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OJS3 Plugin for parsing JATS XML and displaying it on article detail page

License: GNU General Public License v3.0

PHP 56.40% CSS 14.92% JavaScript 24.29% Smarty 4.39%

jats-xml jats ojs3-plugin

jatsparserplugin's Introduction

JATSParserPlugin

OJS3 Plugin for parsing JATS XML and displaying it on article detail page.

Features

JATS XML to HTML conversion.
JATS XML to PDF conversion.
Article's metadata now is taken directly from OJS (no need to populate JATS XML meta nodes).
Article's reference list can be taken from JATS XML or OJS (option in the plugin settings).
Support for figures attached to the XML through OJS dashboard.

How to use?

Installation

Download the latest release
Upload the plugin from the admin dashboard Website Settings -> Plugins -> Upload a New Plugin (make sure php.ini variables upload_max_filesize and post_max_size a set to equal or more than 16M) or unpack the archive into the plugins/generic/ folder.
Activate the plugin from the dashboard.
To change image logo in resulted PDF just replace JATSParser/logo/logo.jpg file by yours.

Usage

After activation the plugin adds new item to the publication form: The first select option contains the list of XML files uploaded to the production ready stage where is possible to pick the file that will be converted and saved as article's full-text. Before saving, a result of a conversion can be previewed. Under the hood the conversion process transforms JATS XML into HTML and saves the results in the database.

After publication full-text will be shown on the article landing page under the abstract.

Installation for development

Navigate to plugins/generic folder starting from OJS webroot.
git clone --recursive https://github.com/Vitaliy-1/JATSParserPlugin.git jatsParser.
To install support for JATS to PDF conversion: cd jatsParser/JATSParser and composer install.

Requirements

PHP 7.3 or higher
OJS 3.1+
Lens Galley Plugin must be turned off

Examples

Example of the JATS XML: https://github.com/Vitaliy-1/JATSParser/blob/main/examples/example.xml
HTML example: https://e-medjournal.com/index.php/psp/article/view/213
PDF example: https://uk.e-medjournal.com/index.php/psp/article/view/296/486

Release notes

2.2.0

Starting from this version JATS Parser Plugin starts to serve HTML statically and will no longer support rendering of the full-text on the fly on the galley page. Instead full-text is generated on demand from production ready JATS XML files and saved as a part of the publication.

jatsparserplugin's People

Contributors

Stargazers

Watchers

jatsparserplugin's Issues

stable-3_3_0: wrong path to the dependent files

Remove rendering of the Galley page

As full-text becomes a property of a publication and is served statically, on-the-fly conversion of JATS XML galley should be removed.

delete a HTML and languages support

Hi, when I try the plugin (prerelease 2.1.9) it works fine, but I found two issues:

(1) with an article written in Spanish, the HTML file was included in both languages, and
(2) when I delete the XML file, the HTML was not be deleted

for solve this problem I just disable the plugin, but the plugin is very good and I hope you can improve those things or tell me if you know some solution

Thank you!!

Example XML on Readme.md is dead link

The sample XML file provided on Readme.md is not working (error 404). Could you please update the link?

Revise generated HTML

Does HTML contain all needed tags, attributes, and their values?

Add Handler for Generated PDF page

Ensure image URL is properly encoded

The Texture plugin doesn't escape spaces in the URI of the image in the JATS XML output. To reproduce:

Create new JATS XML file
Open with Texture
Create a new Figure, upload a file with a filename that contains spaces, e.g. fig 1.jpg as per forum thread.
Save the file and explore tags related to a new figure:

<graphic id="graphic-2b9ee4ad70b4c56ec056012bf94bd7fa" mimetype="image" mime-subtype="jpeg" xlink:href="fig 1.jpg"/>

according to the JATS XML specification: https://jats.nlm.nih.gov/publishing/tag-library/1.3d1/attribute/xlink-href.html

As specified in XML Linking Language (XLink) Version 1.0, the value of an @xLink:href must be a valid URI.

if considering encoded one: xlink:href="fig%201.jpg

Escape URLs in the HTML output
Should/can it be escaped in Texture?

