Create a fully changed insight article to review export

[Cooryd]

• Use 72787 as the base article (it's an insight).
• change every field to check every xml section.
• Send over to Fred for review

[Cooryd]

Hi @FAtherden-eLife could you validate the XML at https://libero-editor--staging.elifesciences.org/api/v1/articles/72787/export when you get a chance please?

[fred-atherden]

Thanks @Cooryd. I've taken a look, there are some remaining issues:

DTD issues (in order to be valid JATS)

double <article-title>

<title-group><article-title><article-title>Altered Western diet shifts immune cell balance</article-title></article-title></title-group>

<caption> needs to be before <graphic> in <fig>

e.g.

<fig id="fig1" position="float">
    <label>NewFig1</label>
    <graphic mime-subtype="tiff"
        xlink:href="a4971c90-4585-4d42-8495-bf00e351cf4d/elife-67269-fig1 (1).tif" mimetype="image"/>
    <caption>
        <title>A newly added figure</title>
        <p>new figure legend</p>
        <p>new figure attr</p>
    </caption>
    <permissions>
        <copyright-statement>License statement</copyright-statement>
        <copyright-year>2021</copyright-year>
        <copyright-holder>License holder</copyright-holder>
        <license xlink:href="http://creativecommons.org/licenses/by/4.0/">
            <license-p>License one</license-p>
        </license>
    </permissions>
</fig>

<surname> needs to be placed before <given-names> in <name>

e.g.:

<name><given-names>Reference</given-names><surname>Book</surname></name>

Other issues (flagged by Schematron)

Unnecessary line breaks in article permissions (very minor)

<license-p>This article is distributed under the terms of the 
    <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">
        Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author 
    and source are credited.</license-p>

copyright-year, copyright-holder and copyright-statement missing from <permissions>

<permissions><ali:free_to_read/><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><ali:license_ref>http://creativecommons.org/licenses/by/4.0/</ali:license_ref><license-p>This article is distributed under the terms of the 
    <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">
        Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author 
    and source are credited.</license-p></license></permissions>

presume they would have been present in the original? I can't seem to add that info in the Editor - I think it should be automatically derived from the author list/pub date.

reference citations/reference ids do not align

e.g.

Refined sugars, cereals and vegetable oils, meat from domesticated animals, added sodium, and, in some groups, dairy foods, are now widespread components that would have been largely alien before the advent of farming, animal husbandry and industrialization (<xref ref-type="bibr" rid="bib11">Cordain et al., 2005</xref>).

In the XML, the ref with the id bib11 is Mackenbach, 2007:

<ref id="bib11">
    <element-citation publication-type="journal">
        <person-group person-group-type="author">
            <name>
                <given-names>JP</given-names>
                <surname>Mackenbach</surname>
            </name>
        </person-group>
        <fpage>105</fpage>
        <lpage>109</lpage>
        <year iso-8601-date="2007">2007</year>
        <article-title>The Mediterranean diet story illustrates that "why" questions are as
            important as "how" questions in disease explanation</article-title>
        <source>Journal of Clinical Epidemiology</source>
        <pub-id pub-id-type="doi">10.1016/j.jclinepi.2006.05.001</pub-id>
        <pub-id pub-id-type="pmid">17208115</pub-id>
        <volume>60</volume>
    </element-citation>
</ref>

fig citations/fig ids do not align

e.g.

<p>Some extra body text in it’s own paragraph tag. (<xref ref-type="fig" rid="fig2">NewFig1)</xref></p>

fig with id fig2 is Figure 1 (NewFig1 has the id fig1).

[Cooryd]

I've broken the feedback down into individual issues.