Oxygen XML Forum

Dear Sir or Madam,

I just recently began to learn working with JATS NISO XML documents and I was instructed to try Oxygen XML Editor. So far more or less everything is running just fine, but I stumbled upon two issues and I'd need some help:

1. I found in the manuals an option to edit tables in JATS mode. I started the Oxygen XML Editor, then selected new JATS document (Orange - Authoring) and created some usual elements liks paragraphs, list items, etc. Now, whetever I try, I'm unable to find the options to insert/edit tables. I also attached the screenshot how these options should look like (from your online manuals), but there are all other options available just the ones for tables aren't visible in the menu. What am I doing wrong? It's written in online manuals that the options should be available when inserting and working on a table. I did insert a "table-wrap", then right-click on it, but there aren't any extra table options available. I also tried to manually add then some other table items like "table", "colgroup", "col", etc., and actaully tried to search all possible places without the XML Editor, but without any luck. I'm surely missing something, I just don't know what and where to begin.
2. I live in Slovenia where we use some scaron signs like "ŠĐČĆŽ - šđčćž". I noticed that when I convert the XML to "JATS/BITS single HTML page" all letters are displayed just fine. But when I try to generate the "JATS/BITS PDF preview", just letters Ž and Š are displayed ok, but letters Č and Ć aren't ok. If I try to insert a string like "ŠĐČĆŽ šđčćž" it looks then like this:

HTML version: ŠĐČĆŽ šđčćž (all ok)
PDF version: Š###Ž š###ž (not ok)

What could be the issue?

Thank you in advance for your help and kind regards from Slovenia.

Tomaz Kavcic.

Dear Tomaz,

The JATS editing support in Oxygen does not yet have table support, its availability is incorrectly advertised in our user's manual and we'll correct this. I will update this forum thread if we add this support in a future Oxygen version.
The XML structure of a JATS table should look like this: you can insert it in the Text editing mode and then the table should be displayed in the Author visual editing mode.

About the problem with the characters not being properly rendered in the PDF, you need to modify the fonts in the XSLT stylesheets used to generate the PDF, I tried to use the "Arial Unicode MS" font to generate the PDF and it seems to work. I will send you via email the changes you need to make on your side to make this work.

Regards,
Radu

Dear Radu,

thank you for your kind answer.

In regards to (html) table editing, it's all clear to me now. Basically, it seems the JATS table code (except for the table-wrapper and some specific tags) looks exactly the same as classic html code. So, for instance, the easiest way would bo to use a simple wysiwyg html editor to create a table without any css formatting, then paste the clean html table code to oxygen and fill the missing tags manually. Is there maybe a better/easier way to do this that you would suggest for finishing this job?

I also tested the modified jats-xslfo.xsl file you sent me, but it seems I'm out of luck. The result is still with "###" signs instead of original "đčć" characters. I also tried to file-compare original and modified .xsl files and it seems there's lots of differences between these two versions, not just the two lines where font was changed from sans-serif to "Arial Unicode MS". I tested this on latest v22 and also on v21.

Lastly, if I may, just two more beginner's questions.

a) After installing Oxygen XML with my academic licence I get three links (editor, author, developer). I need the app only for creating and editing JATS files and I see no difference whichever version I run. What are the actual difference between these versions and which one should I use?

b) When creating new JATS document, there are three options (book, publishing, authoring). If I understand thing correctly, the difference is only between some restrictions in tag sets and one is actual a subset of another. Wikipedia says there are green, blue, orange. So, if we're trying to publish a journal, then I guess we should use a blue variant which is described as "...intended for general use in journal production and publication". Is this correct or would it be better to use the "green" one so we can extend it some more if we need?

Hi Tomaz,

Please see some comments below:

In regards to (html) table editing, it's all clear to me now. Basically, it seems the JATS table code (except for the table-wrapper and some specific tags) looks exactly the same as classic html code. So, for instance, the easiest way would bo to use a simple wysiwyg html editor to create a table without any css formatting, then paste the clean html table code to oxygen and fill the missing tags manually. Is there maybe a better/easier way to do this that you would suggest for finishing this job?

Actually JATS seems to provide for two separate table models, CALS and HTML:

https://github.com/wendellpiez/JATSKit/issues/5

but I think you should stick with HTML tables, you can also create XHTML documents in Oxygen and edit them in the Author visual editing mode, use the support we already have for XHTML to create the tables, then copy paste them to the Jats article.
I have a colleague who worked some time ago on the JATS tables support but he did not finalize it, if we come up with some incipient support for inserting tables in JATS I will try to give you a framework to test on your side.

I also tested the modified jats-xslfo.xsl file you sent me, but it seems I'm out of luck. The result is still with "###" signs instead of original "đčć" characters. I also tried to file-compare original and modified .xsl files and it seems there's lots of differences between these two versions, not just the two lines where font was changed from sans-serif to "Arial Unicode MS". I tested this on latest v22 and also on v21.

I think my modification was made against the XSLT stylesheets in an Oxygen 22.1 installation.
Can you tell me again what transformation scenario you are using for publishing? Is it the JATS/BITS PDF preview (XSL-FO) - open PDF or something else? Also for what Oxygen version do you want to make this work? I can try again to make the changes on my side, double check and send them to you via email.

a) After installing Oxygen XML with my academic licence I get three links (editor, author, developer). I need the app only for creating and editing JATS files and I see no difference whichever version I run. What are the actual difference between these versions and which one should I use?

The XML Editor contains all the features of our product, it allows for XML visual editing, publishing and for editing XML file types like XSLT stylesheets, XML Schemas, DTDs.
The XML Developer does not allow for visual editing, it's mostly intended for editing XML in the Text editing mode and for editing XSLT stylesheets, XML Schemas and DTDs.
The XML Author can be used for visual editing but it cannot be used to edit XSLT stylesheets, XML Schemas or DTDs.
Your academic license allows you to use the full XML Editor, so if you always start the "editor" shortcut the application will contain all the features unlocked.

b) When creating new JATS document, there are three options (book, publishing, authoring). If I understand thing correctly, the difference is only between some restrictions in tag sets and one is actual a subset of another. Wikipedia says there are green, blue, orange. So, if we're trying to publish a journal, then I guess we should use a blue variant which is described as "...intended for general use in journal production and publication". Is this correct or would it be better to use the "green" one so we can extend it some more if we need?

I have no idea about the differences between the tag sets, we do not use JATS for anything ourselves. I also suspect that there are differences in elements between them. Wendell Piez, the original developer of the framework used to edit Jats in Oxygen also maintains a JATS users list:

http://www.mulberrytech.com/JATS/JATS-List/

maybe you can try to register and ask there.

Regards,
Radu