Revise rendering of XML galleys

Recent updates to the parser allow conversion results to be recorded into the database directly. In turn, this data is used to display full-textx on the article landing page alongside with metadata, which makes on the fly rendering of XML galleys redundant.

JATSParserPlugin Issues

Hi, Vitaliy great fan of your work. Thank you for all your help.

I tried to install the parser plugin and i am running into issues.

old gregg theme has been updated and after installing the parser plugin i an no longer able to access the pugins tab in settings it just rotates. It only happens for journals for which oldgregg is the theme
for classic theme the parser plugin settings are not visible. Just a blue bar thats it.

Remove sidebar from galley page for child themes of the Default theme

Support for references

- Parse references from JATS XML and save the raw text in the citations table.
- Reflect the reference structure in the citation_settings table.
- Consider making a background for the support of different citation styles.

Update for 3.2.1-2

Hi, I'm testing the plugin on 3.2.1-2 and get multiple errors.

Is planned launch an update for this version of OJS?

Thank you in advance

Add galley-level settings for the default XML galley

By default, the first XML galley fetched will be displayed on the article landing page. Add option to the galley grid to pick the galley for being displayed. Consider other options, like omit galley parsing.

Localize PDF output according to the chosen locale

TCPDF: add external CSS

Consider an option to add external CSS by users:

By substitution of the predefined CSS file in plugin's directory.
By uploading through plugin's settings.

Link to production ready files does not work

The link in the full text tab to production-ready files does not work. This may work in 3.3, but it won't in 3.2.1. Let's remove the link for now.

Table cell content is not displayed if surrounded by <p> </p> tags

Hi Vitaliy, hope you are doing well.
Our online text editor (Typeset.io) has recently changed their JATS formatting, and now they are including

tags surrounding every table cell content. So,

<td id="tc-ee8f2569c952" align="center">
  <p id="p-7a21351a9ec2">Colonoscopia</p>
</td>

must be manually rearranged to

<td id="tc-ee8f2569c952" align="center">
   Colonoscopia
</td>

to be displayed using oldGregg. When using default OJS template, the cell content shows fine, even with

tags on cell content.

Maybe this is a JatsParser problem. Do you think is it possible to correct it?

Many thanks in advance.

Issue with save xml

Dear sir

We have uploaded xml in production stage and now when we save we got error An unexpected error occurred. You may have been logged out.new ojs 3.2.2_1

Simplify the process of copying submission files and their metadata

Don't create a new file for a copied submission file (e.g., when importing a galley), use a file id of a submission file that is being copied.
Clone a submission file and its metadata. Review what metadata should be changed. Relevant for importing XML galleys and creating PDF galley. Example:

$newSubmissionFile = clone $submissionFile;
$newSubmissionFile->setData('fileStage', $fileStage);
$newSubmissionFile->setData('sourceSubmissionFileId', $submissionFile->getId());
$newSubmissionFile = Services::get('submissionFile')->add($newSubmissionFile, Application::get()->getRequest());

Fatal error when showing references from OJS

Current PDF font doesn't support all languages

E.g., Korean; consider changing to another.

Fatal error when extracting citations

When I try to extract the citations I get a fatal error. In the plugin settings I've selected "force to display references from JATS XML".

