JATSParserPlugin not installing in 3.2.1

Hi, I’m trying tot install the JATSParserPlugin. I get PHP errors on some required files like vendor/autoload.php. But the files are present. I don’t fully understand the location of the JATSParser folder. Should it be like this:

generic
 - JATSParser
 - JATSParserPlugin

or this

generic
 - JATSParserPlugin
 -- JATSParser

Thanks in advance!
Gr Bas
Application Version - OJS 3.2.1

Hi @basD,

There isn’t a release made compatible with OJS 3.2.1 for JATS Parser Plugin but you can use the plugin’s master branch. There are 2 known OJS-related issues that you may encounter while using the plugin:

  1. Problem with saving full-text if it exceeds 64kb, fixed in OJS 3.3: OJS3 - DB field type TEXT is cutting off long content · Issue #6096 · pkp/pkp-lib · GitHub
  2. Linking between in-text citations and correspondent references. This hasn’t been fixed yet, expecting somewhere around OJS 3.3.1

For installation just follow the guideline Installation for development: GitHub - Vitaliy-1/JATSParserPlugin: OJS3 Plugin for parsing JATS XML and displaying it on article detail page. The location folder should be jatsParser inside the generic dir. Let me know if problems occur.

Thanks @Vitaliy. Gonna try it.

Similar problems here. My OJS instance is 3.2.1.2.

If I download the JATSParserPlugin the pre-release 2.1.9-1 and I try to upload and install in the sites/plugin y get this error:

Notification: Files of this type can not be uploaded.

2021-01-10_21-26

and nothing happens.

If I try the Installation for development I get this problem:

/var/www/ojs/plugins/generic/jatsParser/JATSParser# composer install
[Composer\Json\JsonValidationException]
"./composer.json" does not match the expected JSON schema:
- name : Does not match the regex pattern ^[a-z0-9]([_.-]?[a-z0-9]+)*/[a-z0-9](([_.]?|-{0,2})[a-z0-9]+)*$

My Composer version is 2.0.8

Thank you in advance.

Hi @isaac.marco

There should be a .tar.gz file above the zip files on Github page. You should download & upload that file

Regards
PNG görüntüsü 2

Thanks @Vitaliy, the plugin is working. It now renders the XML. The only thing it doesnt render are the footnotes. Did I do something wrong?
Gr Bas

Hi @basD,

Glad that you made it work.
Footnotes support isn’t implemented yet.

Ah, ok thanks @Vitaliy

Thank you. Downloading jatsParser-2.1.9-2.tar.gz (a yesterday prelease) I could install the plugin in my OJS 3.2.1.2 and the “Create full text” option works OK for me, but when I “Create PDF Galley” I always get this error:

An unexpected error occurred. You may have been logged out. Please reload the page and try again.

But I’m logged :frowning:

These are the error logs I see in my server Debian Pastezone

Hi @Vitaliy
I’m using pre-release 2.1.9-2 of Jats Parser Plugin with OJS 3.2.1-4.
I use it for creating full HTML text from JATS XML files.
It works pretty well, except for references:
the produced HTML contains links to references in-text citations but the citations themselves are non in the HTML.
The same XML files performed well in a previous version of OJS 3.1.2-4 where oldGregg Theme with embedded JatsParser was used.

Any idea why references are not fetched from the XML?

Thanks a lot

Hi @razzi,

Indeed, references were removed from the full-text but they still can be added from the JATS to OJS through a references tab of the publication. The option appears after full-text generation (may require page reload).
jats-refs
In the plugin settings it’s possible to pick the appropriate citation style format. The only drawback is that it’s impossible right now to preserve the reference structure, that’s planned for future version of OJS and the plugin.

Thanks for quick feedback @Vitaliy
In my case, I can’t see the new “References” tab.
Reloaded the page: no effect.
image

What is the correct PlugIn Configuration for references? See emage below:

image

Concerning the citation style configuratioin, does it affect only the HTML output or also refers to the structure of citations in XML?

Last question: what do you mean with “it’s impossible right now to preserve the reference structure”?

Can you double-check if references are activated in the workflow settings?
refs_activated

If references are structured in JATS XML, it’s possible to format them according to the preferred style in the output. See best practices according to JATS guidelines: Element: Element Citation
References are saved in OJS database, each separately, in raw format.

