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jatspreviewstylesheets's Introduction

NISO Journal Article Tag Suite (JATS) version 1.0

Preview XSLT stylesheets

For documentation on these stylesheets, see:

  • quickstart.pdf -- "Bare bones" instructions
  • user-docs.pdf -- User documentation including assumptions and limitations
  • technical-docs.pdf -- More technical documentation, especially for those who wish to customize their environment or the stylesheets

Or the same documents in HTML format.

These same documents are included with tagging according to NISO JATS 1.0, from which the PDF and HTML was generated:

  • quickstart.xml
  • user-docs.xml
  • technical-docs.xml

As such, they are suitable for testing the stylesheets.

As described in the documentation, these XSLT 1.0 transformations will work standalone:

  • xslt/main/jats-html.xsl
  • xslt/main/jats-xslfo.xsl

To provide additional functionality, these stylesheets are also called into pipelines, which may be invoked using stylesheets included in the shells/saxon directory:

  • jats-APAcit-html.xsl
  • jats-APAcit-xslfo.xsl
  • jats-PMCcit-html.xsl
  • jats-PMCcit-print-fo.xsl
  • jats-PMCcit-web-html.xsl
  • jats-PMCcit-xhtml.xsl
  • jats-PMCcit-xslfo.xsl
  • jats-oasis-PMCcit-fo.xsl

As described in the documentation, these are XSLT 2.0 with Saxon extensions, and require a recent version of the Saxon processor to run. (Tested under Saxon 9.4.)

Or if XProc is preferred, use the XProc versions (with the same names) given in the shells/xproc directory.

Plus, there is a CSS stylesheet to be used with HTML results of any of these processes (including the HTML versions of the documentation): *jats-preview.css

The file saxon-bug-readme.txt describes a bug that may be encountered when using one of the stylesheets with certain versions of Saxon (or with XProc invoking Saxon), which is most easily addressed by upgrading the tool (to a copy distributed since the bug was reported and fixed).

The following files are included in this distribution (as described in the documentation). Directories are in bold.

  • jats-preview.css
  • quickstart.html
  • quickstart.pdf
  • quickstart.xml
  • readme.txt
  • README.md
  • saxon-bug-readme.txt
  • technical-docs.html
  • technical-docs.pdf
  • technical-docs.xml
  • userguide.html
  • userguide.pdf
  • userguide.xml
  • shells
    • saxon
      • jats-APAcit-html.xsl
      • jats-APAcit-xslfo.xsl
      • jats-oasis-PMCcit-fo.xsl
      • jats-PMCcit-html.xsl
      • jats-PMCcit-print-fo.xsl
      • jats-PMCcit-web-html.xsl
      • jats-PMCcit-xhtml.xsl
      • jats-PMCcit-xslfo.xsl
    • xproc
      • jats-APAcit-html.xpl
      • jats-APAcit-xslfo.xpl
      • jats-oasis-PMCcit-fo.xpl
      • jats-PMCcit-html.xpl
      • jats-PMCcit-print-fo.xpl
      • jats-PMCcit-web-html.xpl
      • jats-PMCcit-xhtml.xpl
      • jats-PMCcit-xslfo.xpl
  • xslt
    • citations-prep
      • jats-APAcit.xsl
      • jats-PMCcit.xsl
    • main
      • jats-html.xsl
      • jats-xslfo.xsl
      • shell-utility.xsl *xhtml-tables-fo.xsl
      • oasis-tables
      • oasis-table-html.xsl
      • oasis-table-support.xsl
      • oasis-table.sch
    • post
      • xhtml-ns.xsl
    • prep
      • jats-printfilter.xsl
      • jats-webfilter.xsl
      • oasis-tables-html.xsl

Our policy on merging changes:

These stylesheets are provided as a point of entry for JATS users who may not have the resources to create them from scratch. Because there are many varied implementations of JATS, you should have no expectation that these stylesheets will create production ready files in any arbitrary system. Instead, the stylesheets should be customized for your particular needs.

Because we view these stylesheets as a template for a customized solution, not the solution itself, we will accept changes that fix an actual bug, but we will not merge in changes that we view as “customization”. For example, we will accept changes that fix a problem which otherwise leads to failure in creating a final output file, but we will not accept changes that focus on presentational aspects of the final output (such as font changes, margin changes, graphics sizing, etc).