[29-Oct-2020 17:27:04 Europe/London] Slim Application Error:
Type: Exception
Message: String could not be parsed as XML
File: /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JATSParser/vendor/seboettg/citeproc-php/src/CiteProc.php
Line: 213
Trace: #0 /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JATSParser/vendor/seboettg/citeproc-php/src/CiteProc.php(213): SimpleXMLElement->__construct('')
#1 /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JATSParser/vendor/seboettg/citeproc-php/src/CiteProc.php(168): Seboettg\CiteProc\CiteProc->init(false)
#2 /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JATSParser/src/JATSParser/HTML/Document.php(234): Seboettg\CiteProc\CiteProc->render(Array, 'bibliography')
#3 /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JATSParser/src/JATSParser/HTML/Document.php(44): JATSParser\HTML\Document->extractReferences(Array)
#4 /home/nate/Projects/pkp/ojs-stable/plugins/generic/jatsParser/JatsParserPlugin.inc.php(647): JATSParser\HTML\Document->setReferences('', 'en-US', false)
#5 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/plugins/HookRegistry.inc.php(107): JatsParserPlugin->editPublicationReferences('Publication::ed...', Array)
#6 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/services/PKPPublicationService.inc.php(524): HookRegistry::call('Publication::ed...', Array)
#7 /home/nate/Projects/pkp/ojs-stable/lib/pkp/api/v1/submissions/PKPSubmissionHandler.inc.php(704): PKP\Services\PKPPublicationService->edit(Object(Publication), Array, Object(Request))
#8 [internal function]: PKPSubmissionHandler->editPublication(Object(Slim\Http\Request), Object(APIResponse), Array)
#9 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/Handlers/Strategies/RequestResponse.php(40): call_user_func(Array, Object(Slim\Http\Request), Object(APIResponse), Array)
#10 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/Route.php(281): Slim\Handlers\Strategies\RequestResponse->__invoke(Array, Object(Slim\Http\Request), Object(APIResponse), Array)
#11 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(117): Slim\Route->__invoke(Object(Slim\Http\Request), Object(APIResponse))
#12 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/Route.php(268): Slim\Route->callMiddlewareStack(Object(Slim\Http\Request), Object(APIResponse))
#13 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/App.php(503): Slim\Route->run(Object(Slim\Http\Request), Object(APIResponse))
#14 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/security/authorization/internal/ApiAuthorizationMiddleware.inc.php(77): Slim\App->__invoke(Object(Slim\Http\Request), Object(APIResponse))
#15 [internal function]: ApiAuthorizationMiddleware->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Slim\App))
#16 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(ApiAuthorizationMiddleware), Array)
#17 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Slim\App))
#18 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Slim\App))
#19 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/security/authorization/internal/ApiCsrfMiddleware.inc.php(46): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#20 [internal function]: ApiCsrfMiddleware->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#21 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(ApiCsrfMiddleware), Array)
#22 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#23 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#24 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/security/authorization/internal/ApiTokenDecodingMiddleware.inc.php(82): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#25 [internal function]: ApiTokenDecodingMiddleware->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#26 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(ApiTokenDecodingMiddleware), Array)
#27 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#28 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#29 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/handler/APIHandler.inc.php(68): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#30 [internal function]: APIHandler->{closure}(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#31 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(Closure), Array)
#32 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#33 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#34 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/handler/APIHandler.inc.php(127): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#35 [internal function]: APIHandler->{closure}(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#36 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(Closure), Array)
#37 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#38 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#39 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/handler/APIHandler.inc.php(132): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#40 [internal function]: APIHandler->{closure}(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#41 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/DeferredCallable.php(57): call_user_func_array(Object(Closure), Array)
#42 [internal function]: Slim\DeferredCallable->__invoke(Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#43 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(70): call_user_func(Object(Slim\DeferredCallable), Object(Slim\Http\Request), Object(APIResponse), Object(Closure))
#44 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/MiddlewareAwareTrait.php(117): Slim\App->Slim\{closure}(Object(Slim\Http\Request), Object(APIResponse))
#45 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/App.php(392): Slim\App->callMiddlewareStack(Object(Slim\Http\Request), Object(APIResponse))
#46 /home/nate/Projects/pkp/ojs-stable/lib/pkp/lib/vendor/slim/slim/Slim/App.php(297): Slim\App->process(Object(Slim\Http\Request), Object(APIResponse))
#47 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/core/APIRouter.inc.php(115): Slim\App->run()
#48 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/core/Dispatcher.inc.php(143): APIRouter->route(Object(Request))
#49 /home/nate/Projects/pkp/ojs-stable/lib/pkp/classes/core/PKPApplication.inc.php(281): Dispatcher->dispatch(Object(Request))
#50 /home/nate/Projects/pkp/ojs-stable/index.php(68): PKPApplication->execute()
#51 {main}
View in rendered output by enabling the "displayErrorDetails" setting.

