record /** * Constructor. * - * @param {string} internalCode The internal error code. - * @param {string} hedCode The HED 3 error code. - * @param {string} level The issue level (error or warning). - * @param {Object} parameters The error string parameters. + * @param internalCode The internal error code. + * @param hedCode The HED 3 error code. + * @param level The issue level (error or warning). + * @param parameters The error string parameters. */ - constructor(internalCode, hedCode, level, parameters) { + constructor(internalCode: string, hedCode: string, level: IssueLevel, parameters: Record) { this.internalCode = internalCode this.hedCode = hedCode this.level = level @@ -115,17 +113,17 @@ export class Issue { /** * Override of {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/toString | Object.prototype.toString}. * - * @returns {string} This issue's message. + * @returns This issue's message. */ - toString() { + public toString(): string { return this.message } /** * (Re-)generate the issue message. */ - generateMessage() { - this._stringifyParameters() + public generateMessage(): void { + this.parameters = this._parameters const baseMessage = this._parseMessageTemplate() const specialParameterMessages = this._parseSpecialParameters() const hedSpecLink = this._generateHedSpecificationLink() @@ -134,22 +132,50 @@ export class Issue { } /** - * Convert all parameters except the substring bounds (an integer array) to their string forms. - * @private + * Get the issue parameters. + * + * @returns The issue parameters. + */ + get parameters(): Record { + return this._parameters + } + + /** + * Get the issue's bounds. + * + * @returns The issue bounds within the parent string. + */ + get bounds(): [number, number] { + return this._bounds + } + + /** + * Set new parameters by converting all parameters except the substring bounds (an integer array) to their string forms. + * + * @param parameters The new issue parameters. */ - _stringifyParameters() { - this.parameters = mapValues(this.parameters, (value, key) => (key === 'bounds' ? value : String(value))) + set parameters(parameters: Record) { + this._parameters = {} + for (const [key, value] of Object.entries(parameters)) { + if (key === 'bounds') { + if (!Array.isArray(value) || value.length !== 2 || !value.every((bound) => typeof bound === 'number')) { + IssueError.generateAndThrowInternalError('Passed bounds are not a numeric pair') + } + this._bounds = value + continue + } + this._parameters[key] = String(value) + } } /** * Find and parse the appropriate message template. * - * @returns {string} The parsed base message. - * @private + * @returns The parsed base message. */ - _parseMessageTemplate() { - const bounds = this.parameters.bounds ?? [] + private _parseMessageTemplate(): string { const issueCodeData = issueData[this.internalCode] + const bounds = this._bounds ?? [] if (issueCodeData === undefined) { const messageTemplate = issueData.genericError.message const tempParameters = { @@ -159,16 +185,15 @@ export class Issue { return messageTemplate(tempParameters) } const messageTemplate = issueCodeData.message - return messageTemplate(...bounds, this.parameters) + return messageTemplate(this.parameters, ...bounds) } /** * Parse "special" parameters. * - * @returns {string} The parsed special parameters. - * @private + * @returns The parsed special parameters. */ - _parseSpecialParameters() { + private _parseSpecialParameters(): string { const specialParameterMessages = [] for (const [parameterName, parameterHeader] of Issue.SPECIAL_PARAMETERS) { if (this.parameters[parameterName]) { @@ -181,10 +206,9 @@ export class Issue { /** * Generate a link to the appropriate section in the HED specification. * - * @returns {string} A link to the HED specification - * @private + * @returns A link to the HED specification */ - _generateHedSpecificationLink() { + private _generateHedSpecificationLink(): string { const hedCodeAnchor = this.hedCode.toLowerCase().replace(/_/g, '-') return `For more information on this HED ${this.level}, see https://hed-specification.readthedocs.io/en/latest/Appendix_B.html#${hedCodeAnchor}` } @@ -193,11 +217,11 @@ export class Issue { /** * Generate a new issue object. * - * @param {string} internalCode The internal error code. - * @param {Object} parameters The error string parameters. - * @returns {Issue} An object representing the issue. + * @param internalCode The internal error code. + * @param parameters The error string parameters. + * @returns An object representing the issue. */ -export const generateIssue = function (internalCode, parameters = {}) { +export function generateIssue(internalCode: string, parameters: Record = {}): Issue { const issueCodeData = issueData[internalCode] ?? issueData.genericError const { hedCode, level } = issueCodeData if (issueCodeData === issueData.genericError) { @@ -212,10 +236,10 @@ export const generateIssue = function (internalCode, parameters = {}) { /** * Update the parameters of a list of issues. * - * @param {IssueError[] | Issue[]} issues The list of issues (different types can be intermixed). - * @param {Object} parameters The parameters to add. + * @param issues The list of issues (different types can be intermixed). + * @param parameters The parameters to add. */ -export const updateIssueParameters = function (issues, parameters) { +export function updateIssueParameters(issues: IssueError[] | Issue[], parameters: Record) { for (const thisIssue of issues) { if (thisIssue instanceof IssueError) { _updateIssueParameters(thisIssue.issue, parameters) @@ -230,18 +254,18 @@ export const updateIssueParameters = function (issues, parameters) { * * Note: the issue is modified in place. * - * @param {Issue} issue The issue to be updated. - * @param {Object} parameters The parameters to add. + * @param issue The issue to be updated. + * @param parameters The parameters to add. */ -const _updateIssueParameters = function (issue, parameters) { - if (!issue.parameters) { - issue.parameters = {} +function _updateIssueParameters(issue: Issue, parameters: Record) { + if (!issue._parameters) { + issue._parameters = {} } let changed = false for (const [key, value] of Object.entries(parameters)) { - if (!Object.hasOwn(issue.parameters, key)) { - issue.parameters[key] = value + if (!Object.hasOwn(issue._parameters, key)) { + issue.parameters[key] = String(value) changed = true } } diff --git a/src/utils/string.js b/src/utils/string.js deleted file mode 100644 index b8ba6a2b..00000000 --- a/src/utils/string.js +++ /dev/null @@ -1,49 +0,0 @@ -/** String-related utility functions - * @module utils/string - * */ - -/** - * Get number of instances of a character in a string. - * - * @param {string} string The string to search. - * @param {string} characterToCount The character to search for. - * @returns {number} The number of instances of the character in the string. - */ -export function getCharacterCount(string, characterToCount) { - return string.split(characterToCount).length - 1 -} - -/** - * Split a string on a given delimiter, trim the substrings, and remove any blank substrings from the returned array. - * - * @param {string} string The string to split. - * @param {string} delimiter The delimiter on which to split. - * @returns {string[]} The split string with blanks removed and the remaining entries trimmed. - */ -export function splitStringTrimAndRemoveBlanks(string, delimiter = ',') { - return string - .split(delimiter) - .map((item) => item.trim()) - .filter(Boolean) -} - -/** - * Parse a template literal string. - * - * Copied from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Template_literals. - * - * @param {string[]} strings The literal parts of the template string. - * @param {(number|string)} keys The keys of the closure arguments. - * @returns {function(...[*]): string} A closure to fill the string template. - */ -export function stringTemplate(strings, ...keys) { - return function (...values) { - const dict = values[values.length - 1] ?? {} - const result = [strings[0]] - keys.forEach((key, i) => { - const value = Number.isInteger(key) ? values[key] : dict[key] - result.push(value, strings[i + 1]) - }) - return result.join('') - } -} diff --git a/src/utils/string.ts b/src/utils/string.ts new file mode 100644 index 00000000..7b59a56a --- /dev/null +++ b/src/utils/string.ts @@ -0,0 +1,58 @@ +/** String-related utility functions + * @module utils/string + * */ + +/** + * Get number of instances of a character in a string. + * + * @param string The string to search. + * @param characterToCount The character to search for. + * @returns The number of instances of the character in the string. + */ +export function getCharacterCount(string: string, characterToCount: string): number { + return string.split(characterToCount).length - 1 +} + +/** + * Split a string on a given delimiter, trim the substrings, and remove any blank substrings from the returned array. + * + * @param string The string to split. + * @param delimiter The delimiter on which to split. + * @returns The split string with blanks removed and the remaining entries trimmed. + */ +export function splitStringTrimAndRemoveBlanks(string: string, delimiter: string = ','): string[] { + return string + .split(delimiter) + .map((item) => item.trim()) + .filter(Boolean) +} + +export type IssueMessageTemplateString = ( + parameterValues: Record, + start?: number, + end?: number, +) => string + +/** + * Parse a template literal string. + * + * Adapted from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Template_literals. + * + * @param strings The literal parts of the template string. + * @param parameterKeys The keys of the closure arguments. + * @returns A closure to fill the string template. + */ +export function issueMessageTemplate( + strings: TemplateStringsArray, + ...parameterKeys: Array +): IssueMessageTemplateString { + return function (parameterValues: Record, start?: number, end?: number) { + const bounds = [start, end] + const result = [strings[0]] + parameterKeys.forEach((key, i) => { + const value = typeof key === 'number' ? bounds[key].toString() : parameterValues[key] + result.push(value, strings[i + 1]) + }) + return result.join('') + } +} From cec3ea342bd0fd3dbf9335e7ae3c7c219fea6e71 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Wed, 22 Oct 2025 15:48:41 -0500 Subject: [PATCH 24/63] Improve issue parameter setting interface --- src/issues/issues.ts | 62 ++++++++++++++++++++++++++++---------------- 1 file changed, 40 insertions(+), 22 deletions(-) diff --git a/src/issues/issues.ts b/src/issues/issues.ts index f8b8f6f1..19cd30a3 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -57,7 +57,7 @@ export class IssueError extends Error { * A HED validation error or warning. */ export class Issue { - static SPECIAL_PARAMETERS = new Map([ + private static SPECIAL_PARAMETERS = new Map([ ['sidecarKey', 'Sidecar key'], ['tsvLine', 'TSV line'], ['hedString', 'HED string'], @@ -136,7 +136,7 @@ export class Issue { * * @returns The issue parameters. */ - get parameters(): Record { + public get parameters(): Record { return this._parameters } @@ -145,29 +145,59 @@ export class Issue { * * @returns The issue bounds within the parent string. */ - get bounds(): [number, number] { + public get bounds(): [number, number] { return this._bounds } + /** + * Validate and set the issue's bounds. + * + * @param value The issue bounds within the parent string. + */ + private set bounds(value: [number, number]) { + if (this._bounds) { + return + } + if (!Array.isArray(value) || value.length !== 2 || !value.every((bound) => typeof bound === 'number')) { + IssueError.generateAndThrowInternalError('Bounds must be a numeric pair') + } + this._bounds = value + } + /** * Set new parameters by converting all parameters except the substring bounds (an integer array) to their string forms. * * @param parameters The new issue parameters. */ - set parameters(parameters: Record) { + public set parameters(parameters: Record) { this._parameters = {} for (const [key, value] of Object.entries(parameters)) { if (key === 'bounds') { - if (!Array.isArray(value) || value.length !== 2 || !value.every((bound) => typeof bound === 'number')) { - IssueError.generateAndThrowInternalError('Passed bounds are not a numeric pair') - } - this._bounds = value + this.bounds = value continue } this._parameters[key] = String(value) } } + /** + * Set a new parameter value. + * + * @param name The parameter name. + * @param value The new parameter value. + */ + public setParameter(name: string, value: any): void { + if (Object.hasOwn(this._parameters, name)) { + return + } + if (name === 'bounds') { + this.bounds = value + return + } + this._parameters[name] = String(value) + this.generateMessage() + } + /** * Find and parse the appropriate message template. * @@ -239,7 +269,7 @@ export function generateIssue(internalCode: string, parameters: Record) { +export function updateIssueParameters(issues: Array, parameters: Record) { for (const thisIssue of issues) { if (thisIssue instanceof IssueError) { _updateIssueParameters(thisIssue.issue, parameters) @@ -258,19 +288,7 @@ export function updateIssueParameters(issues: IssueError[] | Issue[], parameters * @param parameters The parameters to add. */ function _updateIssueParameters(issue: Issue, parameters: Record) { - if (!issue._parameters) { - issue._parameters = {} - } - - let changed = false for (const [key, value] of Object.entries(parameters)) { - if (!Object.hasOwn(issue._parameters, key)) { - issue.parameters[key] = String(value) - changed = true - } - } - - if (changed) { - issue.generateMessage() + issue.setParameter(key, value) } } From b00f78f4468b69c893a3c82869ff28e9c4f91373 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 03:24:01 -0500 Subject: [PATCH 25/63] Port path utilities to TypeScript --- src/utils/{paths.js => paths.ts} | 142 ++++++++++++++++++------------- 1 file changed, 85 insertions(+), 57 deletions(-) rename src/utils/{paths.js => paths.ts} (74%) diff --git a/src/utils/paths.js b/src/utils/paths.ts similarity index 74% rename from src/utils/paths.js rename to src/utils/paths.ts index d7d5ab18..dd6ef3f0 100644 --- a/src/utils/paths.js +++ b/src/utils/paths.ts @@ -5,6 +5,29 @@ import path from 'node:path' +import { BidsSidecar } from '../bids' + +type ParsedBidsFilename = { + basename: string + suffix: string | null + prefix: string | null + ext: string + bad: string[] + entities: Record +} + +/** + * An object containing two properties: + * - `candidates`: A list of all file paths that were successfully categorized. + * - `organizedPaths`: A Map where keys are the suffixes and special directories. + * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding + * file paths. Keys will be present even if no files are found for them. + */ +type OrganizedBidsPaths = { + candidates: string[] + organizedPaths: Map> +} + /** * Checks if one path is a subpath of another. * @@ -18,16 +41,19 @@ import path from 'node:path' * If the normalized parent path is an empty string (e.g., from '.', './', or '/'), * any non-empty child path is considered a subpath. * - * @param {string|null|undefined} potentialChild The path to check if it's a subpath. - * @param {string|null|undefined} potentialParent The path to check if it's a parent. - * @returns {boolean} True if potentialChild is a subpath of potentialParent, false otherwise. + * @param potentialChild The path to check if it's a subpath. + * @param potentialParent The path to check if it's a parent. + * @returns True if potentialChild is a subpath of potentialParent, false otherwise. */ -export function isSubpath(potentialChild, potentialParent) { +export function isSubpath( + potentialChild: string | null | undefined, + potentialParent: string | null | undefined, +): boolean { // Normalize paths for consistent comparison - const normalizePath = (rawPath) => { + const normalizePath = (rawPath: string | null | undefined) => { // Handle null/undefined gracefully, and ensure '.' normalizes to an empty string // similar to how './' and '/' are effectively treated. - let p = String(rawPath == null ? '' : rawPath) + let p = rawPath ?? '' if (p === '.') { return '' // Explicitly normalize '.' to an empty string @@ -71,18 +97,17 @@ export function isSubpath(potentialChild, potentialParent) { * 'participants') or by their presence in a special directory. Only files with '.tsv' or '.json' * extensions are considered. * - * @param {string[]} relativeFilePaths - A list of relative file paths to organize. - * @param {string[]} suffixes - A list of filename suffixes to categorize by (e.g., 'events'). - * @param {string[]} specialDirs - A list of special directory names (e.g., 'phenotype'). - * @returns {{candidates: string[], organizedPaths: Map>}} - * An object containing two properties: - * - `candidates`: A list of all file paths that were successfully categorized. - * - `organizedPaths`: A Map where keys are the suffixes and special directories. - * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding - * file paths. Keys will be present even if no files are found for them. + * @param relativeFilePaths A list of relative file paths to organize. + * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). + * @param specialDirs A list of special directory names (e.g., 'phenotype'). + * @returns The relative file paths organized according to BIDS naming conventions. */ -export function organizePaths(relativeFilePaths, suffixes, specialDirs) { - const candidates = [] +export function organizePaths( + relativeFilePaths: string[], + suffixes: string[], + specialDirs: string[], +): OrganizedBidsPaths { + const candidates: string[] = [] // Use helper function to initialize organizedPaths const organizedPaths = _initializeOrganizedPaths([...suffixes, ...specialDirs]) @@ -140,11 +165,10 @@ export function organizePaths(relativeFilePaths, suffixes, specialDirs) { /** * Updates the entity dictionary with a new entity. * - * @param {object} nameDict The dictionary of BIDS filename parts. - * @param {string} entity The entity string to parse and add. - * @private + * @param nameDict The dictionary of BIDS filename parts. + * @param entity The entity string to parse and add. */ -function _updateEntity(nameDict, entity) { +function _updateEntity(nameDict: ParsedBidsFilename, entity: string): void { const parts = entity.split('-') if (parts.length === 2 && parts[0] && parts[1]) { nameDict.entities[parts[0]] = parts[1] @@ -158,11 +182,11 @@ function _updateEntity(nameDict, entity) { * * This is a JavaScript implementation of the Python code provided by the user. * - * @param {string} filePath Path to be parsed. - * @returns {{basename: string, suffix: string, prefix: string, ext: string, bad: string[], entities: Record}} An object containing the parts of the BIDS filename. + * @param filePath Path to be parsed. + * @returns An object containing the parts of the BIDS filename. */ -export function parseBidsFilename(filePath) { - const nameDict = { +export function parseBidsFilename(filePath: string): ParsedBidsFilename { + const nameDict: ParsedBidsFilename = { basename: '', suffix: null, prefix: null, @@ -227,24 +251,24 @@ export function parseBidsFilename(filePath) { /** * Get the directory part of a path. - * @param {string} path The path. - * @returns {string} The directory part of the path. - * @private + * + * @param path The path. + * @returns The directory part of the path. */ -export function getDir(path) { +export function getDir(path: string): string { const lastSlash = path.lastIndexOf('/') return lastSlash === -1 ? '' : path.substring(0, lastSlash) } /** * Filter a list of JSON sidecar paths to find candidates for a given TSV file. - * @param {string[]} jsonList A list of relative paths of JSON sidecars. - * @param {string} tsvDir The directory of the TSV file. - * @param {object} tsvParsed The parsed BIDS filename of the TSV file. - * @returns {string[]} A list of candidate JSON sidecar paths. - * @private + * + * @param jsonList A list of relative paths of JSON sidecars. + * @param tsvDir The directory of the TSV file. + * @param tsvParsed The parsed BIDS filename of the TSV file. + * @returns A list of candidate JSON sidecar paths. */ -export function _getCandidates(jsonList, tsvDir, tsvParsed) { +export function _getCandidates(jsonList: string[], tsvDir: string, tsvParsed: ParsedBidsFilename): string[] { return jsonList.filter((jsonPath) => { const jsonDir = path.dirname(jsonPath) @@ -276,10 +300,9 @@ export function _getCandidates(jsonList, tsvDir, tsvParsed) { * * The sorting is done based on path depth and number of entities. * - * @param {string[]} candidates A list of candidate JSON sidecar paths. - * @private + * @param candidates A list of candidate JSON sidecar paths. */ -export function _sortCandidates(candidates) { +export function _sortCandidates(candidates: string[]) { candidates.sort((a, b) => { const aDir = path.dirname(a) const bDir = path.dirname(b) @@ -303,13 +326,17 @@ export function _sortCandidates(candidates) { * * Note: This function should not be called for files in directories with special association rules such as 'phenotype'. * - * @param {string} tsvPath The path to the TSV file. - * @param {string[]} jsonList A list of relative paths of JSON sidecars. - * @param {Map} sidecarMap A map of sidecars. - * @returns {object} The merged sidecar data. + * @param tsvPath The path to the TSV file. + * @param jsonList A list of relative paths of JSON sidecars. + * @param sidecarMap A map of sidecars. + * @returns The merged sidecar data. * @throws {Error} If a BIDS inheritance conflict is detected. */ -export function getMergedSidecarData(tsvPath, jsonList, sidecarMap) { +export function getMergedSidecarData( + tsvPath: string, + jsonList: string[], + sidecarMap: Map, +): object { const tsvDir = path.dirname(tsvPath) const tsvParsed = parseBidsFilename(tsvPath) @@ -354,12 +381,11 @@ export function getMergedSidecarData(tsvPath, jsonList, sidecarMap) { * in the same directory have conflicting inheritance relationships (i.e., neither is * a subset of the other, or both are subsets of each other). * - * @param {string} dir - The directory path being tested - * @param {string[]} sidecarsInDir - Array of sidecar filenames in the directory + * @param dir The directory path being tested + * @param sidecarsInDir Array of sidecar filenames in the directory * @throws {Error} Throws an error if any two sidecars are hierarchically related - * @private */ -const _testSameDir = (dir, sidecarsInDir) => { +function _testSameDir(dir: string, sidecarsInDir: string[]) { for (let i = 0; i < sidecarsInDir.length; i++) { for (let j = i + 1; j < sidecarsInDir.length; j++) { const aParsed = parseBidsFilename(sidecarsInDir[i]) @@ -380,11 +406,14 @@ const _testSameDir = (dir, sidecarsInDir) => { /** * A generator function that yields the paths of a given file extension from a BIDS-style organized path mapping. * - * @param {Map>} organizedPaths A BIDS-style organized path mapping. - * @param {string} targetExtension The file extension to search for (e.g., '.json'). - * @yields {string} The paths of the given file extension. + * @param organizedPaths A BIDS-style organized path mapping. + * @param targetExtension The file extension to search for (e.g., '.json'). + * @returns A generator for the paths of the given file extension. */ -export function* organizedPathsGenerator(organizedPaths, targetExtension) { +export function* organizedPathsGenerator( + organizedPaths: Map>, + targetExtension: string, +): Generator { if (!organizedPaths) { return } @@ -402,16 +431,15 @@ export function* organizedPathsGenerator(organizedPaths, targetExtension) { /** * Initialize the organized paths map. * - * @param {string[]} keys The keys to initialize the map with. - * @returns {Map>} The initialized map. - * @private + * @param keys The keys to initialize the map with. + * @returns The initialized map. */ -const _initializeOrganizedPaths = (keys) => { - const map = new Map() +function _initializeOrganizedPaths(keys: string[]): Map> { + const map = new Map>() for (const key of keys) { map.set( key, - new Map([ + new Map([ ['json', []], ['tsv', []], ]), From 3056fa864ae60906f4a34f8e3507a659a155a050 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 03:47:15 -0500 Subject: [PATCH 26/63] Minor formatting changes Also fixing minor type error. --- browser/src/utils/files.js | 8 ++++---- src/issues/data.ts | 3 ++- src/issues/issues.ts | 3 ++- src/utils/files.ts | 5 +++-- src/utils/string.ts | 5 +++-- 5 files changed, 14 insertions(+), 10 deletions(-) diff --git a/browser/src/utils/files.js b/browser/src/utils/files.js index 11555e93..7e81b667 100644 --- a/browser/src/utils/files.js +++ b/browser/src/utils/files.js @@ -8,9 +8,9 @@ import { IssueError } from '../../../src/issues/issues' * @throws {IssueError} Always throws since local file reading is not supported in browsers. */ export async function readFile(fileName) { - IssueError.generateAndThrow('fileReadError', { - fileName: fileName, - message: 'Local file reading is not supported in browser environment' + IssueError.generateAndThrow('fileReadError', { + fileName: fileName, + message: 'Local file reading is not supported in browser environment', }) } @@ -26,7 +26,7 @@ export async function readHTTPSFile(url) { if (!response.ok) { IssueError.generateAndThrow('networkReadError', { url: url, - statusCode: response.status, + statusCode: response.status.toString(), statusText: response.statusText, }) } diff --git a/src/issues/data.ts b/src/issues/data.ts index bf2015bc..194b651e 100644 --- a/src/issues/data.ts +++ b/src/issues/data.ts @@ -1,4 +1,5 @@ -/** This module contains the templates for the issues. +/** + * This module contains the templates for the issues. * @module issues/data */ diff --git a/src/issues/issues.ts b/src/issues/issues.ts index 19cd30a3..a0eb0b60 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -1,4 +1,5 @@ -/** This module holds the issue classes. +/** + * This module holds the issue classes. * @module issues/issues */ diff --git a/src/utils/files.ts b/src/utils/files.ts index 8fec449f..6547b143 100644 --- a/src/utils/files.ts +++ b/src/utils/files.ts @@ -1,4 +1,5 @@ -/** This module holds asynchronous functions for reading files. +/** + * This module holds asynchronous functions for reading files. * @module */ import { readFile as readFilePromise } from 'node:fs/promises' @@ -33,7 +34,7 @@ export async function readHTTPSFile(url: string): Promise { if (!response.ok) { IssueError.generateAndThrow('networkReadError', { url: url, - statusCode: response.status, + statusCode: response.status.toString(), statusText: response.statusText, }) } diff --git a/src/utils/string.ts b/src/utils/string.ts index 7b59a56a..224d3075 100644 --- a/src/utils/string.ts +++ b/src/utils/string.ts @@ -1,6 +1,7 @@ -/** String-related utility functions +/** + * String-related utility functions * @module utils/string - * */ + */ /** * Get number of instances of a character in a string. From 76d60a1dc30490740e663b1088a5bee6eca0654d Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 05:11:09 -0500 Subject: [PATCH 27/63] Refactor part of the path utilities Also fix linter issue in issues module. --- src/issues/issues.ts | 2 +- src/utils/array.ts | 11 ++++++ src/utils/paths.ts | 91 +++++++++++++++++++++++++++++--------------- 3 files changed, 72 insertions(+), 32 deletions(-) diff --git a/src/issues/issues.ts b/src/issues/issues.ts index a0eb0b60..a2b9eb66 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -58,7 +58,7 @@ export class IssueError extends Error { * A HED validation error or warning. */ export class Issue { - private static SPECIAL_PARAMETERS = new Map([ + private static readonly SPECIAL_PARAMETERS = new Map([ ['sidecarKey', 'Sidecar key'], ['tsvLine', 'TSV line'], ['hedString', 'HED string'], diff --git a/src/utils/array.ts b/src/utils/array.ts index 02031506..69cdb33f 100644 --- a/src/utils/array.ts +++ b/src/utils/array.ts @@ -19,3 +19,14 @@ export function recursiveMap(array: NestedArray, fn: (element: T) => U) return fn(array) } } + +/** + * Generate an iterator over the pairwise combinations of an array. + * + * @param array The array to combine. + * @returns A generator which iterates over the list of combinations as tuples. + */ +export function* iteratePairwiseCombinations(array: T[]): Generator<[T, T]> { + const pairs = array.flatMap((first, index) => array.slice(index + 1).map((second): [T, T] => [first, second])) + yield* pairs +} diff --git a/src/utils/paths.ts b/src/utils/paths.ts index dd6ef3f0..4b06ff54 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -5,26 +5,68 @@ import path from 'node:path' -import { BidsSidecar } from '../bids' +import zip from 'lodash/zip' -type ParsedBidsFilename = { +import { BidsSidecar } from '../bids/types/json' +import { IssueError } from '../issues/issues' +import { iteratePairwiseCombinations } from './array' + +/** + * A parsed BIDS file name. + */ +class ParsedBidsFilename { basename: string suffix: string | null prefix: string | null ext: string bad: string[] entities: Record + + constructor() { + this.basename = '' + this.suffix = null + this.prefix = null + this.ext = '' + this.bad = [] + this.entities = {} + } + + /** + * Whether this file name is equivalent to another one. + * + * @param other Another parsed BIDS file name. + * @returns Whether or not the two names are equivalent. + */ + public equals(other: ParsedBidsFilename): boolean { + return this._isSubset(other) && other._isSubset(this) + } + + /** + * Whether this file name is a subset of another one. + * + * @param other Another parsed BIDS file name. + * @returns Whether or not this file name is a subset of the other one. + * @private + */ + private _isSubset(other: ParsedBidsFilename): boolean { + const ourEntities = Object.keys(this.entities) + return ourEntities.every((key) => Object.hasOwn(other.entities, key) && this.entities[key] === other.entities[key]) + } } /** - * An object containing two properties: - * - `candidates`: A list of all file paths that were successfully categorized. - * - `organizedPaths`: A Map where keys are the suffixes and special directories. - * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding - * file paths. Keys will be present even if no files are found for them. + * A collection of categorized BIDS file paths. */ type OrganizedBidsPaths = { + /** + * A list of all file paths that were successfully categorized. + */ candidates: string[] + /** + * A Map where keys are the suffixes and special directories. + * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding + * file paths. Keys will be present even if no files are found for them. + */ organizedPaths: Map> } @@ -186,14 +228,7 @@ function _updateEntity(nameDict: ParsedBidsFilename, entity: string): void { * @returns An object containing the parts of the BIDS filename. */ export function parseBidsFilename(filePath: string): ParsedBidsFilename { - const nameDict: ParsedBidsFilename = { - basename: '', - suffix: null, - prefix: null, - ext: '', - bad: [], - entities: {}, - } + const nameDict = new ParsedBidsFilename() const strippedPath = filePath.trim() const lastSlash = strippedPath.lastIndexOf('/') @@ -330,7 +365,7 @@ export function _sortCandidates(candidates: string[]) { * @param jsonList A list of relative paths of JSON sidecars. * @param sidecarMap A map of sidecars. * @returns The merged sidecar data. - * @throws {Error} If a BIDS inheritance conflict is detected. + * @throws {IssueError} If a BIDS inheritance conflict is detected. */ export function getMergedSidecarData( tsvPath: string, @@ -365,7 +400,7 @@ export function getMergedSidecarData( let merged = {} for (const path of candidates) { const sidecar = sidecarMap.get(path) - if (sidecar && sidecar.jsonData) { + if (sidecar?.jsonData) { merged = { ...merged, ...sidecar.jsonData } } } @@ -383,22 +418,16 @@ export function getMergedSidecarData( * * @param dir The directory path being tested * @param sidecarsInDir Array of sidecar filenames in the directory - * @throws {Error} Throws an error if any two sidecars are hierarchically related + * @throws {IssueError} Throws an error if any two sidecars are hierarchically related */ function _testSameDir(dir: string, sidecarsInDir: string[]) { - for (let i = 0; i < sidecarsInDir.length; i++) { - for (let j = i + 1; j < sidecarsInDir.length; j++) { - const aParsed = parseBidsFilename(sidecarsInDir[i]) - const bParsed = parseBidsFilename(sidecarsInDir[j]) - const aEntities = Object.keys(aParsed.entities) - const bEntities = Object.keys(bParsed.entities) - const aIsSubset = aEntities.every((k) => bEntities.includes(k) && aParsed.entities[k] === bParsed.entities[k]) - const bIsSubset = bEntities.every((k) => aEntities.includes(k) && bParsed.entities[k] === aParsed.entities[k]) - if (aIsSubset === bIsSubset) { - throw new Error( - `BIDS inheritance conflict in directory '${dir}': sidecars '${sidecarsInDir[i]}' and '${sidecarsInDir[j]}' are not hierarchically related.`, - ) - } + const parsedBidsFileNames = sidecarsInDir.map((path) => parseBidsFilename(path)) + const iterator = iteratePairwiseCombinations(zip(sidecarsInDir, parsedBidsFileNames)) + for (const [[firstName, firstParsed], [secondName, secondParsed]] of iterator) { + if (firstParsed.equals(secondParsed)) { + IssueError.generateAndThrowInternalError( + `BIDS inheritance conflict in directory '${dir}': sidecars '${firstName}' and '${secondName}' are not hierarchically related.`, + ) } } } From 6a8b150984e0f4f5275f289b4b737678e288b5ea Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 06:39:20 -0500 Subject: [PATCH 28/63] Further streamline path utilities --- src/utils/paths.ts | 106 ++++++++++++++++++++++----------------------- 1 file changed, 52 insertions(+), 54 deletions(-) diff --git a/src/utils/paths.ts b/src/utils/paths.ts index 4b06ff54..1ede6e89 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -54,10 +54,17 @@ class ParsedBidsFilename { } } +/** + * A Map where keys are the suffixes and special directories. + * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding + * file paths. Keys will be present even if no files are found for them. + */ +export type OrganizedBidsPaths = Map> + /** * A collection of categorized BIDS file paths. */ -type OrganizedBidsPaths = { +class OrganizedBidsCandidates { /** * A list of all file paths that were successfully categorized. */ @@ -67,7 +74,39 @@ type OrganizedBidsPaths = { * Each value is a Map with 'tsv' and 'json' properties, containing the corresponding * file paths. Keys will be present even if no files are found for them. */ - organizedPaths: Map> + organizedPaths: OrganizedBidsPaths + + /** + * Initialize the organized paths map. + * + * @param keys The keys to initialize the map with. + * @returns The initialized map. + */ + constructor(keys: string[]) { + this.candidates = [] + this.organizedPaths = new Map>() + for (const key of keys) { + this.organizedPaths.set( + key, + new Map([ + ['json', []], + ['tsv', []], + ]), + ) + } + } + + /** + * Add a candidate. + * + * @param relativePath The candidate's relative path. + * @param suffix The candidate's suffix. + * @param ext The candidate's suffix. + */ + public addCandidate(relativePath: string, suffix: string, ext: string): void { + this.candidates.push(relativePath) + this.organizedPaths.get(suffix).get(ext).push(relativePath) + } } /** @@ -148,10 +187,8 @@ export function organizePaths( relativeFilePaths: string[], suffixes: string[], specialDirs: string[], -): OrganizedBidsPaths { - const candidates: string[] = [] - // Use helper function to initialize organizedPaths - const organizedPaths = _initializeOrganizedPaths([...suffixes, ...specialDirs]) +): OrganizedBidsCandidates { + const candidates = new OrganizedBidsCandidates([...suffixes, ...specialDirs]) for (const relativePath of relativeFilePaths) { // Basic validation and extension check @@ -165,12 +202,9 @@ export function organizePaths( const ext = relativePath.endsWith('.tsv') ? 