If you believe that you have a customization of the stylesheets that would benefit other users please fork this repository and announce your fork on the JATS mailing list, http://www.mulberrytech.com/JATS/JATS-List/.


This work is in the public domain and may be reproduced, published or otherwise used without the permission of the National Library of Medicine (NLM).

We request only that the NLM is cited as the source of the work.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.


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jatspreviewstylesheets's Issues

Support for JATS 1.2?

Are the stylesheets going to be updated so as to support version 1.2 of JATS?

If not, where one can find publicly available stylesheets to transform JATS 1.2 XML documents to HTML documents?

Parameters for 'auto-label-app', etc.?

It's not clear to me why 'auto-label-app', etc., are variables rather than parameters.

In principle, if they were parameters, it would be possible to add autonumbering in the formatted output of 'Orange' content, where <label> isn't allowed, by setting the parameters when invoking the XSLT processor.

Vancouver referencing style

Hi,

Just wondering, is there a way for article references to be shown in Vancouver style - jats-html.xsl ?

Now:
O CalatayudJM Tenias. Effects of time, temperature and blood cell count on levels of lactate in heparinized whole blood gas samples. Scand J Clin Lab Invest. 2003;63:311–4. 10.1080/0036551031000196012940640

It should be:
Calatayud O, Tenias JM. Effects of time, temperature and blood cell count on levels of lactate in heparinized whole blood gas samples. Scand J Clin Lab Invest 2003;63:311–4. 10.1080/0036551031000196012940640

Regards, Erik

Why full text of an articles sometimes is not available ?

Hey guys, sorry for asking this question here but I figured somebody who is aware of NCBI infrastructure is reading this.

Could you please explain why full text of an articles sometimes is not available ?

Let's use this article as an example
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907408/

EFetch gives only abstract
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&retmode=xml&rettype=full&id=2907408

and oai.cgi says it doesn't exist at all !
http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:2907408

How can I get this article ?

Thank you!

jats-html.xsl and jats-PMCcit-html.xpl produce different references

The xml source contains the following:

<ref id="R18"><label>18</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Greenspan</surname><given-names>JA</given-names></name><name><surname>McMahon</surname><given-names>SA</given-names></name><name><surname>Chebet</surname><given-names>JJ</given-names></name><name><surname>Mpunga</surname><given-names>M</given-names></name><name><surname>Urassa</surname><given-names>DP</given-names></name><name><surname>Winch</surname><given-names>PJ</given-names></name></person-group><article-title>Sources of community health worker motivation: a qualitative study in Morogoro Region, Tanzania.</article-title><source>Hum Resour Health</source><year>2013</year><volume>11</volume><fpage>52</fpage><pub-id pub-id-type="doi">10.1186/1478-4491-11-52</pub-id><pub-id pub-id-type="pmid">24112292</pub-id></mixed-citation></ref>

Using XML Calabash from the command line:
java -jar xmlcalabash-1.1.21-98.jar -i source=XYZ.xml -o result=XYZ.htm shells/xproc/jats-PMCcit-html.xpl

renders the reference correctly:
18 Greenspan JA, McMahon SA, Chebet JJ, Mpunga M, Urassa DP, Winch PJ, authors. Sources of community health worker motivation: a qualitative study in Morogoro Region, Tanzania. Hum Resour Health. 2013;11:52DOI: 10.1186/1478-4491-11-52. [24112292]

But applying jats-html.xsl on the exact same xml source for on-the-fly display directly in the browser produces the following wrong result:
18 JA GreenspanSA McMahonJJ ChebetM MpungaDP UrassaPJ WinchSources of community health worker motivation: a qualitative study in Morogoro Region, Tanzania.Hum Resour Health2013115210.1186/1478-4491-11-5224112292

Any idea why?

TIA

Can we remove dependencies on saxon extensions?

The readme mentions that these depend on some saxon extensions:

As described in the documentation, these are XSLT 2.0 with Saxon extensions, and require a recent version of the Saxon processor to run. (Tested under Saxon 9.4.)

It would be nice if we could make them processor-independent, or, at least, only dependent on Saxon HE (extensions require either PE or EE).

If that's not possible, could we update the README to be more specific, that PE or EE is required?

P.S. This was reported by a potential user.

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