And here's the XML file I'm trying to extract citations from:

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN" "https://jats.nlm.nih.gov/publishing/1.2/JATS-journalpublishing1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <article-meta>
      <title-group>
        <article-title>Test xml workflow</article-title>
      </title-group>
      <contrib-group content-type="author">
        <contrib contrib-type="person">
          <name>
            <surname>admin</surname>
            <given-names>admin</given-names>
          </name>
          <email>[email protected]</email>
          <xref ref-type="aff" rid="aff-1"/>
        </contrib>
      </contrib-group>
      <aff id="aff-1">
        <institution/>
        <country/>
      </aff>
      <history>
        <date date-type="received" iso-8601-date="2020-10-29">
          <day>29</day>
          <month>10</month>
          <year>2020</year>
        </date>
      </history>
    </article-meta>
  </front>
  
  
<body id="body">
    <sec id="sec-1">
      <title>Introduction test</title>
      <p id="_paragraph-2"><bold id="_bold-1">Juvenile idiopathic </bold><bold id="_bold-2"><italic id="_italic-1">arthritis</italic></bold><bold id="_bold-3"> (JIA)</bold> <sup id="_superscript-1">often</sup> causes <sub id="_subscript-1">significant</sub> functional  throughout the lifespan [1,2]. Medical workers who are aware of the JIA’s clinical course specifics in adolescence can provide better assistance at the transition stage when a patient’s healthcare shifts from a pediatric to an adult health services [3, 4,5]. The patient's transmission is a multidimensional, interdisciplinary and active process, which addresses the medical, socio-psychological and educational/professional needs of adolescents with JIA [6,7,8]. Previous studies have shown that the use of specific questionnaires (CHQ, Peds-QL) don’t allow fully assess psychometric changes in young adults. In particular, the interpretation of these studies’ results on Peds-QL is limited due to a small sample size [10]. On the contrary, when using HR-QOL, Haverman L. et al. (2011) found significant changes in the quality of life in children and adolescents with JIA [11].</p>
      <sec id="sec-1_1">
        <title>Heading 2</title>
        <list list-type="order" id="list-52b58034d0b7f98c27466f54c2b083f6">
          <list-item>
            <p>First</p>
          </list-item>
          <list-item>
            <p>Second</p>
            <list list-type="order">
              <list-item>
                <p>Level 2 First</p>
                <list list-type="order">
                  <list-item>
                    <p>Level 3 First</p>
                  </list-item>
                  <list-item>
                    <p>Level 3 Second</p>
                  </list-item>
                </list>
              </list-item>
              <list-item>
                <p>Level 2 Second</p>
              </list-item>
            </list>
          </list-item>
          <list-item>
            <p>Third</p>
            <list list-type="order">
              <list-item>
                <p>Level 2 Third</p>
              </list-item>
            </list>
          </list-item>
        </list>
        <p id="_paragraph-3">The HAQ questionnaire is widely used in clinical practice for the study rheumatic diseases in adults, particularly in rheumatoid arthritis [12]. This questionnaire is a useful tool for evaluation of functional status, its change during treatment . HAQ score is also associated with disease activity, mortality, and need in joint replacement [12, 13]. Most often, for the quality of life (QoL) assessment in adult patients, the SF-36 questionnaire is used [13]. Indeed, QoL in adulthood may be influenced by sociological, economic, philosophical and ethical factors, which can be less informative in childhood. For patients in the transitional period from pediatric to adult medical care, it is necessary to investigate the effectiveness of various medical examination methods for measuring QoL.</p>