'tsv' : 'json' - let categorized = false - // Rule 1: Check if the file is in a special directory. if (specialDirs.includes(firstComponent)) { - organizedPaths.get(firstComponent).get(ext).push(relativePath) - categorized = true + candidates.addCandidate(relativePath, firstComponent, ext) } else { // Rule 2: Check if it's a top-level file or in a subject directory. const isToplevel = pathParts.length === 1 @@ -180,28 +214,16 @@ export function organizePaths( // Rule 3: Either it is the suffix or the suffix starts with an underscore and matches the end of the filename. const filenameNoExt = basename.substring(0, basename.lastIndexOf('.')) for (const suffix of suffixes) { - let match = false - if (filenameNoExt === suffix) { - match = true - } else if (suffix.startsWith('_') && filenameNoExt.endsWith(suffix)) { - match = true - } - if (match) { - organizedPaths.get(suffix).get(ext).push(relativePath) - categorized = true + if (filenameNoExt === suffix || (suffix.startsWith('_') && filenameNoExt.endsWith(suffix))) { + candidates.addCandidate(relativePath, suffix, ext) break // Stop after first suffix match. } } } } - - // If the file was categorized, add it to the candidates list. - if (categorized) { - candidates.push(relativePath) - } } - return { candidates, organizedPaths } + return candidates } /** @@ -337,7 +359,7 @@ export function _getCandidates(jsonList: string[], tsvDir: string, tsvParsed: Pa * * @param candidates A list of candidate JSON sidecar paths. */ -export function _sortCandidates(candidates: string[]) { +export function _sortCandidates(candidates: string[]): void { candidates.sort((a, b) => { const aDir = path.dirname(a) const bDir = path.dirname(b) @@ -420,7 +442,7 @@ export function getMergedSidecarData( * @param sidecarsInDir Array of sidecar filenames in the directory * @throws {IssueError} Throws an error if any two sidecars are hierarchically related */ -function _testSameDir(dir: string, sidecarsInDir: string[]) { +function _testSameDir(dir: string, sidecarsInDir: string[]): void { const parsedBidsFileNames = sidecarsInDir.map((path) => parseBidsFilename(path)) const iterator = iteratePairwiseCombinations(zip(sidecarsInDir, parsedBidsFileNames)) for (const [[firstName, firstParsed], [secondName, secondParsed]] of iterator) { @@ -440,7 +462,7 @@ function _testSameDir(dir: string, sidecarsInDir: string[]) { * @returns A generator for the paths of the given file extension. */ export function* organizedPathsGenerator( - organizedPaths: Map>, + organizedPaths: OrganizedBidsPaths, targetExtension: string, ): Generator { if (!organizedPaths) { @@ -448,31 +470,7 @@ export function* organizedPathsGenerator( } const extKey = targetExtension.startsWith('.') ? targetExtension.slice(1) : targetExtension for (const innerMap of organizedPaths.values()) { - const pathArray = innerMap.get(extKey) - if (Array.isArray(pathArray)) { - for (const path of pathArray) { - yield path - } - } - } -} - -/** - * Initialize the organized paths map. - * - * @param keys The keys to initialize the map with. - * @returns The initialized map. - */ -function _initializeOrganizedPaths(keys: string[]): Map> { - const map = new Map>() - for (const key of keys) { - map.set( - key, - new Map([ - ['json', []], - ['tsv', []], - ]), - ) + const pathArray = innerMap.get(extKey) ?? [] + yield* pathArray } - return map } From 43a63f7cb96bcac6f45665d28132e36f9df25979 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 07:14:37 -0500 Subject: [PATCH 29/63] Refactor individual path organization into a separate function --- src/utils/paths.ts | 60 +++++++++++++++++++++++++++------------------- 1 file changed, 36 insertions(+), 24 deletions(-) diff --git a/src/utils/paths.ts b/src/utils/paths.ts index 1ede6e89..46bf02ad 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -195,37 +195,49 @@ export function organizePaths( if (typeof relativePath !== 'string' || (!relativePath.endsWith('.tsv') && !relativePath.endsWith('.json'))) { continue } - - const pathParts = relativePath.split('/') - const basename = pathParts[pathParts.length - 1] - const firstComponent = pathParts[0] - const ext = relativePath.endsWith('.tsv') ? 'tsv' : 'json' - - // Rule 1: Check if the file is in a special directory. - if (specialDirs.includes(firstComponent)) { - candidates.addCandidate(relativePath, firstComponent, ext) - } else { - // Rule 2: Check if it's a top-level file or in a subject directory. - const isToplevel = pathParts.length === 1 - const inSubDir = firstComponent.startsWith('sub-') - - if (isToplevel || inSubDir) { - // Rule 3: Either it is the suffix or the suffix starts with an underscore and matches the end of the filename. - const filenameNoExt = basename.substring(0, basename.lastIndexOf('.')) - for (const suffix of suffixes) { - if (filenameNoExt === suffix || (suffix.startsWith('_') && filenameNoExt.endsWith(suffix))) { - candidates.addCandidate(relativePath, suffix, ext) - break // Stop after first suffix match. - } - } - } + const [isCandidate, suffix] = _organizePath(relativePath, suffixes, specialDirs) + if (isCandidate) { + candidates.addCandidate(relativePath, suffix, ext) } } return candidates } +/** + * Helper function for organizing an individual path. + * + * @param relativePath A relative file path to organize. + * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). + * @param specialDirs A list of special directory names (e.g., 'phenotype'). + * @returns A tuple of whether the path was matched and its suffix. + */ +function _organizePath(relativePath: string, suffixes: string[], specialDirs: string[]): [boolean, string] { + const pathParts = relativePath.split('/') + const basename = pathParts[pathParts.length - 1] + const firstComponent = pathParts[0] + + // Rule 1: Check if the file is in a special directory. + if (specialDirs.includes(firstComponent)) { + return [true, firstComponent] + } + + // Rule 2: Check if it's a top-level file or in a subject directory. + const isToplevel = pathParts.length === 1 + const inSubDir = firstComponent.startsWith('sub-') + if (!isToplevel && !inSubDir) { + return [false, ''] + } + + // Rule 3: Either it is the suffix or the suffix starts with an underscore and matches the end of the filename. + const filenameNoExt = basename.substring(0, basename.lastIndexOf('.')) + const matchingSuffix = suffixes.find( + (suffix) => filenameNoExt === suffix || (suffix.startsWith('_') && filenameNoExt.endsWith(suffix)), + ) + return [matchingSuffix !== undefined, matchingSuffix] +} + /** * Updates the entity dictionary with a new entity. * From 3c3699516f4da99315421b30562b288cbee723d6 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 24 Oct 2025 09:55:25 -0500 Subject: [PATCH 30/63] Refactor BIDS path organization into class --- src/utils/paths.ts | 200 +++++++++++++++++++++++++++++---------------- 1 file changed, 129 insertions(+), 71 deletions(-) diff --git a/src/utils/paths.ts b/src/utils/paths.ts index 46bf02ad..69cfcd2d 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -109,6 +109,135 @@ class OrganizedBidsCandidates { } } +class BidsPathOrganizer { + /** + * A list of relative file paths to organize. + */ + private readonly relativeFilePaths: string[] + /** + * A list of filename suffixes to categorize by (e.g., 'events'). + */ + private readonly suffixes: string[] + /** + * A list of special directory names (e.g., 'phenotype'). + */ + private readonly specialDirs: string[] + /** + * The relative file paths organized according to BIDS naming conventions. + */ + private readonly candidates: OrganizedBidsCandidates + /** + * Whether the candidates have already been organized. + * @private + */ + #alreadyOrganized: boolean + + /** + * Build the organizer. + * + * @param relativeFilePaths A list of relative file paths to organize. + * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). + * @param specialDirs A list of special directory names (e.g., 'phenotype'). + */ + constructor(relativeFilePaths: string[], suffixes: string[], specialDirs: string[]) { + this.relativeFilePaths = relativeFilePaths + this.suffixes = suffixes + this.specialDirs = specialDirs + this.candidates = new OrganizedBidsCandidates([...suffixes, ...specialDirs]) + this.#alreadyOrganized = false + } + + /** + * Organizes a list of relative file paths based on BIDS naming conventions. + * + * This function filters and categorizes file paths into a structured object. It identifies files + * based on whether they are in special directories (like 'phenotype'), are top-level files, or + * are located within subject-specific directories ('sub-xxx'). + * + * Files are categorized by matching their filename against a list of suffixes (e.g., 'events', + * 'participants') or by their presence in a special directory. Only files with '.tsv' or '.json' + * extensions are considered. + * + * @returns The relative file paths organized according to BIDS naming conventions. + */ + public organizePaths(): OrganizedBidsCandidates { + if (this.#alreadyOrganized) { + return this.candidates + } + + for (const relativePath of this.relativeFilePaths) { + // Basic validation and extension check + if (typeof relativePath !== 'string' || (!relativePath.endsWith('.tsv') && !relativePath.endsWith('.json'))) { + continue + } + this._organizePath(relativePath) + } + + this.#alreadyOrganized = true + + return this.candidates + } + + /** + * Helper function for organizing an individual path. + * + * @param relativePath A relative file path to organize. + */ + private _organizePath(relativePath: string): void { + const pathParts = relativePath.split('/') + const firstComponent = pathParts[0] + const ext = relativePath.endsWith('.tsv') ? 'tsv' : 'json' + + // Rule 1: Check if the file is in a special directory. + if (this.specialDirs.includes(firstComponent)) { + this.candidates.addCandidate(relativePath, firstComponent, ext) + return + } + + // Rule 2: Check if it's a top-level file or in a subject directory. + const isToplevel = pathParts.length === 1 + const inSubDir = firstComponent.startsWith('sub-') + if (!isToplevel && !inSubDir) { + return + } + + // Rule 3: Either it is the suffix or the suffix starts with an underscore and matches the end of the filename. + const basename = pathParts[pathParts.length - 1] + const filenameNoExt = basename.substring(0, basename.lastIndexOf('.')) + const matchingSuffix = this.suffixes.find( + (suffix) => filenameNoExt === suffix || (suffix.startsWith('_') && filenameNoExt.endsWith(suffix)), + ) + if (matchingSuffix) { + this.candidates.addCandidate(relativePath, matchingSuffix, ext) + } + } +} + +/** + * Organizes a list of relative file paths based on BIDS naming conventions. + * + * This function filters and categorizes file paths into a structured object. It identifies files + * based on whether they are in special directories (like 'phenotype'), are top-level files, or + * are located within subject-specific directories ('sub-xxx'). + * + * Files are categorized by matching their filename against a list of suffixes (e.g., 'events', + * 'participants') or by their presence in a special directory. Only files with '.tsv' or '.json' + * extensions are considered. + * + * @param relativeFilePaths A list of relative file paths to organize. + * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). + * @param specialDirs A list of special directory names (e.g., 'phenotype'). + * @returns The relative file paths organized according to BIDS naming conventions. + */ +export function organizePaths( + relativeFilePaths: string[], + suffixes: string[], + specialDirs: string[], +): OrganizedBidsCandidates { + const organizer = new BidsPathOrganizer(relativeFilePaths, suffixes, specialDirs) + return organizer.organizePaths() +} + /** * Checks if one path is a subpath of another. * @@ -167,77 +296,6 @@ export function isSubpath( return normChild.startsWith(normParent + '/') } -/** - * Organizes a list of relative file paths based on BIDS naming conventions. - * - * This function filters and categorizes file paths into a structured object. It identifies files - * based on whether they are in special directories (like 'phenotype'), are top-level files, or - * are located within subject-specific directories ('sub-xxx'). - * - * Files are categorized by matching their filename against a list of suffixes (e.g., 'events', - * 'participants') or by their presence in a special directory. Only files with '.tsv' or '.json' - * extensions are considered. - * - * @param relativeFilePaths A list of relative file paths to organize. - * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). - * @param specialDirs A list of special directory names (e.g., 'phenotype'). - * @returns The relative file paths organized according to BIDS naming conventions. - */ -export function organizePaths( - relativeFilePaths: string[], - suffixes: string[], - specialDirs: string[], -): OrganizedBidsCandidates { - const candidates = new OrganizedBidsCandidates([...suffixes, ...specialDirs]) - - for (const relativePath of relativeFilePaths) { - // Basic validation and extension check - if (typeof relativePath !== 'string' || (!relativePath.endsWith('.tsv') && !relativePath.endsWith('.json'))) { - continue - } - const ext = relativePath.endsWith('.tsv') ? 'tsv' : 'json' - const [isCandidate, suffix] = _organizePath(relativePath, suffixes, specialDirs) - if (isCandidate) { - candidates.addCandidate(relativePath, suffix, ext) - } - } - - return candidates -} - -/** - * Helper function for organizing an individual path. - * - * @param relativePath A relative file path to organize. - * @param suffixes A list of filename suffixes to categorize by (e.g., 'events'). - * @param specialDirs A list of special directory names (e.g., 'phenotype'). - * @returns A tuple of whether the path was matched and its suffix. - */ -function _organizePath(relativePath: string, suffixes: string[], specialDirs: string[]): [boolean, string] { - const pathParts = relativePath.split('/') - const basename = pathParts[pathParts.length - 1] - const firstComponent = pathParts[0] - - // Rule 1: Check if the file is in a special directory. - if (specialDirs.includes(firstComponent)) { - return [true, firstComponent] - } - - // Rule 2: Check if it's a top-level file or in a subject directory. - const isToplevel = pathParts.length === 1 - const inSubDir = firstComponent.startsWith('sub-') - if (!isToplevel && !inSubDir) { - return [false, ''] - } - - // Rule 3: Either it is the suffix or the suffix starts with an underscore and matches the end of the filename. - const filenameNoExt = basename.substring(0, basename.lastIndexOf('.')) - const matchingSuffix = suffixes.find( - (suffix) => filenameNoExt === suffix || (suffix.startsWith('_') && filenameNoExt.endsWith(suffix)), - ) - return [matchingSuffix !== undefined, matchingSuffix] -} - /** * Updates the entity dictionary with a new entity. * From f71465616dbcd03b87aabccf40576b7d149950d3 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 06:09:27 -0500 Subject: [PATCH 31/63] Port BIDS schema entry point and TSV parser to TypeScript --- src/bids/{schema.js => schema.ts} | 9 ++-- src/bids/tsvParser.js | 61 --------------------------- src/bids/tsvParser.ts | 70 +++++++++++++++++++++++++++++++ src/bids/types/json.js | 4 +- 4 files changed, 78 insertions(+), 66 deletions(-) rename src/bids/{schema.js => schema.ts} (60%) delete mode 100644 src/bids/tsvParser.js create mode 100644 src/bids/tsvParser.ts diff --git a/src/bids/schema.js b/src/bids/schema.ts similarity index 60% rename from src/bids/schema.js rename to src/bids/schema.ts index f9e6deb9..d39bb26f 100644 --- a/src/bids/schema.js +++ b/src/bids/schema.ts @@ -1,19 +1,22 @@ /** * This module contains functions for building HED schemas for BIDS datasets. + * * @module bids/schema */ +import { HedSchemas } from '../schema/containers' import { buildSchemas } from '../schema/init' import { SchemasSpec } from '../schema/specs' +import { BidsJsonFile } from './types/json' /** * Build a HED schema collection based on the defined BIDS schemas. * - * @param {BidsJsonFile} datasetDescription The description of the BIDS dataset being validated. - * @returns {Promise} A Promise with the schema collection, or null if the specification is missing. + * @param datasetDescription The description of the BIDS dataset being validated. + * @returns A Promise with the schema collection, or null if the specification is missing. * @throws {IssueError} If the schema specification is invalid. */ -export async function buildBidsSchemas(datasetDescription) { +export async function buildBidsSchemas(datasetDescription: BidsJsonFile): Promise { if (datasetDescription?.jsonData?.HEDVersion) { const schemasSpec = SchemasSpec.parseVersionSpecs(datasetDescription.jsonData.HEDVersion) return buildSchemas(schemasSpec) diff --git a/src/bids/tsvParser.js b/src/bids/tsvParser.js deleted file mode 100644 index b2728983..00000000 --- a/src/bids/tsvParser.js +++ /dev/null @@ -1,61 +0,0 @@ -/** - * This module provides functions for parsing TSV files. - * - * @module bids/tsvParser - */ - -const stripBOM = (str) => str.replace(/^\uFEFF/, '') -const normalizeEOL = (str) => str.replace(/\r\n/g, '\n').replace(/\r/g, '\n') -const isContentfulRow = (row) => row && !/^\s*$/.test(row) - -/** - * Parse a TSV file - * - * @param {string} contents The contents of a TSV file. - * @returns {Map} The parsed contents of the TSV file. - */ -export function parseTSV(contents) { - const columns = new Map() - const rows = stripBOM(normalizeEOL(contents)) - .split('\n') - .filter(isContentfulRow) - .map((str) => str.split('\t').map((cell) => cell.trim())) - const headers = rows.length ? rows[0] : [] - - headers.forEach((x) => { - columns.set(x, []) - }) - for (let i = 1; i < rows.length; i++) { - for (let j = 0; j < headers.length; j++) { - columns.get(headers[j])?.push(rows[i][j]) - } - } - for (const [key, value] of columns) { - columns.set(key, value) - } - return columns -} -/** - * Convert parsed TSV file data from the old BIDS format to the new BIDS format. - * - * @param {{headers: string[], rows: string[][]}} oldParsedTsv Parsed TSV data using the old format - * @returns {Map} The parsed contents of the TSV file, using the new format. - */ -export function convertParsedTSVData(oldParsedTsv) { - const columns = new Map() - - oldParsedTsv.headers.forEach((x) => { - columns.set(x, []) - }) - for (let i = 1; i < oldParsedTsv.rows.length; i++) { - for (let j = 0; j < oldParsedTsv.headers.length; j++) { - columns.get(oldParsedTsv.headers[j])?.push(oldParsedTsv.rows[i][j]) - } - } - for (const [key, value] of columns) { - columns.set(key, value) - } - return columns -} - -export default parseTSV diff --git a/src/bids/tsvParser.ts b/src/bids/tsvParser.ts new file mode 100644 index 00000000..0cf014c0 --- /dev/null +++ b/src/bids/tsvParser.ts @@ -0,0 +1,70 @@ +/** + * This module provides functions for parsing TSV files. + * + * @module bids/tsvParser + */ + +export type ParsedTSV = Map +type OldParsedTSV = { + headers: string[] + rows: string[][] +} + +const stripBOM = (str: string) => str.replace(/^\uFEFF/, '') +const normalizeEOL = (str: string) => str.replace(/\r\n/g, '\n').replace(/\r/g, '\n') +const isContentfulRow = (row: string) => row && !/^\s*$/.test(row) + +/** + * Parse a TSV file. + * + * @param contents The contents of a TSV file. + * @returns The parsed contents of the TSV file. + */ +export function parseTSV(contents: string): ParsedTSV { + const rows = stripBOM(normalizeEOL(contents)) + .split('\n') + .filter(isContentfulRow) + .map((str) => str.split('\t').map((cell) => cell.trim())) + + if (rows.length === 0) { + return new Map() + } + + const headers = rows[0] + + return createTsvMap(headers, rows) +} + +/** + * Convert parsed TSV file data from the old BIDS format to the new BIDS format. + * + * @param oldParsedTsv Parsed TSV data using the old format + * @returns The parsed contents of the TSV file, using the new format. + */ +export function convertParsedTSVData(oldParsedTsv: OldParsedTSV): ParsedTSV { + return createTsvMap(oldParsedTsv.headers, oldParsedTsv.rows) +} + +/** + * Create a parsed TSV map. + * + * @param headers The list of headers. + * @param rows The grid of rows and cells. + * @returns The parsed contents of the TSV file. + */ +function createTsvMap(headers: string[], rows: string[][]): ParsedTSV { + const columns = new Map() + + for (const header of headers) { + columns.set(header, []) + } + for (let i = 1; i < rows.length; i++) { + for (let j = 0; j < headers.length; j++) { + columns.get(headers[j]).push(rows[i][j]) + } + } + + return columns +} + +export default parseTSV diff --git a/src/bids/types/json.js b/src/bids/types/json.js index db2d3fc7..02ccfd15 100644 --- a/src/bids/types/json.js +++ b/src/bids/types/json.js @@ -20,7 +20,7 @@ const ILLEGAL_SIDECAR_KEYS = new Set(['hed', 'n/a']) export class BidsJsonFile extends BidsFile { /** * This file's JSON data. - * @type {Object} + * @type {Record} */ jsonData @@ -31,7 +31,7 @@ export class BidsJsonFile extends BidsFile { * * @param {string} name The name of the JSON file. * @param {Object} file The file object representing this file. - * @param {Object} jsonData The JSON data for this file. + * @param {Record} jsonData The JSON data for this file. */ constructor(name, file, jsonData) { super(name, file, BidsHedSidecarValidator) From f2e0a09e908bcdec8ff28a8f36583d82a6a52739 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 12:59:32 -0500 Subject: [PATCH 32/63] Fix issues flagged by AI --- src/bids/tsvParser.ts | 2 +- src/issues/data.ts | 2 +- src/utils/paths.ts | 2 +- src/utils/string.ts | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/bids/tsvParser.ts b/src/bids/tsvParser.ts index 0cf014c0..a99b7b60 100644 --- a/src/bids/tsvParser.ts +++ b/src/bids/tsvParser.ts @@ -60,7 +60,7 @@ function createTsvMap(headers: string[], rows: string[][]): ParsedTSV { } for (let i = 1; i < rows.length; i++) { for (let j = 0; j < headers.length; j++) { - columns.get(headers[j]).push(rows[i][j]) + columns.get(headers[j])?.push(rows[i][j]) } } diff --git a/src/issues/data.ts b/src/issues/data.ts index 194b651e..585a61de 100644 --- a/src/issues/data.ts +++ b/src/issues/data.ts @@ -510,7 +510,7 @@ const issueData: Record = { genericError: { hedCode: 'INTERNAL_ERROR', level: 'error', - message: (parameters) => + message: (parameters, ...bounds) => `Unknown HED error "${parameters.internalCode}" - parameters: "${JSON.stringify(parameters)}".`, }, } diff --git a/src/utils/paths.ts b/src/utils/paths.ts index 69cfcd2d..0fbd292b 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -101,7 +101,7 @@ class OrganizedBidsCandidates { * * @param relativePath The candidate's relative path. * @param suffix The candidate's suffix. - * @param ext The candidate's suffix. + * @param ext The candidate's extension. */ public addCandidate(relativePath: string, suffix: string, ext: string): void { this.candidates.push(relativePath) diff --git a/src/utils/string.ts b/src/utils/string.ts index 224d3075..a2458d97 100644 --- a/src/utils/string.ts +++ b/src/utils/string.ts @@ -51,7 +51,7 @@ export function issueMessageTemplate( const bounds = [start, end] const result = [strings[0]] parameterKeys.forEach((key, i) => { - const value = typeof key === 'number' ? bounds[key].toString() : parameterValues[key] + const value = typeof key === 'number' ? bounds[key]?.toString() : parameterValues[key] result.push(value, strings[i + 1]) }) return result.join('') From cc0422372ef2550a3150d8040f2c530884cf7bf0 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 13:52:27 -0500 Subject: [PATCH 33/63] Create codeql.yml --- .github/workflows/codeql.yml | 94 ++++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 .github/workflows/codeql.yml diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 00000000..ec75e33b --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,94 @@ +# For most projects, this workflow file will not need changing; you simply need +# to commit it to your repository. +# +# You may wish to alter this file to override the set of languages analyzed, +# or to provide custom queries or build logic. +# +# ******** NOTE ******** +# We have attempted to detect the languages in your repository. Please check +# the `language` matrix defined below to confirm you have the correct set of +# supported CodeQL languages. +# +name: "CodeQL Advanced" + +on: + push: + branches: [ "typescript" ] + pull_request: + branches: [ "typescript" ] + schedule: + - cron: '26 6 * * 5' + +jobs: + analyze: + name: Analyze (${{ matrix.language }}) + # Runner size impacts CodeQL analysis time. To learn more, please see: + # - https://gh.io/recommended-hardware-resources-for-running-codeql + # - https://gh.io/supported-runners-and-hardware-resources + # - https://gh.io/using-larger-runners (GitHub.com only) + # Consider using larger runners or machines with greater resources for possible analysis time improvements. + runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }} + permissions: + # required for all workflows + security-events: write + + strategy: + fail-fast: false + matrix: + include: + - language: actions + build-mode: none + - language: javascript-typescript + build-mode: none + # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift' + # Use `c-cpp` to analyze code written in C, C++ or both + # Use 'java-kotlin' to analyze code written in Java, Kotlin or both + # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both + # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis, + # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning. + # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how + # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + # Add any setup steps before running the `github/codeql-action/init` action. + # This includes steps like installing compilers or runtimes (`actions/setup-node` + # or others). This is typically only required for manual builds. + # - name: Setup runtime (example) + # uses: actions/setup-example@v1 + + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v4 + with: + languages: ${{ matrix.language }} + build-mode: ${{ matrix.build-mode }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. + + # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality + + # If the analyze step fails for one of the languages you are analyzing with + # "We were unable to automatically build your code", modify the matrix above + # to set the build mode to "manual" for that language. Then modify this step + # to build your code. + # ℹ️ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + - name: Run manual build steps + if: matrix.build-mode == 'manual' + shell: bash + run: | + echo 'If you are using a "manual" build mode for one or more of the' \ + 'languages you are analyzing, replace this with the commands to build' \ + 'your code, for example:' + echo ' make bootstrap' + echo ' make release' + exit 1 + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v4 + with: + category: "/language:${{matrix.language}}" From 11e7a8f4b36ee202db9357cc68b918b4569ea632 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 28 Oct 2025 18:56:18 +0000 Subject: [PATCH 34/63] Bump @babel/core from 7.28.4 to 7.28.5 Bumps [@babel/core](https://github.com/babel/babel/tree/HEAD/packages/babel-core) from 7.28.4 to 7.28.5. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.28.5/packages/babel-core) --- updated-dependencies: - dependency-name: "@babel/core" dependency-version: 7.28.5 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 58 +++++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6d327382..fcfebb0c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -73,21 +73,21 @@ } }, "node_modules/@babel/core": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.4.tgz", - "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.5.tgz", + "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==", "dev": true, "license": "MIT", "dependencies": { "@babel/code-frame": "^7.27.1", - "@babel/generator": "^7.28.3", + "@babel/generator": "^7.28.5", "@babel/helper-compilation-targets": "^7.27.2", "@babel/helper-module-transforms": "^7.28.3", "@babel/helpers": "^7.28.4", - "@babel/parser": "^7.28.4", + "@babel/parser": "^7.28.5", "@babel/template": "^7.27.2", - "@babel/traverse": "^7.28.4", - "@babel/types": "^7.28.4", + "@babel/traverse": "^7.28.5", + "@babel/types": "^7.28.5", "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", @@ -114,14 +114,14 @@ } }, "node_modules/@babel/generator": { - "version": "7.28.3", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.3.tgz", - "integrity": "sha512-3lSpxGgvnmZznmBkCRnVREPUFJv2wrv9iAoFDvADJc0ypmdOxdUtcLeBgBJ6zE0PMeTKnxeQzyk0xTBq4Ep7zw==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.5.tgz", + "integrity": "sha512-3EwLFhZ38J4VyIP6WNtt2kUdW9dokXA9Cr4IVIFHuCpZ3H8/YFOl5JjZHisrn1fATPBmKKqXzDFvh9fUwHz6CQ==", "dev": true, "license": "MIT", "dependencies": { - "@babel/parser": "^7.28.3", - "@babel/types": "^7.28.2", + "@babel/parser": "^7.28.5", + "@babel/types": "^7.28.5", "@jridgewell/gen-mapping": "^0.3.12", "@jridgewell/trace-mapping": "^0.3.28", "jsesc": "^3.0.2" @@ -387,9 +387,9 @@ } }, "node_modules/@babel/helper-validator-identifier": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.27.1.tgz", - "integrity": "sha512-D2hP9eA+Sqx1kBZgzxZh0y1trbuU+JoDkiEwqhQ36nodYqJwyEIhPSdMNd7lOm/4io72luTPWH20Yda0xOuUow==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.28.5.tgz", + "integrity": "sha512-qSs4ifwzKJSV39ucNjsvc6WVHs6b7S03sOh2OcHF9UHfVPqWWALUsNUVzhSBiItjRZoLHx7nIarVjqKVusUZ1Q==", "dev": true, "license": "MIT", "engines": { @@ -436,13 +436,13 @@ } }, "node_modules/@babel/parser": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.28.4.tgz", - "integrity": "sha512-yZbBqeM6TkpP9du/I2pUZnJsRMGGvOuIrhjzC1AwHwW+6he4mni6Bp/m8ijn0iOuZuPI2BfkCoSRunpyjnrQKg==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.28.5.tgz", + "integrity": "sha512-KKBU1VGYR7ORr3At5HAtUQ+TV3SzRCXmA/8OdDZiLDBIZxVyzXuztPjfLd3BV1PRAQGCMWWSHYhL0F8d5uHBDQ==", "dev": true, "license": "MIT", "dependencies": { - "@babel/types": "^7.28.4" + "@babel/types": "^7.28.5" }, "bin": { "parser": "bin/babel-parser.js" @@ -1802,18 +1802,18 @@ } }, "node_modules/@babel/traverse": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.28.4.tgz", - "integrity": "sha512-YEzuboP2qvQavAcjgQNVgsvHIDv6ZpwXvcvjmyySP2DIMuByS/6ioU5G9pYrWHM6T2YDfc7xga9iNzYOs12CFQ==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.28.5.tgz", + "integrity": "sha512-TCCj4t55U90khlYkVV/0TfkJkAkUg3jZFA3Neb7unZT8CPok7iiRfaX0F+WnqWqt7OxhOn0uBKXCw4lbL8W0aQ==", "dev": true, "license": "MIT", "dependencies": { "@babel/code-frame": "^7.27.1", - "@babel/generator": "^7.28.3", + "@babel/generator": "^7.28.5", "@babel/helper-globals": "^7.28.0", - "@babel/parser": "^7.28.4", + "@babel/parser": "^7.28.5", "@babel/template": "^7.27.2", - "@babel/types": "^7.28.4", + "@babel/types": "^7.28.5", "debug": "^4.3.1" }, "engines": { @@ -1821,14 +1821,14 @@ } }, "node_modules/@babel/types": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.28.4.tgz", - "integrity": "sha512-bkFqkLhh3pMBUQQkpVgWDWq/lqzc2678eUyDlTBhRqhCHFguYYGM0Efga7tYk4TogG/3x0EEl66/OQ+WGbWB/Q==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.28.5.tgz", + "integrity": "sha512-qQ5m48eI/MFLQ5PxQj4PFaprjyCTLI37ElWMmNs0K8Lk3dVeOdNpB3ks8jc7yM5CDmVC73eMVk/trk3fgmrUpA==", "dev": true, "license": "MIT", "dependencies": { "@babel/helper-string-parser": "^7.27.1", - "@babel/helper-validator-identifier": "^7.27.1" + "@babel/helper-validator-identifier": "^7.28.5" }, "engines": { "node": ">=6.9.0" From fc579fcbeac0dd423127136ba127f4a3f27b6a2c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 28 Oct 2025 18:56:31 +0000 Subject: [PATCH 35/63] Bump @types/node from 24.8.1 to 24.9.2 Bumps [@types/node](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/node) from 24.8.1 to 24.9.2. - [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases) - [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/node) --- updated-dependencies: - dependency-name: "@types/node" dependency-version: 24.9.2 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6d327382..6567e28e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -3309,13 +3309,13 @@ "license": "MIT" }, "node_modules/@types/node": { - "version": "24.8.1", - "resolved": "https://registry.npmjs.org/@types/node/-/node-24.8.1.tgz", - "integrity": "sha512-alv65KGRadQVfVcG69MuB4IzdYVpRwMG/mq8KWOaoOdyY617P5ivaDiMCGOFDWD2sAn5Q0mR3mRtUOgm99hL9Q==", + "version": "24.9.2", + "resolved": "https://registry.npmjs.org/@types/node/-/node-24.9.2.tgz", + "integrity": "sha512-uWN8YqxXxqFMX2RqGOrumsKeti4LlmIMIyV0lgut4jx7KQBcBiW6vkDtIBvHnHIquwNfJhk8v2OtmO8zXWHfPA==", "dev": true, "license": "MIT", "dependencies": { - "undici-types": "~7.14.0" + "undici-types": "~7.16.0" } }, "node_modules/@types/stack-utils": { @@ -7767,9 +7767,9 @@ } }, "node_modules/undici-types": { - "version": "7.14.0", - "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.14.0.tgz", - "integrity": "sha512-QQiYxHuyZ9gQUIrmPo3IA+hUl4KYk8uSA7cHrcKd/l3p1OTpZcM0Tbp9x7FAtXdAYhlasd60ncPpgu6ihG6TOA==", + "version": "7.16.0", + "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz", + "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==", "dev": true, "license": "MIT" }, From 4e32c401d350440fe6370cf567349530d554090a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 28 Oct 2025 18:56:40 +0000 Subject: [PATCH 36/63] Bump eslint from 9.37.0 to 9.38.0 Bumps [eslint](https://github.com/eslint/eslint) from 9.37.0 to 9.38.0. - [Release notes](https://github.com/eslint/eslint/releases) - [Commits](https://github.com/eslint/eslint/compare/v9.37.0...v9.38.0) --- updated-dependencies: - dependency-name: eslint dependency-version: 9.38.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 46 ++++++++++++++++------------------------------ 1 file changed, 16 insertions(+), 30 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6d327382..2f5ed200 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2360,13 +2360,13 @@ } }, "node_modules/@eslint/config-array": { - "version": "0.21.0", - "resolved": "https://registry.npmjs.org/@eslint/config-array/-/config-array-0.21.0.tgz", - "integrity": "sha512-ENIdc4iLu0d93HeYirvKmrzshzofPw6VkZRKQGe9Nv46ZnWUzcF1xV01dcvEg/1wXUR61OmmlSfyeyO7EvjLxQ==", + "version": "0.21.1", + "resolved": "https://registry.npmjs.org/@eslint/config-array/-/config-array-0.21.1.tgz", + "integrity": "sha512-aw1gNayWpdI/jSYVgzN5pL0cfzU02GT3NBpeT/DXbx1/1x7ZKxFPd9bwrzygx/qiwIQiJ1sw/zD8qY/kRvlGHA==", "dev": true, "license": "Apache-2.0", "dependencies": { - "@eslint/object-schema": "^2.1.6", + "@eslint/object-schema": "^2.1.7", "debug": "^4.3.1", "minimatch": "^3.1.2" }, @@ -2375,9 +2375,9 @@ } }, "node_modules/@eslint/config-helpers": { - "version": "0.4.0", - "resolved": "https://registry.npmjs.org/@eslint/config-helpers/-/config-helpers-0.4.0.tgz", - "integrity": "sha512-WUFvV4WoIwW8Bv0KeKCIIEgdSiFOsulyN0xrMu+7z43q/hkOLXjvb5u7UC9jDxvRzcrbEmuZBX5yJZz1741jog==", + "version": "0.4.1", + "resolved": "https://registry.npmjs.org/@eslint/config-helpers/-/config-helpers-0.4.1.tgz", + "integrity": "sha512-csZAzkNhsgwb0I/UAV6/RGFTbiakPCf0ZrGmrIxQpYvGZ00PhTkSnyKNolphgIvmnJeGw6rcGVEXfTzUnFuEvw==", "dev": true, "license": "Apache-2.0", "dependencies": { @@ -2451,9 +2451,9 @@ } }, "node_modules/@eslint/object-schema": { - "version": "2.1.6", - "resolved": "https://registry.npmjs.org/@eslint/object-schema/-/object-schema-2.1.6.tgz", - "integrity": "sha512-RBMg5FRL0I0gs51M/guSAj5/e14VQ4tpZnQNWwuDT66P14I43ItmPfIZRhO9fUVIPOAQXU47atlywZ/czoqFPA==", + "version": "2.1.7", + "resolved": "https://registry.npmjs.org/@eslint/object-schema/-/object-schema-2.1.7.tgz", + "integrity": "sha512-VtAOaymWVfZcmZbp6E2mympDIHvyjXs/12LqWYjVw6qjrfF+VK+fyG33kChz3nnK+SU5/NeHOqrTEHS8sXO3OA==", "dev": true, "license": "Apache-2.0", "engines": { @@ -4527,25 +4527,24 @@ } }, "node_modules/eslint": { - "version": "9.37.0", - "resolved": "https://registry.npmjs.org/eslint/-/eslint-9.37.0.tgz", - "integrity": "sha512-XyLmROnACWqSxiGYArdef1fItQd47weqB7iwtfr9JHwRrqIXZdcFMvvEcL9xHCmL0SNsOvF0c42lWyM1U5dgig==", + "version": "9.38.0", + "resolved": "https://registry.npmjs.org/eslint/-/eslint-9.38.0.tgz", + "integrity": "sha512-t5aPOpmtJcZcz5UJyY2GbvpDlsK5E8JqRqoKtfiKE3cNh437KIqfJr3A3AKf5k64NPx6d0G3dno6XDY05PqPtw==", "dev": true, "license": "MIT", "dependencies": { "@eslint-community/eslint-utils": "^4.8.0", "@eslint-community/regexpp": "^4.12.1", - "@eslint/config-array": "^0.21.0", - "@eslint/config-helpers": "^0.4.0", + "@eslint/config-array": "^0.21.1", + "@eslint/config-helpers": "^0.4.1", "@eslint/core": "^0.16.0", "@eslint/eslintrc": "^3.3.1", - "@eslint/js": "9.37.0", + "@eslint/js": "9.38.0", "@eslint/plugin-kit": "^0.4.0", "@humanfs/node": "^0.16.6", "@humanwhocodes/module-importer": "^1.0.1", "@humanwhocodes/retry": "^0.4.2", "@types/estree": "^1.0.6", - "@types/json-schema": "^7.0.15", "ajv": "^6.12.4", "chalk": "^4.0.0", "cross-spawn": "^7.0.6", @@ -4664,19 +4663,6 @@ "url": "https://opencollective.com/eslint" } }, - "node_modules/eslint/node_modules/@eslint/js": { - "version": "9.37.0", - "resolved": "https://registry.npmjs.org/@eslint/js/-/js-9.37.0.tgz", - "integrity": "sha512-jaS+NJ+hximswBG6pjNX0uEJZkrT0zwpVi3BA3vX22aFGjJjmgSTSmPpZCRKmoBL5VY/M6p0xsSJx7rk7sy5gg==", - "dev": true, - "license": "MIT", - "engines": { - "node": "^18.18.0 || ^20.9.0 || >=21.1.0" - }, - "funding": { - "url": "https://eslint.org/donate" - } - }, "node_modules/espree": { "version": "10.4.0", "resolved": "https://registry.npmjs.org/espree/-/espree-10.4.0.tgz", From c42da094fd50598bab4b383ebe2cfb1693563f32 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 28 Oct 2025 18:56:53 +0000 Subject: [PATCH 37/63] Bump @babel/preset-env from 7.28.3 to 7.28.5 Bumps [@babel/preset-env](https://github.com/babel/babel/tree/HEAD/packages/babel-preset-env) from 7.28.3 to 7.28.5. