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Wendell Piez edited this page Apr 18, 2016 · 24 revisions

On this page:

  • What's JATSKit, the JATS framework for oXygen
  • How to install it
  • What's in it
  • How to extend it
  • Feature requests / developers' discussion

For all matters related to JATS:

For oXygen XML editor:

What's the JATS framework for oXygen

Licensed users of oXygen XML Editor or Author (http://oxygenxml.com) who wish to work in the JATS format or with JATS-formatted data can take advantage of CSS stylesheets (for authoring) and XSLT transformations (for production of HTML and other outputs) bundled in a framework that recognizes these document types by their Formal Public Identifiers (FPIs). Included document types are JATS journal articles conformant to the Blue ("Publishing") and narrower Orange ("Authoring") XML formats, along with NLM BITS 2.0, a book description format built on the same infrastructure.

The current version of the framework has been developed and tested with oXygen 17.1.

How to install it

In oXygen Help > Install New Add-ons, into "Show Add-ons from:" paste the URL

https://github.com/wendellpiez/JATSKit/raw/master/oXygenJATSframework.xml

Please persevere, agreeing to license terms and to the installation of an unsigned add-on. Note that this is an open source project whose code base is open for your inspection. (Do not ordinarily accept unsigned add-ons!)

Or: GOTO Installation

What's in it

CSS stylesheets for editing JATS data in oXygen Author, the WYSIWYG-like, formatted "pretty" view of the editor.

CSS provides not only pretty formatting, but also widgetry for some elements, e.g. graphics and links. These include forms controls for things like ID assignments. CSS stylesheets can be switched in and out and used together or separately.

Copies of the DTDs, JATS version 1.1 in various forms:

  • Authoring ("Orange") with MathML3
  • Publishing ("Blue"), with and without OASIS tables and MathML3
  • BITS 2.0 (book description format), also with and without OASIS tables, and MathML3

If you wish to use JATSKit with other DTDs, for example the "Green" DTDs or older JATS or NLM DTDs, the framework can be extended to support this. More details on how to do this are on the page on DTD Versions.

Document templates

Starting new instances of each of these is available from File/New:

  • Article (valid to Orange)
  • Article (valid to Blue with either type of tables)
  • Book (valid to BITS 0.2 with either type of tables)

Schematron for specialized (QA) checking

  • Schematron rules are applied to check against certain extra-DTD constraints over and above the JATS content models, such as "top level book-part elements must all have IDs assigned". Some Schematron logic has actionable "quick fixes" associated. A "JATSKit QA" Schematron is provided as an example on which to build.

Preview stylesheets for HTML and PDF production

Prewired scenarios for HTML preview production using adaptations of the NLM/NCBI JATS Preview stylesheets (https://github.com/NCBITools/JATSPreviewStylesheets).

Additionally, XSL-FO developers will find an entry point for supporting PDF production via an XSL-FO pathway.

Embedded documentation

Documentation from the official Tag Libraries is integrated into the editor, with links to the official pages on line.

Refactoring transformations

"Document-level refactoring" amounts to applying transformation logic at the file level to any file open in the editor or available on the file system, either singly or in batches. As demonstrations, JATSKit offers refactoring operations to apply JATS/BITS FPIs (formal public identifiers) to documents as well as to rewrite ID values (and references to them) in XML files according to a logic appropriate for JATS (or BITS).

Prototype EPUB3 production

Got BITS? Go straight to EPUB3 using XProc inside oXygen. Again all the stylesheets can be tweaked and tuned to produce the transformation results exactly the way you want them - to facilitate this, another XProc pipeline in JATSKit will produce the same EPUB3 except 'unwrapped', a "mock ebook" as a static set of HTML resources you can read on your file system.

Smart paste

Thanks to our friends at oXygen, the editor does better than you might think pasting arbitrary content from web pages or MS Word, into JATS documents. Again this is something subject to modification and improvement.

How to extend JATSKit

oXygen has a nice video on how to set up a framework with a tour of framework internals. (They even use an earlier version of JATS as their example: not bad!) Costin Sandoi explains everything at http://www.oxygenxml.com/demo/FrameworkConfiguration.html. Of course, you modify an existing framework in much the same way as you create a new one.

You can add to or replace CSS or XSLT. Or you can perform routine modifications to support your own use of JATS. For example, if you have your own stylesheets (or your own profiles for the Preview stylesheets included) you can add transformation scenarios to use them.

Feature requests / developers' discussion

See Plans for plans.

Or write to me or to the JATS-List at www.mulberrytech.com if you have ideas or requests, or to volunteer to implement.

-- Wendell Piez (wapiez -at- wendellpiez -dot- com)

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