        <p id="_paragraph-4"><bold id="_bold-4">The study aimed</bold> to determine the impact of the disease on the QoL in young adults with JIA during the transition from a pediatric to an adult healthcare service. </p>
      </sec>
    </sec>
    <sec id="sec-2">
      <title>Materials and methods</title>
      <sec id="sec-2_1">
        <title>materials</title>
        <p id="_paragraph-5">A study sample included 89 young people aged 16 to 22 years old with a history of JIA, regardless <xref id="_xref-1" ref-type="bibr" rid="bib1">[?]</xref> of the active inflammation severity at the time of examination and 25  healthy young volunteers that formed the control group. The experimental group comprised of patients from different Ukrainian who were diagnosed with the JIA according to the classification criteria of the International League of Associations for Rheumatology - ILAR [14] between 1984 and 2014 without severe concomitant pathology. Upon reaching adulthood, all patients with JIA were examined by an adult rheumatologist during outpatient visits or inpatient at the Oleksandrivka City Clinical Hospital in Kyiv between April 2015 and February 2017. In the study were analyzed demographic and clinical data, including age, gender, delayed diagnosis of JIA, disease duration, number of swollen joints, limitation of joint mobility, disease activity, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP). Pain and overall well-being were measured using the visual analogue scale (VAS). The functional status was evaluated using the HAQ questionnaire (Health Survey). Disease activity and the presence of remission were determined according to the American Association of Rheumatologists criteria [15].</p>
      </sec>
      <sec id="sec-2_2">
        <title>methods</title>
        <sec id="sec-2_2_1">
          <title>First Method</title>
          <p id="_paragraph-6">Additionally, the data regarding current JIA treatment were analyzed, including the use of non-steroidal anti-inflammatory drugs (NSAIDs), glucocorticoids (GCs), methotrexate, leflunomide, hydroxychloroquine, azathioprine and biological therapy (IL-1Ra, anti-TNF agents (etanercept, adalimumab), abatacept and tocilizumab).</p>
          <p id="_paragraph-7">The QoL of patients with JIA and the control group was assessed using the Short-Form-36 questionnaire (SF-36). We used licensed access containing (license No. QM037587) for Non-Profit Academic Research from the Management of Scientific Grants and Research (OGSR) provided by OptumInsight Life Sciences, Inc..</p>
        </sec>
        <sec id="sec-2_2_2">
          <title>Second Method</title>
          <p id="_paragraph-8">Praesent vitae pretium nisi. Vestibulum vitae nunc quis velit volutpat faucibus. Donec ultrices, enim sit amet maximus tincidunt, massa metus imperdiet mi, id finibus est nisl fermentum nibh. Donec blandit, nunc quis vestibulum fringilla, libero orci varius justo, sit amet malesuada felis elit id nisl. Mauris ornare sollicitudin tellus, in scelerisque ante pharetra a. Suspendisse non odio orci. Pellentesque sem metus, mattis eget vulputate eget, semper ac leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam mattis nibh porttitor elit blandit, at ullamcorper neque dapibus.</p>
        </sec>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>Statistical analysis</title>
      <p id="_paragraph-9">Statistical analysis was performed using descriptive statistics, Student's criteria for unbound variables, and one-way ANOVA dispersion analysis. The data are presented as the mean ± standard deviation (SD) for continuous variables and numbers (percentages) for categorical variables. Statistically significant was the probability value p &lt;0,05. The correlation was determined by the Pearson method for a two-way mixed model. In the analysis, software packages "Statistica 6.0" was used by Copyright StatSoft, Inc. 1984-2001.</p>