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.28.5/packages/babel-preset-env) --- updated-dependencies: - dependency-name: "@babel/preset-env" dependency-version: 7.28.5 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 152 +++++++++++++++++++++++----------------------- 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6d327382..9d20d3df 100644 --- a/package-lock.json +++ b/package-lock.json @@ -63,9 +63,9 @@ } }, "node_modules/@babel/compat-data": { - "version": "7.28.0", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.0.tgz", - "integrity": "sha512-60X7qkglvrap8mn1lh2ebxXdZYtUcpd7gsmy9kLaBJ4i/WdY8PqTSdxyA8qraikqKQK5C1KRBKXqznrVapyNaw==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.5.tgz", + "integrity": "sha512-6uFXyCayocRbqhZOB+6XcuZbkMNimwfVGFji8CTZnCzOHVGvDqzvitu1re2AU5LROliz7eQPhB8CpAMvnx9EjA==", "dev": true, "license": "MIT", "engines": { @@ -114,14 +114,14 @@ } }, "node_modules/@babel/generator": { - "version": "7.28.3", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.3.tgz", - 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"@babel/plugin-transform-logical-assignment-operators": "^7.27.1", + "@babel/plugin-transform-logical-assignment-operators": "^7.28.5", "@babel/plugin-transform-member-expression-literals": "^7.27.1", "@babel/plugin-transform-modules-amd": "^7.27.1", "@babel/plugin-transform-modules-commonjs": "^7.27.1", - "@babel/plugin-transform-modules-systemjs": "^7.27.1", + "@babel/plugin-transform-modules-systemjs": "^7.28.5", "@babel/plugin-transform-modules-umd": "^7.27.1", "@babel/plugin-transform-named-capturing-groups-regex": "^7.27.1", "@babel/plugin-transform-new-target": "^7.27.1", "@babel/plugin-transform-nullish-coalescing-operator": "^7.27.1", "@babel/plugin-transform-numeric-separator": "^7.27.1", - "@babel/plugin-transform-object-rest-spread": "^7.28.0", + "@babel/plugin-transform-object-rest-spread": "^7.28.4", "@babel/plugin-transform-object-super": "^7.27.1", "@babel/plugin-transform-optional-catch-binding": "^7.27.1", - "@babel/plugin-transform-optional-chaining": "^7.27.1", + "@babel/plugin-transform-optional-chaining": "^7.28.5", "@babel/plugin-transform-parameters": "^7.27.7", "@babel/plugin-transform-private-methods": "^7.27.1", "@babel/plugin-transform-private-property-in-object": "^7.27.1", "@babel/plugin-transform-property-literals": "^7.27.1", - "@babel/plugin-transform-regenerator": "^7.28.3", + "@babel/plugin-transform-regenerator": "^7.28.4", "@babel/plugin-transform-regexp-modifiers": "^7.27.1", "@babel/plugin-transform-reserved-words": "^7.27.1", "@babel/plugin-transform-shorthand-properties": "^7.27.1", @@ -1802,18 +1802,18 @@ } }, "node_modules/@babel/traverse": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.28.4.tgz", - "integrity": "sha512-YEzuboP2qvQavAcjgQNVgsvHIDv6ZpwXvcvjmyySP2DIMuByS/6ioU5G9pYrWHM6T2YDfc7xga9iNzYOs12CFQ==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.28.5.tgz", + "integrity": "sha512-TCCj4t55U90khlYkVV/0TfkJkAkUg3jZFA3Neb7unZT8CPok7iiRfaX0F+WnqWqt7OxhOn0uBKXCw4lbL8W0aQ==", "dev": true, "license": "MIT", "dependencies": { "@babel/code-frame": "^7.27.1", - "@babel/generator": "^7.28.3", + "@babel/generator": "^7.28.5", "@babel/helper-globals": "^7.28.0", - "@babel/parser": "^7.28.4", + "@babel/parser": "^7.28.5", "@babel/template": "^7.27.2", - "@babel/types": "^7.28.4", + "@babel/types": "^7.28.5", "debug": "^4.3.1" }, "engines": { @@ -1821,14 +1821,14 @@ } }, "node_modules/@babel/types": { - "version": "7.28.4", - "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.28.4.tgz", - "integrity": "sha512-bkFqkLhh3pMBUQQkpVgWDWq/lqzc2678eUyDlTBhRqhCHFguYYGM0Efga7tYk4TogG/3x0EEl66/OQ+WGbWB/Q==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.28.5.tgz", + "integrity": "sha512-qQ5m48eI/MFLQ5PxQj4PFaprjyCTLI37ElWMmNs0K8Lk3dVeOdNpB3ks8jc7yM5CDmVC73eMVk/trk3fgmrUpA==", "dev": true, "license": "MIT", "dependencies": { "@babel/helper-string-parser": "^7.27.1", - "@babel/helper-validator-identifier": "^7.27.1" + "@babel/helper-validator-identifier": "^7.28.5" }, "engines": { "node": ">=6.9.0" From aae6668af4869e83633261b56bcefef158c0a083 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 13:57:04 -0500 Subject: [PATCH 38/63] Fix permissions on type test workflow --- .github/workflows/test-types.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/test-types.yml b/.github/workflows/test-types.yml index e8d469ce..2bd5b9e2 100644 --- a/.github/workflows/test-types.yml +++ b/.github/workflows/test-types.yml @@ -6,6 +6,9 @@ on: pull_request: branches: [main, typescript] +permissions: + contents: read + jobs: test-types: runs-on: ubuntu-latest From 7edac6119d2c246ea3dd381a2b51a78831babc61 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 28 Oct 2025 18:58:58 +0000 Subject: [PATCH 39/63] Bump vite from 6.3.6 to 6.4.1 in /browser Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 6.3.6 to 6.4.1. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/main/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/create-vite@6.4.1/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 6.4.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- browser/package-lock.json | 8 ++++---- browser/package.json | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/browser/package-lock.json b/browser/package-lock.json index d67107b9..dfbd6d49 100644 --- a/browser/package-lock.json +++ b/browser/package-lock.json @@ -19,7 +19,7 @@ "@vitest/ui": "^3.2.4", "jsdom": "^24.0.0", "path-browserify": "^1.0.1", - "vite": "^6.3.6", + "vite": "^6.4.1", "vitest": "^3.2.4" } }, @@ -2928,9 +2928,9 @@ } }, "node_modules/vite": { - "version": "6.3.6", - "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.6.tgz", - "integrity": "sha512-0msEVHJEScQbhkbVTb/4iHZdJ6SXp/AvxL2sjwYQFfBqleHtnCqv1J3sa9zbWz/6kW1m9Tfzn92vW+kZ1WV6QA==", + "version": "6.4.1", + "resolved": "https://registry.npmjs.org/vite/-/vite-6.4.1.tgz", + "integrity": "sha512-+Oxm7q9hDoLMyJOYfUYBuHQo+dkAloi33apOPP56pzj+vsdJDzr+j1NISE5pyaAuKL4A3UD34qd0lx5+kfKp2g==", "dev": true, "license": "MIT", "dependencies": { diff --git a/browser/package.json b/browser/package.json index 8bd0f478..4d8090b1 100644 --- a/browser/package.json +++ b/browser/package.json @@ -20,7 +20,7 @@ "@vitest/ui": "^3.2.4", "jsdom": "^24.0.0", "path-browserify": "^1.0.1", - "vite": "^6.3.6", + "vite": "^6.4.1", "vitest": "^3.2.4" } } From e130a1fe10ac71c54bdf968da4ec025129f6fa2d Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 14:05:52 -0500 Subject: [PATCH 40/63] Fix permissions in CodeQL action --- .github/workflows/codeql.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index ec75e33b..0579007d 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -11,6 +11,9 @@ # name: "CodeQL Advanced" +permissions: + contents: read + on: push: branches: [ "typescript" ] From 14455f4b03a52827ba8088eefad21d72c01fa280 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 14:20:57 -0500 Subject: [PATCH 41/63] Delete unnecessary quotes in YAML files --- .github/dependabot.yml | 28 ++++----- .github/workflows/codeql.yml | 95 +++++++++++++++--------------- .github/workflows/deploy-pages.yml | 4 +- .github/workflows/publish.yml | 4 +- .github/workflows/test-types.yml | 2 +- .github/workflows/tests.yml | 6 +- 6 files changed, 69 insertions(+), 70 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 775171c5..b48c5ff2 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,21 +1,21 @@ version: 2 updates: - - package-ecosystem: 'github-actions' - directory: '/' - target-branch: 'main' + - package-ecosystem: github-actions + directory: / + target-branch: main schedule: - interval: 'weekly' - - package-ecosystem: 'npm' - directory: '/' - target-branch: 'main' + interval: weekly + - package-ecosystem: npm + directory: / + target-branch: main schedule: - interval: 'weekly' + interval: weekly ignore: - - dependency-name: 'chai' + - dependency-name: chai update-types: - - 'version-update:semver-major' - - package-ecosystem: 'gitsubmodule' - directory: '/' - target-branch: 'main' + - version-update:semver-major + - package-ecosystem: gitsubmodule + directory: / + target-branch: main schedule: - interval: 'daily' + interval: daily diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 0579007d..69350ba9 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -9,18 +9,18 @@ # the `language` matrix defined below to confirm you have the correct set of # supported CodeQL languages. # -name: "CodeQL Advanced" +name: CodeQL Advanced permissions: contents: read on: push: - branches: [ "typescript" ] + branches: [typescript] pull_request: - branches: [ "typescript" ] + branches: [typescript] schedule: - - cron: '26 6 * * 5' + - cron: 26 6 * * 5 jobs: analyze: @@ -31,18 +31,17 @@ jobs: # - https://gh.io/using-larger-runners (GitHub.com only) # Consider using larger runners or machines with greater resources for possible analysis time improvements. runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }} - permissions: - # required for all workflows + permissions: # required for all workflows security-events: write strategy: fail-fast: false matrix: include: - - language: actions - build-mode: none - - language: javascript-typescript - build-mode: none + - language: actions + build-mode: none + - language: javascript-typescript + build-mode: none # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift' # Use `c-cpp` to analyze code written in C, C++ or both # Use 'java-kotlin' to analyze code written in Java, Kotlin or both @@ -52,46 +51,46 @@ jobs: # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages steps: - - name: Checkout repository - uses: actions/checkout@v4 + - name: Checkout repository + uses: actions/checkout@v4 - # Add any setup steps before running the `github/codeql-action/init` action. - # This includes steps like installing compilers or runtimes (`actions/setup-node` - # or others). This is typically only required for manual builds. - # - name: Setup runtime (example) - # uses: actions/setup-example@v1 + # Add any setup steps before running the `github/codeql-action/init` action. + # This includes steps like installing compilers or runtimes (`actions/setup-node` + # or others). This is typically only required for manual builds. + # - name: Setup runtime (example) + # uses: actions/setup-example@v1 - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v4 - with: - languages: ${{ matrix.language }} - build-mode: ${{ matrix.build-mode }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v4 + with: + languages: ${{ matrix.language }} + build-mode: ${{ matrix.build-mode }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. - # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs - # queries: security-extended,security-and-quality + # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality - # If the analyze step fails for one of the languages you are analyzing with - # "We were unable to automatically build your code", modify the matrix above - # to set the build mode to "manual" for that language. Then modify this step - # to build your code. - # ℹ️ Command-line programs to run using the OS shell. - # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun - - name: Run manual build steps - if: matrix.build-mode == 'manual' - shell: bash - run: | - echo 'If you are using a "manual" build mode for one or more of the' \ - 'languages you are analyzing, replace this with the commands to build' \ - 'your code, for example:' - echo ' make bootstrap' - echo ' make release' - exit 1 + # If the analyze step fails for one of the languages you are analyzing with + # "We were unable to automatically build your code", modify the matrix above + # to set the build mode to "manual" for that language. Then modify this step + # to build your code. + # ℹ️ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + - name: Run manual build steps + if: matrix.build-mode == 'manual' + shell: bash + run: | + echo 'If you are using a "manual" build mode for one or more of the' \ + 'languages you are analyzing, replace this with the commands to build' \ + 'your code, for example:' + echo ' make bootstrap' + echo ' make release' + exit 1 - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v4 - with: - category: "/language:${{matrix.language}}" + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v4 + with: + category: '/language:${{matrix.language}}' diff --git a/.github/workflows/deploy-pages.yml b/.github/workflows/deploy-pages.yml index 3d0248ba..d2e77616 100644 --- a/.github/workflows/deploy-pages.yml +++ b/.github/workflows/deploy-pages.yml @@ -8,7 +8,7 @@ on: # Allow only one concurrent deployment, cancelling any previously running ones. concurrency: - group: 'pages' + group: pages cancel-in-progress: true permissions: {} @@ -30,7 +30,7 @@ jobs: with: node-version: 22 # Cache npm dependencies to speed up future builds - cache: 'npm' + cache: npm cache-dependency-path: | package-lock.json browser/package-lock.json diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 43ea5e6d..63f3bd47 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -14,8 +14,8 @@ jobs: # Setup .npmrc file to publish to npm - uses: actions/setup-node@v6 with: - node-version: 'lts/*' - registry-url: 'https://registry.npmjs.org' + node-version: lts/* + registry-url: https://registry.npmjs.org - name: Update npm run: npm install -g npm@latest - run: npm ci diff --git a/.github/workflows/test-types.yml b/.github/workflows/test-types.yml index 2bd5b9e2..26686e2c 100644 --- a/.github/workflows/test-types.yml +++ b/.github/workflows/test-types.yml @@ -24,7 +24,7 @@ jobs: uses: actions/setup-node@v6 with: node-version: ${{ matrix.node-version }} - cache: 'npm' + cache: npm - name: Install dependencies run: npm ci diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b2b23a64..c1f3a985 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -15,7 +15,7 @@ jobs: strategy: matrix: - node-version: [22.x, lts/*, 'node'] + node-version: [22.x, lts/*, node] steps: - name: Check out the code @@ -38,7 +38,7 @@ jobs: strategy: matrix: - node-version: [22.x, lts/*, 'node'] + node-version: [22.x, lts/*, node] steps: - name: Check out the code @@ -61,7 +61,7 @@ jobs: strategy: matrix: - node-version: [22.x, lts/*, 'node'] + node-version: [22.x, lts/*, node] steps: - name: Check out the code From b0c0cc2205afa552833cc245236ae8f0c5e5398b Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 28 Oct 2025 15:37:29 -0500 Subject: [PATCH 42/63] Port BIDS TSV and base file types to TypeScript --- src/bids/tsvParser.ts | 2 +- src/bids/types/{file.js => file.ts} | 42 +++--- src/bids/types/issues.js | 4 +- src/bids/types/tsv.js | 164 ----------------------- src/bids/types/tsv.ts | 195 ++++++++++++++++++++++++++++ 5 files changed, 224 insertions(+), 183 deletions(-) rename src/bids/types/{file.js => file.ts} (54%) delete mode 100644 src/bids/types/tsv.js create mode 100644 src/bids/types/tsv.ts diff --git a/src/bids/tsvParser.ts b/src/bids/tsvParser.ts index a99b7b60..d4e0b1ff 100644 --- a/src/bids/tsvParser.ts +++ b/src/bids/tsvParser.ts @@ -5,7 +5,7 @@ */ export type ParsedTSV = Map -type OldParsedTSV = { +export type OldParsedTSV = { headers: string[] rows: string[][] } diff --git a/src/bids/types/file.js b/src/bids/types/file.ts similarity index 54% rename from src/bids/types/file.js rename to src/bids/types/file.ts index 7a4c83bb..8846813b 100644 --- a/src/bids/types/file.js +++ b/src/bids/types/file.ts @@ -5,44 +5,54 @@ */ import { BidsHedIssue } from './issues' +import { BidsValidator } from '../validator/validator' import { generateIssue } from '../../issues/issues' +import { HedSchemas } from '../../schema/containers' + +type BidsValidatorConstructor = { + new (file: BidsFile, schemas: HedSchemas): ValidatorClass +} /** * A BIDS file. */ -export class BidsFile { +export class BidsFile { /** * The name of this file. - * @type {string} */ - name + readonly name: string /** * The Object representing this file data. * This is used to generate {@link BidsHedIssue} objects. - * @type {Object} */ - file + readonly file: any /** * The validator class used to validate this file. - * @private */ - _validatorClass + private readonly _validatorClass: BidsValidatorConstructor - constructor(name, file, validatorClass) { + /** + * Constructor. + * + * @param name The name of this file. + * @param file The Object representing this file data. + * @param validatorClass The validator class used to validate this file. + */ + constructor(name: string, file: any, validatorClass: BidsValidatorConstructor) { this.name = name this.file = file this._validatorClass = validatorClass } /** - * Validate this validator's tsv file. + * Validate this validator's file. * - * @param {HedSchemas} schemas - The HED schemas used to validate this file. - * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file. + * @param schemas The HED schemas used to validate this file. + * @returns Any issues found during validation of this TSV file. */ - validate(schemas) { + validate(schemas: HedSchemas): BidsHedIssue[] { if (!this.hasHedData) { return [] } @@ -70,18 +80,18 @@ export class BidsFile { /** * Determine whether this file has any HED data. * - * @returns {boolean} + * @returns Whether this file has any HED data. */ - get hasHedData() { + get hasHedData(): boolean { return false } /** * The validator class used to validate this file. * - * @returns {function} The validator class used to validate this file. + * @returns The validator class used to validate this file. */ - get validatorClass() { + get validatorClass(): BidsValidatorConstructor { return this._validatorClass } } diff --git a/src/bids/types/issues.js b/src/bids/types/issues.js index baec8dfe..c56438bf 100644 --- a/src/bids/types/issues.js +++ b/src/bids/types/issues.js @@ -184,7 +184,7 @@ export class BidsHedIssue { * @param {object?} extraParameters Any extra parameters to inject into the {@link Issue} objects. * @returns {BidsHedIssue[]} An array of BIDS-compatible issues. */ - static fromHedIssues(hedIssues, file, extraParameters) { + static fromHedIssues(hedIssues, file, extraParameters = {}) { if (hedIssues.length === 0) { return [] } else if (hedIssues instanceof IssueError) { @@ -204,7 +204,7 @@ export class BidsHedIssue { * @param {object?} extraParameters Any extra parameters to inject into the {@link Issue} object. * @returns {BidsHedIssue} The BIDS-compatible issue. */ - static fromHedIssue(hedIssue, file, extraParameters) { + static fromHedIssue(hedIssue, file, extraParameters = {}) { Object.assign(hedIssue.parameters, extraParameters) hedIssue.generateMessage() return new BidsHedIssue(hedIssue, file) diff --git a/src/bids/types/tsv.js b/src/bids/types/tsv.js deleted file mode 100644 index 89ac1a6e..00000000 --- a/src/bids/types/tsv.js +++ /dev/null @@ -1,164 +0,0 @@ -/** - * This module contains classes for representing BIDS TSV files and their components. - * - * @module bids/types/tsv - */ -import isPlainObject from 'lodash/isPlainObject' - -import { BidsFile } from './file' -import { convertParsedTSVData, parseTSV } from '../tsvParser' -import { BidsSidecar } from './json' -import BidsHedTsvValidator from '../validator/tsvValidator' -import { IssueError } from '../../issues/issues' - -/** - * A BIDS TSV file. - */ -export class BidsTsvFile extends BidsFile { - /** - * This file's parsed TSV data. - * @type {Map} - */ - parsedTsv - - /** - * HED strings in the "HED" column of the TSV data. - * @type {string[]} - */ - hedColumnHedStrings - - /** - * The pseudo-sidecar object representing the merged sidecar data. - * @type {BidsSidecar} - */ - mergedSidecar - - constructor(name, file, tsvData, mergedDictionary = {}, defManager = null) { - super(name, file, BidsHedTsvValidator) - - if (typeof tsvData === 'string') { - this.parsedTsv = parseTSV(tsvData) - } else if (tsvData instanceof Map) { - this.parsedTsv = new Map(tsvData) - } else if (isPlainObject(tsvData)) { - this.parsedTsv = convertParsedTSVData(tsvData) - } else { - const msg = 'The tsvData was not a string, Map or plain object, so a BidsTsvFile could not be created.' - IssueError.generateAndThrow('internalError', { message: msg, filePath: file.path }) - } - - this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager) - this._parseHedColumn() - } - - /** - * Parse the HED column from the TSV data. - * @private - */ - _parseHedColumn() { - const hedColumn = this.parsedTsv.get('HED') - if (hedColumn === undefined) { - this.hedColumnHedStrings = [] - } else { - this.hedColumnHedStrings = hedColumn.map((hedCell) => (hedCell && hedCell !== 'n/a' ? hedCell : '')) - } - } - - /** - * Determine whether this file has any HED data. - * - * @returns {boolean} - */ - get hasHedData() { - return this.parsedTsv.has('HED') || this.mergedSidecar.hasHedData - } - - /** - * Whether this TSV file is a timeline file. - * - * @returns {boolean} - */ - get isTimelineFile() { - return this.parsedTsv.has('onset') - } -} - -/** - * An element in a BIDS TSV file. - */ -export class BidsTsvElement { - /** - * The string representation of this row - * @type {string} - */ - hedString - - /** - * The ParsedHedString representation of this row - * @type {import('../../parser/parsedHedString.js').ParsedHedString} - */ - parsedHedString - - /** - * The file this row belongs to (usually just the path). - * @type {Object} - */ - file - - /** - * The onset represented by this row or a NaN. - * @type {Number} - */ - onset - - /** - * The line number(s) (including the header) represented by this row. - * @type {string} - */ - tsvLine - - constructor(hedString, tsvFile, onset, tsvLine) { - this.hedString = hedString - this.parsedHedString = null - this.file = tsvFile.file - this.fileName = tsvFile.name - this.onset = onset - this.tsvLine = tsvLine - } - - /** - * Override of {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/toString | Object.prototype.toString}. - * - * @returns {string} The string representation of this element. - */ - toString() { - const onsetString = this.onset ? ` with onset=${this.onset.toString()}` : '' - return this.hedString + ` in TSV file "${this.fileName}" at line(s) ${this.tsvLine}` + onsetString - } - - /** - * Create a string list of a list of BidsTsvElement objects. - * @param {BidsTsvElement[]} elements - A list of elements to construct line numbers from. - * @returns {string} - A string with the list of line numbers for error messages. - */ - static getTsvLines(elements) { - return elements.map((element) => element.tsvLine).join(',') - } -} - -/** - * A row in a BIDS TSV file. - */ -export class BidsTsvRow extends BidsTsvElement { - /** - * The map of column name to value for this row. - * @type {Map} - */ - rowCells - - constructor(hedString, tsvFile, tsvLine, rowCells) { - const onset = rowCells.has('onset') ? rowCells.get('onset') : undefined - super(hedString, tsvFile, onset, tsvLine.toString()) - this.rowCells = rowCells - } -} diff --git a/src/bids/types/tsv.ts b/src/bids/types/tsv.ts new file mode 100644 index 00000000..17631ad9 --- /dev/null +++ b/src/bids/types/tsv.ts @@ -0,0 +1,195 @@ +/** + * This module contains classes for representing BIDS TSV files and their components. + * + * @module bids/types/tsv + */ +import isPlainObject from 'lodash/isPlainObject' + +import { BidsFile } from './file' +import { convertParsedTSVData, parseTSV, OldParsedTSV, ParsedTSV } from '../tsvParser' +import { BidsSidecar } from './json' +import BidsHedTsvValidator from '../validator/tsvValidator' +import { IssueError } from '../../issues/issues' +import { DefinitionManager } from '../../parser/definitionManager' +import ParsedHedString from '../../parser/parsedHedString' + +/** + * A BIDS TSV file. + */ +export class BidsTsvFile extends BidsFile { + /** + * This file's parsed TSV data. + */ + parsedTsv: ParsedTSV + + /** + * HED strings in the "HED" column of the TSV data. + */ + hedColumnHedStrings: string[] + + /** + * The pseudo-sidecar object representing the merged sidecar data. + */ + mergedSidecar: BidsSidecar + + /** + * Constructor. + * + * @param name The name of this file. + * @param file The Object representing this file data. + * @param tsvData This file's TSV data. + * @param mergedDictionary This file's merged JSON dictionary. + * @param defManager This file's definition manager. + */ + constructor( + name: string, + file: any, + tsvData: string | ParsedTSV | OldParsedTSV, + mergedDictionary: Record = {}, + defManager: DefinitionManager = null, + ) { + super(name, file, BidsHedTsvValidator) + + if (typeof tsvData === 'string') { + this.parsedTsv = parseTSV(tsvData) + } else if (tsvData instanceof Map) { + this.parsedTsv = new Map(tsvData) + } else if (isPlainObject(tsvData)) { + this.parsedTsv = convertParsedTSVData(tsvData) + } else { + const msg = 'The tsvData was not a string, Map or plain object, so a BidsTsvFile could not be created.' + IssueError.generateAndThrow('internalError', { message: msg, filePath: file.path }) + } + + this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager) + this._parseHedColumn() + } + + /** + * Parse the HED column from the TSV data. + */ + private _parseHedColumn(): void { + const hedColumn = this.parsedTsv.get('HED') + if (hedColumn === undefined) { + this.hedColumnHedStrings = [] + } else { + this.hedColumnHedStrings = hedColumn.map((hedCell) => (hedCell && hedCell !== 'n/a' ? hedCell : '')) + } + } + + /** + * Determine whether this file has any HED data. + * + * @returns Whether this file has any HED data. + */ + public get hasHedData(): boolean { + return this.parsedTsv.has('HED') || this.mergedSidecar.hasHedData + } + + /** + * Whether this TSV file is a timeline file. + * + * @returns Whether this TSV file is a timeline file. + */ + public get isTimelineFile(): boolean { + return this.parsedTsv.has('onset') + } +} + +/** + * An element in a BIDS TSV file. + */ +export class BidsTsvElement { + /** + * The string representation of this element. + */ + hedString: string + + /** + * The ParsedHedString representation of this element. + */ + parsedHedString: ParsedHedString | null + + /** + * The file this element belongs to (usually just the path). + */ + file: any + + /** + * The name of the file this element belongs to (usually just the path). + */ + fileName: string + + /** + * The onset represented by this element or a NaN. + * + * @todo This probably should be a number. Move numeric conversion to this file? + */ + onset: string + + /** + * The line number(s) (including the header) represented by this element. + */ + tsvLine: string + + /** + * Constructor. + * + * @param hedString The string representation of this element. + * @param tsvFile The file this element belongs to (usually just the path). + * @param onset The onset represented by this element or a NaN. + * @param tsvLine The line number(s) (including the header) represented by this element. + */ + constructor(hedString: string, tsvFile: BidsTsvFile, onset: string, tsvLine: string) { + this.hedString = hedString + this.parsedHedString = null + this.file = tsvFile.file + this.fileName = tsvFile.name + this.onset = onset + this.tsvLine = tsvLine + } + + /** + * Override of {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/toString | Object.prototype.toString}. + * + * @returns The string representation of this element. + */ + public toString(): string { + const onsetString = this.onset ? ` with onset=${this.onset}` : '' + return this.hedString + ` in TSV file "${this.fileName}" at line(s) ${this.tsvLine}` + onsetString + } + + /** + * Create a string list of a list of BidsTsvElement objects. + * + * @param elements A list of elements to construct line numbers from. + * @returns A string with the list of line numbers for error messages. + */ + public static getTsvLines(elements: BidsTsvElement[]): string { + return elements.map((element) => element.tsvLine).join(',') + } +} + +/** + * A row in a BIDS TSV file. + */ +export class BidsTsvRow extends BidsTsvElement { + /** + * The map of column name to value for this row. + */ + rowCells: Map + + /** + * Constructor. + * + * @param hedString The string representation of this row. + * @param tsvFile The file this row belongs to (usually just the path). + * @param tsvLine The line number (including the header) represented by this row. + * @param rowCells The map of column name to value for this row. + */ + constructor(hedString: string, tsvFile: BidsTsvFile, tsvLine: number, rowCells: Map) { + const onset = rowCells.get('onset') ?? '' + super(hedString, tsvFile, onset, tsvLine.toString()) + this.rowCells = rowCells + } +} From 1d9c16f1f275812f792bc426f3c3ccd307626f43 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Thu, 30 Oct 2025 02:04:58 -0500 Subject: [PATCH 43/63] Port BIDS issue module to TypeScript Also add visibility modifiers to BidsFile. I disabled a test related to the file field from Issue, as the port revealed that the field didn't exist on Issue (and thus the test was unsound). No code currently injects a file field into a HED Issue object. Whether that will change has been deferred. --- browser/src/validate_dataset.jsx | 6 +- browser/src/validate_file.jsx | 4 +- src/bids/types/file.ts | 18 ++-- src/bids/types/{issues.js => issues.ts} | 121 ++++++++++++------------ tests/otherTests/issues.spec.js | 2 +- 5 files changed, 75 insertions(+), 76 deletions(-) rename src/bids/types/{issues.js => issues.ts} (62%) diff --git a/browser/src/validate_dataset.jsx b/browser/src/validate_dataset.jsx index 41f7052d..012e3b01 100644 --- a/browser/src/validate_dataset.jsx +++ b/browser/src/validate_dataset.jsx @@ -3,9 +3,9 @@ import { createRoot } from 'react-dom/client' import { FolderInput } from './components/FolderInput' import { ErrorDisplay } from './components/ErrorDisplay' import { BidsWebAccessor } from './bids/BidsWebAccessor.js' -import { BidsDataset } from '@hed-javascript-root/src/bids/types/dataset.js' -import { IssueError } from '@hed-javascript-root/src/issues/issues.js' -import { BidsHedIssue } from '@hed-javascript-root/src/bids/types/issues.js' +import { BidsDataset } from '@hed-javascript-root/src/bids/types/dataset' +import { IssueError } from '@hed-javascript-root/src/issues/issues' +import { BidsHedIssue } from '@hed-javascript-root/src/bids/types/issues' // --- Add TailwindCSS to the document head for immediate styling --- ;(() => { diff --git a/browser/src/validate_file.jsx b/browser/src/validate_file.jsx index c0f630b5..fe544ee9 100644 --- a/browser/src/validate_file.jsx +++ b/browser/src/validate_file.jsx @@ -10,8 +10,8 @@ import { buildBidsSchemas, } from '@hed-javascript-root/src/bids/index.js' import { buildSchemasFromVersion } from './schema/init.js' -import { generateIssue, IssueError } from '@hed-javascript-root/src/issues/issues.js' -import parseTSV from '@hed-javascript-root/src/bids/tsvParser.js' +import { generateIssue, IssueError } from '@hed-javascript-root/src/issues/issues' +import parseTSV from '@hed-javascript-root/src/bids/tsvParser' // --- Main Application Component --- diff --git a/src/bids/types/file.ts b/src/bids/types/file.ts index 8846813b..e2cc5414 100644 --- a/src/bids/types/file.ts +++ b/src/bids/types/file.ts @@ -20,18 +20,18 @@ export class BidsFile { /** * The name of this file. */ - readonly name: string + public readonly name: string /** * The Object representing this file data. * This is used to generate {@link BidsHedIssue} objects. */ - readonly file: any + public readonly file: any /** * The validator class used to validate this file. */ - private readonly _validatorClass: BidsValidatorConstructor + readonly #validatorClass: BidsValidatorConstructor /** * Constructor. @@ -40,10 +40,10 @@ export class BidsFile { * @param file The Object representing this file data. * @param validatorClass The validator class used to validate this file. */ - constructor(name: string, file: any, validatorClass: BidsValidatorConstructor) { + protected constructor(name: string, file: any, validatorClass: BidsValidatorConstructor) { this.name = name this.file = file - this._validatorClass = validatorClass + this.#validatorClass = validatorClass } /** @@ -52,7 +52,7 @@ export class BidsFile { * @param schemas The HED schemas used to validate this file. * @returns Any issues found during validation of this TSV file. */ - validate(schemas: HedSchemas): BidsHedIssue[] { + public validate(schemas: HedSchemas): BidsHedIssue[] { if (!this.hasHedData) { return [] } @@ -82,7 +82,7 @@ export class BidsFile { * * @returns Whether this file has any HED data. */ - get hasHedData(): boolean { + public get hasHedData(): boolean { return false } @@ -91,7 +91,7 @@ export class BidsFile { * * @returns The validator class used to validate this file. */ - get validatorClass(): BidsValidatorConstructor { - return this._validatorClass + public get validatorClass(): BidsValidatorConstructor { + return this.#validatorClass } } diff --git a/src/bids/types/issues.js b/src/bids/types/issues.ts similarity index 62% rename from src/bids/types/issues.js rename to src/bids/types/issues.ts index c56438bf..6c9f1514 100644 --- a/src/bids/types/issues.js +++ b/src/bids/types/issues.ts @@ -2,11 +2,11 @@ * Provides a wrapper for HED validation issues that is compatible with the BIDS validator. * @module bids/types/issues */ -import { generateIssue, IssueError } from '../../issues/issues' -/** - * @typedef {import('../../issues/issues.ts').Issue} Issue - */ +import { generateIssue, Issue, IssueError } from '../../issues/issues' +import { IssueLevel } from '../../issues/data' + +type BidsIssueCode = 'HED_ERROR' | 'HED_WARNING' /** * A wrapper for a HED validation issue that is compatible with the BIDS validator. @@ -17,59 +17,51 @@ import { generateIssue, IssueError } from '../../issues/issues' export class BidsHedIssue { /** * The file associated with this issue. - * @type {object} */ - file + file: any /** * The underlying HED issue object. - * @type {Issue} */ - hedIssue + hedIssue: Issue /** * The BIDS-compliant issue code. - * @type {string} */ - code + code: BidsIssueCode /** * The HED-specific issue code. - * @type {string} */ - subCode + subCode: string /** * The severity of the issue (e.g., 'error' or 'warning'). - * @type {string} */ - severity + severity: IssueLevel /** * The human-readable issue message. - * @type {string} */ - issueMessage + issueMessage: string /** * The line number where the issue occurred. - * @type {number} */ - line + line: string /** * The path to the file where the issue occurred. - * @type {string} */ - location + location: string /** * Constructs a BidsHedIssue object. * - * @param {Issue} hedIssue The HED issue object to be wrapped. - * @param {object} file The file object associated with this issue. + * @param hedIssue The HED issue object to be wrapped. + * @param file The file object associated with this issue. */ - constructor(hedIssue, file) { + constructor(hedIssue: Issue, file: any) { this.hedIssue = hedIssue this.file = file @@ -89,11 +81,11 @@ export class BidsHedIssue { /** * Transforms a list of issues into a Map, keyed by severity level. * - * @param {BidsHedIssue[]} issues A list of BIDS HED issues. - * @returns {Map} A map where keys are severity levels and values are arrays of issues. + * @param issues A list of BIDS HED issues. + * @returns A map where keys are severity levels and values are arrays of issues. */ - static splitErrors(issues) { - const issueMap = new Map() + static splitErrors(issues: BidsHedIssue[]): Map { + const issueMap = new Map() for (const issue of issues) { if (!issueMap.has(issue.severity)) { issueMap.set(issue.severity, []) @@ -106,11 +98,11 @@ export class BidsHedIssue { /** * Categorizes a list of issues by their subCode values. * - * @param {BidsHedIssue[]} issues A list of BIDS HED issues. - * @returns {Map} A map where keys are HED issue codes and values are arrays of issues. + * @param issues A list of BIDS HED issues. + * @returns A map where keys are HED issue codes and values are arrays of issues. */ - static categorizeByCode(issues) { - const codeMap = new Map() + static categorizeByCode(issues: BidsHedIssue[]): Map { + const codeMap = new Map() for (const issue of issues) { if (!codeMap.has(issue.subCode)) { codeMap.set(issue.subCode, []) @@ -123,12 +115,12 @@ export class BidsHedIssue { /** * Reduces a list of issues to one of each subCode that occurred in the incoming list, summarizing the occurrences. * - * @param {BidsHedIssue[]} issues A list of BIDS HED issues. - * @returns {BidsHedIssue[]} A new list of issues with one issue of each type. + * @param issues A list of BIDS HED issues. + * @returns A new list of issues with one issue of each type. */ - static reduceIssues(issues) { + static reduceIssues(issues: BidsHedIssue[]): BidsHedIssue[] { const categorizedIssues = BidsHedIssue.categorizeByCode(issues) - const reducedIssues = [] + const reducedIssues: BidsHedIssue[] = [] for (const issueList of categorizedIssues.values()) { if (issueList.length === 0) { continue @@ -154,12 +146,16 @@ export class BidsHedIssue { * If `limitErrors` is true, the output will be reduced to one issue of each subCode type in the list. * The message of each "representative" issue will be updated to summarize the number of occurrences and files. * - * @param {BidsHedIssue[]} issues A list of BIDS HED issues. - * @param {boolean} checkWarnings Whether to include warnings in the output. - * @param {boolean} limitErrors Whether to reduce the list of issues to one of each type. - * @returns {BidsHedIssue[]} The processed list of issues. - */ - static processIssues(issues, checkWarnings = false, limitErrors = false) { + * @param issues A list of BIDS HED issues. + * @param checkWarnings Whether to include warnings in the output. + * @param limitErrors Whether to reduce the list of issues to one of each type. + * @returns The processed list of issues. + */ + static processIssues( + issues: BidsHedIssue[], + checkWarnings: boolean = false, + limitErrors: boolean = false, + ): BidsHedIssue[] { const issueMap = BidsHedIssue.splitErrors(issues) const errorIssues = issueMap.get('error') ?? [] const warningIssues = issueMap.get('warning') ?? [] @@ -179,18 +175,22 @@ export class BidsHedIssue { /** * Converts one or more HED issues into BIDS-compatible issues. * - * @param {Error|Issue[]} hedIssues One or more HED-format issues. - * @param {object} file A BIDS-format file object used to generate {@link BidsHedIssue} objects. - * @param {object?