README

CLI for generating JATS XML citations from DOIs using multiple academic data providers.

Basic Usage (Single DOI)

php doi2jats.php <DOI>

Example:

php doi2jats.php 10.30430/gjae.2023.0350

Multiple DOIs

php doi2jats.php <DOI1> <DOI2> <DOI3> ...

Example:

php doi2jats.php 10.30430/gjae.2023.0350 10.52825/bis.v1i.42

Advanced Options

# Verbose output with processing details
php doi2jats.php -v 10.30430/gjae.2023.0350 10.52825/bis.v1i.42

# Ref-List format (all citations in ref-list)
php doi2jats.php -f reflist 10.30430/gjae.2023.0350 10.52825/bis.v1i.42

# Back  format with numbering
php doi2jats.php --format back 10.30430/gjae.2023.0350 10.52825/bis.v1i.42

# Verbose + reflist format
php doi2jats.php -v -f reflist 10.30430/gjae.2023.0350 10.52825/bis.v1i.42

Installation

Using Composer (Recommended)

composer require citation-generator/doi2jats

php vendor/citation-generator/doi2jats/doi2jats.php -h

Using github

git clone https://github.com/withanage/doi2jats/
cd doi2jats
composer install

Using github without Composer

The application includes a fallback PSR-4 autoloader, so it works without Composer.

Usage

Command-Line Options

Output Formats

Individual (Default)

Each citation as separate XML documents:

<!-- DOI: 10.30430/gjae.2023.0350 -->
<?xml version="1.0" encoding="UTF-8"?>
<element-citation publication-type="journal">
  ...
</element-citation>

<!-- DOI: 10.52825/bis.v1i.42 -->
<?xml version="1.0" encoding="UTF-8"?>
<element-citation publication-type="journal">
  ...
</element-citation>

Reflist

All citations wrapped in a reference list:

<?xml version="1.0" encoding="UTF-8"?>
<ref-list>
  <ref id="ref1">
    <element-citation publication-type="journal">
      ...
    </element-citation>
  </ref>
  <ref id="ref2">
    <element-citation publication-type="journal">
      ...
    </element-citation>
  </ref>
</ref-list>

Back

Full back format with labels:

<?xml version="1.0" encoding="UTF-8"?>
<back>
  <ref-list>
    <title>References</title>
    <ref id="bib1">
      <label>1.</label>
      <element-citation publication-type="journal">
        ...
      </element-citation>
    </ref>
    <ref id="bib2">
      <label>2.</label>
      <element-citation publication-type="journal">
        ...
      </element-citation>
    </ref>
  </ref-list>
</back>

Error Handling

The application handles various error scenarios:

• Invalid DOI format: Shows specific error for malformed DOIs
• Network failures: handles API timeouts and connection issues

Example with Errors

$ php doi2jats.php -v 10.30430/gjae.2023.0350 invalid-doi 10.52825/bis.v1i.42
Processing 3 DOI(s) in 'individual' format...
Processing DOI 1/3: 10.30430/gjae.2023.0350
Processing DOI 2/3: invalid-doi
  Error: Invalid DOI format: invalid-doi
Processing DOI 3/3: 10.52825/bis.v1i.42

<!-- DOI: 10.30430/gjae.2023.0350 -->
<?xml version="1.0" encoding="UTF-8"?>
<element-citation publication-type="journal">
  ...
</element-citation>

<!-- ERROR for DOI: invalid-doi - Invalid DOI format: invalid-doi -->

<!-- DOI: 10.52825/bis.v1i.42 -->
<?xml version="1.0" encoding="UTF-8"?>
<element-citation publication-type="journal">
  ...
</element-citation>

=== SUMMARY ===
Total DOIs processed: 3
Successful: 2
Failed: 1

Failed DOIs:
  - invalid-doi: Invalid DOI format: invalid-doi

Development

• PHP Coding and code reading knowledge required. Tool does not contain method documentation.

Testing

composer test

Adding New Providers

1. Create a new class implementing CitationProviderInterface
2. Extend AbstractCitationProvider for common functionality
3. Add it to the providers array in Application

Requirements

• PHP 8.1 or higher
• ext-dom
• ext-json

Contribution

• Lead and concept : Dulip Withanage (TIB) https://www.tib.eu