    </sec>
    <sec id="sec-4">
      <title>Results</title>
      <p id="_paragraph-10">There was conducted an analysis of demographic and anthropometric data from 89 young patients with JIA and 25 healthy volunteers (Table 1). The mean age of patients was 19.4 ± 1.8 years, which did not significantly differ from the mean age in control group. The average duration of the disease was 8.7 ± 5.1 years and the average age of the disease onset - 10.2 ± 4.9 years. The mean time from the disease’s onset to the diagnosis was estimeated at 15.6 ± 25.9 months.</p>
      <table-wrap id="_table-figure-1">
        <label>Table 1</label>
        <caption>
          <p id="_paragraph-11"/>
        </caption>
        <table id="_table-1">
          <tbody>
            <tr id="table-row-d10d37b1b7852169035f595a3cf6a4f4">
              <td id="5e7916eef73d305abb4215c763926f06" colspan="2">2 colspans</td>
              <td id="ae41e2fe7c4ae530528d9ea38976570b" rowspan="2" colspan="2">2 colspans 2 rowspans</td>
            </tr>
            <tr id="table-row-6891913daedab280971d2634b19da2d2">
              <td id="fc474b1e7d1b56eac69bdf2798c74959" rowspan="3" colspan="2">2 colspans 3 colspans 3 paragpraphs<bold id="_bold-5">2nd bold paraphrai with </bold><bold id="_bold-6"><italic id="_italic-2">italic</italic></bold><bold id="_bold-7"><italic id="_italic-3">3rd bold italic with </italic></bold><bold id="_bold-8"><italic id="_italic-4"><sup id="_superscript-2">superscript</sup></italic></bold></td>
              <td id="dead1769474eaeeffa4bf8e2b4c67f18">1</td>
              <td id="56030a6352213c744760a94bb8908105">1</td>
            </tr>
            <tr id="table-row-1655223fa5c16e7054f17fd06c3758b1">
              <td id="56396a28cf893a4385c8715f5a228d8a">1</td>
              <td id="fd6ac5f542ff4ea0d7b1d59d4bb0d197">1</td>
            </tr>
            <tr id="table-row-8cca49700aa2dda3f331b9eedcc53cb5">
              <td id="9531c685a3c3e4c569227016ee8ba039">1</td>
              <td id="ec19093d18e2d52d1b0548b37e05d814">1</td>
            </tr>
            <tr id="table-row-b6a7b82bd2afa2f71987a928845e9fa2">
              <td id="8c7a5f3e988855f8a3bf2f524929e700" colspan="2">2 colspans</td>
              <td id="61cbdae98788e35518801f944e1e6012">1 colspan</td>
              <td id="d228061e849c1161e4608f45fbfbb339">1 colspan</td>
            </tr>
            <tr id="table-row-4461604523ad755a7cb0fa78630da3ff">
              <td id="584a190cbf82b94a04d0ba0a863affac" colspan="4">4 colspans</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
      <p id="_paragraph-12">The oligoarthritis form of JIA was diagnosed in 34 patients, including 20 patients with persistent and 14 with common form. The polyarthritis variant was found in 24 patients, from whom 10 had seropositive and 14 had seronegative polyarthritis. Enthesitis-related arthritis and psoriatic arthritis were diagnosed in 18 patients, and systemic JIA - in 13 patients.</p>
      <p id="_paragraph-13">Most patients (67.4%) had previously received glucocorticoids (GCs) before baseline period, and at the time of observation, only 27% received GCs. 14 patients received only NSAIDs. 75 patients received DMARD, including methotrexate (n=55), plaquenil (n=12), sulfasalazine (n=6), azathioprine (n=2). 23 patients received immunobiological therapy before or at the time of examination; 19 patients were prescribed monoclonal antibodies to the TNF-19 (etanercept - 16 patients, adalimumab - 3 patients), 2 - tocylumizabac, and remaining 2 - rituximab. Remission was diagnosed in 37 (41.6%) patients with a history of JIA.</p>
      <table-wrap id="_table-figure-2">
        <label>Table 2</label>
        <caption>
          <title>Demographic characteristics of patients with JIA.</title>
          <p id="_paragraph-15">All patients from JIA and control group received quality assessment questionnaires SF-36 and functional status HAQ. The results of the evaluation are presented in Table 2.</p>