} extraParameters Any extra parameters to inject into the {@link Issue} objects. - * @returns {BidsHedIssue[]} An array of BIDS-compatible issues. - */ - static fromHedIssues(hedIssues, file, extraParameters = {}) { - if (hedIssues.length === 0) { - return [] - } else if (hedIssues instanceof IssueError) { + * @param hedIssues One or more HED-format issues. + * @param file A BIDS-format file object used to generate {@link BidsHedIssue} objects. + * @param extraParameters Any extra parameters to inject into the {@link Issue} objects. + * @returns An array of BIDS-compatible issues. + */ + static fromHedIssues( + hedIssues: Error | Issue[], + file: object, + extraParameters: Record = {}, + ): BidsHedIssue[] { + if (hedIssues instanceof IssueError) { return [BidsHedIssue.fromHedIssue(hedIssues.issue, file, extraParameters)] } else if (hedIssues instanceof Error) { return [new BidsHedIssue(generateIssue('internalError', { message: hedIssues.message }), file ?? null)] + } else if (hedIssues.length === 0) { + return [] } else { return hedIssues.map((hedIssue) => BidsHedIssue.fromHedIssue(hedIssue, file, extraParameters)) } @@ -199,12 +199,12 @@ export class BidsHedIssue { /** * Converts a single HED issue into a BIDS-compatible issue. * - * @param {Issue} hedIssue A HED-format issue. - * @param {object} file A BIDS-format file object used to generate a {@link BidsHedIssue} object. - * @param {object?} extraParameters Any extra parameters to inject into the {@link Issue} object. - * @returns {BidsHedIssue} The BIDS-compatible issue. + * @param hedIssue A HED-format issue. + * @param file A BIDS-format file object used to generate a {@link BidsHedIssue} object. + * @param extraParameters Any extra parameters to inject into the {@link Issue} object. + * @returns The BIDS-compatible issue. */ - static fromHedIssue(hedIssue, file, extraParameters = {}) { + static fromHedIssue(hedIssue: Issue, file: object, extraParameters: Record = {}): BidsHedIssue { Object.assign(hedIssue.parameters, extraParameters) hedIssue.generateMessage() return new BidsHedIssue(hedIssue, file) @@ -213,17 +213,16 @@ export class BidsHedIssue { /** * Transforms a list of mixed-format issues into BIDS-compatible issues. * - * @param {Array} issues A list of mixed-format issues. - * @param {object} file A BIDS-format file object used to generate {@link BidsHedIssue} objects. - * @returns {BidsHedIssue[]} An array of BIDS-compatible issues. + * @param issues A list of mixed-format issues. + * @param file A BIDS-format file object used to generate {@link BidsHedIssue} objects. + * @returns An array of BIDS-compatible issues. */ - static transformToBids(issues, file = null) { + static transformToBids(issues: Array, file: object = null): BidsHedIssue[] { return issues.map((issue) => { if (issue instanceof BidsHedIssue) { return issue } else if (issue instanceof IssueError) { - const issueFile = issue.issue.file || file - return BidsHedIssue.fromHedIssue(issue.issue, issueFile, issue.issue.parameters) + return BidsHedIssue.fromHedIssue(issue.issue, file, issue.issue.parameters) } else if (issue instanceof Error) { return new BidsHedIssue(generateIssue('internalError', { message: issue.message }), file) } else { diff --git a/tests/otherTests/issues.spec.js b/tests/otherTests/issues.spec.js index 9fddf50f..615bd6b6 100644 --- a/tests/otherTests/issues.spec.js +++ b/tests/otherTests/issues.spec.js @@ -20,7 +20,7 @@ describe('BidsHedIssue', () => { expect(result[0].file).toBe(testFile) }) - it('should use the file from IssueError if available', () => { + it.skip('should use the file from IssueError if available', () => { const issueFile = { path: '/test/issueFile.tsv' } const issue = generateIssue('genericError') issue.file = issueFile From 3b89e5986492e64c5f2991a166a9b890d293fafb Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Thu, 30 Oct 2025 03:40:51 -0500 Subject: [PATCH 44/63] Port BIDS validator classes and reorganize more issue code --- src/bids/types/file.ts | 11 +- src/bids/types/issues.ts | 60 ++++--- src/bids/types/json.js | 6 +- src/bids/types/tsv.ts | 50 +++--- ...idecarValidator.js => sidecarValidator.ts} | 61 +++---- .../{tsvValidator.js => tsvValidator.ts} | 152 ++++++++---------- src/bids/validator/validator.js | 40 ----- src/bids/validator/validator.ts | 43 +++++ src/issues/issues.ts | 71 ++++---- tests/jsonTestData/bidsTests.data.js | 18 ++- tests/otherTests/issueParameters.spec.js | 10 +- 11 files changed, 283 insertions(+), 239 deletions(-) rename src/bids/validator/{sidecarValidator.js => sidecarValidator.ts} (73%) rename src/bids/validator/{tsvValidator.js => tsvValidator.ts} (76%) delete mode 100644 src/bids/validator/validator.js create mode 100644 src/bids/validator/validator.ts diff --git a/src/bids/types/file.ts b/src/bids/types/file.ts index e2cc5414..4c2e3d18 100644 --- a/src/bids/types/file.ts +++ b/src/bids/types/file.ts @@ -16,7 +16,7 @@ type BidsValidatorConstructor = { /** * A BIDS file. */ -export class BidsFile { +export abstract class BidsFile { /** * The name of this file. */ @@ -46,6 +46,15 @@ export class BidsFile { this.#validatorClass = validatorClass } + /** + * Override of {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/toString | Object.prototype.toString}. + * + * @returns The file name. + */ + public toString(): string { + return this.name + } + /** * Validate this validator's file. * diff --git a/src/bids/types/issues.ts b/src/bids/types/issues.ts index 6c9f1514..374c7e3f 100644 --- a/src/bids/types/issues.ts +++ b/src/bids/types/issues.ts @@ -18,50 +18,52 @@ export class BidsHedIssue { /** * The file associated with this issue. */ - file: any + public readonly file: any /** * The underlying HED issue object. */ - hedIssue: Issue + public readonly hedIssue: Issue /** * The BIDS-compliant issue code. */ - code: BidsIssueCode + public readonly code: BidsIssueCode /** * The HED-specific issue code. */ - subCode: string + public readonly subCode: string /** * The severity of the issue (e.g., 'error' or 'warning'). */ - severity: IssueLevel + public readonly severity: IssueLevel /** * The human-readable issue message. */ - issueMessage: string + public issueMessage: string /** * The line number where the issue occurred. */ - line: string + public readonly line: string /** * The path to the file where the issue occurred. */ - location: string + public readonly location: string /** * Constructs a BidsHedIssue object. * + * @deprecated Direct use of this constructor is not recommended. Use {@link BidsHedIssue.fromHedIssues}. + * * @param hedIssue The HED issue object to be wrapped. * @param file The file object associated with this issue. */ - constructor(hedIssue: Issue, file: any) { + public constructor(hedIssue: Issue, file: any) { this.hedIssue = hedIssue this.file = file @@ -78,13 +80,22 @@ export class BidsHedIssue { this.location = file?.path } + /** + * Override of {@link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Object/toString | Object.prototype.toString}. + * + * @returns The issue message. + */ + public toString(): string { + return this.issueMessage + } + /** * Transforms a list of issues into a Map, keyed by severity level. * * @param issues A list of BIDS HED issues. * @returns A map where keys are severity levels and values are arrays of issues. */ - static splitErrors(issues: BidsHedIssue[]): Map { + public static splitErrors(issues: BidsHedIssue[]): Map { const issueMap = new Map() for (const issue of issues) { if (!issueMap.has(issue.severity)) { @@ -101,7 +112,7 @@ export class BidsHedIssue { * @param issues A list of BIDS HED issues. * @returns A map where keys are HED issue codes and values are arrays of issues. */ - static categorizeByCode(issues: BidsHedIssue[]): Map { + public static categorizeByCode(issues: BidsHedIssue[]): Map { const codeMap = new Map() for (const issue of issues) { if (!codeMap.has(issue.subCode)) { @@ -118,7 +129,7 @@ export class BidsHedIssue { * @param issues A list of BIDS HED issues. * @returns A new list of issues with one issue of each type. */ - static reduceIssues(issues: BidsHedIssue[]): BidsHedIssue[] { + public static reduceIssues(issues: BidsHedIssue[]): BidsHedIssue[] { const categorizedIssues = BidsHedIssue.categorizeByCode(issues) const reducedIssues: BidsHedIssue[] = [] for (const issueList of categorizedIssues.values()) { @@ -151,7 +162,7 @@ export class BidsHedIssue { * @param limitErrors Whether to reduce the list of issues to one of each type. * @returns The processed list of issues. */ - static processIssues( + public static processIssues( issues: BidsHedIssue[], checkWarnings: boolean = false, limitErrors: boolean = false, @@ -180,7 +191,7 @@ export class BidsHedIssue { * @param extraParameters Any extra parameters to inject into the {@link Issue} objects. * @returns An array of BIDS-compatible issues. */ - static fromHedIssues( + public static fromHedIssues( hedIssues: Error | Issue[], file: object, extraParameters: Record = {}, @@ -204,9 +215,8 @@ export class BidsHedIssue { * @param extraParameters Any extra parameters to inject into the {@link Issue} object. * @returns The BIDS-compatible issue. */ - static fromHedIssue(hedIssue: Issue, file: object, extraParameters: Record = {}): BidsHedIssue { - Object.assign(hedIssue.parameters, extraParameters) - hedIssue.generateMessage() + public static fromHedIssue(hedIssue: Issue, file: object, extraParameters: Record = {}): BidsHedIssue { + hedIssue.addParameters(extraParameters) return new BidsHedIssue(hedIssue, file) } @@ -217,7 +227,7 @@ export class BidsHedIssue { * @param file A BIDS-format file object used to generate {@link BidsHedIssue} objects. * @returns An array of BIDS-compatible issues. */ - static transformToBids(issues: Array, file: object = null): BidsHedIssue[] { + public static transformToBids(issues: Array, file: object = null): BidsHedIssue[] { return issues.map((issue) => { if (issue instanceof BidsHedIssue) { return issue @@ -230,4 +240,18 @@ export class BidsHedIssue { } }) } + + /** + * Add new parameters to the underlying HED issues of a list of BIDS issues and regenerate the issue messages. + * + * @param issues A list of BIDS-compatible issues. + * @param parameters The parameters to add. + */ + public static addIssueParameters(issues: BidsHedIssue[], parameters: Record): void { + for (const issue of issues) { + const hedIssue = issue.hedIssue + hedIssue.addParameters(parameters) + issue.issueMessage = hedIssue.message + } + } } diff --git a/src/bids/types/json.js b/src/bids/types/json.js index 02ccfd15..0afc6f6f 100644 --- a/src/bids/types/json.js +++ b/src/bids/types/json.js @@ -9,7 +9,7 @@ import { parseHedString } from '../../parser/parser' import ParsedHedString from '../../parser/parsedHedString' import { BidsFile } from './file' import BidsHedSidecarValidator from '../validator/sidecarValidator' -import { IssueError, updateIssueParameters } from '../../issues/issues' +import { IssueError, addIssueParameters } from '../../issues/issues' import { DefinitionManager, Definition } from '../../parser/definitionManager' const ILLEGAL_SIDECAR_KEYS = new Set(['hed', 'n/a']) @@ -145,8 +145,8 @@ export class BidsSidecar extends BidsJsonFile { fullValidation && !this.columnSpliceReferences.has(name), ) const updateParams = { sidecarKey: name, filePath: this.file?.path } - updateIssueParameters(errorIssues, updateParams) - updateIssueParameters(warningIssues, updateParams) + addIssueParameters(errorIssues, updateParams) + addIssueParameters(warningIssues, updateParams) errors.push(...errorIssues) warnings.push(...warningIssues) if (sidecarKey.isValueKey) { diff --git a/src/bids/types/tsv.ts b/src/bids/types/tsv.ts index 17631ad9..164bc081 100644 --- a/src/bids/types/tsv.ts +++ b/src/bids/types/tsv.ts @@ -20,17 +20,17 @@ export class BidsTsvFile extends BidsFile { /** * This file's parsed TSV data. */ - parsedTsv: ParsedTSV + public readonly parsedTsv: ParsedTSV /** * HED strings in the "HED" column of the TSV data. */ - hedColumnHedStrings: string[] + public readonly hedColumnHedStrings: string[] /** * The pseudo-sidecar object representing the merged sidecar data. */ - mergedSidecar: BidsSidecar + public readonly mergedSidecar: BidsSidecar /** * Constructor. @@ -50,30 +50,42 @@ export class BidsTsvFile extends BidsFile { ) { super(name, file, BidsHedTsvValidator) + this.parsedTsv = this._parseTsv(tsvData, file) + this.hedColumnHedStrings = this._parseHedColumn() + this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager) + } + + /** + * Parse the TSV file. + * + * @param tsvData This file's TSV data. + * @param file The Object representing this file data. + * @returns The parsed TSV data. + */ + private _parseTsv(tsvData: string | ParsedTSV | OldParsedTSV, file: any): ParsedTSV { if (typeof tsvData === 'string') { - this.parsedTsv = parseTSV(tsvData) + return parseTSV(tsvData) } else if (tsvData instanceof Map) { - this.parsedTsv = new Map(tsvData) + return new Map(tsvData) } else if (isPlainObject(tsvData)) { - this.parsedTsv = convertParsedTSVData(tsvData) + return convertParsedTSVData(tsvData) } else { const msg = 'The tsvData was not a string, Map or plain object, so a BidsTsvFile could not be created.' IssueError.generateAndThrow('internalError', { message: msg, filePath: file.path }) } - - this.mergedSidecar = new BidsSidecar(name, this.file, mergedDictionary, defManager) - this._parseHedColumn() } /** * Parse the HED column from the TSV data. + * + * @returns The parsed HED column. */ - private _parseHedColumn(): void { + private _parseHedColumn(): string[] { const hedColumn = this.parsedTsv.get('HED') if (hedColumn === undefined) { - this.hedColumnHedStrings = [] + return [] } else { - this.hedColumnHedStrings = hedColumn.map((hedCell) => (hedCell && hedCell !== 'n/a' ? hedCell : '')) + return hedColumn.map((hedCell) => (hedCell && hedCell !== 'n/a' ? hedCell : '')) } } @@ -103,34 +115,34 @@ export class BidsTsvElement { /** * The string representation of this element. */ - hedString: string + public readonly hedString: string /** * The ParsedHedString representation of this element. */ - parsedHedString: ParsedHedString | null + public parsedHedString: ParsedHedString | null /** * The file this element belongs to (usually just the path). */ - file: any + public readonly file: any /** * The name of the file this element belongs to (usually just the path). */ - fileName: string + public readonly fileName: string /** * The onset represented by this element or a NaN. * * @todo This probably should be a number. Move numeric conversion to this file? */ - onset: string + public readonly onset: string /** * The line number(s) (including the header) represented by this element. */ - tsvLine: string + public readonly tsvLine: string /** * Constructor. @@ -177,7 +189,7 @@ export class BidsTsvRow extends BidsTsvElement { /** * The map of column name to value for this row. */ - rowCells: Map + public readonly rowCells: Map /** * Constructor. diff --git a/src/bids/validator/sidecarValidator.js b/src/bids/validator/sidecarValidator.ts similarity index 73% rename from src/bids/validator/sidecarValidator.js rename to src/bids/validator/sidecarValidator.ts index d1f26910..55c8e391 100644 --- a/src/bids/validator/sidecarValidator.js +++ b/src/bids/validator/sidecarValidator.ts @@ -2,11 +2,13 @@ * @module bids/validator/sidecarValidator */ +import { BidsValidator } from './validator' import { BidsHedIssue } from '../types/issues' +import { BidsSidecar } from '../types/json' import ParsedHedString from '../../parser/parsedHedString' -import { generateIssue, IssueError, updateIssueParameters } from '../../issues/issues' +import { generateIssue, IssueError } from '../../issues/issues' +import { HedSchemas } from '../../schema/containers' import { getCharacterCount } from '../../utils/string' -import { BidsValidator } from './validator' /** * Validator for HED data in BIDS JSON sidecars. @@ -14,26 +16,24 @@ import { BidsValidator } from './validator' export class BidsHedSidecarValidator extends BidsValidator { /** * The BIDS sidecar being validated. - * @type {BidsSidecar} */ - sidecar + private readonly sidecar: BidsSidecar /** * Constructor for the BidsHedSidecarValidator. * - * @param {BidsSidecar} sidecar - The BIDS sidecar being validated. - * @param {HedSchemas} hedSchemas - The schemas used for the sidecar validation. + * @param sidecar The BIDS sidecar being validated. + * @param hedSchemas The schemas used for the sidecar validation. */ - constructor(sidecar, hedSchemas) { + public constructor(sidecar: BidsSidecar, hedSchemas: HedSchemas) { super(hedSchemas) this.sidecar = sidecar } /** * Validate a BIDS JSON sidecar file. Errors and warnings are stored. - * */ - validate() { + public validate(): void { // Allow schema to be set a validation time -- this is checked by the superclass of BIDS file const [errorIssues, warningIssues] = this.sidecar.parseSidecarKeys(this.hedSchemas, false) this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.sidecar.file)) @@ -56,10 +56,10 @@ export class BidsHedSidecarValidator extends BidsValidator { /** * Validate this sidecar's HED strings. * - * @returns {BidsHedIssue[]} All issues found. + * @returns All issues found. */ - _validateStrings() { - const issues = [] + private _validateStrings(): BidsHedIssue[] { + const issues: BidsHedIssue[] = [] for (const [sidecarKeyName, hedData] of this.sidecar.parsedHedData) { if (hedData instanceof ParsedHedString) { @@ -83,28 +83,26 @@ export class BidsHedSidecarValidator extends BidsValidator { /** * Check definitions and placeholders for a string associated with a sidecar key. * - * @param {string} sidecarKeyName - The name of the sidecar key associated with string to be checked. - * @param {ParsedHedString} hedString - The parsed string to be checked. - * @returns {BidsHedIssue[]} - Issues associated with the check. - * @private + * @param sidecarKeyName The name of the sidecar key associated with string to be checked. + * @param hedString The parsed string to be checked. + * @returns Issues associated with the check. */ - _checkDetails(sidecarKeyName, hedString) { + private _checkDetails(sidecarKeyName: string, hedString: ParsedHedString): BidsHedIssue[] { const issues = this._checkDefs(sidecarKeyName, hedString, true) issues.push(...this._checkPlaceholders(sidecarKeyName, hedString)) - updateIssueParameters(issues, { sidecarKey: sidecarKeyName, filePath: this.sidecar?.file?.path }) + BidsHedIssue.addIssueParameters(issues, { sidecarKey: sidecarKeyName, filePath: this.sidecar?.file?.path }) return issues } /** * Validate the Def and Def-expand usage against the sidecar definitions. * - * @param {string} sidecarKeyName - Name of the sidecar key for this HED string - * @param {ParsedHedString} hedString - The parsed HED string object associated with this key. - * @param {boolean} placeholdersAllowed - If true, placeholders are allowed here. - * @returns {BidsHedIssue[]} - Issues encountered such as missing definitions or improper Def-expand values. - * @private + * @param sidecarKeyName Name of the sidecar key for this HED string + * @param hedString The parsed HED string object associated with this key. + * @param placeholdersAllowed If true, placeholders are allowed here. + * @returns Issues encountered such as missing definitions or improper Def-expand values. */ - _checkDefs(sidecarKeyName, hedString, placeholdersAllowed) { + private _checkDefs(sidecarKeyName: string, hedString: ParsedHedString, placeholdersAllowed: boolean): BidsHedIssue[] { let issues = this.sidecar.definitions.validateDefs(hedString, this.hedSchemas, placeholdersAllowed) if (issues.length > 0) { return BidsHedIssue.fromHedIssues(issues, this.sidecar.file, { sidecarKey: sidecarKeyName }) @@ -113,7 +111,14 @@ export class BidsHedSidecarValidator extends BidsValidator { return BidsHedIssue.fromHedIssues(issues, this.sidecar.file, { sidecarKey: sidecarKeyName }) } - _checkPlaceholders(sidecarKeyName, hedString) { + /** + * Validate the placeholders. + * + * @param sidecarKeyName Name of the sidecar key for this HED string + * @param hedString The parsed HED string object associated with this key. + * @returns Issues encountered relating to invalid placeholders. + */ + private _checkPlaceholders(sidecarKeyName: string, hedString: ParsedHedString): BidsHedIssue[] { const numberPlaceholders = getCharacterCount(hedString.hedString, '#') const sidecarKey = this.sidecar.sidecarKeys.get(sidecarKeyName) if (!sidecarKey.valueString && !sidecarKey.hasDefinitions && numberPlaceholders > 0) { @@ -145,10 +150,10 @@ export class BidsHedSidecarValidator extends BidsValidator { /** * Validate this sidecar's curly braces -- checking recursion and missing columns. * - * @returns {BidsHedIssue[]} All issues found. + * @returns All issues found. */ - _validateCurlyBraces() { - const issues = [] + private _validateCurlyBraces(): BidsHedIssue[] { + const issues: BidsHedIssue[] = [] const references = this.sidecar.columnSpliceMapping for (const [key, referredKeys] of references) { diff --git a/src/bids/validator/tsvValidator.js b/src/bids/validator/tsvValidator.ts similarity index 76% rename from src/bids/validator/tsvValidator.js rename to src/bids/validator/tsvValidator.ts index ad9a861c..7ed76887 100644 --- a/src/bids/validator/tsvValidator.js +++ b/src/bids/validator/tsvValidator.ts @@ -2,7 +2,7 @@ * @module bids/validator/tsvValidator */ import { BidsHedIssue } from '../types/issues' -import { BidsTsvElement, BidsTsvRow } from '../types/tsv' +import { BidsTsvElement, BidsTsvFile, BidsTsvRow } from '../types/tsv' import { BidsValidator } from './validator' import { parseHedString, parseStandaloneString } from '../../parser/parser' import ParsedHedString from '../../parser/parsedHedString' @@ -10,6 +10,7 @@ import { generateIssue } from '../../issues/issues' import { ReservedChecker } from '../../parser/reservedChecker' import { cleanupEmpties, getTagListString } from '../../parser/parseUtils' import { EventManager } from '../../parser/eventManager' +import { HedSchemas } from '../../schema/containers' /** * Validator for HED data in BIDS TSV files. @@ -17,32 +18,30 @@ import { EventManager } from '../../parser/eventManager' export class BidsHedTsvValidator extends BidsValidator { /** * The BIDS TSV file being validated. - * @type {BidsTsvFile} */ - tsvFile + private readonly tsvFile: BidsTsvFile /** * The singleton instance of the checker for reserved requirements. - * @type {ReservedChecker} */ - reserved + private readonly reserved: ReservedChecker /** * Constructor. * - * @param {BidsTsvFile} tsvFile - The BIDS TSV file being validated. - * @param {HedSchemas} hedSchemas - The HED schemas used to validate the tsv file. + * @param tsvFile The BIDS TSV file being validated. + * @param hedSchemas The HED schemas used to validate the tsv file. */ - constructor(tsvFile, hedSchemas) { + public constructor(tsvFile: BidsTsvFile, hedSchemas: HedSchemas) { super(hedSchemas) this.tsvFile = tsvFile this.reserved = ReservedChecker.getInstance() } /** - * Validate a BIDS TSV file. This method returns the complete issue list for convenience. + * Validate a BIDS TSV file. */ - validate() { + public validate(): void { // Validate the BIDS sidecar if it exists and return if there are errors if (this.tsvFile.mergedSidecar) { const issues = this.tsvFile.mergedSidecar.validate(this.hedSchemas) @@ -67,7 +66,7 @@ export class BidsHedTsvValidator extends BidsValidator { if (this.errors.length > 0) { return } - this.validateDataset(bidsEvents) + this._validateDataset(bidsEvents) if (this.errors.length === 0 && this.tsvFile.mergedSidecar?.hasHedData) { this._checkMissingHedWarning() this._checkMissingValueWarnings() @@ -76,9 +75,8 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Check for a warning if the HED column is used as a splice but no HED column exists. - * @private */ - _checkMissingHedWarning() { + private _checkMissingHedWarning(): void { // Check for HED column used as splice but no HED column if (this.tsvFile.mergedSidecar.columnSpliceReferences.has('HED') && !this.tsvFile.parsedTsv.has('HED')) { this.warnings.push(BidsHedIssue.fromHedIssue(generateIssue('hedUsedAsSpliceButNoTsvHed', {}), this.tsvFile.file)) @@ -87,9 +85,8 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Check for categorical column value in tsv but not in sidecar. - * @private */ - _checkMissingValueWarnings() { + private _checkMissingValueWarnings(): void { for (const columnName of this.tsvFile.parsedTsv.keys()) { const sidecarColumn = this.tsvFile.mergedSidecar?.sidecarKeys.get(columnName) if (!sidecarColumn || sidecarColumn.isValueKey) { @@ -113,10 +110,8 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Validate this TSV file's HED column. - * - * @private */ - _validateHedColumn() { + private _validateHedColumn(): void { if (this.tsvFile.hedColumnHedStrings.length > 0) { this.tsvFile.hedColumnHedStrings.flatMap((hedString, rowIndexMinusTwo) => this._validateHedColumnString(hedString, rowIndexMinusTwo + 2), @@ -127,15 +122,14 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Validate a string in this TSV file's HED column. * - * @param {string} hedString - The string to be validated. - * @param {number} rowIndex - The index of this row in the TSV file. - * @private + * @param hedString The string to be validated. + * @param rowIndex The index of this row in the TSV file. */ - _validateHedColumnString(hedString, rowIndex) { + private _validateHedColumnString(hedString: string, rowIndex: number) { if (!hedString) { return } - const [parsedString, errorIssues, warningIssues] = parseStandaloneString( + const [, errorIssues, warningIssues] = parseStandaloneString( hedString, this.hedSchemas, this.tsvFile.mergedSidecar.definitions, @@ -147,8 +141,10 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Validate the HED data in a combined event TSV file/sidecar BIDS data collection. + * + * @param elements The elements representing the tsv file. */ - validateDataset(elements) { + private _validateDataset(elements: BidsTsvElement[]): void { // Final top-tag detection cannot be done until the strings are fully assembled and finalized. this._checkNoTopTags(elements) if (this.errors.length > 0) { @@ -166,10 +162,9 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Check the temporal relationships among events. * - * @param {BidsTsvElement[]} elements - The elements representing the tsv file. - * @private + * @param elements The elements representing the tsv file. */ - _validateTemporal(elements) { + private _validateTemporal(elements: BidsTsvElement[]): void { // Check basic temporal conflicts such as Offset before Onset, or temporal tags with same def at same time. const eventManager = new EventManager() const [eventList, temporalIssues] = eventManager.parseEvents(elements) @@ -191,11 +186,9 @@ export class BidsHedTsvValidator extends BidsValidator { * Duplicate onsets are relatively rare and duplicates for single rows are checked when a ParsedHedString is * constructed. * - * @param {BidsTsvElement[]} elements - The elements representing the tsv file. - * @returns {BidsHedIssue[]} - Errors in temporal relationships among events. - * @private + * @param elements The elements representing the tsv file. */ - _checkDuplicatesAcrossRows(elements) { + private _checkDuplicatesAcrossRows(elements: BidsTsvElement[]): void { const duplicateMap = this._getOnsetMap(elements) for (const elementList of duplicateMap.values()) { if (elementList.length === 1) { @@ -213,11 +206,10 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Get map of onsets to BidsTsvElements. * - * @param {BidsTsvElement[]} elements - The elements representing the tsv file. - * @returns {Map} - Map of onset value to a list of elements with that onset. - * @private + * @param elements The elements representing the tsv file. + * @returns Map of onset value to a list of elements with that onset. */ - _getOnsetMap(elements) { + private _getOnsetMap(elements: BidsTsvElement[]): Map { const onsetMap = new Map() for (const element of elements) { if (!element.hedString) { @@ -235,10 +227,9 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Top group tag requirements may not be satisfied until all splices have been done. * - * @param {BidsTsvElement[]} elements - The elements to be checked. - * @private + * @param elements The elements to be checked. */ - _checkNoTopTags(elements) { + private _checkNoTopTags(elements: BidsTsvElement[]): void { for (const element of elements) { const topTags = element.parsedHedString ? element.parsedHedString.topLevelTags : [] const badTags = topTags.filter((tag) => ReservedChecker.hasTopLevelTagGroupAttribute(tag)) @@ -257,9 +248,9 @@ export class BidsHedTsvValidator extends BidsValidator { /** * Verify that this non-temporal file does not contain any temporal tags. * - * @param {BidsTsvElement[]} elements - The elements representing a tsv file (with HED string parsed). + * @param elements The elements representing a tsv file (with HED string parsed). */ - _checkNoTime(elements) { + private _checkNoTime(elements: BidsTsvElement[]): void { for (const element of elements) { if (element.parsedHedString.tags.some((tag) => this.reserved.timelineTags.has(tag.schemaTag.name))) { this.errors.push( @@ -277,28 +268,26 @@ export class BidsHedTsvValidator extends BidsValidator { * Class that performs basic parsing and splicing. */ export class BidsHedTsvParser { - static nullSet = new Set([null, undefined, '', 'n/a']) - static braceRegEx = /\{([^{}]*?)\}/g + private static readonly nullSet = new Set([null, undefined, '', 'n/a']) + private static readonly braceRegEx = /\{([^{}]*?)\}/g /** * The BIDS TSV file being parsed. - * @type {BidsTsvFile} */ - tsvFile + private readonly tsvFile: BidsTsvFile /** * The HED schema collection being parsed against. - * @type {HedSchemas} */ - hedSchemas + private readonly hedSchemas: HedSchemas /** * Constructor. * - * @param {BidsTsvFile} tsvFile The BIDS TSV file being parsed. - * @param {HedSchemas} hedSchemas The HED schema collection being parsed against. + * @param tsvFile The BIDS TSV file being parsed. + * @param hedSchemas The HED schema collection being parsed against. */ - constructor(tsvFile, hedSchemas) { + constructor(tsvFile: BidsTsvFile, hedSchemas: HedSchemas) { this.tsvFile = tsvFile this.hedSchemas = hedSchemas } @@ -306,9 +295,9 @@ export class BidsHedTsvParser { /** * Combine the BIDS sidecar HED data into a BIDS TSV file's HED data. * - * @returns {Array} - Returns a two-element array [BidsTsvElement[], BidsHedIssue[], BidsHedIssue[]]. + * @returns The TSV rows, the list of errors, and the list of warnings. */ - parse() { + public parse(): [BidsTsvElement[], BidsHedIssue[], BidsHedIssue[]] { const tsvHedRows = this._generateHedRows() const tsvElements = this._parseHedRows(tsvHedRows) const [errors, warnings] = this._parseElementStrings(tsvElements) @@ -318,17 +307,17 @@ export class BidsHedTsvParser { /** * Parse element HED strings. * - * @param {BidsTsvElement[]} elements - The objects representing tsv rows with their parsed HEd strings. - * @returns {Array} - [BidsHedIssue[], BidsHedIssue[]] The errors and warnings resulting in creating the parsed HED strings. + * @param elements The objects representing tsv rows with their parsed HEd strings. + * @returns The errors and warnings resulting in creating the parsed HED strings. */ - _parseElementStrings(elements) { + private _parseElementStrings(elements: BidsTsvElement[]): [BidsHedIssue[], BidsHedIssue[]] { if (elements.length === 0) { return [[], []] } // Add the parsed HED strings to the elements and quite if there are serious errors - const errors = [] - const warnings = [] + const errors: BidsHedIssue[] = [] + const warnings: BidsHedIssue[] = [] for (const element of elements) { const [parsedHedString, errorIssues, warningIssues] = parseHedString( element.hedString, @@ -347,15 +336,14 @@ export class BidsHedTsvParser { /** * Generate a list of rows with column-to-value mappings. * - * @returns {Array} A list of single-row column-to-value mappings. - * @private + * @returns A list of single-row column-to-value mappings. */ - _generateHedRows() { + private _generateHedRows(): Map[] { const tsvHedColumns = Array.from(this.tsvFile.parsedTsv.entries()).filter( ([header]) => this.tsvFile.mergedSidecar.hedData.has(header) || header === 'HED' || header === 'onset', ) - const tsvHedRows = [] + const tsvHedRows: Map[] = [] for (const [header, data] of tsvHedColumns) { data.forEach((value, index) => { tsvHedRows[index] ??= new Map() @@ -368,12 +356,11 @@ export class BidsHedTsvParser { /** * Parse the rows in the TSV file into HED strings. * - * @param {Map[]} tsvHedRows - A list of single-row column-to-value mappings. - * @returns {BidsTsvRow[]} - A list of row-based parsed HED strings. - * @private + * @param tsvHedRows A list of single-row column-to-value mappings. + * @returns A list of row-based parsed HED strings. */ - _parseHedRows(tsvHedRows) { - const hedRows = [] + private _parseHedRows(tsvHedRows: Map[]): BidsTsvRow[] { + const hedRows: BidsTsvRow[] = [] tsvHedRows.forEach((row, index) => { const hedRow = this._parseHedRow(row, index + 2) if (hedRow !== null) { @@ -386,15 +373,14 @@ export class BidsHedTsvParser { /** * Parse a row in a TSV file into a BIDS row. * - * @param {Map} rowCells - The column-to-value mapping for a single row. - * @param {number} tsvLine - The index of this row in the TSV file. - * @returns {BidsTsvRow} - A parsed HED string. - * @private + * @param rowCells The column-to-value mapping for a single row. + * @param tsvLine The index of this row in the TSV file. + * @returns A parsed HED string. */ - _parseHedRow(rowCells, tsvLine) { - const hedStringParts = [] + private _parseHedRow(rowCells: Map, tsvLine: number): BidsTsvRow { + const hedStringParts: string[] = [] const columnMap = this._getColumnMapping(rowCells) - this.spliceValues(columnMap) + this._spliceValues(columnMap) for (const [columnName, columnValue] of rowCells.entries()) { // If a splice, it can't be used in an assembled HED string. @@ -418,12 +404,11 @@ export class BidsHedTsvParser { /** * Generate a mapping from tsv columns to strings (may have splices in the strings) * - * @param {Map} rowCells - The column-to-value mapping for a single row. - * @returns {Map} - A mapping of column names to their corresponding parsed sidecar strings. - * @private + * @param rowCells The column-to-value mapping for a single row. + * @returns A mapping of column names to their corresponding parsed sidecar strings. */ - _getColumnMapping(rowCells) { - const columnMap = new Map() + private _getColumnMapping(rowCells: Map): Map { + const columnMap = new Map() if (rowCells.has('HED')) { columnMap.set('HED', rowCells.get('HED')) @@ -459,11 +444,11 @@ export class BidsHedTsvParser { /** * Update the map to splice-in the values for columns that have splices. * - * @param {Map} columnMap - Map of column name to HED string for a row. + * @param columnMap Map of column name to HED string for a row. * * Note: Updates the map in place. */ - spliceValues(columnMap) { + private _spliceValues(columnMap: Map) { if (!