meca 1.0.3 → 1.0.5

package/package.json

@@ -1,9 +1,9 @@
 {
   "name": "meca",
-  "version": "1.0.3",
+  "version": "1.0.5",
   "description": "Types and utilities for working with MECA",
   "author": "Rowan Cockett <rowan@curvenote.com>",
-  "homepage": "https://github.com/curvenote/meca",
+  "homepage": "https://github.com/curvenote/jats",
   "license": "MIT",
   "sideEffects": false,
   "type": "module",
@@ -22,11 +22,11 @@
   },
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/curvenote/meca.git"
+    "url": "git+https://github.com/curvenote/jats.git"
   },
   "bin": "./dist/meca.cjs",
   "scripts": {
-    "copy:dtd": "cp ./static/MECA_manifest.dtd dist/MECA_manifest.dtd",
+    "copy:dtd": "cp ./static/manifest-1.0.dtd dist/manifest-1.0.dtd; cp ./static/transfer-1.0.dtd dist/transfer-1.0.dtd",
     "copy:version": "echo \"const version = '\"$npm_package_version\"';\nexport default version;\" > src/version.ts",
     "clean": "rm -rf dist",
     "unlink": "npm uninstall -g meca;",
@@ -36,16 +36,17 @@
     "test:watch": "npm run copy:version && vitest watch",
     "lint": "eslint \"src/**/*.ts*\" -c ./.eslintrc.cjs",
     "lint:format": "prettier --check \"src/**/*.{ts,tsx,md}\"",
-    "build:esm": "tsc --project ./tsconfig.json --module es2015 --outDir dist --declaration",
+    "build:esm": "tsc",
     "build:cli": "esbuild src/cli/index.ts --bundle --outfile=dist/meca.cjs --platform=node",
     "build": "npm-run-all -l clean copy:version -p build:esm build:cli -s copy:dtd"
   },
   "bugs": {
-    "url": "https://github.com/curvenote/meca/issues"
+    "url": "https://github.com/curvenote/jats/issues"
   },
   "dependencies": {
     "adm-zip": "^0.5.10",
-    "jats-xml": "^1.0.3",
+    "jats-xml": "^1.0.5",
+    "node-fetch": "^3.3.1",
     "xml-js": "^1.6.11"
   },
   "peerDependencies": {
@@ -56,7 +57,7 @@
     "@types/adm-zip": "^0.5.0",
     "chalk": "^5.2.0",
     "commander": "^10.0.1",
-    "myst-cli-utils": "^1.0.0",
+    "myst-cli-utils": "^2.0.0",
     "myst-common": "^1.0.0",
     "myst-frontmatter": "^1.0.0"
   }

