jats-cli

Node CLI for working with JATS XML documents.

Read, write, and convert JATS XML and log summaries from the command line.

To use from the command line, use the -g to create a global install, which will provide a jats CLI:

npm install -g jats-cli
jats -v

What is JATS?

JATS is a NISO standard for Journal Article Tags Schema, which is a way to define the XML structure of a scientific article semantically. This includes the front-matter (authors, funding, title, abstract, etc.), the body of the article (sections, figures, equations, tables, etc.), and back-matter (references, footnotes, etc.). The JATS can also contain sub-articles.

The standard documents are hosted by the NIH https://jats.nlm.nih.gov/. There are three flavours, this library currently uses in most cases the most precriptive tag set (for article authoring). Another helpful resource is https://jats4r.org/, which provides other examples and recomendations for JATS.

Note that most publishers do not provide the XML as a first class output - they should, it is an important part of open-science to have the content programatically accessible and interoperable. It is only FAIR 😉.

From the command line

Commands available:

download: attempt to find the JATS file and download it locally.

jats download https://elifesciences.org/articles/81952 -o article.jats

For some Open Access PMC articles, you may download associated files with the --data option.

jats download PMC11025918 --data

convert: convert a JATS file to MyST-compatible JSON. The --frontmatter project option will write frontmatter to a myst.yml file.

jats convert article.jats --frontmatter project

summary: summarize the contents of the JATS, given a URL, DOI, or local file

jats summary https://elifesciences.org/articles/81952
jats summary 10.1371/journal.pclm.0000068
jats summary /local/article.jats

This will provide a summary, including a list of what the JATS file contains.

validate: validate local file against JATS Archive DTD schema. By default, this uses JATS 1.3.

jats validate article.jats --jats 1.2 --mathmml 2

test: test a JATS file against a list of unit tests in YAML

The test cases are useful for known exports and expecting specific pieces of information in the XML.

jats test article.jats --cases tests.yml

cases:
  - title: Correct publisher ID (publisher-id)
    select: 'front > journal-meta > journal-id[journal-id-type="publisher-id"] > *'
    equals:
      type: text
      value: plos
  - title: Every orcid is authenticated
    selectAll: 'front > article-meta > contrib-group > contrib > contrib-id'
    equals:
      contrib-id-type: orcid
      authenticated: 'true'

As of v1.0.0 this package is ESM only.