(this.tsvFile.mergedSidecar?.columnSpliceMapping?.size > 0)) { return } @@ -483,12 +468,11 @@ export class BidsHedTsvParser { /** * Replace a HED string containing slices with a resolved version for the column value in a row. * - * @param {string} unspliced - A HED string possibly with unresolved splices. - * @param {Map} columnMap - The map of column name to HED string for a row. - * @returns {string} - The fully resolved HED string with no splices. - * @private + * @param unspliced A HED string possibly with unresolved splices. + * @param columnMap The map of column name to HED string for a row. + * @returns The fully resolved HED string with no splices. */ - _replaceSplices(unspliced, columnMap) { + private _replaceSplices(unspliced: string, columnMap: Map): string { const result = unspliced.replace(BidsHedTsvParser.braceRegEx, (match, content) => { // Resolve the replacement value const resolved = columnMap.has(content) ? columnMap.get(content) : '' diff --git a/src/bids/validator/validator.js b/src/bids/validator/validator.js deleted file mode 100644 index b1a5dcbc..00000000 --- a/src/bids/validator/validator.js +++ /dev/null @@ -1,40 +0,0 @@ -/** - * Validator base class for HED data in BIDS TSV files. - * @abstract bids/validator/validator - */ -export class BidsValidator { - /** - * The HED schema collection being validated against. - * @type {HedSchemas} - */ - hedSchemas - - /** - * The issues found during validation. - * @type {BidsHedIssue[]} - */ - errors - - /** - * The warnings found during validation. - * @type {BidsHedIssue[]} - */ - warnings - - /** - * Constructor. - * - * @param {HedSchemas} hedSchemas - The HED schemas used for validation. - */ - constructor(hedSchemas) { - this.hedSchemas = hedSchemas // Will be set when the file is validated - this.errors = [] - this.warnings = [] - } - - /** - * Validate a BIDS file. Overridden by particular types of BIDS files. - * @abstract - */ - validate() {} -} diff --git a/src/bids/validator/validator.ts b/src/bids/validator/validator.ts new file mode 100644 index 00000000..794187d7 --- /dev/null +++ b/src/bids/validator/validator.ts @@ -0,0 +1,43 @@ +/** + * Validator base class for HED data in BIDS TSV files. + * @module bids/validator/validator + */ + +import { BidsHedIssue } from '../types/issues' +import { HedSchemas } from '../../schema/containers' + +/** + * Validator base class for HED data in BIDS TSV files. + */ +export abstract class BidsValidator { + /** + * The HED schema collection being validated against. + */ + hedSchemas: HedSchemas + + /** + * The errors found during validation. + */ + errors: BidsHedIssue[] + + /** + * The warnings found during validation. + */ + warnings: BidsHedIssue[] + + /** + * Constructor. + * + * @param hedSchemas The HED schemas used for validation. + */ + protected constructor(hedSchemas: HedSchemas) { + this.hedSchemas = hedSchemas + this.errors = [] + this.warnings = [] + } + + /** + * Validate a BIDS file. Overridden by particular types of BIDS files. + */ + public abstract validate(): void +} diff --git a/src/issues/issues.ts b/src/issues/issues.ts index a2b9eb66..55f69e62 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -68,22 +68,17 @@ export class Issue { /** * The internal error code. */ - internalCode: string + public readonly internalCode: string /** * The HED 3 error code. */ - hedCode: string + public readonly hedCode: string /** * The issue level (error or warning). */ - level: IssueLevel - - /** - * The detailed error message. - */ - message: string + public readonly level: IssueLevel /** * The bounds of this issue. @@ -108,7 +103,6 @@ export class Issue { this.hedCode = hedCode this.level = level this.parameters = parameters - this.generateMessage() } /** @@ -121,15 +115,17 @@ export class Issue { } /** - * (Re-)generate the issue message. + * Generate the detailed error message. + * + * @returns This issue's message. */ - public generateMessage(): void { + public get message(): string { this.parameters = this._parameters const baseMessage = this._parseMessageTemplate() const specialParameterMessages = this._parseSpecialParameters() const hedSpecLink = this._generateHedSpecificationLink() - this.message = `${this.level.toUpperCase()}: [${this.hedCode}] ${baseMessage} ${specialParameterMessages} (${hedSpecLink}.)` + return `${this.level.toUpperCase()}: [${this.hedCode}] ${baseMessage} ${specialParameterMessages} (${hedSpecLink}.)` } /** @@ -182,13 +178,26 @@ export class Issue { } /** - * Set a new parameter value. + * Determine whether this issue has a given parameter. + * + * @param name The parameter name to check. + * @returns Whether this issue already has a parameter by that name. + */ + public hasParameter(name: string): boolean { + if (name === 'bounds') { + return this._bounds !== undefined + } + return Object.hasOwn(this._parameters, name) + } + + /** + * Add a new parameter value. * * @param name The parameter name. * @param value The new parameter value. */ - public setParameter(name: string, value: any): void { - if (Object.hasOwn(this._parameters, name)) { + public addParameter(name: string, value: any): void { + if (this.hasParameter(name)) { return } if (name === 'bounds') { @@ -196,7 +205,17 @@ export class Issue { return } this._parameters[name] = String(value) - this.generateMessage() + } + + /** + * Add multiple parameters for this Issue. + * + * @param parameters The new values of the parameters. + */ + public addParameters(parameters: Record): void { + for (const [key, value] of Object.entries(parameters)) { + this.addParameter(key, value) + } } /** @@ -270,26 +289,12 @@ export function generateIssue(internalCode: string, parameters: Record, parameters: Record) { +export function addIssueParameters(issues: Array, parameters: Record) { for (const thisIssue of issues) { if (thisIssue instanceof IssueError) { - _updateIssueParameters(thisIssue.issue, parameters) + thisIssue.issue.addParameters(parameters) } else if (thisIssue instanceof Issue) { - _updateIssueParameters(thisIssue, parameters) + thisIssue.addParameters(parameters) } } } - -/** - * Update the parameters for an Issue. - * - * Note: the issue is modified in place. - * - * @param issue The issue to be updated. - * @param parameters The parameters to add. - */ -function _updateIssueParameters(issue: Issue, parameters: Record) { - for (const [key, value] of Object.entries(parameters)) { - issue.setParameter(key, value) - } -} diff --git a/tests/jsonTestData/bidsTests.data.js b/tests/jsonTestData/bidsTests.data.js index 130dda91..b47f85be 100644 --- a/tests/jsonTestData/bidsTests.data.js +++ b/tests/jsonTestData/bidsTests.data.js @@ -1303,7 +1303,7 @@ export const bidsTestData = [ eventsString: 'onset\tduration\tvehicle\tspeed\n' + '19\t6\ttrain\t5\n', sidecarErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingPlaceholder', { string: 'Blue,Speed', sidecarKey: 'speed' }), + generateIssue('missingPlaceholder', { string: 'Blue,Speed', sidecarKey: 'speed', filePath: 'invalid-no-placeholder-value-column.json' }), { path: 'invalid-no-placeholder-value-column.json', }, @@ -1312,7 +1312,7 @@ export const bidsTestData = [ tsvErrors: [], comboErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingPlaceholder', { string: 'Blue,Speed', sidecarKey: 'speed' }), + generateIssue('missingPlaceholder', { string: 'Blue,Speed', sidecarKey: 'speed', filePath: 'invalid-no-placeholder-value-column.tsv' }), { path: 'invalid-no-placeholder-value-column.tsv', }, @@ -1332,7 +1332,7 @@ export const bidsTestData = [ eventsString: 'onset\tduration\tvehicle\tspeed\n' + '19\t6\ttrain\t5\n', sidecarErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('invalidSidecarPlaceholder', { sidecarKey: 'speed', string: 'Label/#, Speed/# mph' }), + generateIssue('invalidSidecarPlaceholder', { sidecarKey: 'speed', string: 'Label/#, Speed/# mph', filePath: 'invalid-multiple-placeholders-in-value-column.json' }), { path: 'invalid-multiple-placeholders-in-value-column.json', }, @@ -1341,7 +1341,7 @@ export const bidsTestData = [ tsvErrors: [], comboErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('invalidSidecarPlaceholder', { sidecarKey: 'speed', string: 'Label/#, Speed/# mph' }), + generateIssue('invalidSidecarPlaceholder', { sidecarKey: 'speed', string: 'Label/#, Speed/# mph', filePath: 'invalid-multiple-placeholders-in-value-column.tsv' }), { path: 'invalid-multiple-placeholders-in-value-column.tsv', }, @@ -1524,6 +1524,7 @@ export const bidsTestData = [ contents: '', defContents: '(Acceleration/4.5 m-per-s^2,Red)', sidecarKey: 'speed', + filePath: 'invalid-def-expand-no-group.json', }), { path: 'invalid-def-expand-no-group.json', @@ -1537,6 +1538,7 @@ export const bidsTestData = [ contents: '', defContents: '(Acceleration/4.5 m-per-s^2,Red)', sidecarKey: 'speed', + filePath: 'invalid-def-expand-no-group.tsv', }), { path: 'invalid-def-expand-no-group.tsv', @@ -1557,7 +1559,7 @@ export const bidsTestData = [ eventsString: 'onset\tduration\tspeed\n' + '19\t6\t5\n', sidecarErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingDefinitionForDef', { definition: 'missingdef', sidecarKey: 'speed' }), + generateIssue('missingDefinitionForDef', { definition: 'missingdef', sidecarKey: 'speed', filePath: 'invalid-missing-definition-for-def.json' }), { path: 'invalid-missing-definition-for-def.json', }, @@ -1566,7 +1568,7 @@ export const bidsTestData = [ tsvErrors: [], comboErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingDefinitionForDef', { definition: 'missingdef', sidecarKey: 'speed' }), + generateIssue('missingDefinitionForDef', { definition: 'missingdef', sidecarKey: 'speed', filePath: 'invalid-missing-definition-for-def.tsv' }), { path: 'invalid-missing-definition-for-def.tsv', }, @@ -1586,7 +1588,7 @@ export const bidsTestData = [ eventsString: 'onset\tduration\tspeed\n' + '19\t6\t5\n', sidecarErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingDefinitionForDefExpand', { definition: 'missingdefexpand', sidecarKey: 'speed' }), + generateIssue('missingDefinitionForDefExpand', { definition: 'missingdefexpand', sidecarKey: 'speed', filePath: 'invalid-missing-definition-for-def-expand.json' }), { path: 'invalid-missing-definition-for-def-expand.json', }, @@ -1595,7 +1597,7 @@ export const bidsTestData = [ tsvErrors: [], comboErrors: [ BidsHedIssue.fromHedIssue( - generateIssue('missingDefinitionForDefExpand', { definition: 'missingdefexpand', sidecarKey: 'speed' }), + generateIssue('missingDefinitionForDefExpand', { definition: 'missingdefexpand', sidecarKey: 'speed', filePath: 'invalid-missing-definition-for-def-expand.tsv' }), { path: 'invalid-missing-definition-for-def-expand.tsv', }, diff --git a/tests/otherTests/issueParameters.spec.js b/tests/otherTests/issueParameters.spec.js index bb89a7c5..249a8e7c 100644 --- a/tests/otherTests/issueParameters.spec.js +++ b/tests/otherTests/issueParameters.spec.js @@ -1,6 +1,6 @@ import { describe, test } from '@jest/globals' import { BidsSidecar } from '../../src/bids/types/json' -import { IssueError, generateIssue, updateIssueParameters } from '../../src/issues/issues' +import { IssueError, generateIssue, addIssueParameters } from '../../src/issues/issues' describe('Issue Parameters Tests', () => { // Common test data @@ -456,7 +456,7 @@ describe('Issue Parameters Tests', () => { parameterB: 'valueB', } - updateIssueParameters(issues, newParameters) + addIssueParameters(issues, newParameters) expect(issue1.issue.parameters).toHaveProperty('parameter1', 'value1') expect(issue1.issue.parameters).toHaveProperty('parameter2', 'value2') @@ -478,7 +478,7 @@ describe('Issue Parameters Tests', () => { parameter2: 'value2', } - updateIssueParameters(issues, newParameters) + addIssueParameters(issues, newParameters) expect(issue.issue.parameters).toHaveProperty('parameter1', 'originalValue') expect(issue.issue.parameters).toHaveProperty('parameter2', 'value2') @@ -488,7 +488,7 @@ describe('Issue Parameters Tests', () => { const issues = [] const newParameters = { parameter1: 'value1' } - expect(() => updateIssueParameters(issues, newParameters)).not.toThrow() + expect(() => addIssueParameters(issues, newParameters)).not.toThrow() }) test('should handle an empty parameters object', () => { @@ -498,7 +498,7 @@ describe('Issue Parameters Tests', () => { const newParameters = {} - updateIssueParameters(issues, newParameters) + addIssueParameters(issues, newParameters) expect(issue.issue.parameters).toEqual(originalParameters) }) From 54f186261efc6ab0ec3304e635e676f52bb2f0d2 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 31 Oct 2025 21:27:53 -0500 Subject: [PATCH 45/63] Simplify code based on suggestions --- src/bids/types/file.ts | 12 ++++++------ src/bids/types/issues.ts | 2 +- src/bids/types/tsv.ts | 2 +- src/bids/validator/tsvValidator.ts | 3 --- src/issues/issues.ts | 1 - 5 files changed, 8 insertions(+), 12 deletions(-) diff --git a/src/bids/types/file.ts b/src/bids/types/file.ts index 4c2e3d18..5601cfbd 100644 --- a/src/bids/types/file.ts +++ b/src/bids/types/file.ts @@ -9,14 +9,14 @@ import { BidsValidator } from '../validator/validator' import { generateIssue } from '../../issues/issues' import { HedSchemas } from '../../schema/containers' -type BidsValidatorConstructor = { - new (file: BidsFile, schemas: HedSchemas): ValidatorClass +type BidsValidatorConstructor = { + new (file: BidsFile, schemas: HedSchemas): BidsValidator } /** * A BIDS file. */ -export abstract class BidsFile { +export abstract class BidsFile { /** * The name of this file. */ @@ -31,7 +31,7 @@ export abstract class BidsFile { /** * The validator class used to validate this file. */ - readonly #validatorClass: BidsValidatorConstructor + readonly #validatorClass: BidsValidatorConstructor /** * Constructor. @@ -40,7 +40,7 @@ export abstract class BidsFile { * @param file The Object representing this file data. * @param validatorClass The validator class used to validate this file. */ - protected constructor(name: string, file: any, validatorClass: BidsValidatorConstructor) { + protected constructor(name: string, file: any, validatorClass: BidsValidatorConstructor) { this.name = name this.file = file this.#validatorClass = validatorClass @@ -100,7 +100,7 @@ export abstract class BidsFile { * * @returns The validator class used to validate this file. */ - public get validatorClass(): BidsValidatorConstructor { + public get validatorClass(): BidsValidatorConstructor { return this.#validatorClass } } diff --git a/src/bids/types/issues.ts b/src/bids/types/issues.ts index 374c7e3f..83655900 100644 --- a/src/bids/types/issues.ts +++ b/src/bids/types/issues.ts @@ -232,7 +232,7 @@ export class BidsHedIssue { if (issue instanceof BidsHedIssue) { return issue } else if (issue instanceof IssueError) { - return BidsHedIssue.fromHedIssue(issue.issue, file, issue.issue.parameters) + return BidsHedIssue.fromHedIssue(issue.issue, file) } else if (issue instanceof Error) { return new BidsHedIssue(generateIssue('internalError', { message: issue.message }), file) } else { diff --git a/src/bids/types/tsv.ts b/src/bids/types/tsv.ts index 164bc081..14fd5067 100644 --- a/src/bids/types/tsv.ts +++ b/src/bids/types/tsv.ts @@ -16,7 +16,7 @@ import ParsedHedString from '../../parser/parsedHedString' /** * A BIDS TSV file. */ -export class BidsTsvFile extends BidsFile { +export class BidsTsvFile extends BidsFile { /** * This file's parsed TSV data. */ diff --git a/src/bids/validator/tsvValidator.ts b/src/bids/validator/tsvValidator.ts index 7ed76887..bcbe6694 100644 --- a/src/bids/validator/tsvValidator.ts +++ b/src/bids/validator/tsvValidator.ts @@ -449,9 +449,6 @@ export class BidsHedTsvParser { * Note: Updates the map in place. */ private _spliceValues(columnMap: Map) { - if (!(this.tsvFile.mergedSidecar?.columnSpliceMapping?.size > 0)) { - return - } // Only iterate over the column names that have splices for (const column of this.tsvFile.mergedSidecar.columnSpliceMapping.keys()) { // if (!columnMap.has(column)) { diff --git a/src/issues/issues.ts b/src/issues/issues.ts index 55f69e62..43bc4ce4 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -120,7 +120,6 @@ export class Issue { * @returns This issue's message. */ public get message(): string { - this.parameters = this._parameters const baseMessage = this._parseMessageTemplate() const specialParameterMessages = this._parseSpecialParameters() const hedSpecLink = this._generateHedSpecificationLink() From 681eabe754f5cfadbe62ee0d5a1754a7e8c93f93 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Tue, 4 Nov 2025 09:31:31 -0600 Subject: [PATCH 46/63] Port BIDS dataset to TypeScript Also fix issue parameter types. --- src/bids/schema.ts | 4 +- src/bids/types/{dataset.js => dataset.ts} | 123 ++++++++++------------ src/bids/types/file.ts | 4 +- src/bids/types/issues.ts | 16 +-- src/bids/types/tsv.ts | 6 +- src/bids/validator/sidecarValidator.ts | 4 +- src/bids/validator/tsvValidator.ts | 4 +- src/bids/validator/validator.ts | 2 +- src/issues/data.ts | 2 +- src/issues/issues.ts | 49 +++++---- src/schema/containers.ts | 4 +- src/schema/entries.ts | 2 +- src/schema/init.ts | 2 +- src/schema/loader.ts | 13 ++- src/schema/parser.ts | 2 +- src/schema/schemaMerger.ts | 4 +- src/utils/array.ts | 9 ++ src/utils/paths.ts | 5 +- src/utils/xml.ts | 2 +- tests/otherTests/dataset.spec.js | 4 +- 20 files changed, 125 insertions(+), 136 deletions(-) rename src/bids/types/{dataset.js => dataset.ts} (75%) diff --git a/src/bids/schema.ts b/src/bids/schema.ts index d39bb26f..47633bd3 100644 --- a/src/bids/schema.ts +++ b/src/bids/schema.ts @@ -4,10 +4,10 @@ * @module bids/schema */ -import { HedSchemas } from '../schema/containers' +import { type HedSchemas } from '../schema/containers' import { buildSchemas } from '../schema/init' import { SchemasSpec } from '../schema/specs' -import { BidsJsonFile } from './types/json' +import { type BidsJsonFile } from './types/json' /** * Build a HED schema collection based on the defined BIDS schemas. diff --git a/src/bids/types/dataset.js b/src/bids/types/dataset.ts similarity index 75% rename from src/bids/types/dataset.js rename to src/bids/types/dataset.ts index 1df31e06..ecad091d 100644 --- a/src/bids/types/dataset.js +++ b/src/bids/types/dataset.ts @@ -2,13 +2,20 @@ * This module contains the {@link BidsDataset} class, which represents a BIDS dataset for HED validation. * @module bids/types/dataset */ + +import path from 'node:path' + import { BidsFileAccessor } from '../datasetParser' import { BidsSidecar } from './json' import { BidsTsvFile } from './tsv' import { generateIssue, IssueError } from '../../issues/issues' import { getMergedSidecarData, organizedPathsGenerator } from '../../utils/paths' import { BidsHedIssue } from './issues' -import path from 'node:path' +import { type HedSchemas } from '../../schema/containers' + +type BidsFileAccessorConstructor = { + create(datasetRootDirectory: string | object): Promise +} /** * A BIDS dataset. @@ -49,40 +56,34 @@ export class BidsDataset { /** * Map of BIDS sidecar files that contain HED annotations. * The keys are relative paths and the values are BidsSidecar objects. - * @type {Map} */ - sidecarMap + public sidecarMap: Map /** * The dataset's root directory as an absolute path (Node.js context). - * @type {string|null} */ - datasetRootDirectory + public readonly datasetRootDirectory: string | null /** * The HED schemas used to validate this dataset. - * @type {HedSchemas} */ - hedSchemas + private hedSchemas: HedSchemas /** * The BIDS file accessor. - * @type {BidsFileAccessor} - * @public */ - fileAccessor + public fileAccessor: BidsFileAccessor /** * Constructor for a BIDS dataset. * - * @param {BidsFileAccessor} accessor An instance of BidsFileAccessor (or its subclasses). - * @throws {Error} If accessor is not an instance of BidsFileAccessor. - * @private + * @param accessor An instance of BidsFileAccessor (or its subclasses). + * @throws {IssueError} If accessor is not an instance of BidsFileAccessor. * @see BidsDataset.create */ - constructor(accessor) { + private constructor(accessor: BidsFileAccessor) { if (!(accessor instanceof BidsFileAccessor)) { - throw new Error('BidsDataset constructor requires an instance of BidsFileAccessor.\n') + IssueError.generateAndThrowInternalError('BidsDataset constructor requires an instance of BidsFileAccessor') } this.fileAccessor = accessor this.datasetRootDirectory = accessor.datasetRootDirectory // Set from fileAccessor @@ -97,34 +98,25 @@ export class BidsDataset { * Note: This method will fail to create a BidsDataset if a valid HED schema cannot be loaded or any of the * JSON sidecars cannot be loaded. It does not perform HED validation. * - * @param {string | object} rootOrFiles The root directory of the dataset or a file-like object. - * @param {function} fileAccessorClass The BidsFileAccessor class to use for accessing files. - * @returns {Promise<[BidsDataset|null, BidsHedIssue[]]>} A Promise that resolves to a two-element array containing the BidsDataset instance (or null if creation failed) and an array of issues. - * + * @param rootOrFiles The root directory of the dataset or a file-like object. + * @param fileAccessorClass The BidsFileAccessor class to use for accessing files. + * @returns A Promise that resolves to a two-element array containing the BidsDataset instance (or null if creation failed) and an array of issues. */ - static async create(rootOrFiles, fileAccessorClass) { + static async create( + rootOrFiles: string | object, + fileAccessorClass: BidsFileAccessorConstructor, + ): Promise<[BidsDataset | null, BidsHedIssue[]]> { let dataset = null - const issues = [] + const issues: BidsHedIssue[] = [] try { const accessor = await fileAccessorClass.create(rootOrFiles) dataset = new BidsDataset(accessor) const schemaIssues = await dataset.setHedSchemas() issues.push(...schemaIssues) - if (dataset.hedSchemas === null) { - return [null, issues] - } const sidecarIssues = await dataset.setSidecars() issues.push(...sidecarIssues) } catch (error) { - if (error instanceof IssueError) { - issues.push(error.issue) - } else { - issues.push({ - code: 'INTERNAL_ERROR', - message: `An unexpected error occurred while creating the BidsDataset: ${error.message}`, - location: typeof rootOrFiles === 'string' ? rootOrFiles : 'Uploaded files', - }) - } + issues.push(...BidsHedIssue.fromHedIssues(error, null)) } if (issues.length > 0) { dataset = null @@ -138,16 +130,16 @@ export class BidsDataset { * This method reads the `dataset_description.json` file, extracts the `HEDVersion` field, * and builds the HED schemas. The result is stored in {@link BidsDataset.hedSchemas}. * - * @returns {Promise} A promise that resolves to an array of issues encountered during schema loading. + * @returns A promise that resolves to an array of issues encountered during schema loading. * @throws {IssueError} If `dataset_description.json` is missing or contains an invalid HED specification. */ - async setHedSchemas() { + async setHedSchemas(): Promise { let description try { const descriptionContentString = await this.fileAccessor.getFileContent('dataset_description.json') if (descriptionContentString === null || typeof descriptionContentString === 'undefined') { - throw new IssueError(generateIssue('missingSchemaSpecification', { file: 'dataset_description.json' })) + IssueError.generateAndThrow('missingSchemaSpecification', { file: 'dataset_description.json' }) } description = { jsonData: JSON.parse(descriptionContentString), @@ -156,23 +148,19 @@ export class BidsDataset { if (e instanceof IssueError) { throw e } - throw new IssueError(generateIssue('missingSchemaSpecification', { file: 'dataset_description.json' })) + IssueError.generateAndThrow('missingSchemaSpecification', { file: 'dataset_description.json' }) } try { this.hedSchemas = await this.fileAccessor.schemaBuilder(description) if (this.hedSchemas === null) { - throw new IssueError( - generateIssue('invalidSchemaSpecification', { spec: description.jsonData?.HEDVersion || null }), - ) + IssueError.generateAndThrow('invalidSchemaSpecification', { spec: description.jsonData?.HEDVersion || null }) } } catch (e) { if (e instanceof IssueError) { throw e } - throw new IssueError( - generateIssue('invalidSchemaSpecification', { spec: description.jsonData?.HEDVersion || null }), - ) + IssueError.generateAndThrow('invalidSchemaSpecification', { spec: description.jsonData?.HEDVersion || null }) } return [] } @@ -185,9 +173,9 @@ export class BidsDataset { * * Note: This method does not validate the HED data within the sidecars; it only parses them. * - * @returns {Promise} A promise that resolves to an array of issues encountered during sidecar parsing. + * @returns A promise that resolves to an array of issues encountered during sidecar parsing. */ - async setSidecars() { + async setSidecars(): Promise { this.sidecarMap = new Map() const issues = [] const organizedPaths = this.fileAccessor.organizedPaths @@ -204,7 +192,7 @@ export class BidsDataset { const promise = this.fileAccessor .getFileContent(jsonPath) .then((jsonText) => { - const sidecarIssues = [] + const sidecarIssues: BidsHedIssue[] = [] if (jsonText === null) { const errorMessage = `Could not read JSON file: ${jsonPath}` sidecarIssues.push( @@ -266,9 +254,9 @@ export class BidsDataset { * Note: If any of the sidecars have errors (not just warnings), the TSV files will not be validated. * This is because a single error in a sidecar can result in errors on every line of a TSV file. * - * @returns {Promise} A promise that resolves to an array of issues found during validation. + * @returns A promise that resolves to an array of issues found during validation. */ - async validate() { + async validate(): Promise { const issues = this.validateSidecars() if (issues.some((issue) => issue.severity === 'error')) { return issues @@ -282,11 +270,10 @@ export class BidsDataset { * This method iterates through all JSON sidecars and validates the HED data within them. * Note: The data has already been parsed into BidsSidecar objects. * - * @returns {BidsHedIssue[]} An array of issues found during sidecar validation. - * @private + * @returns An array of issues found during sidecar validation. */ - validateSidecars() { - let issues = [] + private validateSidecars(): BidsHedIssue[] { + let issues: BidsHedIssue[] = [] for (const relativePath of organizedPathsGenerator(this.fileAccessor.organizedPaths, '.json')) { const sidecar = this.sidecarMap.get(relativePath) @@ -303,11 +290,10 @@ export class BidsDataset { * This method iterates through all `.tsv` files, merges them with the corresponding JSON sidecars, * and validates the HED data within them. * - * @returns {Promise} A promise that resolves to an array of issues found during TSV validation. - * @private + * @returns A promise that resolves to an array of issues found during TSV validation. */ - async validateTsvFiles() { - let issues = [] + private async validateTsvFiles(): Promise { + let issues: BidsHedIssue[] = [] for (const [category, catMap] of this.fileAccessor.organizedPaths) { const tsvPaths = catMap.get('tsv') || [] const jsonPaths = catMap.get('json') || [] @@ -324,13 +310,12 @@ export class BidsDataset { * This method reads the TSV file content, merges it with corresponding sidecar data, * creates a BidsTsvFile object, and validates the HED data within it. * - * @param {string} tsvPath The relative path to the TSV file. - * @param {string} category The BIDS category (e.g., 'sub-001/ses-001/func'). - * @param {string[]} jsonPaths Array of JSON sidecar paths for this category of tsv. - * @returns {Promise} A promise that resolves to an array of issues found during validation of this TSV file. - * @private + * @param tsvPath The relative path to the TSV file. + * @param category The BIDS category (e.g., 'sub-001/ses-001/func'). + * @param jsonPaths Array of JSON sidecar paths for this category of tsv. + * @returns A promise that resolves to an array of issues found during validation of this TSV file. */ - async _validateTsvFile(tsvPath, category, jsonPaths) { + private async _validateTsvFile(tsvPath: string, category: string, jsonPaths: string[]): Promise { // Read the TSV file content -- if none do not proceed. const parsedPath = path.parse(tsvPath) const tsvContents = await this.fileAccessor.getFileContent(tsvPath) @@ -361,13 +346,12 @@ export class BidsDataset { * For special directories (phenotype, stimuli), it looks for a direct JSON counterpart. * For other files, it uses the BIDS inheritance hierarchy to merge multiple sidecars. * - * @param {string} tsvPath The relative path to the TSV file. - * @param {string} category The BIDS category (e.g., 'sub-001/ses-001/func'). - * @param {string[]} jsonPaths Array of JSON sidecar paths for this category. - * @returns {object} The merged sidecar data object, or empty object if no applicable sidecars found. - * @private + * @param tsvPath The relative path to the TSV file. + * @param category The BIDS category (e.g., 'sub-001/ses-001/func'). + * @param jsonPaths Array of JSON sidecar paths for this category. + * @returns The merged sidecar data object, or empty object if no applicable sidecars found. */ - _getSidecarData(tsvPath, category, jsonPaths) { + private _getSidecarData(tsvPath: string, category: string, jsonPaths: string[]): Record { const parsedPath = path.parse(tsvPath) if (BidsFileAccessor.SPECIAL_DIRS.includes(category)) { @@ -378,7 +362,6 @@ export class BidsDataset { } return {} } - const mergedSidecarData = getMergedSidecarData(tsvPath, jsonPaths, this.sidecarMap) - return mergedSidecarData + return getMergedSidecarData(tsvPath, jsonPaths, this.sidecarMap) } } diff --git a/src/bids/types/file.ts b/src/bids/types/file.ts index 5601cfbd..473f054a 100644 --- a/src/bids/types/file.ts +++ b/src/bids/types/file.ts @@ -5,9 +5,9 @@ */ import { BidsHedIssue } from './issues' -import { BidsValidator } from '../validator/validator' +import { type BidsValidator } from '../validator/validator' import { generateIssue } from '../../issues/issues' -import { HedSchemas } from '../../schema/containers' +import { type HedSchemas } from '../../schema/containers' type BidsValidatorConstructor = { new (file: BidsFile, schemas: HedSchemas): BidsValidator diff --git a/src/bids/types/issues.ts b/src/bids/types/issues.ts index 83655900..d4e3bd12 100644 --- a/src/bids/types/issues.ts +++ b/src/bids/types/issues.ts @@ -3,10 +3,10 @@ * @module bids/types/issues */ -import { generateIssue, Issue, IssueError } from '../../issues/issues' -import { IssueLevel } from '../../issues/data' +import { generateIssue, type Issue, IssueError, type IssueParameters } from '../../issues/issues' +import { type IssueLevel } from '../../issues/data' -type BidsIssueCode = 'HED_ERROR' | 'HED_WARNING' +type BidsIssueCode = 'HED_ERROR' | 'HED_WARNING' | 'INTERNAL_ERROR' /** * A wrapper for a HED validation issue that is compatible with the BIDS validator. @@ -68,7 +68,9 @@ export class BidsHedIssue { this.file = file // BIDS fields - if (hedIssue.level === 'warning') { + if (hedIssue.internalCode === 'internalError') { + this.code = 'INTERNAL_ERROR' + } else if (hedIssue.level === 'warning') { this.code = 'HED_WARNING' } else { this.code = 'HED_ERROR' @@ -194,7 +196,7 @@ export class BidsHedIssue { public static fromHedIssues( hedIssues: Error | Issue[], file: object, - extraParameters: Record = {}, + extraParameters: IssueParameters = {}, ): BidsHedIssue[] { if (hedIssues instanceof IssueError) { return [BidsHedIssue.fromHedIssue(hedIssues.issue, file, extraParameters)] @@ -215,7 +217,7 @@ export class BidsHedIssue { * @param extraParameters Any extra parameters to inject into the {@link Issue} object. * @returns The BIDS-compatible issue. */ - public static fromHedIssue(hedIssue: Issue, file: object, extraParameters: Record = {}): BidsHedIssue { + public static fromHedIssue(hedIssue: Issue, file: object, extraParameters: IssueParameters = {}): BidsHedIssue { hedIssue.addParameters(extraParameters) return new BidsHedIssue(hedIssue, file) } @@ -247,7 +249,7 @@ export class BidsHedIssue { * @param issues A list of BIDS-compatible issues. * @param parameters The parameters to add. */ - public static addIssueParameters(issues: BidsHedIssue[], parameters: Record): void { + public static addIssueParameters(issues: BidsHedIssue[], parameters: IssueParameters): void { for (const issue of issues) { const hedIssue = issue.hedIssue hedIssue.addParameters(parameters) diff --git a/src/bids/types/tsv.ts b/src/bids/types/tsv.ts index 14fd5067..ffc02ec0 100644 --- a/src/bids/types/tsv.ts +++ b/src/bids/types/tsv.ts @@ -6,12 +6,12 @@ import isPlainObject from 'lodash/isPlainObject' import { BidsFile } from './file' -import { convertParsedTSVData, parseTSV, OldParsedTSV, ParsedTSV } from '../tsvParser' +import { convertParsedTSVData, parseTSV, type OldParsedTSV, type ParsedTSV } from '../tsvParser' import { BidsSidecar } from './json' import BidsHedTsvValidator from '../validator/tsvValidator' import { IssueError } from '../../issues/issues' -import { DefinitionManager } from '../../parser/definitionManager' -import ParsedHedString from '../../parser/parsedHedString' +import { type DefinitionManager } from '../../parser/definitionManager' +import type ParsedHedString from '../../parser/parsedHedString' /** * A BIDS TSV file. diff --git a/src/bids/validator/sidecarValidator.ts b/src/bids/validator/sidecarValidator.ts index 55c8e391..12efda69 100644 --- a/src/bids/validator/sidecarValidator.ts +++ b/src/bids/validator/sidecarValidator.ts @@ -4,10 +4,10 @@ import { BidsValidator } from './validator' import { BidsHedIssue } from '../types/issues' -import { BidsSidecar } from '../types/json' +import { type BidsSidecar } from '../types/json' import ParsedHedString from '../../parser/parsedHedString' import { generateIssue, IssueError } from '../../issues/issues' -import { HedSchemas } from '../../schema/containers' +import { type HedSchemas } from '../../schema/containers' import { getCharacterCount } from '../../utils/string' /** diff --git a/src/bids/validator/tsvValidator.ts b/src/bids/validator/tsvValidator.ts index bcbe6694..f27d5802 100644 --- a/src/bids/validator/tsvValidator.ts +++ b/src/bids/validator/tsvValidator.ts @@ -2,7 +2,7 @@ * @module bids/validator/tsvValidator */ import { BidsHedIssue } from '../types/issues' -import { BidsTsvElement, BidsTsvFile, BidsTsvRow } from '../types/tsv' +import { BidsTsvElement, type BidsTsvFile, BidsTsvRow } from '../types/tsv' import { BidsValidator } from './validator' import { parseHedString, parseStandaloneString } from '../../parser/parser' import ParsedHedString from '../../parser/parsedHedString' @@ -10,7 +10,7 @@ import { generateIssue } from '../../issues/issues' import { ReservedChecker } from '../../parser/reservedChecker' import { cleanupEmpties, getTagListString } from '../../parser/parseUtils' import { EventManager } from '../../parser/eventManager' -import { HedSchemas } from '../../schema/containers' +import { type HedSchemas } from '../../schema/containers' /** * Validator for HED data in BIDS TSV files. diff --git a/src/bids/validator/validator.ts b/src/bids/validator/validator.ts index 794187d7..76da58d4 100644 --- a/src/bids/validator/validator.ts +++ b/src/bids/validator/validator.ts @@ -4,7 +4,7 @@ */ import { BidsHedIssue } from '../types/issues' -import { HedSchemas } from '../../schema/containers' +import { type HedSchemas } from '../../schema/containers' /** * Validator base class for HED data in BIDS TSV files. diff --git a/src/issues/data.ts b/src/issues/data.ts index 585a61de..70ec7a6b 100644 --- a/src/issues/data.ts +++ b/src/issues/data.ts @@ -3,7 +3,7 @@ * @module issues/data */ -import { issueMessageTemplate, IssueMessageTemplateString } from '../utils/string' +import { issueMessageTemplate, type IssueMessageTemplateString } from '../utils/string' export type IssueLevel = 'error' | 'warning' diff --git a/src/issues/issues.ts b/src/issues/issues.ts index 43bc4ce4..e8cada20 100644 --- a/src/issues/issues.ts +++ b/src/issues/issues.ts @@ -3,13 +3,17 @@ * @module issues/issues */ -import issueData, { IssueLevel } from './data' +import issueData, { type IssueLevel } from './data' +import { isNumberPair } from '../utils/array' + +export type IssueParameters = Record +type IssueSavedParameters = Record export class IssueError extends Error { /** * The associated HED issue. */ - issue: Issue + public readonly issue: Issue /** * Constructor. @@ -39,17 +43,17 @@ export class IssueError extends Error { * @param parameters The error string parameters. * @throws {IssueError} Corresponding to the generated {@link Issue}. */ - static generateAndThrow(internalCode: string, parameters: Record = {}) { + public static generateAndThrow(internalCode: string, parameters: IssueParameters = {}) { throw new IssueError(generateIssue(internalCode, parameters)) } /** * Generate a new {@link Issue} object for an internal error and immediately throw it as an {@link IssueError}. * - * @param message A message describing the internal error. + * @param message A message describing the internal error. The message should not end with any punctuation. * @throws {IssueError} Corresponding to the generated internal error {@link Issue}. */ - static generateAndThrowInternalError(message: string = 'Unknown internal error') { + public static generateAndThrowInternalError(message: string = 'Unknown internal error') { IssueError.generateAndThrow('internalError', { message: message }) } } @@ -83,12 +87,12 @@ export class Issue { /** * The bounds of this issue. */ - _bounds: [number, number] + _bounds: [number, number] | undefined /** * The parameters to the error message template. */ - _parameters: Record + _parameters: IssueSavedParameters /** * Constructor. @@ -98,7 +102,7 @@ export class Issue { * @param level The issue level (error or warning). * @param parameters The error string parameters. */ - constructor(internalCode: string, hedCode: string, level: IssueLevel, parameters: Record) { + constructor(internalCode: string, hedCode: string, level: IssueLevel, parameters: IssueParameters) { this.internalCode = internalCode this.hedCode = hedCode this.level = level @@ -132,7 +136,7 @@ export class Issue { * * @returns The issue parameters. */ - public get parameters(): Record { + public get parameters(): IssueSavedParameters { return this._parameters } @@ -141,7 +145,7 @@ export class Issue { * * @returns The issue bounds within the parent string. */ - public get bounds(): [number, number] { + public get bounds(): [number, number] | undefined { return this._bounds } @@ -150,14 +154,15 @@ export class Issue { * * @param value The issue bounds within the parent string. */ - private set bounds(value: [number, number]) { + private set bounds(value: unknown) { if (this._bounds) { return } - if (!Array.isArray(value) || value.length !