meca 0.0.0 → 1.0.3

package/dist/validate/dtd.d.ts

@@ -0,0 +1,20 @@
+import type { ISession, JatsOptions } from 'jats-xml';
+/**
+ * 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 declare function validateMeca(session: ISession, file: string, opts: Partial<JatsOptions>): Promise<boolean>;
+/**
+ * Validate a given file as MECA bundle
+ *
+ * Logs confirmation message if valid and throws an error if invalid.
+ */
+export declare function validateMecaWrapper(session: ISession, file: string, opts: Partial<JatsOptions>): Promise<void>;

package/dist/validate/dtd.js

@@ -0,0 +1,166 @@
+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

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

package/dist/validate/index.js

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

package/dist/version.d.ts

@@ -0,0 +1,2 @@
+declare const version = "1.0.3";
+export default version;

package/dist/version.js

@@ -0,0 +1,2 @@
+const version = '1.0.3';
+export default version;

package/package.json

@@ -1,11 +1,63 @@
 {
   "name": "meca",
-  "version": "0.0.0",
-  "description": "Manuscript Exchange Common Approach",
-  "main": "index.js",
+  "version": "1.0.3",
+  "description": "Types and utilities for working with MECA",
+  "author": "Rowan Cockett <rowan@curvenote.com>",
+  "homepage": "https://github.com/curvenote/meca",
+  "license": "MIT",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "files": [
+    "dist"
+  ],
+  "keywords": [
+    "jats",
+    "open-science",
+    "publishing"
+  ],
+  "publishConfig": {
+    "access": "public"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/curvenote/meca.git"
+  },
+  "bin": "./dist/meca.cjs",
   "scripts": {
-    "test": "echo \"Error: no test specified\" && exit 1"
+    "copy:dtd": "cp ./static/MECA_manifest.dtd dist/MECA_manifest.dtd",
+    "copy:version": "echo \"const version = '\"$npm_package_version\"';\nexport default version;\" > src/version.ts",
+    "clean": "rm -rf dist",
+    "unlink": "npm uninstall -g meca;",
+    "link": "npm run unlink; npm link;",
+    "dev": "npm run copy:version && npm run link && esbuild src/cli/index.ts --bundle --outfile=dist/meca.cjs --platform=node --watch && npm run copy:dtd",
+    "test": "npm run copy:version && vitest run",
+    "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: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"
   },
-  "author": "Rowan Cockett <rowan@curvenote.com>",
-  "license": "MIT"
+  "bugs": {
+    "url": "https://github.com/curvenote/meca/issues"
+  },
+  "dependencies": {
+    "adm-zip": "^0.5.10",
+    "jats-xml": "^1.0.3",
+    "xml-js": "^1.6.11"
+  },
+  "peerDependencies": {
+    "chalk": "^5.2.0",
+    "commander": "^10.0.1"
+  },
+  "devDependencies": {
+    "@types/adm-zip": "^0.5.0",
+    "chalk": "^5.2.0",
+    "commander": "^10.0.1",
+    "myst-cli-utils": "^1.0.0",
+    "myst-common": "^1.0.0",
+    "myst-frontmatter": "^1.0.0"
+  }
 }