jats-generator

Generate JATS XML file from journal article data.

Using objects defined in elifearticle as data structure, this library generates JATS XML output for a research article.

No article body content is supported yet, though this library can output at least the following:

• Journal metadata (journal title, publisher name, issn, volume)
• Article metadata (title, doi, pub date, history dates, abstract, copyright, subject categories, research organisms)
• Authors, editors, group authors, author affiliations, correspondence, conflicts of interest
• Permissions (copyright statement, copyright year, copyright holder, license)
• Datasets
• Funding data
• Ethics

One way to populate the elifearticle objects with data, as is used by eLife from CSV files, relies on using the ejpcsvparser library by using generate.build_article_from_csv(), resulting in an Article object. The Article can then be used as input to generate.build_xml() or generate.build_xml_to_disk() which will produce the JATS XML output.

A configparser object can be populated from the jatsgenerator.cfg file, where a different config section per journal name can be included, and building it using the jatsgenerator.config module,

Some sample CSV data input and JATS XML output files can be found in the tests/test_data/ folder, which are the basis for the automated tests.

Requirements and install

a) Install from pypi package index

pip install jatsgenerator

b) Install locally

Clone the git repo

git clone https://github.com/elifesciences/jats-generator.git

Create a python virtual environment and activate it

./install.sh

Configuration

The jatsgenerator.cfg configuration file provided in this repository can be changed in order to write slightly different JATS XML output, depending on the journal.

Example usage

This library is meant to be integrated into another operational system, where the elifearticle objects can be populated with sufficient data to produce complete JATS XMl output, however the following is a simple example using interactive Python:

>>> from elifearticle.article import Article, Contributor
>>> from jatsgenerator import generate
>>> from jatsgenerator.conf import raw_config, parse_raw_config
>>> article_object = Article("10.7554/eLife.00666", "Article title")
>>> article_object.abstract = "An abstract."
>>> article_object.add_contributor(Contributor("author", "Surname", "Given"))
>>> article_object.add_contributor(Contributor("editor", "Orr", "Edit"))
>>> jats_config = parse_raw_config(raw_config("elife"))
>>> article_xml_object = generate.build_xml(None, article_object, jats_config)
>>> print(article_xml_object.output_xml())

The JATS XML output, pretty formatted, will look something like this:

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d3 20150301//EN"  "JATS-archivearticle1.dtd">
<article article-type="research-article" dtd-version="1.1d3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">
<!--generated by jats-generator at 2021-09-02 14:18:33 from version 6cd2bf35c814117f5e5966ec415e01cedbdcd7de-->
    <front>
        <journal-meta>
            <journal-id journal-id-type="nlm-ta">elife</journal-id>
            <journal-id journal-id-type="publisher-id">eLife</journal-id>
            <journal-title-group>
                <journal-title>eLife</journal-title>
            </journal-title-group>
            <issn publication-format="electronic">2050-084X</issn>
            <publisher>
                <publisher-name>eLife Sciences Publications, Ltd</publisher-name>
            </publisher>
        </journal-meta>
        <article-meta>
            <article-id pub-id-type="doi">10.7554/eLife.00666</article-id>
            <title-group>
                <article-title>Article title</article-title>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author">
                    <name>
                        <surname>Surname</surname>
                        <given-names>Given</given-names>
                    </name>
                </contrib>
            </contrib-group>
            <contrib-group content-type="section">
                <contrib contrib-type="editor">
                    <name>
                        <surname>Orr</surname>
                        <given-names>Edit</given-names>
                    </name>
                    <role>Reviewing editor</role>
                </contrib>
            </contrib-group>
            <abstract>
                <p>An abstract.</p>
            </abstract>
        </article-meta>
    </front>
    <back>
        <sec id="s1" sec-type="additional-information">
            <title>Additional information</title>
        </sec>
    </back>
</article>

Run code tests

Use pytest for testing, install it if missing:

pip install pytest

Run tests

pytest

Run tests with coverage

coverage run -m pytest

then report on code coverage

converage report -m

License

Licensed under MIT.