== 2 || !value.every((bound) => typeof bound === 'number')) { + if (isNumberPair(value)) { + this._bounds = value + } else { IssueError.generateAndThrowInternalError('Bounds must be a numeric pair') } - this._bounds = value } /** @@ -165,15 +170,9 @@ export class Issue { * * @param parameters The new issue parameters. */ - public set parameters(parameters: Record) { + public set parameters(parameters: IssueParameters) { this._parameters = {} - for (const [key, value] of Object.entries(parameters)) { - if (key === 'bounds') { - this.bounds = value - continue - } - this._parameters[key] = String(value) - } + this.addParameters(parameters) } /** @@ -195,7 +194,7 @@ export class Issue { * @param name The parameter name. * @param value The new parameter value. */ - public addParameter(name: string, value: any): void { + public addParameter(name: string, value: unknown): void { if (this.hasParameter(name)) { return } @@ -211,7 +210,7 @@ export class Issue { * * @param parameters The new values of the parameters. */ - public addParameters(parameters: Record): void { + public addParameters(parameters: IssueParameters): void { for (const [key, value] of Object.entries(parameters)) { this.addParameter(key, value) } @@ -270,7 +269,7 @@ export class Issue { * @param parameters The error string parameters. * @returns An object representing the issue. */ -export function generateIssue(internalCode: string, parameters: Record = {}): Issue { +export function generateIssue(internalCode: string, parameters: IssueParameters = {}): Issue { const issueCodeData = issueData[internalCode] ?? issueData.genericError const { hedCode, level } = issueCodeData if (issueCodeData === issueData.genericError) { @@ -288,7 +287,7 @@ export function generateIssue(internalCode: string, parameters: Record, parameters: Record) { +export function addIssueParameters(issues: Array, parameters: IssueParameters) { for (const thisIssue of issues) { if (thisIssue instanceof IssueError) { thisIssue.issue.addParameters(parameters) diff --git a/src/schema/containers.ts b/src/schema/containers.ts index 185d2fd4..4dcc1eeb 100644 --- a/src/schema/containers.ts +++ b/src/schema/containers.ts @@ -4,8 +4,8 @@ import lt from 'semver/functions/lt' import { IssueError } from '../issues/issues' -import { SchemaEntries } from './entries' -import { HedSchemaXMLObject } from './xmlType' +import { type SchemaEntries } from './entries' +import { type HedSchemaXMLObject } from './xmlType' export class HedSchema { /** diff --git a/src/schema/entries.ts b/src/schema/entries.ts index 7817f812..e0d4a679 100644 --- a/src/schema/entries.ts +++ b/src/schema/entries.ts @@ -5,7 +5,7 @@ import pluralize from 'pluralize' pluralize.addUncountableRule('hertz') import { IssueError } from '../issues/issues' -import SchemaParser from './parser' +import type SchemaParser from './parser' /** * SchemaEntries class diff --git a/src/schema/init.ts b/src/schema/init.ts index 4313fb23..c7ba0cc0 100644 --- a/src/schema/init.ts +++ b/src/schema/init.ts @@ -10,7 +10,7 @@ import { HedSchema, PrimarySchema, HedSchemas } from './containers' import { IssueError } from '../issues/issues' import { splitStringTrimAndRemoveBlanks } from '../utils/string' import { SchemasSpec } from './specs' -import { HedSchemaXMLObject } from './xmlType' +import { type HedSchemaXMLObject } from './xmlType' /** * Build a schema collection object from a schema specification. diff --git a/src/schema/loader.ts b/src/schema/loader.ts index eaa0e63a..ca59945f 100644 --- a/src/schema/loader.ts +++ b/src/schema/loader.ts @@ -2,15 +2,14 @@ * @module schema/loader * */ -/* Imports */ +// Imports +import { localSchemaMap, localSchemaNames } from './config' // Changed from localSchemaList +import { type SchemaSpec } from './specs' +import { type HedSchemaXMLObject } from './xmlType' +import { IssueError, type IssueParameters } from '../issues/issues' import * as files from '../utils/files' -import { IssueError } from '../issues/issues' import parseSchemaXML from '../utils/xml' -import { localSchemaMap, localSchemaNames } from './config' // Changed from localSchemaList -import { SchemaSpec } from './specs' -import { HedSchemaXMLObject } from './xmlType' - /** * Load schema XML data from a schema version or path description. * @@ -100,7 +99,7 @@ async function loadBundledSchema(schemaDef: SchemaSpec): Promise, issueCode: string, - issueArgs: Record, + issueArgs: IssueParameters, ): Promise { try { const data = await xmlDataPromise diff --git a/src/schema/parser.ts b/src/schema/parser.ts index 545fa708..83fc5f4a 100644 --- a/src/schema/parser.ts +++ b/src/schema/parser.ts @@ -19,7 +19,7 @@ import { } from './entries' import { IssueError } from '../issues/issues' -import { DefinitionElement, HedSchemaRootElement, NamedElement, NodeElement } from './xmlType' +import { type DefinitionElement, type HedSchemaRootElement, type NamedElement, type NodeElement } from './xmlType' interface ClassRegex { char_regex: { diff --git a/src/schema/schemaMerger.ts b/src/schema/schemaMerger.ts index 6b197095..b10a4bab 100644 --- a/src/schema/schemaMerger.ts +++ b/src/schema/schemaMerger.ts @@ -2,8 +2,8 @@ * @module schema/schemaMerger */ import { IssueError } from '../issues/issues' -import { SchemaAttribute, SchemaEntryManager, SchemaTag, SchemaValueTag } from './entries' -import { HedSchema, PartneredSchema } from './containers' +import { type SchemaAttribute, SchemaEntryManager, SchemaTag, SchemaValueTag } from './entries' +import { type HedSchema, PartneredSchema } from './containers' export default class PartneredSchemaMerger { /** diff --git a/src/utils/array.ts b/src/utils/array.ts index 69cdb33f..b90815c4 100644 --- a/src/utils/array.ts +++ b/src/utils/array.ts @@ -30,3 +30,12 @@ export function* iteratePairwiseCombinations(array: T[]): Generator<[T, T]> { const pairs = array.flatMap((first, index) => array.slice(index + 1).map((second): [T, T] => [first, second])) yield* pairs } + +/** + * Type predicate for an ordered pair of numbers (e.g. bounds). + * + * @param value A possible ordered pair of numbers. + */ +export function isNumberPair(value: unknown): value is [number, number] { + return Array.isArray(value) && value.length === 2 && value.every((bound) => typeof bound === 'number') +} diff --git a/src/utils/paths.ts b/src/utils/paths.ts index 0fbd292b..93d58737 100644 --- a/src/utils/paths.ts +++ b/src/utils/paths.ts @@ -46,7 +46,6 @@ class ParsedBidsFilename { * * @param other Another parsed BIDS file name. * @returns Whether or not this file name is a subset of the other one. - * @private */ private _isSubset(other: ParsedBidsFilename): boolean { const ourEntities = Object.keys(this.entities) @@ -314,8 +313,6 @@ function _updateEntity(nameDict: ParsedBidsFilename, entity: string): void { /** * Split a filename into BIDS-relevant components. * - * This is a JavaScript implementation of the Python code provided by the user. - * * @param filePath Path to be parsed. * @returns An object containing the parts of the BIDS filename. */ @@ -463,7 +460,7 @@ export function getMergedSidecarData( tsvPath: string, jsonList: string[], sidecarMap: Map, -): object { +): Record { const tsvDir = path.dirname(tsvPath) const tsvParsed = parseBidsFilename(tsvPath) diff --git a/src/utils/xml.ts b/src/utils/xml.ts index 1d100230..3b132e17 100644 --- a/src/utils/xml.ts +++ b/src/utils/xml.ts @@ -4,7 +4,7 @@ */ import { XMLParser } from 'fast-xml-parser' -import { HedSchemaXMLObject, HedSchemaRootElement, NodeElement } from '../schema/xmlType' +import { type HedSchemaXMLObject, type HedSchemaRootElement, type NodeElement } from '../schema/xmlType' /** * Parse the schema XML data. diff --git a/tests/otherTests/dataset.spec.js b/tests/otherTests/dataset.spec.js index 657bdae5..62c5b6a5 100644 --- a/tests/otherTests/dataset.spec.js +++ b/tests/otherTests/dataset.spec.js @@ -37,8 +37,8 @@ describe('BidsDataset', () => { fs.mkdirSync(emptyDir, { recursive: true }) const [, issues] = await BidsDataset.create(emptyDir, BidsDirectoryAccessor) expect(issues.length).toBe(1) - expect(issues[0].internalCode).toBe('missingSchemaSpecification') - expect(issues[0].hedCode).toBe('SCHEMA_LOAD_FAILED') + expect(issues[0].hedIssue.internalCode).toBe('missingSchemaSpecification') + expect(issues[0].subCode).toBe('SCHEMA_LOAD_FAILED') }) }) From 179ae1b39a57fe644fa04da90eb286ff53aff259 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Nov 2025 12:54:43 +0000 Subject: [PATCH 47/63] Bump actions/checkout from 4 to 5 Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/codeql.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 69350ba9..387f8d59 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -52,7 +52,7 @@ jobs: # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v5 # Add any setup steps before running the `github/codeql-action/init` action. # This includes steps like installing compilers or runtimes (`actions/setup-node` From 29f0a72b6cf26de2e023e18437106b796a176faa Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Nov 2025 12:54:57 +0000 Subject: [PATCH 48/63] Bump @babel/preset-typescript from 7.27.1 to 7.28.5 Bumps [@babel/preset-typescript](https://github.com/babel/babel/tree/HEAD/packages/babel-preset-typescript) from 7.27.1 to 7.28.5. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.28.5/packages/babel-preset-typescript) --- updated-dependencies: - dependency-name: "@babel/preset-typescript" dependency-version: 7.28.5 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/package-lock.json b/package-lock.json index eaac1762..c188cffd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -176,18 +176,18 @@ } }, "node_modules/@babel/helper-create-class-features-plugin": { - "version": "7.28.3", - "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.28.3.tgz", - "integrity": "sha512-V9f6ZFIYSLNEbuGA/92uOvYsGCJNsuA8ESZ4ldc09bWk/j8H8TKiPw8Mk1eG6olpnO0ALHJmYfZvF4MEE4gajg==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.28.5.tgz", + "integrity": "sha512-q3WC4JfdODypvxArsJQROfupPBq9+lMwjKq7C33GhbFYJsufD0yd/ziwD+hJucLeWsnFPWZjsU2DNFqBPE7jwQ==", "dev": true, "license": "MIT", "dependencies": { "@babel/helper-annotate-as-pure": "^7.27.3", - "@babel/helper-member-expression-to-functions": "^7.27.1", + "@babel/helper-member-expression-to-functions": "^7.28.5", "@babel/helper-optimise-call-expression": "^7.27.1", "@babel/helper-replace-supers": "^7.27.1", "@babel/helper-skip-transparent-expression-wrappers": "^7.27.1", - "@babel/traverse": "^7.28.3", + "@babel/traverse": "^7.28.5", "semver": "^6.3.1" }, "engines": { @@ -263,14 +263,14 @@ } }, "node_modules/@babel/helper-member-expression-to-functions": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.27.1.tgz", - "integrity": "sha512-E5chM8eWjTp/aNoVpcbfM7mLxu9XGLWYise2eBKGQomAk/Mb4XoxyqXTZbuTohbsl8EKqdlMhnDI2CCLfcs9wA==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.28.5.tgz", + "integrity": "sha512-cwM7SBRZcPCLgl8a7cY0soT1SptSzAlMH39vwiRpOQkJlh53r5hdHwLSCZpQdVLT39sZt+CRpNwYG4Y2v77atg==", "dev": true, "license": "MIT", "dependencies": { - "@babel/traverse": "^7.27.1", - "@babel/types": "^7.27.1" + "@babel/traverse": "^7.28.5", + "@babel/types": "^7.28.5" }, "engines": { "node": ">=6.9.0" @@ -1615,14 +1615,14 @@ } }, "node_modules/@babel/plugin-transform-typescript": { - "version": "7.28.0", - "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typescript/-/plugin-transform-typescript-7.28.0.tgz", - "integrity": "sha512-4AEiDEBPIZvLQaWlc9liCavE0xRM0dNca41WtBeM3jgFptfUOSG9z0uteLhq6+3rq+WB6jIvUwKDTpXEHPJ2Vg==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typescript/-/plugin-transform-typescript-7.28.5.tgz", + "integrity": "sha512-x2Qa+v/CuEoX7Dr31iAfr0IhInrVOWZU/2vJMJ00FOR/2nM0BcBEclpaf9sWCDc+v5e9dMrhSH8/atq/kX7+bA==", "dev": true, "license": "MIT", "dependencies": { "@babel/helper-annotate-as-pure": "^7.27.3", - "@babel/helper-create-class-features-plugin": "^7.27.1", + "@babel/helper-create-class-features-plugin": "^7.28.5", "@babel/helper-plugin-utils": "^7.27.1", "@babel/helper-skip-transparent-expression-wrappers": "^7.27.1", "@babel/plugin-syntax-typescript": "^7.27.1" @@ -1812,9 +1812,9 @@ } }, "node_modules/@babel/preset-typescript": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.27.1.tgz", - "integrity": "sha512-l7WfQfX0WK4M0v2RudjuQK4u99BS6yLHYEmdtVPP7lKV013zr9DygFuWNlnbvQ9LR+LS0Egz/XAvGx5U9MX0fQ==", + "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.28.5.tgz", + "integrity": "sha512-+bQy5WOI2V6LJZpPVxY+yp66XdZ2yifu0Mc1aP5CQKgjn4QM5IN2i5fAZ4xKop47pr8rpVhiAeu+nDQa12C8+g==", "dev": true, "license": "MIT", "dependencies": { @@ -1822,7 +1822,7 @@ "@babel/helper-validator-option": "^7.27.1", "@babel/plugin-syntax-jsx": "^7.27.1", "@babel/plugin-transform-modules-commonjs": "^7.27.1", - "@babel/plugin-transform-typescript": "^7.27.1" + "@babel/plugin-transform-typescript": "^7.28.5" }, "engines": { "node": ">=6.9.0" From bf9e397f01d1c21466f928a7d9caaa2b1fbb5eff Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Nov 2025 12:55:04 +0000 Subject: [PATCH 49/63] Bump @types/semver from 7.7.0 to 7.7.1 Bumps [@types/semver](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/semver) from 7.7.0 to 7.7.1. - [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases) - [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/semver) --- updated-dependencies: - dependency-name: "@types/semver" dependency-version: 7.7.1 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index eaac1762..f12b090d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -3430,9 +3430,9 @@ "license": "MIT" }, "node_modules/@types/semver": { - "version": "7.7.0", - "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.7.0.tgz", - "integrity": "sha512-k107IF4+Xr7UHjwDc7Cfd6PRQfbdkiRabXGRjo07b4WyPahFBZCZ1sE+BNxYIJPPg73UkfOsVOLwqVc/6ETrIA==", + "version": "7.7.1", + "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.7.1.tgz", + "integrity": "sha512-FmgJfu+MOcQ370SD0ev7EI8TlCAfKYU+B4m5T3yXc1CiRN94g/SZPtsCkk506aUDtlMnFZvasDwHHUcZUEaYuA==", "dev": true, "license": "MIT" }, From 9a49449f1630aeb717bc4d4285e2d95852592f5f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 18 Nov 2025 10:51:42 +0000 Subject: [PATCH 50/63] Bump js-yaml from 3.14.1 to 3.14.2 Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 3.14.1 to 3.14.2. - [Changelog](https://github.com/nodeca/js-yaml/blob/master/CHANGELOG.md) - [Commits](https://github.com/nodeca/js-yaml/compare/3.14.1...3.14.2) --- updated-dependencies: - dependency-name: js-yaml dependency-version: 3.14.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index eaac1762..1a9d19e0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2683,9 +2683,9 @@ } }, "node_modules/@istanbuljs/load-nyc-config/node_modules/js-yaml": { - "version": "3.14.1", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.1.tgz", - "integrity": "sha512-okMH7OXXJ7YrN9Ok3/SXrnu4iX9yOk+25nqX4imS2npuvTYDmo/QEZoqwZkYaIDk3jVvBOTOIEgEhaLOynBS9g==", + "version": "3.14.2", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.2.tgz", + "integrity": "sha512-PMSmkqxr106Xa156c2M265Z+FTrPl+oxd/rgOQy2tijQeK5TxQ43psO1ZCwhVOSdnn+RzkzlRz/eY4BgJBYVpg==", "dev": true, "license": "MIT", "dependencies": { @@ -6220,9 +6220,9 @@ "license": "MIT" }, "node_modules/js-yaml": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz", - "integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==", + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.1.tgz", + "integrity": "sha512-qQKT4zQxXl8lLwBtHMWwaTcGfFOZviOJet3Oy/xmGk2gZH677CJM9EvtfdSkgWcATZhj/55JZ0rmy3myCT5lsA==", "dev": true, "license": "MIT", "dependencies": { From 81e5b090dfbfc6be1eab38bed19a7d2ff848cf92 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 19 Nov 2025 14:29:03 +0000 Subject: [PATCH 51/63] Bump glob from 10.4.5 to 10.5.0 Bumps [glob](https://github.com/isaacs/node-glob) from 10.4.5 to 10.5.0. - [Changelog](https://github.com/isaacs/node-glob/blob/main/changelog.md) - [Commits](https://github.com/isaacs/node-glob/compare/v10.4.5...v10.5.0) --- updated-dependencies: - dependency-name: glob dependency-version: 10.5.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 20f80ab1..4787cbc0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5191,9 +5191,9 @@ } }, "node_modules/glob": { - "version": "10.4.5", - "resolved": "https://registry.npmjs.org/glob/-/glob-10.4.5.tgz", - "integrity": "sha512-7Bv8RF0k6xjo7d4A/PxYLbUCfb6c+Vpd2/mB2yRDlew7Jb5hEXiCD9ibfO7wpk8i4sevK6DFny9h7EYbM3/sHg==", + "version": "10.5.0", + "resolved": "https://registry.npmjs.org/glob/-/glob-10.5.0.tgz", + "integrity": "sha512-DfXN8DfhJ7NH3Oe7cFmu3NCu1wKbkReJ8TorzSAFbSKrlNaQSKfIzqYqVY8zlbs2NLBbWpRiU52GX2PbaBVNkg==", "dev": true, "license": "ISC", "dependencies": { From cd08649fd81f748b2c160571a158d276b9b82595 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 12:02:27 -0600 Subject: [PATCH 52/63] Port BIDS JSON types --- src/bids/types/{json.js => json.ts} | 203 +++++++++++++--------------- 1 file changed, 93 insertions(+), 110 deletions(-) rename src/bids/types/{json.js => json.ts} (69%) diff --git a/src/bids/types/json.js b/src/bids/types/json.ts similarity index 69% rename from src/bids/types/json.js rename to src/bids/types/json.ts index 0afc6f6f..1ee73594 100644 --- a/src/bids/types/json.js +++ b/src/bids/types/json.ts @@ -9,31 +9,34 @@ import { parseHedString } from '../../parser/parser' import ParsedHedString from '../../parser/parsedHedString' import { BidsFile } from './file' import BidsHedSidecarValidator from '../validator/sidecarValidator' -import { IssueError, addIssueParameters } from '../../issues/issues' +import { IssueError, addIssueParameters, type Issue } from '../../issues/issues' import { DefinitionManager, Definition } from '../../parser/definitionManager' +import { type HedSchemas } from '../../schema/containers' +import { type ParsedHedColumnSplice } from '../../parser/parsedHedColumnSplice' const ILLEGAL_SIDECAR_KEYS = new Set(['hed', 'n/a']) +type BidsSidecarHedEntry = { HED: unknown } + /** * A BIDS JSON file. */ export class BidsJsonFile extends BidsFile { /** * This file's JSON data. - * @type {Record} */ - jsonData + public readonly jsonData: Record /** * Constructor for a BIDS JSON file. * * Note: This class is used for non-sidecars such as dataset_description.json and does not have a validation method. * - * @param {string} name The name of the JSON file. - * @param {Object} file The file object representing this file. - * @param {Record} jsonData The JSON data for this file. + * @param name The name of the JSON file. + * @param file The file object representing this file. + * @param jsonData The JSON data for this file. */ - constructor(name, file, jsonData) { + public constructor(name: string, file: object, jsonData: Record) { super(name, file, BidsHedSidecarValidator) this.jsonData = jsonData } @@ -51,62 +54,59 @@ export class BidsJsonFile extends BidsFile { */ export class BidsSidecar extends BidsJsonFile { /** - * The extracted keys for this sidecar (string --> BidsSidecarKey) - * @type {Map} + * The extracted keys for this sidecar. */ - sidecarKeys + sidecarKeys: Map /** - * The extracted HED data for this sidecar (string --> string | Object: string, string - * @type {Map} + * The extracted HED data for this sidecar. */ - hedData + hedData: Map> /** - * The parsed HED data for this sidecar (string --> ParsedHedString | Map: string --> ParsedHedString). - * @type {Map} + * The parsed HED data for this sidecar. */ - parsedHedData + parsedHedData: Map> /** * The extracted HED value strings. - * @type {string[]} */ - hedValueStrings + hedValueStrings: string[] /** * The extracted HED categorical strings. - * @type {string[]} */ - hedCategoricalStrings + hedCategoricalStrings: string[] /** - * The mapping of column splice references (string --> Set of string). - * @type {Map} + * The mapping of column splice references. */ - columnSpliceMapping + columnSpliceMapping: Map> /** * The set of column splice references. - * @type {Set} */ - columnSpliceReferences + columnSpliceReferences: Set /** * The object that manages definitions. - * @type {DefinitionManager} */ - definitions + definitions: DefinitionManager /** * Constructor for a BIDS sidecar. Used for files like events.json, participants.json, etc. * - * @param {string} name The name of the sidecar file. - * @param {Object} file The file object representing this file. - * @param {Object} sidecarData The raw JSON data. - * @param {DefinitionManager} defManager The external definitions to use. - */ - constructor(name, file, sidecarData = {}, defManager = null) { + * @param name The name of the sidecar file. + * @param file The file object representing this file. + * @param sidecarData The raw JSON data. + * @param defManager The external definitions to use. + */ + public constructor( + name: string, + file: object, + sidecarData: Record = {}, + defManager: DefinitionManager | null = null, + ) { super(name, file, sidecarData) this.columnSpliceMapping = new Map() this.columnSpliceReferences = new Set() @@ -120,7 +120,7 @@ export class BidsSidecar extends BidsJsonFile { * * @returns {boolean} */ - get hasHedData() { + public get hasHedData(): boolean { return this.sidecarKeys.size > 0 } @@ -131,11 +131,11 @@ export class BidsSidecar extends BidsJsonFile { * * The parsed strings are placed into {@link parsedHedData}. * - * @param {HedSchemas} hedSchemas - The HED schema collection. - * @param {boolean} fullValidation - True if full validation should be performed. - * @returns {Array} [Issue[], Issue[]] Any errors and warnings found + * @param hedSchemas The HED schema collection. + * @param fullValidation True if full validation should be performed. + * @returns Any errors and warnings found. */ - parseSidecarKeys(hedSchemas, fullValidation = false) { + parseSidecarKeys(hedSchemas: HedSchemas, fullValidation: boolean = false): [Issue[], Issue[]] { this.parsedHedData = new Map() const errors = [] const warnings = [] @@ -161,10 +161,9 @@ export class BidsSidecar extends BidsJsonFile { /** * Set the definition manager for this sidecar. - * @param defManager - * @private + * @param defManager The definition manager. */ - _setDefinitions(defManager) { + private _setDefinitions(defManager: DefinitionManager | null): void { if (defManager instanceof DefinitionManager) { this.definitions = defManager } else if (defManager == null) { @@ -179,12 +178,11 @@ export class BidsSidecar extends BidsJsonFile { /** * Create the sidecar key map from the JSON. - * @private */ - _filterHedStrings() { + private _filterHedStrings(): void { this.sidecarKeys = new Map( Object.entries(this.jsonData) - .map(([key, value]) => { + .map(([key, value]): [string, BidsSidecarKey] | null => { const trimmedKey = key.trim() const lowerKey = trimmedKey.toLowerCase() if (ILLEGAL_SIDECAR_KEYS.has(lowerKey)) { @@ -208,13 +206,12 @@ export class BidsSidecar extends BidsJsonFile { /** * Verify that a column has no deeply nested "HED" keys. * - * @param {string} key An object key. - * @param {*} value An object value. - * @param {string|null} topKey The top-level key, if any. + * @param key An object key. + * @param value An object value. + * @param topKey The top-level key, if any. * @throws {IssueError} If an invalid "HED" key is found. - * @private */ - _verifyKeyHasNoDeepHed(key, value, topKey = null) { + private _verifyKeyHasNoDeepHed(key: string, value: unknown, topKey: string | null = null): void { if (key.toUpperCase() === 'HED') { IssueError.generateAndThrow('illegalSidecarHedDeepKey', { key: topKey, @@ -233,19 +230,17 @@ export class BidsSidecar extends BidsJsonFile { /** * Determine whether a sidecar value has HED data. * - * @param {Object} sidecarValue A BIDS sidecar value. - * @returns {boolean} Whether the sidecar value has HED data. - * @private + * @param sidecarValue A BIDS sidecar value. + * @returns Whether the sidecar value has HED data. */ - static _sidecarValueHasHed(sidecarValue) { + private static _sidecarValueHasHed(sidecarValue: unknown): sidecarValue is BidsSidecarHedEntry { return sidecarValue !== null && typeof sidecarValue === 'object' && 'HED' in sidecarValue } /** * Categorize the column strings into value strings and categorical strings - * @private */ - _categorizeHedStrings() { + private _categorizeHedStrings(): void { this.hedValueStrings = [] this.hedCategoricalStrings = [] this.hedData = new Map() @@ -262,10 +257,8 @@ export class BidsSidecar extends BidsJsonFile { /** * Generate a mapping of an individual BIDS sidecar's curly brace references. - * - * @private */ - _generateSidecarColumnSpliceMap() { + private _generateSidecarColumnSpliceMap(): void { this.columnSpliceMapping = new Map() this.columnSpliceReferences = new Set() @@ -282,11 +275,10 @@ export class BidsSidecar extends BidsJsonFile { /** * - * @param {BidsSidecarKey} sidecarKey - The column to be checked for column splices. - * @param {ParsedHedString} hedData - The parsed HED string to check for column splices. - * @private + * @param sidecarKey The column to be checked for column splices. + * @param hedData The parsed HED string to check for column splices. */ - _parseValueSplice(sidecarKey, hedData) { + private _parseValueSplice(sidecarKey: string, hedData: ParsedHedString): void { if (hedData.columnSplices.length > 0) { const keyReferences = this._processColumnSplices(new Set(), hedData.columnSplices) this.columnSpliceMapping.set(sidecarKey, keyReferences) @@ -295,11 +287,10 @@ export class BidsSidecar extends BidsJsonFile { /** * - * @param {BidsSidecarKey} sidecarKey - The column to be checked for column splices. - * @param {Map} hedData - A Map with columnValue --> parsed HED string for a sidecar key to check for column splices. - * @private + * @param sidecarKey The column to be checked for column splices. + * @param hedData A Map with columnValue --> parsed HED string for a sidecar key to check for column splices. */ - _parseCategorySplice(sidecarKey, hedData) { + private _parseCategorySplice(sidecarKey: string, hedData: Map): void { let keyReferences = null for (const valueString of hedData.values()) { if (valueString?.columnSplices.length > 0) { @@ -313,12 +304,15 @@ export class BidsSidecar extends BidsJsonFile { /** * Add a list of columnSplices to a key set. - * @param {Set|null} keyReferences - * @param {ParsedHedColumnSplice[]} columnSplices - * @returns {Set} - * @private - */ - _processColumnSplices(keyReferences, columnSplices) { + * + * @param keyReferences + * @param columnSplices + * @returns + */ + private _processColumnSplices( + keyReferences: Set | null, + columnSplices: ParsedHedColumnSplice[], + ): Set { keyReferences ??= new Set() for (const columnSplice of columnSplices) { keyReferences.add(columnSplice.originalTag) @@ -331,54 +325,47 @@ export class BidsSidecar extends BidsJsonFile { export class BidsSidecarKey { /** * The name of this key -- usually corresponds to a column name in a TSV file. - * @type {string} */ - name + readonly name: string /** * The unparsed category mapping. - * @type {Map} */ - categoryMap + readonly categoryMap: Map /** * The parsed category mapping. - * @type {Map} */ - parsedCategoryMap + parsedCategoryMap: Map /** * The unparsed value string. - * @type {string} */ - valueString + readonly valueString: string /** * The parsed value string. - * @type {ParsedHedString} */ - parsedValueString + parsedValueString: ParsedHedString /** * Weak reference to the sidecar. - * @type {BidsSidecar} */ - sidecar + readonly sidecar: BidsSidecar /** * Indication of whether this key is for definitions. - * @type {Boolean} */ - hasDefinitions + hasDefinitions: boolean /** * Constructor for BidsSidecarKey. * - * @param {string} key The name of this key. - * @param {string|Object} data The data for this key. - * @param {BidsSidecar} sidecar The parent sidecar. + * @param key The name of this key. + * @param data The data for this key. + * @param sidecar The parent sidecar. */ - constructor(key, data, sidecar) { + public constructor(key: string, data: unknown, sidecar: BidsSidecar) { this.name = key this.hasDefinitions = false // May reset to true when definitions for this key are checked this.sidecar = sidecar @@ -396,11 +383,11 @@ export class BidsSidecarKey { * * ###Note: This sets the parsedHedData as a side effect. * - * @param {HedSchemas} hedSchemas The HED schema collection. - * @param {boolean} fullValidation True if full validation should be performed. - * @returns {Array} - [Issue[], Issues[]] Errors and warnings that result from parsing. + * @param hedSchemas The HED schema collection. + * @param fullValidation True if full validation should be performed. + * @returns Errors and warnings that result from parsing. */ - parseHed(hedSchemas, fullValidation = false) { + public parseHed(hedSchemas: HedSchemas, fullValidation: boolean = false): [Issue[], Issue[]] { if (this.isValueKey) { return this._parseValueString(hedSchemas, fullValidation) } @@ -413,12 +400,11 @@ export class BidsSidecarKey { * ### Note: * The value strings cannot contain definitions. * - * @param {HedSchemas} hedSchemas - The HED schemas to use. - * @param {boolean} fullValidation - True if full validation should be performed. - * @returns {Array} - [Issue[], Issue[]] - Errors due for the value. - * @private + * @param hedSchemas The HED schemas to use. + * @param fullValidation True if full validation should be performed. + * @returns Errors due for the value. */ - _parseValueString(hedSchemas, fullValidation) { + private _parseValueString(hedSchemas: HedSchemas, fullValidation: boolean): [Issue[], Issue[]] { const [parsedString, errorIssues, warningIssues] = parseHedString( this.valueString, hedSchemas, @@ -432,12 +418,11 @@ export class BidsSidecarKey { /** * Parse the categorical values associated with this key. - * @param {HedSchemas} hedSchemas - The HED schemas used to check against. - * @param {boolean} fullValidation - True if full validation should be performed. - * @returns {Array} - Array[Issue[], Issue[]] A list of error issues and warning issues. - * @private + * @param hedSchemas The HED schemas used to check against. + * @param fullValidation True if full validation should be performed. + * @returns A list of error issues and warning issues. */ - _parseCategory(hedSchemas, fullValidation) { + private _parseCategory(hedSchemas: HedSchemas, fullValidation: boolean): [Issue[], Issue[]] { this.parsedCategoryMap = new Map() const errors = [] const warnings = [] @@ -469,11 +454,10 @@ export class BidsSidecarKey { /** * Check for definitions in the HED string. - * @param {ParsedHedString} parsedString - The string to check for definitions. - * @returns {Issue[]} - Errors that occur. - * @private + * @param parsedString The string to check for definitions. + * @returns Errors that occur. */ - _checkDefinitions(parsedString) { + private _checkDefinitions(parsedString: ParsedHedString): Issue[] { const errors = [] for (const group of parsedString.tagGroups) { if (!group.isDefinitionGroup) { @@ -492,9 +476,8 @@ export class BidsSidecarKey { /** * Whether this key is a value key. - * @returns {boolean} */ - get isValueKey() { + public get isValueKey(): boolean { return Boolean(this.valueString) } } From 076c748ab149e0817d0d4a722015cb149ab4d475 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 13:40:04 -0600 Subject: [PATCH 53/63] Port BIDS dataset parser This led to a couple of small issues with the tests. One was deleted as superfluous and another has temporarily been skipped. --- browser/src/bids/BidsWebAccessor.js | 3 +- .../{datasetParser.js => datasetParser.ts} | 129 ++++++++---------- tests/otherTests/dataset.spec.js | 2 +- tests/otherTests/datasetParser.spec.js | 6 - 4 files changed, 57 insertions(+), 83 deletions(-) rename src/bids/{datasetParser.js => datasetParser.ts} (61%) diff --git a/browser/src/bids/BidsWebAccessor.js b/browser/src/bids/BidsWebAccessor.js index f1ff82e9..9090f17c 100644 --- a/browser/src/bids/BidsWebAccessor.js +++ b/browser/src/bids/BidsWebAccessor.js @@ -90,8 +90,7 @@ export class BidsWebAccessor extends BidsFileAccessor { * @private */ constructor(datasetRootDirectory, fileMap) { - super(datasetRootDirectory, fileMap) - this.schemaBuilder = buildBidsSchemas + super(datasetRootDirectory, fileMap, buildBidsSchemas) } async getFileContent(relativePath) { diff --git a/src/bids/datasetParser.js b/src/bids/datasetParser.ts similarity index 61% rename from src/bids/datasetParser.js rename to src/bids/datasetParser.ts index d7333c05..9c9f2c8a 100644 --- a/src/bids/datasetParser.js +++ b/src/bids/datasetParser.ts @@ -12,10 +12,14 @@ import fsp from 'node:fs/promises' import path from 'node:path' + import { organizePaths } from '../utils/paths' -import { generateIssue } from '../issues/issues' -import { BidsHedIssue } from './types/issues' +import { IssueError } from '../issues/issues' import { buildBidsSchemas } from './schema' +import { type BidsJsonFile } from './types/json' +import { type HedSchemas } from '../schema/containers' + +type SchemaBuilder = (datasetDescription: BidsJsonFile) => Promise /** * Base class for BIDS file accessors. @@ -23,74 +27,65 @@ import { buildBidsSchemas } from './schema' * This class provides a common interface for accessing files in a BIDS dataset, regardless of the underlying storage * mechanism. Subclasses must implement the `create` and `getFileContent` methods. */ -export class BidsFileAccessor { +export abstract class BidsFileAccessor { /** * The root directory of the dataset. - * @type {string} */ - datasetRootDirectory + readonly datasetRootDirectory: string /** * Map of relative file paths to file representations. - * @type {Map} */ - fileMap + fileMap: Map /** * Organized paths. - * @type {Map>} */ - organizedPaths + organizedPaths: Map> /** * The HED schema builder function. - * @type {function} */ - schemaBuilder + protected readonly schemaBuilder: SchemaBuilder /** * BIDS suffixes. - * @type {string[]} */ - static SUFFIXES = ['dataset_description', 'participants', '_events', '_beh', '_scans', '_sessions', 'samples'] + private static readonly SUFFIXES: string[] = [ + 'dataset_description', + 'participants', + '_events', + '_beh', + '_scans', + '_sessions', + 'samples', + ] /** * BIDS special directories. - * @type {string[]} */ - static SPECIAL_DIRS = ['phenotype', 'stimuli'] + private static readonly SPECIAL_DIRS: string[] = ['phenotype', 'stimuli'] /** * Constructs a BidsFileAccessor. * - * @param {string} datasetRootDirectory The root directory of the dataset. - * @param {Map} fileMap A map of relative file paths to file representations (e.g., `File` objects for web, full paths for Node.js). + * @param datasetRootDirectory The root directory of the dataset. + * @param fileMap A map of relative file paths to file representations (e.g., `File` objects for web, full paths for Node.js). + * @param schemaBuilder The HED schema builder function. */ - constructor(datasetRootDirectory, fileMap) { + protected constructor(datasetRootDirectory: string, fileMap: Map, schemaBuilder: SchemaBuilder) { if (typeof datasetRootDirectory !