package/dist/validate/dtd.js

@@ -1,166 +0,0 @@
-import fs from 'fs';
-import path from 'path';
-import os from 'os';
-import AdmZip from 'adm-zip';
-import chalk from 'chalk';
-import { xml2js } from 'xml-js';
-import { validateJatsAgainstDtd, xmllintValidate } from 'jats-xml';
-const KNOWN_ITEM_TYPES = [
-    'article-metadata',
-    'article-supporting-file',
-    'manuscript',
-    'manuscript-supporting-file',
-    'article-source',
-    'article-source-environment',
-    'article-source-directory',
-];
-const MANIFEST = 'manifest.xml';
-const MANIFEST_DTD = 'MECA_manifest.dtd';
-/**
- * Function to log debug message for passing check
- */
-function debugCheck(session, msg) {
-    session.log.debug(chalk.green(`✓ ${msg}`));
-}
-/**
- * Function to log an error and clean temp folder
- */
-function errorAndClean(session, msg, tempFolder) {
-    session.log.error(msg);
-    removeTempFolder(tempFolder);
-    return false;
-}
-function removeTempFolder(tempFolder) {
-    if (tempFolder && fs.existsSync(tempFolder)) {
-        if (fs.rmSync) {
-            // Node >= 14.14
-            fs.rmSync(tempFolder, { recursive: true });
-        }
-        else {
-            // Node < 14.14
-            fs.rmdirSync(tempFolder, { recursive: true });
-        }
-    }
-}
-function createTempFolder() {
-    return fs.mkdtempSync(path.join(os.tmpdir(), 'meca'));
-}
-/**
- * Extract list of simple manifest item from valid manifest XML
- */
-function extractManifestItems(manifestString) {
-    var _a, _b, _c, _d, _e;
-    const manifest = xml2js(manifestString);
-    const items = (_e = (_d = (_c = (_b = (_a = manifest.elements) === null || _a === void 0 ? void 0 : _a.find((element) => element.name === 'manifest')) === null || _b === void 0 ? void 0 : _b.elements) === null || _c === void 0 ? void 0 : _c.filter((element) => element.name === 'item')) === null || _d === void 0 ? void 0 : _d.map((item) => {
-        var _a, _b, _c;
-        const instanceAttrs = (_b = (_a = item.elements) === null || _a === void 0 ? void 0 : _a.find((element) => element.name === 'instance')) === null || _b === void 0 ? void 0 : _b.attributes;
-        const href = instanceAttrs === null || instanceAttrs === void 0 ? void 0 : instanceAttrs['xlink:href'];
-        if (!href)
-            return undefined;
-        return {
-            href,
-            itemType: (_c = item.attributes) === null || _c === void 0 ? void 0 : _c['item-type'],
-            mediaType: instanceAttrs['media-type'],
-        };
-    }).filter((item) => !!item)) !== null && _e !== void 0 ? _e : [];
-    return items;
-}
-/**
- * Validate a given file as MECA bundle
- *
- * Returns true if file is valid.
- *
- * Validation checks:
- * - File exists and is zip format
- * - Bundle includes manifest.xlm which validates against DTD
- * - manifest matches items present in the bundle
- * - manifest item types match known types
- * - JATS items validate
- */
-export async function validateMeca(session, file, opts) {
-    if (!fs.existsSync(file))
-        return errorAndClean(session, `Input file does not exists: ${file}`);
-    let mecaZip;
-    try {
-        mecaZip = new AdmZip(file);
-    }
-    catch {
-        return errorAndClean(session, `Input file is not a zip archive: ${file}`);
-    }
-    debugCheck(session, 'is zip archive');
-    const manifestEntry = mecaZip.getEntry(MANIFEST);
-    if (!manifestEntry) {
-        return errorAndClean(session, `Input zip archive does not include required manifest file '${MANIFEST}'`);
-    }
-    debugCheck(session, `includes ${MANIFEST}`);
-    const localDtdFile = fs.existsSync(path.join(__dirname, MANIFEST_DTD))
-        ? path.join(__dirname, MANIFEST_DTD)
-        : path.join(__dirname, '..', MANIFEST_DTD);
-    if (!fs.existsSync(localDtdFile)) {
-        throw new Error(`Unable to locate manifest DTD file ${MANIFEST_DTD} in meca lib distribution`);
-    }
-    const tempFolder = createTempFolder();
-    mecaZip.extractEntryTo(MANIFEST, tempFolder);
-    const manifestIsValid = await xmllintValidate(session, path.join(tempFolder, MANIFEST), localDtdFile);
-    if (!manifestIsValid) {
-        return errorAndClean(session, `${MANIFEST} DTD validation failed`, tempFolder);
-    }
-    debugCheck(session, `${MANIFEST} passes schema validation`);
-    const manifestString = manifestEntry.getData().toString();
-    const manifestItems = extractManifestItems(manifestString);
-    const zipEntries = mecaZip.getEntries();
-    const manifestExtras = manifestItems
-        .filter((item) => !zipEntries.map((entry) => entry.entryName).includes(item.href))
-        .map((item) => item.href);
-    const zipExtras = zipEntries
-        .filter((entry) => entry.entryName !== MANIFEST)
-        .filter((entry) => !entry.isDirectory)
-        .filter((entry) => !manifestItems.map((item) => item.href).includes(entry.entryName))
-        .map((entry) => entry.entryName);
-    if (zipExtras.length) {
-        session.log.warn(`MECA bundle includes items missing from manifest:\n- ${zipExtras.join('\n- ')}`);
-    }
-    if (manifestExtras.length) {
-        return errorAndClean(session, `manifest items missing from MECA bundle:\n- ${manifestExtras.join('\n- ')}`, tempFolder);
-    }
-    debugCheck(session, 'manfiest matches MECA bundle contents');
-    manifestItems.forEach((item) => {
-        if (!item.mediaType) {
-            session.log.warn(`manifest item missing media-type: ${item.href}`);
-        }
-        if (!item.itemType) {
-            session.log.warn(`manifest item missing item-type: ${item.href} `);
-        }
-        else if (!KNOWN_ITEM_TYPES.includes(item.itemType)) {
-            session.log.warn(`manifest item has unknown item-type "${item.itemType}": ${item.href} `);
-        }
-    });
-    const jatsFiles = manifestItems
-        .filter((item) => item.itemType === 'article-metadata')
-        .map((item) => item.href);
-    const invalidJatsFiles = (await Promise.all(jatsFiles.map(async (jatsFile) => {
-        mecaZip.extractEntryTo(jatsFile, tempFolder);
-        const isValid = await validateJatsAgainstDtd(session, path.join(tempFolder, ...jatsFile.split('/')), opts);
-        return isValid ? undefined : jatsFile;
-    }))).filter((jatsFile) => !!jatsFile);
-    if (invalidJatsFiles.length) {
-        return errorAndClean(session, `JATS DTD validation failed:\n- ${invalidJatsFiles.join('\n- ')}`, tempFolder);
-    }
-    debugCheck(session, 'JATS validation passed');
-    removeTempFolder(tempFolder);
-    return true;
-}
-/**
- * Validate a given file as MECA bundle
- *
- * Logs confirmation message if valid and throws an error if invalid.
- */
-export async function validateMecaWrapper(session, file, opts) {
-    const success = await validateMeca(session, file, opts);
-    if (success) {
-        session.log.info(chalk.greenBright('MECA validation passed!'));
-    }
-    else {
-        throw new Error('MECA validation failed.');
-    }
-}

package/dist/validate/index.d.ts

@@ -1 +0,0 @@
-export * from './dtd.js';

package/dist/validate/index.js

@@ -1 +0,0 @@
-export * from './dtd.js';