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microsimulation / ijm

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https://microsimulation.org/ijm/
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Data and code availability missing #199

Closed pbronka closed 6 months ago

pbronka commented 7 months ago

Hi @gnott,

We've spotted this bug with missing data and code availability statements on the web. They still seem to appear in the XMLs, but since Issue 15(2) they seem to get lost in the conversion process. Could you please have a look at this?

Describe the bug "Data and code" availability statement used to be included in the web version of articles, e.g. https://microsimulation.pub/articles/00239/figures

However it is missing since Issue 15(2) Summer 2022. It seems to be present in the XML files, but not in the json files from that issue onwards.

Expected behavior "Data and code" availability statement should be present in all research articles.

gnott commented 7 months ago

Well spotted @pbronka, this isn't something I check.

In the older XML files, the<back> element contains a section tag like the following,

<sec sec-type="data-availability" id="s8">

The newer XML files the similar data is like this example,

<fn fn-type="data-sharing-statement">
<title>Data and code availability</title>
<p>Please contact the authors for information on data and code availability.</p>
</fn>

The XML parsing library is looking for the <sec> tag of sec-type="data-availability".

Going forward, is it possible to use the older, supported, XML format?

In the IJM generation code branch, it is possible I can change the parser to also support the other style of XML, however the articles with missing data would need to be regenerated. My suggestion is to revert back to the supported style of XML going forward.

To repair the existing articles, it might be possible to add the statement to the JSON without requiring each article XML files to be modified.

pbronka commented 7 months ago

Thank you @gnott. I've discussed this with Exeter and, going forward, we will revert to the old style XML format.

To repair the existing articles, it might be possible to add the statement to the JSON without requiring each article XML files to be modified.

How should we add this to the JSON files?

gnott commented 7 months ago

How should we add this to the JSON files?

Easier said than done. I modified the parser code locally to generate the missing data, and I include these in PR https://github.com/microsimulation/ijm/pull/200

pbronka commented 7 months ago

Thank you for that @gnott

pbronka commented 6 months ago

Fixed in previous articles and reverted to old XML format going forward, which seems to work well - closing.