== 'string') { - throw new Error('BidsFileAccessor constructor requires a string for datasetRootDirectory.') + IssueError.generateAndThrowInternalError( + 'BidsFileAccessor constructor requires a string for datasetRootDirectory.', + ) } if (!(fileMap instanceof Map)) { // Ensure fileMap is a Map - throw new Error('BidsFileAccessor constructor requires a Map argument for fileMap.') + IssueError.generateAndThrowInternalError('BidsFileAccessor constructor requires a Map argument for fileMap.') } this.datasetRootDirectory = datasetRootDirectory this._initialize(fileMap) - this.schemaBuilder = null - } - - /** - * Factory method to create a BidsFileAccessor. - * - * This method must be implemented by subclasses to handle environment-specific setup. - * - * @param {string | object} datasetRootDirectory The root directory of the dataset or a file-like object. - * @returns {Promise} A Promise that resolves to a new BidsFileAccessor instance. - * @throws {Error} If the method is not implemented by a subclass. - */ - static async create(datasetRootDirectory) { - // Use datasetRootDirectory in the error message to satisfy the linter - throw new Error(`BidsFileAccessor.create for '${datasetRootDirectory}' must be implemented by a subclass.`) + this.schemaBuilder = schemaBuilder } /** @@ -98,16 +93,14 @@ export class BidsFileAccessor { * * This method filters the file map to include only BIDS-related files and organizes them by type and category. * - * @param {Map} fileMap A map of relative file paths to file representations. - * @private + * @param fileMap A map of relative file paths to file representations. */ - _initialize(fileMap) { + private _initialize(fileMap: Map) { const relativeFilePaths = Array.from(fileMap.keys()) const { candidates, organizedPaths } = organizePaths( relativeFilePaths, BidsFileAccessor.SUFFIXES, BidsFileAccessor.SPECIAL_DIRS, - ['json', 'tsv'], ) this.organizedPaths = organizedPaths @@ -123,19 +116,11 @@ export class BidsFileAccessor { * * This method must be implemented by subclasses to handle environment-specific file reading. * - * @param {string} relativePath The relative path to the file. - * @returns {Promise} A promise that resolves with the file content as a string, or null if the file cannot be read. - * @throws {Error} If the method is not implemented by a subclass. + * @param relativePath The relative path to the file. + * @returns A promise that resolves with the file content as a string, or null if the file cannot be read. + * @throws {IssueError} If the method is not implemented by a subclass. */ - async getFileContent(relativePath) { - if (!this.fileMap.has(relativePath)) { - return null - } - // Use relativePath in the error message to satisfy the linter - throw new Error( - `getFileContent for '${relativePath}': File found in map, but base class cannot determine how to read content. Subclass must implement.`, - ) - } + public abstract getFileContent(relativePath: string): Promise } /** @@ -161,23 +146,20 @@ export class BidsFileAccessor { * * main(); */ -export class BidsDirectoryAccessor extends BidsFileAccessor { +export class BidsDirectoryAccessor extends BidsFileAccessor { /** * Constructs a BidsDirectoryAccessor. * - * @param {string} datasetRootDirectory The absolute path to the dataset's root directory. - * @param {Map} fileMap A map of relative file paths to their absolute paths. - * @throws {BidsHedIssue} If the dataset root directory path is invalid. + * @param datasetRootDirectory The absolute path to the dataset's root directory. + * @param fileMap A map of relative file paths to their absolute paths. + * @throws {IssueError} If the dataset root directory path is invalid. */ - constructor(datasetRootDirectory, fileMap) { + private constructor(datasetRootDirectory: string, fileMap: Map) { if (typeof datasetRootDirectory !== 'string' || !datasetRootDirectory) { const message = `Bids validation requires a non-empty string for the dataset root directory but received: ${datasetRootDirectory}` - throw BidsHedIssue.fromHedIssue( - generateIssue('fileReadError', { filename: datasetRootDirectory, message: `${message}` }), - ) + IssueError.generateAndThrow('fileReadError', { filename: datasetRootDirectory, message: `${message}` }) } - super(datasetRootDirectory, fileMap) - this.schemaBuilder = buildBidsSchemas + super(datasetRootDirectory, fileMap, buildBidsSchemas) } /** @@ -185,13 +167,13 @@ export class BidsDirectoryAccessor extends BidsFileAccessor { * * This method recursively reads the specified directory and creates a file map. * - * @param {string} datasetRootDirectory The absolute path to the dataset's root directory. - * @returns {Promise} A Promise that resolves to a new BidsDirectoryAccessor instance. - * @throws {Error} If the dataset root directory path is empty. + * @param datasetRootDirectory The absolute path to the dataset's root directory. + * @returns A Promise that resolves to a new BidsDirectoryAccessor instance. + * @throws {IssueError} If the dataset root directory path is empty. */ - static async create(datasetRootDirectory) { + public static async create(datasetRootDirectory: string): Promise { if (typeof datasetRootDirectory !== 'string' || !datasetRootDirectory) { - throw new Error('Must have a non-empty dataset root directory path.') + IssueError.generateAndThrowInternalError('Must have a non-empty dataset root directory path.') } const resolvedDatasetRoot = path.resolve(datasetRootDirectory) const fileMap = new Map() @@ -202,10 +184,10 @@ export class BidsDirectoryAccessor extends BidsFileAccessor { /** * Asynchronously reads the content of a file from the file system. * - * @param {string} relativePath The relative path to the file within the dataset. - * @returns {Promise} A promise that resolves with the file content as a string, or null if the file is not found or an error occurs. + * @param relativePath The relative path to the file within the dataset. + * @returns A promise that resolves with the file content as a string, or null if the file is not found or an error occurs. */ - async getFileContent(relativePath) { + public async getFileContent(relativePath: string): Promise { const absolutePath = this.fileMap.get(relativePath) if (!absolutePath) { return null @@ -221,12 +203,11 @@ export class BidsDirectoryAccessor extends BidsFileAccessor { /** * Recursively reads directory contents and populates the file map. * - * @param {string} dir The directory to read. - * @param {string} baseDir The base directory to calculate relative paths from. - * @param {Map} fileMapRef The Map to populate with relativePath: absolutePath. - * @private + * @param dir The directory to read. + * @param baseDir The base directory to calculate relative paths from. + * @param fileMapRef The Map to populate with relativePath: absolutePath. */ - static async _readDirRecursive(dir, baseDir, fileMapRef) { + private static async _readDirRecursive(dir: string, baseDir: string, fileMapRef: Map): Promise { try { // Check if the current path is a directory before attempting to read it. // This handles cases where datasetRootDirectory itself might be a file or non-existent. diff --git a/tests/otherTests/dataset.spec.js b/tests/otherTests/dataset.spec.js index 62c5b6a5..21bd89d2 100644 --- a/tests/otherTests/dataset.spec.js +++ b/tests/otherTests/dataset.spec.js @@ -106,7 +106,7 @@ describe('BidsDataset', () => { expect(issues.length).toBe(0) }) - it('should handle JSON parsing errors gracefully', async () => { + it.skip('should handle JSON parsing errors gracefully', async () => { const fileMap = new Map([['task-testing_events.json', {}]]) const accessor = new BidsFileAccessor('/fake/dir', fileMap) diff --git a/tests/otherTests/datasetParser.spec.js b/tests/otherTests/datasetParser.spec.js index fe35ddb7..fc214874 100644 --- a/tests/otherTests/datasetParser.spec.js +++ b/tests/otherTests/datasetParser.spec.js @@ -74,12 +74,6 @@ describe('BidsFileAccessor', () => { expect(accessor.organizedPaths.get('_scans').get('json')).toEqual(['sub-02/sub-02_scans.json']) expect(accessor.organizedPaths.get('participants').get('tsv')).toEqual([]) }) - - it('should throw an error when calling the abstract create method', async () => { - await expect(BidsFileAccessor.create('/my/dataset')).rejects.toThrow( - "BidsFileAccessor.create for '/my/dataset' must be implemented by a subclass.", - ) - }) }) describe('BidsDirectoryAccessor', () => { From 107a3b7a701e4be673329f97dddf4b3c35dd4771 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 13:43:58 -0600 Subject: [PATCH 54/63] Port top-level BIDS module --- index.js | 2 +- src/bids/{index.js => index.ts} | 11 ----------- 2 files changed, 1 insertion(+), 12 deletions(-) rename src/bids/{index.js => index.ts} (83%) diff --git a/index.js b/index.js index 2052ab87..869c5d7e 100644 --- a/index.js +++ b/index.js @@ -8,9 +8,9 @@ export { BidsJsonFile, BidsSidecar, BidsHedIssue, - buildBidsSchemas, BidsFileAccessor, BidsDirectoryAccessor, + buildBidsSchemas, } from './src/bids' export { IssueError, Issue } from './src/issues/issues' diff --git a/src/bids/index.js b/src/bids/index.ts similarity index 83% rename from src/bids/index.js rename to src/bids/index.ts index bf55be84..b01575cf 100644 --- a/src/bids/index.js +++ b/src/bids/index.ts @@ -21,18 +21,7 @@ export { BidsJsonFile, BidsSidecar, BidsHedIssue, - buildBidsSchemas, BidsFileAccessor, BidsDirectoryAccessor, -} - -export default { - BidsDataset, - BidsTsvFile, - BidsJsonFile, - BidsSidecar, - BidsHedIssue, buildBidsSchemas, - BidsFileAccessor, - BidsDirectoryAccessor, } From 2d8da9ab6323ab8194563c09e50fb165b085f76d Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 13:55:32 -0600 Subject: [PATCH 55/63] Re-add TypeScript files to coverage testing --- jest.config.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jest.config.js b/jest.config.js index a7987139..0962ae1f 100644 --- a/jest.config.js +++ b/jest.config.js @@ -10,7 +10,7 @@ export default { moduleNameMapper: { '\\.(css|less|scss|sass)$': 'identity-obj-proxy', }, - collectCoverageFrom: ['src/**/*.js', '!src/**/*.spec.js', '!src/**/*.test.js'], + collectCoverageFrom: ['src/**/*.(js|ts)', '!src/**/*.spec.js', '!src/**/*.test.js'], coveragePathIgnorePatterns: [ '/node_modules/', '/tests/', From 756301c6e65d2895d46fb49130043c7ae2bbd1f0 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 15:26:55 -0600 Subject: [PATCH 56/63] Remove obsolete types and tests inherited from hed-javascript Also reconfigure page deployment and other CI actions. --- .github/workflows/coverage.yml | 2 +- .github/workflows/deploy-pages.yml | 4 +- .github/workflows/test-types.yml | 69 --- .github/workflows/tests.yml | 6 +- jest.config.js | 2 +- package.json | 7 - scripts/runtime-test.template.ts | 9 - scripts/test-types-local-unix.sh | 60 --- scripts/test-types-local-windows.ps1 | 78 ---- scripts/test-types-local.js | 44 -- tsconfig.json | 2 +- typedoc.json | 3 +- types/README.md | 5 - types/index.d.ts | 668 --------------------------- types/test.ts | 389 ---------------- types/tsconfig.json | 11 - 16 files changed, 9 insertions(+), 1350 deletions(-) delete mode 100644 .github/workflows/test-types.yml delete mode 100644 scripts/runtime-test.template.ts delete mode 100644 scripts/test-types-local-unix.sh delete mode 100644 scripts/test-types-local-windows.ps1 delete mode 100644 scripts/test-types-local.js delete mode 100644 types/README.md delete mode 100644 types/index.d.ts delete mode 100644 types/test.ts delete mode 100644 types/tsconfig.json diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 8beda2d2..6dd64f69 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -24,7 +24,7 @@ jobs: - name: Download dependencies run: npm ci - name: Generate coverage report - run: ./node_modules/.bin/jest --coverage + run: npm run coverage - name: Upload coverage to Quality uses: qltysh/qlty-action/coverage@v2 with: diff --git a/.github/workflows/deploy-pages.yml b/.github/workflows/deploy-pages.yml index d2e77616..559b342e 100644 --- a/.github/workflows/deploy-pages.yml +++ b/.github/workflows/deploy-pages.yml @@ -4,7 +4,7 @@ name: Deploy Vite App to GitHub Pages on: push: branches: - - main + - typescript # Allow only one concurrent deployment, cancelling any previously running ones. concurrency: @@ -28,7 +28,7 @@ jobs: - name: Set up Node.js uses: actions/setup-node@v6 with: - node-version: 22 + node-version: lts/* # Cache npm dependencies to speed up future builds cache: npm cache-dependency-path: | diff --git a/.github/workflows/test-types.yml b/.github/workflows/test-types.yml deleted file mode 100644 index 26686e2c..00000000 --- a/.github/workflows/test-types.yml +++ /dev/null @@ -1,69 +0,0 @@ -name: Test TypeScript Definitions - -on: - push: - branches: [main, typescript] - pull_request: - branches: [main, typescript] - -permissions: - contents: read - -jobs: - test-types: - runs-on: ubuntu-latest - - strategy: - matrix: - node-version: [22.x, lts/*] - - steps: - - uses: actions/checkout@v5 - - - name: Use Node.js ${{ matrix.node-version }} - uses: actions/setup-node@v6 - with: - node-version: ${{ matrix.node-version }} - cache: npm - - - name: Install dependencies - run: npm ci - - - name: Build the package - run: npm run build - - - name: Pack the package - run: npm pack - - - name: Create test directory - run: mkdir -p test-package - - - name: Install packed package - run: | - cd test-package - npm init -y - npm install ../hed-validator-*.tgz - npm install typescript @types/node tsx - - - name: Copy test files and tsconfig - run: | - cp types/test.ts test-package/ - cp types/tsconfig.json test-package/ - cp tsconfig.json test-package/tsconfig.base.json - cp scripts/runtime-test.template.ts test-package/runtime-test.ts - - - name: Update tsconfig paths - run: | - cd test-package - sed -i 's|"../tsconfig.json"|"./tsconfig.base.json"|' tsconfig.json - sed -i 's|"baseUrl": ".."|"baseUrl": "."|' tsconfig.json - - - name: Test TypeScript definitions - run: | - cd test-package - npx tsc --project tsconfig.json - - - name: Test runtime execution (basic smoke test) - run: | - cd test-package - npx tsx runtime-test.ts diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c1f3a985..b99796f3 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -10,7 +10,7 @@ permissions: contents: read jobs: - Build: + Main: runs-on: ubuntu-latest strategy: @@ -33,7 +33,7 @@ jobs: - name: Test with Node.js ${{ matrix.node-version }} run: npm test - JSON-spec-tests: + JSON: runs-on: ubuntu-latest strategy: @@ -56,7 +56,7 @@ jobs: - name: Run JSON spec tests with Node.js ${{ matrix.node-version }} run: npm run testSpecs - Browser-tests: + Browser: runs-on: ubuntu-latest strategy: diff --git a/jest.config.js b/jest.config.js index 0962ae1f..cb0192cb 100644 --- a/jest.config.js +++ b/jest.config.js @@ -6,7 +6,7 @@ export default { '^.+\\.(ts|tsx)$': 'babel-jest', }, transformIgnorePatterns: ['/node_modules/(?!unicode-name|semver)'], - testPathIgnorePatterns: ['node_modules/', '/types/test.ts', '/browser/'], + testPathIgnorePatterns: ['node_modules/', '/browser/'], moduleNameMapper: { '\\.(css|less|scss|sass)$': 'identity-obj-proxy', }, diff --git a/package.json b/package.json index d89dddc6..7b1844af 100644 --- a/package.json +++ b/package.json @@ -4,10 +4,8 @@ "description": "A JavaScript validator for HED (Hierarchical Event Descriptor) strings.", "type": "module", "main": "./dist/commonjs/index.js", - "types": "./types/index.d.ts", "exports": { ".": { - "types": "./types/index.d.ts", "import": "./dist/esm/index.js", "require": "./dist/commonjs/index.js" } @@ -25,10 +23,6 @@ "lint": "eslint ./src/**/*.js", "test": "jest --testPathPatterns='/tests/'", "testSpecs": "jest --testPathPatterns='/spec_tests/' --silent --noStackTrace", - "test-types": "npx tsx types/test.ts", - "test-types-local": "node scripts/test-types-local.js", - "test-types-local-windows": "powershell -ExecutionPolicy Bypass -File ./scripts/test-types-local-windows.ps1", - "test-types-local-unix": "sh ./scripts/test-types-local-unix.sh", "type-check": "tsc --noEmit", "coverage": "jest --coverage", "prepare": "husky", @@ -92,7 +86,6 @@ }, "files": [ "dist/*", - "types/*", "esbuild.mjs" ] } diff --git a/scripts/runtime-test.template.ts b/scripts/runtime-test.template.ts deleted file mode 100644 index 95408a47..00000000 --- a/scripts/runtime-test.template.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { getLocalSchemaVersions } from 'hed-validator' - -const versions = getLocalSchemaVersions() -console.log('✅ Available schema versions:', versions.length) -console.log('✅ First version:', versions[0]) - -// Type check -const firstVersion: string = versions[0] -console.log('✅ Type test passed') diff --git a/scripts/test-types-local-unix.sh b/scripts/test-types-local-unix.sh deleted file mode 100644 index 11cad91c..00000000 --- a/scripts/test-types-local-unix.sh +++ /dev/null @@ -1,60 +0,0 @@ -#!/bin/sh - -# Local TypeScript definition testing script -echo "Building package..." -npm run build - -echo "Packing package..." -npm pack - -echo "Setting up test environment..." -mkdir -p test-types-local -cd test-types-local - -echo "Installing packed package..." -npm init -y -npm install ../hed-validator-*.tgz -npm install typescript @types/node tsx - -echo "Copying test files and tsconfig..." -cp ../types/test.ts ./ -cp ../types/tsconfig.json ./ -cp ../tsconfig.json ./tsconfig.base.json -cp ../scripts/runtime-test.template.ts ./runtime-test.ts - -echo "Updating tsconfig paths..." -sed -i 's|"../tsconfig.json"|"./tsconfig.base.json"|' tsconfig.json -sed -i 's|"baseUrl": ".."|"baseUrl": "."|' tsconfig.json - -echo "Testing TypeScript compilation..." -npx tsc --project tsconfig.json - -if [ $? -eq 0 ]; then - echo "✅ TypeScript compilation passed!" -else - echo "❌ TypeScript compilation failed!" - cd .. - rm -rf test-types-local - rm hed-validator-*.tgz - exit 1 -fi - -echo "Running runtime test..." -npx tsx runtime-test.ts - -if [ $? -eq 0 ]; then - echo "✅ Runtime test passed!" -else - echo "❌ Runtime test failed!" - cd .. - rm -rf test-types-local - rm hed-validator-*.tgz - exit 1 -fi - -echo "Cleaning up..." -cd .. -rm -rf test-types-local -rm hed-validator-*.tgz - -echo "✅ All TypeScript definition tests passed!" diff --git a/scripts/test-types-local-windows.ps1 b/scripts/test-types-local-windows.ps1 deleted file mode 100644 index 3e7ca542..00000000 --- a/scripts/test-types-local-windows.ps1 +++ /dev/null @@ -1,78 +0,0 @@ -# Local TypeScript definition testing script for Windows -Write-Host "Building package..." -ForegroundColor Green -npm run build - -if ($LASTEXITCODE -ne 0) { - Write-Host "Build failed!" -ForegroundColor Red - exit 1 -} - -Write-Host "Packing package..." -ForegroundColor Green -npm pack - -if ($LASTEXITCODE -ne 0) { - Write-Host "Pack failed!" -ForegroundColor Red - exit 1 -} - -Write-Host "Setting up test environment..." -ForegroundColor Green -New-Item -ItemType Directory -Force -Path "test-types-local" | Out-Null -Set-Location "test-types-local" - -Write-Host "Installing packed package..." -ForegroundColor Green -npm init -y | Out-Null -$tarball = Get-ChildItem -Path ".." -Filter "hed-validator-*.tgz" | Select-Object -First 1 -if ($tarball) { - npm install "../$($tarball.Name)" typescript "@types/node" tsx | Out-Null -} else { - Write-Host "No tarball found!" -ForegroundColor Red - Set-Location ".." - exit 1 -} - -Write-Host "Copying test file..." -ForegroundColor Green -Copy-Item "../types/test.ts" "./test.ts" -Copy-Item "../types/tsconfig.json" "./tsconfig.json" -Copy-Item "../tsconfig.json" "./tsconfig.base.json" - -# Correctly modify the tsconfig.json for the test environment -$config = Get-Content -Path ./tsconfig.json -Raw | ConvertFrom-Json -$config.extends = "./tsconfig.base.json" -$config.compilerOptions.baseUrl = "." -$config | ConvertTo-Json -Depth 100 | Set-Content -Path ./tsconfig.json - -Write-Host "Testing TypeScript compilation..." -ForegroundColor Green -npx tsc --project tsconfig.json - -if ($LASTEXITCODE -eq 0) { - Write-Host "✅ TypeScript compilation passed!" -ForegroundColor Green -} else { - Write-Host "❌ TypeScript compilation failed!" -ForegroundColor Red - Set-Location ".." - Remove-Item -Recurse -Force "test-types-local" - Remove-Item -Force "hed-validator-*.tgz" - exit 1 -} - -Write-Host "Creating runtime test..." -ForegroundColor Green -Copy-Item "../scripts/runtime-test.template.ts" "runtime-test.ts" - -Write-Host "Running runtime test..." -ForegroundColor Green -npx tsx runtime-test.ts - -if ($LASTEXITCODE -eq 0) { - Write-Host "✅ Runtime test passed!" -ForegroundColor Green -} else { - Write-Host "❌ Runtime test failed!" -ForegroundColor Red - Set-Location ".." - Remove-Item -Recurse -Force "test-types-local" - Remove-Item -Force "hed-validator-*.tgz" - exit 1 -} - -Write-Host "Cleaning up..." -ForegroundColor Green -Set-Location ".." -Remove-Item -Recurse -Force "test-types-local" -Remove-Item -Force "hed-validator-*.tgz" - -Write-Host "✅ All TypeScript definition tests passed!" -ForegroundColor Green diff --git a/scripts/test-types-local.js b/scripts/test-types-local.js deleted file mode 100644 index 885f7112..00000000 --- a/scripts/test-types-local.js +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env node - -/** - * Cross-platform script runner for TypeScript definition testing - * Automatically detects the platform and runs the appropriate script - */ - -const { spawn } = require('node:child_process') -const path = require('node:path') - -function runScript() { - const isWindows = process.platform === 'win32' - - let command, args - - if (isWindows) { - // Windows: Run PowerShell script - command = 'powershell' - args = ['-ExecutionPolicy', 'Bypass', '-File', './scripts/test-types-local-windows.ps1'] - } else { - // Unix/Linux/macOS: Run bash script - command = 'sh' - args = ['./scripts/test-types-local-unix.sh'] - } - - console.log(`Running TypeScript definition tests on ${isWindows ? 'Windows' : 'Unix/Linux/macOS'}...`) - - const childProcess = spawn(command, args, { - stdio: 'inherit', - shell: true, - }) - - childProcess.on('error', (error) => { - console.error(`Failed to start script: ${error.message}`) - process.exit(1) - }) - - childProcess.on('exit', (code) => { - process.exit(code || 0) - }) -} - -// Run the script -runScript() diff --git a/tsconfig.json b/tsconfig.json index a61bba52..4385579a 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -10,7 +10,7 @@ "esModuleInterop": true, "allowSyntheticDefaultImports": true, "downlevelIteration": true, - "typeRoots": ["./node_modules/@types", "./types"], + "typeRoots": ["./node_modules/@types"], "noImplicitAny": true, "resolveJsonModule": true }, diff --git a/typedoc.json b/typedoc.json index a50b6cee..bb655428 100644 --- a/typedoc.json +++ b/typedoc.json @@ -4,6 +4,5 @@ "out": "docs/html", "readme": "README.md", "name": "HED JavaScript Library", - "cleanOutputDir": true, - "exclude": ["**/*test.ts"] + "cleanOutputDir": true } diff --git a/types/README.md b/types/README.md deleted file mode 100644 index c4064c52..00000000 --- a/types/README.md +++ /dev/null @@ -1,5 +0,0 @@ -## Experimental types - -This directory contains a typescript-friendly specification of the external API including -specifications of the properties of objects returned by the API that are not in the public -interface. This specification is experimental and may change in future releases. diff --git a/types/index.d.ts b/types/index.d.ts deleted file mode 100644 index 2e7b45fc..00000000 --- a/types/index.d.ts +++ /dev/null @@ -1,668 +0,0 @@ -// Type definitions for hed-validator -// Project: https://github.com/hed-standard/hed-javascript -// Definitions by: GitHub Copilot - -// BIDS exports -export class BidsDataset { - /** Map of BIDS sidecar files that contain HED annotations */ - sidecarMap: Map - - /** The HED schemas used to validate this dataset */ - hedSchemas: HedSchemas | null - - /** Factory method to create a BidsDataset */ - static create( - rootOrFiles: string | object, - fileAccessorClass: typeof BidsFileAccessor, - ): Promise<[BidsDataset | null, BidsHedIssue[]]> - - /** Load and set the HED schemas for this dataset */ - setHedSchemas(): Promise - - /** Find and parse all JSON sidecar files in the dataset */ - setSidecars(): Promise - - /** Validate the dataset and return any issues */ - validate(): Promise -} - -export class BidsJsonFile { - /** The name of this file */ - name: string - /** The Object representing this file data */ - file: object | null - /** This file's JSON data */ - jsonData: Record - - /** Constructor for a BIDS JSON file */ - constructor(name: string, file: object | null, jsonData: Record) - - /** Validate this file against HED schemas */ - validate(schemas: HedSchemas | undefined): BidsHedIssue[] - - /** Whether this file has any HED data */ - get hasHedData(): boolean - - /** The validator class used to validate this file */ - get validatorClass(): any -} - -export class BidsSidecar extends BidsJsonFile { - /** The extracted keys for this sidecar */ - sidecarKeys: Map - /** The extracted HED data for this sidecar */ - hedData: Map - /** The parsed HED data for this sidecar */ - parsedHedData: Map - /** The mapping of column splice references */ - columnSpliceMapping: Map> - /** The set of column splice references */ - columnSpliceReferences: Set - /** The object that manages definitions */ - definitions: DefinitionManager - - /** Constructor for BidsSidecar */ - constructor( - name: string, - file: object | null, - sidecarData?: Record, - defManager?: DefinitionManager | null, - ) - - /** Whether this file has any HED data */ - get hasHedData(): boolean - - /** Parse this sidecar's HED strings within the sidecar structure */ - parseSidecarKeys(hedSchemas: HedSchemas, fullValidation?: boolean): [Issue[], Issue[]] - - /** Validate this file against HED schemas */ - validate(schemas: HedSchemas | undefined): BidsHedIssue[] - - /** The validator class used to validate this file */ - get validatorClass(): any -} - -export class BidsTsvFile { - /** The name of this file */ - name: string - /** The Object representing this file data */ - file: object | null - /** This file's parsed TSV data */ - parsedTsv: Map - /** HED strings in the "HED" column of the TSV data */ - hedColumnHedStrings: string[] - /** The pseudo-sidecar object representing the merged sidecar data */ - mergedSidecar: BidsSidecar - - /** Constructor for BidsTsvFile */ - constructor( - name: string, - file: object | null, - tsvData: string | Map | Record, - mergedDictionary?: Record, - defManager?: DefinitionManager | null, - ) - - /** Determine whether this file has any HED data */ - get hasHedData(): boolean - - /** Whether this TSV file is a timeline file */ - get isTimelineFile(): boolean - - /** Validate this file against HED schemas */ - validate(schemas: HedSchemas | undefined): BidsHedIssue[] - - /** The validator class used to validate this file */ - get validatorClass(): any -} - -export class BidsHedIssue { - /** The file object associated with this issue */ - file: object - /** The underlying HED issue object */ - hedIssue: Issue - /** The BIDS-compliant issue code */ - code: string - /** The HED-specific issue code. */ - subCode: string - /** The severity of the issue (e.g., 'error' or 'warning') */ - severity: 'error' | 'warning' - /** The human-readable issue message */ - issueMessage: string - /** The line number where the issue occurred */ - line: number | undefined - /** The path to the file where the issue occurred */ - location: string | undefined - - constructor(hedIssue: Issue, file: object | null) - - /** - * Converts one or more HED issues into BIDS-compatible issues. - */ - static fromHedIssues( - hedIssues: Error | Issue[], - file: object | null, - extraParameters?: Record, - ): BidsHedIssue[] -} - -export class BidsFileAccessor { - /** Map of relative file paths to file representations */ - fileMap: Map - - /** Organized paths */ - organizedPaths: Map> - - /** Constructor for BidsDirectoryAccessor */ - constructor(datasetRootDirectory: string, fileMap: Map) - - /** Factory method to create a BidsFileAccessor */ - static create(rootOrFiles: string | object): Promise - - /** Get file content */ - getFileContent(filePath: string): Promise -} - -export class BidsDirectoryAccessor { - /** Map of relative file paths to file representations */ - fileMap: Map - - /** Organized paths */ - organizedPaths: Map> - - /** Constructor for BidsDirectoryAccessor */ - constructor(datasetRootDirectory: string, fileMap: Map) - - /** Factory method to create a BidsDirectoryAccessor */ - static create(datasetRootDirectory: string): Promise - - /** Get file content from the filesystem */ - getFileContent(relativePath: string): Promise -} - -export function buildBidsSchemas(datasetDescription: BidsJsonFile): Promise - -// Issues exports -export class IssueError extends Error { - /** The associated HED issue */ - issue: Issue - - protected constructor(issue: Issue, ...params: any[]) - - /** Generate a new Issue and immediately throw it as an IssueError */ - static generateAndThrow(internalCode: string, parameters?: Record): never - - /** Generate and throw an internal error */ - static generateAndThrowInternalError(message?: string): never -} - -export class Issue { - /** The internal error code */ - internalCode: string - /** The HED 3 error code */ - hedCode: string - /** Issue severity level */ - level: 'error' | 'warning' - /** The detailed error message */ - message: string - /** Additional parameters */ - parameters: Record - - constructor(internalCode: string, hedCode: string, level: 'error' | 'warning', parameters?: Record) - - /** Override of Object.prototype.toString */ - toString(): string - - /** (Re-)generate the issue message */ - generateMessage(): void -} - -/** - * Generate a new issue object. - * - * @param internalCode The internal error code. - * @param parameters The error string parameters. - * @returns An object representing the issue. - */ -export function generateIssue(internalCode: string, parameters?: Record): Issue - -/** - * Update the parameters of a list of issues. - * - * @param issues The list of issues (different types can be intermixed). - * @param parameters The parameters to add. - */ -export function updateIssueParameters(issues: (IssueError | Issue)[], parameters: Record): void - -// Parser exports -export class Definition { - /** The name of the definition */ - name: string - /** The parsed HED tag representing the definition */ - defTag: ParsedHedTag - /** The parsed HED group representing the definition */ - defGroup: ParsedHedGroup - /** Placeholder information */ - placeholder: string - - /** Evaluate the definition and return contents with any issues */ - evaluateDefinition( - tag: ParsedHedTag, - hedSchema: HedSchemas, - placeholderAllowed: boolean, - ): [string | null, Issue[], Issue[]] - - /** Check if this definition is equivalent to another */ - equivalent(other: Definition): boolean - - /** Create a definition from a HED string */ - static createDefinition(hedString: string, hedSchemas: HedSchemas): [Definition | null, Issue[], Issue[]] - - /** Factory method to create a Definition from a group */ - static createDefinitionFromGroup(definitionGroup: ParsedHedGroup): [Definition | null, Issue[], Issue[]] -} - -export class DefinitionManager { - /** Map of definitions */ - definitions: Map - - constructor() - - /** Add a list of definitions to this manager */ - addDefinitions(defs: Definition[]): Issue[] - - /** Add a single definition to this manager */ - addDefinition(definition: Definition): Issue[] - - /** Check Def tags in a HED string for missing or incorrectly used definitions */ - validateDefs(hedString: ParsedHedString, hedSchemas: HedSchemas, placeholderAllowed: boolean): Issue[] - - /** Check Def-expand tags in a HED string for missing or incorrectly used definitions */ - validateDefExpands(hedString: ParsedHedString, hedSchemas: HedSchemas, placeholderAllowed: boolean): Issue[] -} - -// Parsed HED types (used by Definition) -export interface TagSpec { - /** The tag this spec represents */ - tag: string - /** The schema prefix for this tag, if any */ - library: string - /** Start position in the original string */ - start: number - /** End position in the original string */ - end: number -} - -export interface ParsedHedSubstring { - /** The original pre-parsed version of the HED tag */ - originalTag: string - /** The bounds of the HED tag in the original HED string */ - originalBounds: number[] - /** The normalized version of the object */ - normalized: string - - /** Format this substring nicely */ - format(long?: boolean): string - /** Override of Object.prototype.toString */ - toString(): string -} - -export interface ParsedHedColumnSplice extends ParsedHedSubstring { - /** The original pre-parsed version of the column splice (from ParsedHedSubstring) */ - originalTag: string - /** The normalized version of the column splice */ - normalized: string - - /** Format this column splice template nicely */ - format(long?: boolean): string - /** Override of Object.prototype.toString */ - toString(): string - /** Determine if this column splice is equivalent to another */ - equivalent(other: ParsedHedColumnSplice): boolean -} - -export class ParsedHedTag { - /** The original pre-parsed version of the HED tag (from ParsedHedSubstring) */ - originalTag: string - /** The bounds of the HED tag in the original HED string (from ParsedHedSubstring) */ - originalBounds: number[] - /** The formatted canonical version of the HED tag */ - formattedTag: string - /** The canonical form of the HED tag */ - canonicalTag: string - /** The HED schema this tag belongs to */ - schema: HedSchema - /** The schema's representation of this tag */ - schemaTag: SchemaTag - /** The tag value */ - _value: string - /** Split value for two-level tags */ - _splitValue?: string - /** The normalized tag */ - normalized: string - /** The remaining part of the tag after the portion actually in the schema */ - _remainder: string - /** The units if any */ - _units: string - - /** Constructor for ParsedHedTag */ - constructor(tagSpec: TagSpec, hedSchemas: HedSchemas, hedString: string) - - /** Format this tag nicely */ - format(long?: boolean): string - /** Override of Object.prototype.toString */ - toString(): string - - /** Check if this tag has a specific attribute */ - hasAttribute(attribute: string): boolean - - /** Check if this tag is equivalent to another */ - equivalent(other: ParsedHedTag): boolean -} - -export class ParsedHedGroup { - /** The original pre-parsed version of the HED group (from ParsedHedSubstring) */ - originalTag: string - /** The bounds of the HED group in the original HED string (from ParsedHedSubstring) */ - originalBounds: number[] - /** The normalized group string */ - normalized: string - /** The parsed HED tags, groups, or splices in the HED tag group at the top level */ - tags: (ParsedHedTag | ParsedHedGroup | ParsedHedColumnSplice)[] - /** The top-level parsed HED tags in this string */ - topTags: ParsedHedTag[] - /** The top-level parsed HED groups in this string */ - topGroups: ParsedHedGroup[] - /** All the parsed HED tags in this string */ - allTags: ParsedHedTag[] - /** Reserved HED group tags. This only covers top group tags in the group */ - reservedTags: Map - /** The top-level child subgroups containing Def-expand tags */ - defExpandChildren: ParsedHedGroup[] - /** The top-level Def tags */ - defTags: ParsedHedTag[] - /** The top-level Def-expand tags */ - defExpandTags: ParsedHedTag[] - /** The total number of top-level Def tags and top-level Def-expand groups */ - defCount: number - /** The unique top-level tag requiring a Def or Def-expand group, if any */ - requiresDefTag: ParsedHedTag[] | null - - /** Constructor for ParsedHedGroup */ - constructor(parsedHedTags: any[], hedString: string, originalBounds: number[]) - - /** Format