PMC Utils Node Package

A Node.js package for building and validating PMC (PubMed Central) manuscript deposits. This package provides tools for creating properly formatted PMC submission packages, including manifest generation, XML validation, and archive creation.

Features

• Build PMC deposit packages from manifest files
• Generate PMC-compliant manifest text files
• Validate XML against PMC DTD specifications
• Create tar.gz archives for submission
• Support for multiple file types (manuscripts, figures, tables, supplements)
• Local file system integration

Prerequisites

• Node.js (v16 or higher)
• xmllint command-line tool for XML validation
  • On macOS: brew install libxml2
  • On Ubuntu/Debian: apt-get install libxml2-utils
  • On Windows: Install via Chocolatey or MSYS2

Installation

npm install pmc-utils

Usage

Building a PMC Deposit

import { buildDeposit } from 'pmc-utils';

const manifest = {
  taskId: 'example-task-123',
  doi: '10.1234/example.doi',
  agency: 'example-agency',
  metadata: {
    title: 'Example Manuscript',
    authors: [
      {
        fname: 'John',
        lname: 'Doe',
        email: '[email protected]',
        contactType: 'reviewer'
      }
    ],
    journal: {
      issn: '1234-5678',
      issnType: 'electronic',
      title: 'Example Journal'
    },
          grants: [
      {
        funder: 'NIH',
        id: 'R01-123456'
      }
    ]
  },
  files: [
    {
      type: 'manuscript',
      filename: 'manuscript.pdf',
      path: './manuscripts',
      storage: 'local'
    },
    {
      type: 'figure',
      label: 'fig1',
      filename: 'figure1.png',
      path: './figures',
      storage: 'local'
    }
  ]
};

const options = {
  output: './deposits',
  keepFiles: false,
  log: console
};

try {
  const tarFile = await buildDeposit(manifest, options);
  console.log(`Deposit package created at: ${tarFile}`);
} catch (error) {
  console.error('Error creating deposit:', error);
}

Manifest File Format

The package generates a manifest file in the following format:

<file_type> <label> <file_name>

File types supported:

• bulksub_meta_xml: Required metadata file
• manuscript: Manuscript text file(s)
• figure: Figure file
• table: Table file
• supplement: Supplementary material file

Development

Setup

1. Clone the repository
2. Install dependencies:

   npm install

Building

npm run build

Testing

npm test

API Reference

buildDeposit(manifest: AAMDepositManifest, opts: BuildDepositOptions)

Builds a complete PMC deposit package from a manifest object.

Options:

• output: Directory for output files (default: 'deposits')
• keepFiles: Whether to keep temporary files (default: false)
• log: Logger instance (default: console)

preparePMCManifestText(manifest: AAMDepositManifest)

Generates the manifest text file content for a PMC deposit.

validateXml(xml: string)

Validates XML content against the PMC DTD specification.

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Submit a pull request

License

Released under the MIT License