For now, OJS doesn’t allow to preserve citation structure, only raw reference. In means that if JATS XML contains info regarding authors, their surname and family name, article title, journal where article was published, etc., this info will be lost during conversion and it will be saved as a simple string. In near future I’m planning to change this behavior, this allows, e.g., export references in different formats (bib, ris…), supported by reference manager software, like Zotero or Mendeley.

It works now, the references are shows now! Thanks a lot @Vitaliy !
In fact, it was the missing references setting in “Workflow settings”, as you suggested.

As you already wrote, compared with the previous version of the plugin, the references are not connected anymore to the inline citation, even though the link on the citation number is still there. What is missing is anchor on the references.

I also noticed a difference with the previous version:
the link to the DOI of the reference is not displayed anymore.
This is how the reference is displayed with the previous version of the PlugIn:
image

and this is how the same reference is displayed with the new version of the plugin:
image

A part from the differences in the style, the DOI link disappeared.

This is the XML for the above reference:
image

Is there a way for showing the link again?

Cheers

It depends on CSL stylesheet that is used. Some of them may include DOIs: GitHub - citation-style-language/styles: Official repository for Citation Style Language (CSL) citation styles.. It can be set in the plugin’s settings. Just enter a name of the stylesheet (without .csl extension).

As I wrote before, for now it’s impossible to preserve the reference structure, including the anchor. I’m planning to change this in the near future. If it’s the citation style where references are added consequently as they appear in the text, it can be temporarily fixed by assigning the anchor with javascript.

Thanks again, @Vitaliy for your help.
It works with a different CSL stylesheet, indeed.

Also thanks for the javascript work-around suggested for restoring the missing anchors.
I’ll let you know if I’ll find a way to make it work.

Hi Vitaliy. One more question about Citation Style Language used in JATS Parser PlugIn for styling the references.
I’ve found a style that works well enoght with the XML structure of citations in my articles’ JAST files (it’s “american-medical-association”). It gets all the information from the citations except the ext-link tag.

Below an example of XML where you can see the part that is not extracted:

<ref id="ref6"><label>6</label> <mixed-citation publication-type="web"><person-group person-group-type="author"><name><surname>Quaranta</surname><given-names>N</given-names></name><name><surname>Pantaleo</surname> <given-names>A</given-names></name><name><surname>Berrettini</surname> <given-names>S</given-names></name><etal/></person-group>. <source>Strategic plan for the management of ENT and maxillofacial patients during the post-pandemic transition period (SIOeChCF)</source>. <comment><ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://www.sioechcf.it/piano-strategico-per-la-gestione-del-paziente-orl-durante-il-periodo-di-transizione-a-seguito-della-pandemia-covid-19-versione-2">https://www.sioechcf.it/piano-strategico-per-la-gestione-del-paziente-orl-durante-il-periodo-di-transizione-a-seguito-della-pandemia-covid-19-versione-2</ext-link>. Accessed 6 July</comment> <year>2020</year>.</mixed-citation></ref>

This is the XML that is not extracted:
<ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://www.sioechcf.it/piano-strategico-per-la-gestione-del-paziente-orl-durante-il-periodo-di-transizione-a-seguito-della-pandemia-covid-19-versione-2">https://www.sioechcf.it/piano-strategico-per-la-gestione-del-paziente-orl-durante-il-periodo-di-transizione-a-seguito-della-pandemia-covid-19-versione-2</ext-link>.

Do you know if there are different styles where this information is extracted?
do you know if editing the the style file in SCL it is possible to have that information extracted?

Did you inspect the CSL template, I mean how full-text URL is handled there?

Probably they applying it for all except newspaper articles: styles/american-medical-association.csl at master · citation-style-language/styles · GitHub
I’ll take a look.

Thanks, @Vitaliy

I tried to read the CSL file. I was able to change the “doi” label in that file
(styles/american-medical-association.csl at master · citation-style-language/styles · GitHub) and I saw it having effect in the JATS Parser. It means that I was working on the right file.
But I wasn’t able to understand how to modify the CSL for making it parsing the tag I want to be parsed. To me, it’s not clear at all how this CSL template works.
If you can give me some hints I can try further investigations concernig this issue.