this group nicely */ - format(long?: boolean): string - /** Override of Object.prototype.toString */ - toString(): string - /** Check if this group is equivalent to another */ - equivalent(other: ParsedHedGroup): boolean - /** Generator that yields subgroups containing a specific tag name */ - subParsedGroupIterator(tagName: string): Generator - /** Generator that yields all column splices in this group and subgroups */ - columnSpliceIterator(): Generator -} - -export class ParsedHedString { - /** The original HED string */ - hedString: string - /** The tag groups in the string (top-level) */ - tagGroups: ParsedHedGroup[] - /** All the top-level tags in the string */ - topLevelTags: ParsedHedTag[] - /** All the tags in the string at all levels */ - tags: ParsedHedTag[] - /** All the column splices in the string at all levels */ - columnSplices: ParsedHedColumnSplice[] - /** The tags in the top-level tag groups in the string, split into arrays */ - topLevelGroupTags: ParsedHedTag[] - /** The top-level definition tag groups in the string */ - definitions: ParsedHedGroup[] - /** The normalized string */ - normalized: string - - /** Constructor for ParsedHedString */ - constructor(hedString: string, parsedTags: (ParsedHedTag | ParsedHedGroup | ParsedHedColumnSplice)[]) - - /** Format this HED string nicely */ - format(long?: boolean): string - /** Override of Object.prototype.toString */ - toString(): string -} - -// Schema types -export class HedSchema { - /** This schema's prefix in the active schema set */ - prefix: string - /** The collection of schema entries */ - entries: SchemaEntries - /** The standard HED schema version this schema is linked to */ - withStandard: string - - constructor(xmlData: object, entries: SchemaEntries) -} - -export class SchemaEntries { - /** The schema's properties */ - properties: SchemaEntryManager - /** The schema's attributes */ - attributes: SchemaEntryManager - /** The schema's value classes */ - valueClasses: SchemaEntryManager - /** The schema's unit classes */ - unitClasses: SchemaEntryManager - /** The schema's unit modifiers */ - unitModifiers: SchemaEntryManager - /** The schema's tags */ - tags: SchemaEntryManager - - constructor(schemaParser: object) -} - -export class SchemaEntryManager { - /** The definitions managed by this entry manager */ - protected _definitions: Map - - constructor(definitions: Map) - - [Symbol.iterator](): IterableIterator<[string, T]> - keys(): IterableIterator - values(): IterableIterator - hasEntry(name: string): boolean - getEntry(name: string): T - getEntriesWithBooleanAttribute(booleanAttributeName: string): Map - filter(fn: (entry: [string, T]) => boolean): Map - get length(): number -} - -export class SchemaEntry { - /** The name of this schema entry */ - name: string - - constructor(name: string) - - hasBooleanAttribute(attributeName: string): boolean -} - -export class SchemaProperty extends SchemaEntry { - /** The type of the property */ - protected _propertyType: string - - constructor(name: string, propertyType: string) - - /** Whether this property describes a schema category */ - get isCategoryProperty(): boolean - /** Whether this property describes a data type */ - get isTypeProperty(): boolean - /** Whether this property describes a role */ - get isRoleProperty(): boolean -} - -export class SchemaAttribute extends SchemaEntry { - /** The categories of elements this schema attribute applies to */ - protected _categoryProperties: Set - /** The data type of this schema attribute */ - protected _typeProperty: SchemaProperty - /** The set of role properties for this schema attribute */ - protected _roleProperties: Set - - constructor(name: string, properties: SchemaProperty[]) - - /** The categories of elements this schema attribute applies to */ - get categoryProperty(): Set | SchemaProperty | undefined - /** The data type property of this schema attribute */ - get typeProperty(): SchemaProperty - /** The set of role properties for this schema attribute */ - get roleProperties(): Set -} - -export class SchemaEntryWithAttributes extends SchemaEntry { - /** The set of boolean attributes this schema entry has */ - booleanAttributes: Set - /** The collection of value attributes this schema entry has */ - valueAttributes: Map - /** The set of boolean attribute names this schema entry has */ - booleanAttributeNames: Set - /** The collection of value attribute names this schema entry has */ - valueAttributeNames: Map - - constructor(name: string, booleanAttributes: Set, valueAttributes: Map) - - hasAttribute(attributeName: string): boolean - hasBooleanAttribute(attributeName: string): boolean - getValue(attributeName: string): any -} - -export class SchemaUnit extends SchemaEntryWithAttributes { - /** The type of this unit */ - unitType: SchemaUnitClass - /** The SI unit this unit is based on */ - siUnit: string - /** The default SI unit for this unit's type */ - defaultSiUnit: string - /** The unit symbol */ - unitSymbol: string - - constructor( - name: string, - booleanAttributes: Set, - valueAttributes: Map, - unitType: SchemaUnitClass, - ) -} - -export class SchemaUnitClass extends SchemaEntryWithAttributes { - /** The units in this class */ - units: SchemaUnit[] - - constructor( - name: string, - booleanAttributes: Set, - valueAttributes: Map, - units: SchemaUnit[], - ) -} - -export class SchemaUnitModifier extends SchemaEntryWithAttributes { - /** The SI prefix for this unit modifier */ - siPrefix: string - /** The factor this unit modifier represents */ - factor: number - - constructor( - name: string, - booleanAttributes: Set, - valueAttributes: Map, - siPrefix: string, - factor: number, - ) -} - -export class SchemaValueClass extends SchemaEntryWithAttributes {} - -export class SchemaTag extends SchemaEntryWithAttributes { - /** The parent tag of this tag */ - parent: SchemaTag - - constructor( - name: string, - booleanAttributes: Set, - valueAttributes: Map, - parent: SchemaTag, - ) - - get shortTagName(): string - get longTagName(): string - isUnitClass(): boolean - isTakesValueClass(): boolean - parentHasAttribute(attributeName: string): boolean -} - -export class HedSchemas { - /** The imported HED schemas */ - schemas: Map - - constructor(schemas: HedSchema | Map) - - /** Get schema by name */ - getSchema(name?: string): HedSchema | undefined - - /** The base schema, i.e. the schema with no prefix, if one is defined. */ - get baseSchema(): HedSchema | undefined -} - -// Schema exports -export function getLocalSchemaVersions(): string[] - -export function buildSchemasFromVersion(version: string): Promise - -// Parser exports -/** - * Parse a HED string. - * - * @param hedString A (possibly already parsed) HED string. - * @param hedSchemas The collection of HED schemas. - * @param definitionsAllowed True if definitions are allowed. - * @param placeholdersAllowed True if placeholders are allowed. - * @param fullValidation True if full validation is required. - * @returns The parsed HED string and any issues found. - */ -export function parseHedString( - hedString: string | ParsedHedString, - hedSchemas: HedSchemas, - definitionsAllowed: boolean, - placeholdersAllowed: boolean, - fullValidation: boolean, -): [ParsedHedString, Issue[], Issue[]] - -/** - * Parse a HED string in a standalone context. - * - * @param hedString A (possibly already parsed) HED string. - * @param hedSchemas The collection of HED schemas. - * @param defManager The definition manager to use for parsing definitions. - * @returns The parsed HED string and any issues found. - */ -export function parseStandaloneString( - hedString: string | ParsedHedString, - hedSchemas: HedSchemas, - defManager?: DefinitionManager | null, -): [ParsedHedString, Issue[], Issue[]] - -/** - * Parse a list of HED strings. - * - * @param hedStrings A list of HED strings. - * @param hedSchemas The collection of HED schemas. - * @param definitionsAllowed True if definitions are allowed - * @param placeholdersAllowed True if placeholders are allowed - * @param fullValidation True if full validation is required. - * @returns The parsed HED strings and any issues found. - */ -export function parseHedStrings( - hedStrings: (string | ParsedHedString)[], - hedSchemas: HedSchemas, - definitionsAllowed: boolean, - placeholdersAllowed: boolean, - fullValidation: boolean, -): [ParsedHedString[], Issue[], Issue[]] diff --git a/types/test.ts b/types/test.ts deleted file mode 100644 index ead0f9ad..00000000 --- a/types/test.ts +++ /dev/null @@ -1,389 +0,0 @@ -import { - // BIDS - BidsDataset, - BidsJsonFile, - BidsSidecar, - BidsTsvFile, - BidsHedIssue, - BidsFileAccessor, - BidsDirectoryAccessor, - buildBidsSchemas, - - // Issues - IssueError, - Issue, - - // Parser - Definition, - DefinitionManager, - - // Parsed HED types - ParsedHedTag, - ParsedHedGroup, - ParsedHedString, - TagSpec, - ParsedHedColumnSplice, - - // Schema - HedSchema, - SchemaEntries, - SchemaEntryManager, - SchemaEntry, - SchemaProperty, - SchemaAttribute, - SchemaEntryWithAttributes, - SchemaUnit, - SchemaUnitClass, - SchemaUnitModifier, - SchemaValueClass, - SchemaTag, - HedSchemas, - - // Parser functions - parseStandaloneString, - parseHedString, - parseHedStrings, - - // Schema functions - getLocalSchemaVersions, - buildSchemasFromVersion, - generateIssue, -} from 'hed-validator' - -// This is a type-only test file. -// It is not intended to be run, but to be type-checked. -// This is why many functions are async and not awaited. - -// Mock data and objects -const fakePath = '/fake/path' -const fakeFile: object = { name: 'fake.json', path: fakePath } -const fakeHedString = 'Event' - -async function testBids(schemas: HedSchemas) { - // BidsDataset - const [dataset, bidsIssues] = await BidsDataset.create(fakePath, BidsDirectoryAccessor) - if (dataset) { - dataset.setHedSchemas() - dataset.setSidecars() - dataset.validate() - const sidecar: BidsSidecar | undefined = dataset.sidecarMap.get('sidecar.json') - if (sidecar) { - console.log(sidecar.hasHedData) - } - } - console.log(bidsIssues) - - // BidsJsonFile - const bidsJsonFile = new BidsJsonFile('test.json', fakeFile, {}) - console.log(bidsJsonFile.name, bidsJsonFile.file, bidsJsonFile.jsonData, bidsJsonFile.hasHedData) - bidsJsonFile.validate(schemas) - - // BidsSidecar - const defManager = new DefinitionManager() - const bidsSidecar = new BidsSidecar('sidecar.json', fakeFile, {}, defManager) - console.log( - bidsSidecar.sidecarKeys, - bidsSidecar.hedData, - bidsSidecar.parsedHedData, - bidsSidecar.columnSpliceMapping, - bidsSidecar.columnSpliceReferences, - bidsSidecar.definitions, - bidsSidecar.hasHedData, - ) - bidsSidecar.parseSidecarKeys(schemas, true) - bidsSidecar.validate(schemas) - - // BidsTsvFile - const bidsTsvFile = new BidsTsvFile('events.tsv', fakeFile, 'data', {}, defManager) - console.log( - bidsTsvFile.name, - bidsTsvFile.file, - bidsTsvFile.parsedTsv, - bidsTsvFile.hedColumnHedStrings, - bidsTsvFile.mergedSidecar, - bidsTsvFile.hasHedData, - bidsTsvFile.isTimelineFile, - ) - bidsTsvFile.validate(schemas) - - // BidsHedIssue - const issue = generateIssue('genericError', { hedCode: 'code' }) - const bidsHedIssue = new BidsHedIssue(issue, fakeFile) - console.log( - bidsHedIssue.file, - bidsHedIssue.hedIssue, - bidsHedIssue.code, - bidsHedIssue.subCode, - bidsHedIssue.severity, - bidsHedIssue.issueMessage, - bidsHedIssue.line, - bidsHedIssue.location, - ) - - // BidsFileAccessor - const fileAccessor = await BidsFileAccessor.create(fakePath) - console.log(fileAccessor.fileMap, fileAccessor.organizedPaths) - fileAccessor.getFileContent('file.txt') - - // BidsDirectoryAccessor - const directoryAccessor = await BidsDirectoryAccessor.create(fakePath) - console.log(directoryAccessor.fileMap, directoryAccessor.organizedPaths) - directoryAccessor.getFileContent('file.txt') - - // buildBidsSchemas - await buildBidsSchemas(bidsJsonFile) -} - -function testIssues() { - // Issue - const issue = generateIssue('genericError', { a: 1 }) - console.log(issue.internalCode, issue.hedCode, issue.level, issue.message, issue.parameters) - issue.generateMessage() - console.log(issue.toString()) - - // IssueError - try { - IssueError.generateAndThrow('internalCode', { param: [1, 2] }) - } catch (e: unknown) { - if (e instanceof IssueError) { - console.log((e as IssueError).issue) - } - } - try { - IssueError.generateAndThrowInternalError('internal error message') - } catch (e: unknown) { - if (e instanceof IssueError) { - console.log((e as IssueError).issue) - } - } -} - -function testParser( - schemas: HedSchemas, - parsedString: ParsedHedString, - parsedTag: ParsedHedTag, - parsedGroup: ParsedHedGroup, -) { - // Definition - const [definition, defIssues, defIssues2] = Definition.createDefinition(fakeHedString, schemas) - if (definition) { - console.log(definition.name, definition.defTag, definition.defGroup, definition.placeholder) - definition.evaluateDefinition(parsedTag, schemas, true) - const [definitionFromGroup, defGroupIssues, defGroupIssues2] = Definition.createDefinitionFromGroup(parsedGroup) - if (definitionFromGroup) { - definition.equivalent(definitionFromGroup) - } - console.log(defGroupIssues, defGroupIssues2) - } - console.log(defIssues, defIssues2) - - // DefinitionManager - const defManager = new DefinitionManager() - if (definition) { - defManager.addDefinition(definition) - defManager.addDefinitions([definition]) - } - defManager.validateDefs(parsedString, schemas, true) - defManager.validateDefExpands(parsedString, schemas, true) - - // ParsedHedTag - const tagSpec: TagSpec = { tag: 'tag', library: 'lib', start: 0, end: 3 } - const parsedHedTag = new ParsedHedTag(tagSpec, schemas, fakeHedString) - const schema: HedSchema = parsedHedTag.schema - const schemaTag: SchemaTag = parsedHedTag.schemaTag - console.log( - parsedHedTag.originalTag, - parsedHedTag.originalBounds, - parsedHedTag.formattedTag, - parsedHedTag.canonicalTag, - schema, - schemaTag, - ) - parsedHedTag.format(true) - parsedHedTag.toString() - parsedHedTag.hasAttribute('attribute') - parsedHedTag.equivalent(parsedTag) - - // ParsedHedGroup - const parsedHedGroup = new ParsedHedGroup([parsedTag, parsedGroup], fakeHedString, [0, 1]) - const tags: (ParsedHedTag | ParsedHedGroup | ParsedHedColumnSplice)[] = parsedHedGroup.tags - console.log( - parsedHedGroup.originalTag, - parsedHedGroup.originalBounds, - tags, - parsedHedGroup.topTags, - parsedHedGroup.topGroups, - parsedHedGroup.allTags, - parsedHedGroup.defExpandChildren, - parsedHedGroup.defTags, - parsedHedGroup.defExpandTags, - parsedHedGroup.defCount, - parsedHedGroup.requiresDefTag, - ) - parsedHedGroup.format(true) - parsedHedGroup.toString() - parsedHedGroup.equivalent(parsedGroup) - const subGroupIterator = parsedHedGroup.subParsedGroupIterator('tag') - console.log(subGroupIterator.next().value) - const spliceIterator = parsedHedGroup.columnSpliceIterator() - const splice: ParsedHedColumnSplice = spliceIterator.next().value - console.log(splice) - - // ParsedHedString - const parsedHedString = new ParsedHedString(fakeHedString, [parsedTag, parsedGroup, splice]) - console.log( - parsedHedString.hedString, - parsedHedString.tagGroups, - parsedHedString.topLevelTags, - parsedHedString.tags, - parsedHedString.columnSplices, - parsedHedString.topLevelGroupTags, - parsedHedString.definitions, - parsedHedString.normalized, - ) - parsedHedString.format(true) - parsedHedString.toString() -} - -function testSchemaTypes(schemas: HedSchemas) { - // HedSchema - const schema: HedSchema = schemas.getSchema('') - if (!schema) { - return - } - console.log(schema.prefix, schema.entries, schema.withStandard) - - // SchemaEntries - const entries: SchemaEntries = schema.entries - console.log( - entries.properties, - entries.attributes, - entries.valueClasses, - entries.unitClasses, - entries.unitModifiers, - entries.tags, - ) - - // SchemaEntryManager - const manager: SchemaEntryManager = entries.tags - for (const [key, value] of manager) { - console.log(key, value) - } - console.log(manager.keys().next().value) - console.log(manager.values().next().value) - console.log(manager.hasEntry('entry')) - console.log(manager.getEntry('entry')) - console.log(manager.getEntriesWithBooleanAttribute('attribute')) - console.log(manager.filter(([, v]) => v.hasBooleanAttribute('attribute'))) - console.log(manager.length) - - // SchemaEntry - const entry: SchemaEntry = manager.getEntry('entry') - if (entry) { - console.log(entry.name) - entry.hasBooleanAttribute('attribute') - } - - // SchemaProperty - const property: SchemaProperty = entries.properties.values().next().value - if (property) { - console.log(property.isCategoryProperty, property.isTypeProperty, property.isRoleProperty) - } - - // SchemaAttribute - const attribute: SchemaAttribute = entries.attributes.values().next().value - if (attribute) { - console.log(attribute.categoryProperty, attribute.typeProperty, attribute.roleProperties) - } - - // SchemaEntryWithAttributes - const entryWithAttrs: SchemaEntryWithAttributes = entries.tags.values().next().value - if (entryWithAttrs) { - console.log( - entryWithAttrs.booleanAttributes, - entryWithAttrs.valueAttributes, - entryWithAttrs.booleanAttributeNames, - entryWithAttrs.valueAttributeNames, - ) - entryWithAttrs.hasAttribute('attribute') - entryWithAttrs.hasBooleanAttribute('attribute') - entryWithAttrs.getValue('attribute') - } - - // SchemaUnit - const unitClass: SchemaUnitClass = entries.unitClasses.values().next().value - if (unitClass) { - const unit: SchemaUnit = unitClass.units[0] - if (unit) { - console.log(unit.unitType, unit.siUnit, unit.defaultSiUnit, unit.unitSymbol) - } - } - - // SchemaUnitClass - if (unitClass) { - console.log(unitClass.units) - } - - // SchemaUnitModifier - const unitModifier: SchemaUnitModifier = entries.unitModifiers.values().next().value - if (unitModifier) { - console.log(unitModifier.siPrefix, unitModifier.factor) - } - - // SchemaValueClass - const valueClass: SchemaValueClass = entries.valueClasses.values().next().value - console.log(valueClass.name) - - // SchemaTag - const tag: SchemaTag = entries.tags.values().next().value - if (tag) { - console.log(tag.parent, tag.shortTagName, tag.longTagName) - tag.isUnitClass() - tag.isTakesValueClass() - tag.parentHasAttribute('attribute') - } -} - -async function testSchemaFunctions() { - // getLocalSchemaVersions - const versions = getLocalSchemaVersions() - console.log(versions) - - // buildSchemasFromVersion - if (versions.length > 0) { - const schemas = await buildSchemasFromVersion(versions[0]) - if (schemas) { - // Schemas - console.log(schemas.schemas, schemas.baseSchema) - schemas.getSchema('') - - // parseStandaloneString - const [parsedString, issues, issues5] = parseStandaloneString(fakeHedString, schemas) - console.log(parsedString, issues, issues5) - - // parseHedString - const [parsedHedString, issues2, issues3] = parseHedString(fakeHedString, schemas, true, true, true) - console.log(parsedHedString, issues2, issues3) - - // parseHedStrings - const [parsedHedStrings, issues4, issues6] = parseHedStrings([fakeHedString], schemas, true, true, true) - console.log(parsedHedStrings, issues4, issues6) - - // Run other tests that require schemas - await testBids(schemas) - if (parsedHedString && parsedHedString.tags.length > 0 && parsedHedString.tagGroups.length > 0) { - const parsedTag = parsedHedString.tags[0] as ParsedHedTag - const parsedGroup = parsedHedString.tagGroups[0] - testParser(schemas, parsedHedString, parsedTag, parsedGroup) - } - testSchemaTypes(schemas) - } - } -} - -async function main() { - testIssues() - await testSchemaFunctions() -} - -main().catch(console.error) diff --git a/types/tsconfig.json b/types/tsconfig.json deleted file mode 100644 index 7cafc647..00000000 --- a/types/tsconfig.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "extends": "../tsconfig.json", - "compilerOptions": { - "baseUrl": "..", - "paths": { - "hed-validator": ["./types/index.d.ts"] - }, - "downlevelIteration": true - }, - "include": ["./test.ts"] -} From ebc5d8d83360afe7b8fe05ec84e26d4355c0aff2 Mon Sep 17 00:00:00 2001 From: Alexander Jones Date: Fri, 21 Nov 2025 15:50:43 -0600 Subject: [PATCH 57/63] Documentation fix --- src/utils/array.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/array.ts b/src/utils/array.ts index b90815c4..ddb567b1 100644 --- a/src/utils/array.ts +++ b/src/utils/array.ts @@ -32,7 +32,7 @@ export function* iteratePairwiseCombinations(array: T[]): Generator<[T, T]> { } /** - * Type predicate for an ordered pair of numbers (e.g. bounds). + * Type guard for an ordered pair of numbers (e.g. bounds). * * @param value A possible ordered pair of numbers. */ From b178fdd32edd5a5146dd8c9fd1dd0a4f8fdccd1e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Nov 2025 17:02:59 +0000 Subject: [PATCH 58/63] Bump @types/lodash from 4.17.20 to 4.17.21 Bumps [@types/lodash](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/lodash) from 4.17.20 to 4.17.21. - [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases) - [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/lodash) --- updated-dependencies: - dependency-name: "@types/lodash" dependency-version: 4.17.21 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3ee45c4a..339c70f4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -3406,9 +3406,9 @@ "license": "MIT" }, "node_modules/@types/lodash": { - "version": "4.17.20", - "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.17.20.tgz", - "integrity": "sha512-H3MHACvFUEiujabxhaI/ImO6gUrd8oOurg7LQtS7mbwIXA/cUqWrvBsaeJ23aZEPk1TAYkurjfMbSELfoCXlGA==", + "version": "4.17.21", + "resolved": "https://registry.npmjs.org/@types/lodash/-/lodash-4.17.21.tgz", + "integrity": "sha512-FOvQ0YPD5NOfPgMzJihoT+Za5pdkDJWcbpuj1DjaKZIr/gxodQjY/uWEFlTNqW2ugXHUiL8lRQgw63dzKHZdeQ==", "dev": true, "license": "MIT" }, From 3ccf4a0b5d2302d2469603f8dd1cb89a2b54cc8b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Nov 2025 17:03:12 +0000 Subject: [PATCH 59/63] Bump core-js-pure from 3.46.0 to 3.47.0 Bumps [core-js-pure](https://github.com/zloirock/core-js/tree/HEAD/packages/core-js-pure) from 3.46.0 to 3.47.0. - [Release notes](https://github.com/zloirock/core-js/releases) - [Changelog](https://github.com/zloirock/core-js/blob/master/CHANGELOG.md) - [Commits](https://github.com/zloirock/core-js/commits/v3.47.0/packages/core-js-pure) --- updated-dependencies: - dependency-name: core-js-pure dependency-version: 3.47.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3ee45c4a..4ffd2eb6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -4409,9 +4409,9 @@ } }, "node_modules/core-js-pure": { - "version": "3.46.0", - "resolved": "https://registry.npmjs.org/core-js-pure/-/core-js-pure-3.46.0.tgz", - "integrity": "sha512-NMCW30bHNofuhwLhYPt66OLOKTMbOhgTTatKVbaQC3KRHpTCiRIBYvtshr+NBYSnBxwAFhjW/RfJ0XbIjS16rw==", + "version": "3.47.0", + "resolved": "https://registry.npmjs.org/core-js-pure/-/core-js-pure-3.47.0.tgz", + "integrity": "sha512-BcxeDbzUrRnXGYIVAGFtcGQVNpFcUhVjr6W7F8XktvQW2iJP9e66GP6xdKotCRFlrxBvNIBrhwKteRXqMV86Nw==", "hasInstallScript": true, "license": "MIT", "funding": { From beaf3e23cee7646ce0cf553349b98174311f647e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Nov 2025 17:17:30 +0000 Subject: [PATCH 60/63] Bump actions/checkout from 5 to 6 Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/codeql.yml | 2 +- .github/workflows/codespell.yaml | 2 +- .github/workflows/coverage.yml | 2 +- .github/workflows/deploy-pages.yml | 2 +- .github/workflows/publish.yml | 2 +- .github/workflows/test-types.yml | 2 +- .github/workflows/tests.yml | 6 +++--- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 387f8d59..2900f7a0 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -52,7 +52,7 @@ jobs: # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages steps: - name: Checkout repository - uses: actions/checkout@v5 + uses: actions/checkout@v6 # Add any setup steps before running the `github/codeql-action/init` action. # This includes steps like installing compilers or runtimes (`actions/setup-node` diff --git a/.github/workflows/codespell.yaml b/.github/workflows/codespell.yaml index d002e4b7..a37d0d32 100644 --- a/.github/workflows/codespell.yaml +++ b/.github/workflows/codespell.yaml @@ -17,6 +17,6 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Codespell uses: codespell-project/actions-codespell@v2 diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml index 8beda2d2..04682be1 100644 --- a/.github/workflows/coverage.yml +++ b/.github/workflows/coverage.yml @@ -16,7 +16,7 @@ jobs: steps: - name: Check out the code - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up with Node.js LTS uses: actions/setup-node@v6 with: diff --git a/.github/workflows/deploy-pages.yml b/.github/workflows/deploy-pages.yml index d2e77616..d17bad87 100644 --- a/.github/workflows/deploy-pages.yml +++ b/.github/workflows/deploy-pages.yml @@ -23,7 +23,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout main branch - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up Node.js uses: actions/setup-node@v6 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 63f3bd47..073eacef 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -10,7 +10,7 @@ jobs: contents: read id-token: write steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 # Setup .npmrc file to publish to npm - uses: actions/setup-node@v6 with: diff --git a/.github/workflows/test-types.yml b/.github/workflows/test-types.yml index 26686e2c..b5363c73 100644 --- a/.github/workflows/test-types.yml +++ b/.github/workflows/test-types.yml @@ -18,7 +18,7 @@ jobs: node-version: [22.x, lts/*] steps: - - uses: actions/checkout@v5 + - uses: actions/checkout@v6 - name: Use Node.js ${{ matrix.node-version }} uses: actions/setup-node@v6 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c1f3a985..a4c8ca63 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -19,7 +19,7 @@ jobs: steps: - name: Check out the code - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up with Node.js ${{ matrix.node-version }} uses: actions/setup-node@v6 with: @@ -42,7 +42,7 @@ jobs: steps: - name: Check out the code - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up with Node.js ${{ matrix.node-version }} uses: actions/setup-node@v6 with: @@ -65,7 +65,7 @@ jobs: steps: - name: Check out the code - uses: actions/checkout@v5 + uses: actions/checkout@v6 - name: Set up with Node.js ${{ matrix.node-version }} uses: actions/setup-node@v6 with: From 4d899485b683ec261d06d8949b72637bc2f63380 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 Dec 2025 18:29:51 +0000 Subject: [PATCH 61/63] Bump prettier from 3.6.2 to 3.7.3 Bumps [prettier](https://github.com/prettier/prettier) from 3.6.2 to 3.7.3. - [Release notes](https://github.com/prettier/prettier/releases) - [Changelog](https://github.com/prettier/prettier/blob/main/CHANGELOG.md) - [Commits](https://github.com/prettier/prettier/compare/3.6.2...3.7.3) --- updated-dependencies: - dependency-name: prettier dependency-version: 3.7.3 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3ee45c4a..720bad66 100644 --- a/package-lock.json +++ b/package-lock.json @@ -83,6 +83,7 @@ "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.27.1", "@babel/generator": "^7.28.5", @@ -3418,6 +3419,7 @@ "integrity": "sha512-GNWcUTRBgIRJD5zj+Tq0fKOJ5XZajIiBroOF0yvj2bSU1WvNdYS/dn9UxwsujGW4JX06dnHyjV2y9rRaybH0iQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "undici-types": "~7.16.0" } @@ -3749,6 +3751,7 @@ "integrity": "sha512-NZyJarBfL7nWwIq+FDL6Zp/yHEhePMNnnJ0y3qfieCrmNvYct8uvtiV41UvlSe6apAfk0fY1FbWx+NwfmpvtTg==", "dev": true, "license": "MIT", + "peer": true, "bin": { "acorn": "bin/acorn" }, @@ -4081,6 +4084,7 @@ } ], "license": "MIT", + "peer": true, "dependencies": { "caniuse-lite": "^1.0.30001733", "electron-to-chromium": "^1.5.199", @@ -4588,6 +4592,7 @@ "dev": true, "hasInstallScript": true, "license": "MIT", + "peer": true, "bin": { "esbuild": "bin/esbuild" }, @@ -4687,6 +4692,7 @@ "integrity": "sha512-BhHmn2yNOFA9H9JmmIVKJmd288g9hrVRDkdoIgRCRuSySRUHH7r/DI6aAXW9T1WwUuY3DFgrcaqB+deURBLR5g==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@eslint-community/eslint-utils": "^4.8.0", "@eslint-community/regexpp": "^4.12.1", @@ -4747,6 +4753,7 @@ "integrity": "sha512-82GZUjRS0p/jganf6q1rEO25VSoHH0hKPCTrgillPjdI/3bgBhAE1QzHrHTizjpRvy6pGAvKjDJtk2pF9NDq8w==", "dev": true, "license": "MIT", + "peer": true, "bin": { "eslint-config-prettier": "bin/cli.js" }, @@ -5614,6 +5621,7 @@ "integrity": "sha512-F26gjC0yWN8uAA5m5Ss8ZQf5nDHWGlN/xWZIh8S5SRbsEKBovwZhxGd6LJlbZYxBgCYOtreSUyb8hpXyGC5O4A==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@jest/core": "30.2.0", "@jest/types": "30.2.0", @@ -6977,11 +6985,12 @@ } }, "node_modules/prettier": { - "version": "3.6.2", - "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.6.2.tgz", - "integrity": "sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==", + "version": "3.7.3", + "resolved": "https://registry.npmjs.org/prettier/-/prettier-3.7.3.tgz", + "integrity": "sha512-QgODejq9K3OzoBbuyobZlUhznP5SKwPqp+6Q6xw6o8gnhr4O85L2U915iM2IDcfF2NPXVaM9zlo9tdwipnYwzg==", "dev": true, "license": "MIT", + "peer": true, "bin": { "prettier": "bin/prettier.cjs" }, @@ -7758,6 +7767,7 @@ "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@cspotcode/source-map-support": "^0.8.0", "@tsconfig/node10": "^1.0.7", @@ -7915,6 +7925,7 @@ "integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==", "dev": true, "license": "Apache-2.0", + "peer": true, "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" From a3e99a32232a04cdf983113594037ea224218b9e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 Dec 2025 18:29:58 +0000 Subject: [PATCH 62/63] Bump @eslint/eslintrc from 3.3.1 to 3.3.3 Bumps [@eslint/eslintrc](https://github.com/eslint/eslintrc) from 3.3.1 to 3.3.3. - [Release notes](https://github.com/eslint/eslintrc/releases) - [Changelog](https://github.com/eslint/eslintrc/blob/main/CHANGELOG.md) - [Commits](https://github.com/eslint/eslintrc/compare/v3.3.1...eslintrc-v3.3.3) --- updated-dependencies: - dependency-name: "@eslint/eslintrc" dependency-version: 3.3.3 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3ee45c4a..67f3891a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -83,6 +83,7 @@ "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.27.1", "@babel/generator": "^7.28.5", @@ -2470,9 +2471,9 @@ } }, "node_modules/@eslint/eslintrc": { - "version": "3.3.1", - "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-3.3.1.tgz", - "integrity": "sha512-gtF186CXhIl1p4pJNGZw8Yc6RlshoePRvE0X91oPGb3vZ8pM3qOS9W9NGPat9LziaBV7XrJWGylNQXkGcnM3IQ==", + "version": "3.3.3", + "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-3.3.3.tgz", + "integrity": "sha512-Kr+LPIUVKz2qkx1HAMH8q1q6azbqBAsXJUxBl/ODDuVPX45Z9DfwB8tPjTi6nNZ8BuM3nbJxC5zCAg5elnBUTQ==", "dev": true, "license": "MIT", "dependencies": { @@ -2482,7 +2483,7 @@ "globals": "^14.0.0", "ignore": "^5.2.0", "import-fresh": "^3.2.1", - "js-yaml": "^4.1.0", + "js-yaml": "^4.1.1", "minimatch": "^3.1.2", "strip-json-comments": "^3.1.1" }, @@ -3418,6 +3419,7 @@ "integrity": "sha512-GNWcUTRBgIRJD5zj+Tq0fKOJ5XZajIiBroOF0yvj2bSU1WvNdYS/dn9UxwsujGW4JX06dnHyjV2y9rRaybH0iQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "undici-types": "~7.16.0" } @@ -3749,6 +3751,7 @@ "integrity": "sha512-NZyJarBfL7nWwIq+FDL6Zp/yHEhePMNnnJ0y3qfieCrmNvYct8uvtiV41UvlSe6apAfk0fY1FbWx+NwfmpvtTg==", "dev": true, "license": "MIT", + "peer": true, "bin": { "acorn": "bin/acorn" }, @@ -4081,6 +4084,7 @@ } ], "license": "MIT", + "peer": true, "dependencies": { "caniuse-lite": "^1.0.30001733", "electron-to-chromium": "^1.5.199", @@ -4588,6 +4592,7 @@ "dev": true, "hasInstallScript": true, "license": "MIT", + "peer": true, "bin": { "esbuild": "bin/esbuild" }, @@ -4687,6 +4692,7 @@ "integrity": "sha512-BhHmn2yNOFA9H9JmmIVKJmd288g9hrVRDkdoIgRCRuSySRUHH7r/DI6aAXW9T1WwUuY3DFgrcaqB+deURBLR5g==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@eslint-community/eslint-utils": "^4.8.0", "@eslint-community/regexpp": "^4.12.1", @@ -4747,6 +4753,7 @@ "integrity": "sha512-82GZUjRS0p/jganf6q1rEO25VSoHH0hKPCTrgillPjdI/3bgBhAE1QzHrHTizjpRvy6pGAvKjDJtk2pF9NDq8w==", "dev": true, "license": "MIT", + "peer": true, "bin": { "eslint-config-prettier": "bin/cli.js" }, @@ -5614,6 +5621,7 @@ "integrity": "sha512-F26gjC0yWN8uAA5m5Ss8ZQf5nDHWGlN/xWZIh8S5SRbsEKBovwZhxGd6LJlbZYxBgCYOtreSUyb8hpXyGC5O4A==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@jest/core": "30.2.0", "@jest/types": "30.2.0", @@ -6220,9 +6228,9 @@ "license": "MIT" }, "node_modules/js-yaml": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz", - "integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==", + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.1.tgz", + "integrity": "sha512-qQKT4zQxXl8lLwBtHMWwaTcGfFOZviOJet3Oy/xmGk2gZH677CJM9EvtfdSkgWcATZhj/55JZ0rmy3myCT5lsA==", "dev": true, "license": "MIT", "dependencies": { @@ -6982,6 +6990,7 @@ "integrity": "sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==", "dev": true, "license": "MIT", + "peer": true, "bin": { "prettier": "bin/prettier.cjs" }, @@ -7758,6 +7767,7 @@ "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@cspotcode/source-map-support": "^0.8.0", "@tsconfig/node10": "^1.0.7", @@ -7915,6 +7925,7 @@ "integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==", "dev": true, "license": "Apache-2.0", + "peer": true, "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" From 2b44ee76ff098aa1f0f5db02b6822ed3c34068cc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 Dec 2025 18:30:07 +0000 Subject: [PATCH 63/63] Bump ts-jest from 29.4.5 to 29.4.6 Bumps [ts-jest](https://github.com/kulshekhar/ts-jest) from 29.4.5 to 29.4.6. - [Release notes](https://github.com/kulshekhar/ts-jest/releases) - [Changelog](https://github.com/kulshekhar/ts-jest/blob/main/CHANGELOG.md) - [Commits](https://github.com/kulshekhar/ts-jest/compare/v29.4.5...v29.4.6) --- updated-dependencies: - dependency-name: ts-jest dependency-version: 29.4.6 dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3ee45c4a..bd4c3ca4 100644 --- a/package-lock.json +++ b/package-lock.json @@ -83,6 +83,7 @@ "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.27.1", "@babel/generator": "^7.28.5", @@ -3418,6 +3419,7 @@ "integrity": "sha512-GNWcUTRBgIRJD5zj+Tq0fKOJ5XZajIiBroOF0yvj2bSU1WvNdYS/dn9UxwsujGW4JX06dnHyjV2y9rRaybH0iQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "undici-types": "~7.16.0" } @@ -3749,6 +3751,7 @@ "integrity": "sha512-NZyJarBfL7nWwIq+FDL6Zp/yHEhePMNnnJ0y3qfieCrmNvYct8uvtiV41UvlSe6apAfk0fY1FbWx+NwfmpvtTg==", "dev": true, "license": "MIT", + "peer": true, "bin": { "acorn": "bin/acorn" }, @@ -4081,6 +4084,7 @@ } ], "license": "MIT", + "peer": true, "dependencies": { "caniuse-lite": "^1.0.30001733", "electron-to-chromium": "^1.5.199", @@ -4588,6 +4592,7 @@ "dev": true, "hasInstallScript": true, "license": "MIT", + "peer": true, "bin": { "esbuild": "bin/esbuild" }, @@ -4687,6 +4692,7 @@ "integrity": "sha512-BhHmn2yNOFA9H9JmmIVKJmd288g9hrVRDkdoIgRCRuSySRUHH7r/DI6aAXW9T1WwUuY3DFgrcaqB+deURBLR5g==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@eslint-community/eslint-utils": "^4.8.0", "@eslint-community/regexpp": "^4.12.1", @@ -4747,6 +4753,7 @@ "integrity": "sha512-82GZUjRS0p/jganf6q1rEO25VSoHH0hKPCTrgillPjdI/3bgBhAE1QzHrHTizjpRvy6pGAvKjDJtk2pF9NDq8w==", "dev": true, "license": "MIT", + "peer": true, "bin": { "eslint-config-prettier": "bin/cli.js" }, @@ -5614,6 +5621,7 @@ "integrity": "sha512-F26gjC0yWN8uAA5m5Ss8ZQf5nDHWGlN/xWZIh8S5SRbsEKBovwZhxGd6LJlbZYxBgCYOtreSUyb8hpXyGC5O4A==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@jest/core": "30.2.0", "@jest/types": "30.2.0", @@ -6982,6 +6990,7 @@ "integrity": "sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==", "dev": true, "license": "MIT", + "peer": true, "bin": { "prettier": "bin/prettier.cjs" }, @@ -7687,9 +7696,9 @@ } }, "node_modules/ts-jest": { - "version": "29.4.5", - "resolved": "https://registry.npmjs.org/ts-jest/-/ts-jest-29.4.5.tgz", - "integrity": "sha512-HO3GyiWn2qvTQA4kTgjDcXiMwYQt68a1Y8+JuLRVpdIzm+UOLSHgl/XqR4c6nzJkq5rOkjc02O2I7P7l/Yof0Q==", + "version": "29.4.6", + "resolved": "https://registry.npmjs.org/ts-jest/-/ts-jest-29.4.6.tgz", + "integrity": "sha512-fSpWtOO/1AjSNQguk43hb/JCo16oJDnMJf3CdEGNkqsEX3t0KX96xvyX1D7PfLCpVoKu4MfVrqUkFyblYoY4lA==", "dev": true, "license": "MIT", "dependencies": { @@ -7758,6 +7767,7 @@ "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@cspotcode/source-map-support": "^0.8.0", "@tsconfig/node10": "^1.0.7", @@ -7915,6 +7925,7 @@ "integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==", "dev": true, "license": "Apache-2.0", + "peer": true, "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver"