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jats-schematrons's Issues

CREDIT taxonomy issue

Hello.

I am using the XML Validator, but I have encountered a problem in the CREDIT taxonomy. Following the recommendations on the Jats4R page it is stated in the table and in the example that URLs starting with "https" should be used, however the validator only recognises addresses starting with "http". I think it is a bug and that it should be possible to use both options.

I think this would be solved by adding to this file the "https versions" of the URLs(along with the http ones so that they still work). However I don't know Schematron and I'm not sure this is the right solution.

Pablo

Issue with the <break> element.

Hi!

I found a small problem in the JATS4r validator. The problem is that when I use the <break> element, the validator generates an error and does not run the validator.

image

This element is allowed by DTD 1.3. I understand that it is unusual to use it in a body text, as the purpose of jats-xml is not to reproduce the display. However, in a table it can be an important element.

I send you a minimal example

Thanks again for your work!

<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.3 20210610//EN" "https://jats.nlm.nih.gov/publishing/1.3/JATS-journalpublishing1-3.dtd">

<article xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" dtd-version="1.3" specific-use="~!gurí_(+Pandoc)" article-type="introduction" xml:lang="es">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
<journal-title specific-use="original" xml:lang="es">My journal</journal-title>
</journal-title-group>
<issn publication-format="electronic" pub-type="epub">1215-1215</issn>
<publisher>
<publisher-name>A publisher</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<title-group>
<article-title xml:lang="es">The title</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">0000-0001-9343-8658</contrib-id>
<name>
<surname>Messi</surname>
<given-names>Lionel</given-names>
</name>
<xref ref-type="aff" rid="aff-aff1"/>
<email>[email protected]</email>
</contrib>
<aff id="aff-aff1">
<institution-wrap>
<institution>Selección Argentina de Fútbol</institution>
</institution-wrap>
</aff>
</contrib-group>
<pub-date pub-type="epub" date-type="pub" publication-format="electronic">
<year>2023</year>
</pub-date>
<elocation-id>20201</elocation-id>
<permissions>
<license xlink:href="https://creativecommons.org/licenses/by-nc/3.0/">
<ali:license_ref>https://creativecommons.org/licenses/by-nc/3.0/</ali:license_ref>
<license-p>Esta obra está bajo una Licencia Creative Commons Atribución-NoComercial 3.0 Internacional.</license-p>
</license>
</permissions>
</article-meta>
</front>
<body>
<sec id="introducción">
  <title>Introducción</title>
<p>Text.</p>
<table-wrap id="TAB_02">
  <label>Tabla 0.</label>
  <caption><title>Titulo de la segunda tabla </title></caption>
  <table style="border-collapse: collapse; border: none; border-spacing: 0px;">
  	<tbody>
  		<tr>
  			<td>
  				Column 1 
  			</td>
  			<td>
  				Column 2
  			</td>
  			<td>
  				Coloun 3
  			</td>
  		</tr>
  		<tr>
  			<td colspan="3" style="padding-right: 3pt; padding-left: 3pt;">
    This is only a line with a <break>
  				break.
  			</td>
  		</tr>
  	</tbody>
  </table></table-wrap>
</sec>
</body>
<back>
</back>
</article>

Remove "value-of" from output messages

When the list of validations is shown to the user, those which have passed have a message that sometimes looks like "The copyright year should have 4 digits, instead of "2019"", which is confusing.

It would make more sense if it just said "The copyright year should have 4 digits", as we can already show the relevant line of the XML.

More DAS @sec-type error values

@jeffbeckncbi

@sec-type=”data-availability”. Use this attribute on the containing the DAS.

[[Validator result: ERROR: <sec @sec-type=””> with following values found anywhere in XML document: if encounter any @sec-type labelled “Data availability”, “Data Availability”, “Data-Availability”, “data availability statement”, “Data availability statement”, “Data Availability Statement”, “data-availability-statement” “Data-availability-statement”, “Data-Availability-Statement”, “Data_Availability”, “data_availability-statement”, “Data_availability-statement”, “Data_Availability-Statement”, “data_availability”, “Data Accessibility” “Data accessibility”]]

Rebecca Orris has identified a whole bunch more we can add to the exceptions list:
Data availability
Data availability statement(s)
Data accessibility
Data accessibility statement(s)
Availability of data and material(s)
Data and code availability
Code and data availability
Data and software availability
Software and data availability
Availability and data format(s)
Availability of data
Availability of supporting data
Correlates of data availability
Data archiving statement(s)
Data deposition and access
Direct link to deposited data
Raw data availability

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