        </caption>
        <table id="_table-2">
          <tbody>
            <tr id="table-row-0893d4b21435b552619bf5ac659292a7">
              <td id="84352f2cf0b1c9e3c1fff15605f7a0f3"/>
              <td id="cb88dc537a4ca3b79a8bf752757cc13d">Patients with JIA (n=89)</td>
            </tr>
            <tr id="table-row-ed5a8131f4f786481c9b8e42481de9e4">
              <td id="da93df61c31cb5b9974430b903b8ed74">Sex (M/F)</td>
              <td id="28da93516ab1f77aa894909728216ef1">41/48 (control group -12/13</td>
            </tr>
            <tr id="table-row-a06c43a328edce23dc1382861351cd52">
              <td id="5a184ceef2e4ca6c3749da9360fbcede">Middle age </td>
              <td id="695d1ee5f63a5da9ccabd5b74315d63b">19.4±1.8 (control group - 20.1±1.9)</td>
            </tr>
            <tr id="table-row-70c4c50a717ca7b8e0a3214de0ba3a35">
              <td id="7c820760c4f6ad137e067874b5a947b1">Duration of the disease, years</td>
              <td id="7a5a2b2b57df7f97e4df370f60e361f9">8.7±5.1</td>
            </tr>
            <tr id="table-row-7b611b11141bfbae78c34330e015422b">
              <td id="ba1bbb5fdf374964f966e9148649f93d">Age at onset of JIA, years</td>
              <td id="f519c49cda7bf8cf1b120f0f0e2d1f97">10.2±4.9</td>
            </tr>
            <tr id="table-row-a61406a8ab2d1970cabdf8317914146d">
              <td id="e30c7446315edb59f65cc98c79335194">Time from onset to the diagnosis, months.</td>
              <td id="83f2f4b9524a6b97caa4a32dda52089b">15.6±25.9</td>
            </tr>
            <tr id="table-row-c2bf145b8428fe0faff4dd38c47e1a8d">
              <td id="bc9edb6bf66ca6ca6fccc630730d04e1">Persistent oligoarthritis</td>
              <td id="7603ff7421609bd05585d609e3c73bd4">20 (22.5%)</td>
            </tr>
            <tr id="table-row-08037a4f91985c39bf01854ae7004b76">
              <td id="f1b9fccd57e2910e909b9974743b7654">Common oligoarthritis</td>
              <td id="3b45e63f73977e006ce9c592cda0a572">14 (15.7%)</td>
            </tr>
            <tr id="table-row-d99b1039b9812ae7b9fce814c19cfdb2">
              <td id="ed118cce8cf279b7cb8ad022d11473ee">Polyarthritis RF +</td>
              <td id="6dafaa00c5081e87cec79d35108fa2be">10 (11.2%)</td>
            </tr>
            <tr id="table-row-3467341d3be61e95389153bde1cc6123">
              <td id="1c5fb47045c6a5acd340a0a3d643e949">Polyarthritis RF -</td>
              <td id="200ad3fbfa6d5d4e9f01b41cbe8b9add">14 (15.7%)</td>
            </tr>
            <tr id="table-row-dbdffb83bd962c76dfde55c2c48e60d3">
              <td id="970f17f7faf7d5928098c18d45e8b63f">Enthesitis-related arthritis + psoriatic arthritis</td>
              <td id="5f2cefcec93a35c8ef1721782cc5234d">18 (16.9%)</td>
            </tr>
            <tr id="table-row-eac957c95fea159f6cd830d163d0edfe">
              <td id="c0740b9fa2c468590af92eabf58c4c7e">Systemic JIA</td>
              <td id="236d298c0732be1044e988cef6276367">13 (14.6%)</td>
            </tr>
            <tr id="table-row-814cae7cde785f76014059064b5e3ead">
              <td id="7e3683bf1bbf72440a63c9b23e7d303e">GCs took earlier / at the moment</td>
              <td id="7acb465a7d8ffec706e92bde314e7bcf">60 (67.4%)/24 (27%)</td>
            </tr>
            <tr id="table-row-2d629bd6cfb5184cba31942f21b9ef38">
              <td id="4ac1ebe751f52a3c62b0b65af1c001b7">Remission</td>
              <td id="f9343fe0734354100f9dfa88ebaeaa19">37 (41.6%)</td>
            </tr>
            <tr id="table-row-f13e76fc8b3bd1c3a13e57581812218a">
              <td id="59367d36ae9f9392453ae2ad2c81133c">NSAIDs</td>
              <td id="3cf04fc47a6184c0cd2ae4e06cdd4b83">14</td>
            </tr>
            <tr id="table-row-584f9df716f1c3b1448b59fb946ef981">
              <td id="9d90f6778496c13459d435f175176a60" colspan="2">DMARD (n=75)</td>
            </tr>
            <tr id="table-row-228a60aaf977017bbd4e322ee6f442c9">
              <td id="b5a905fbaed7c8dc2e9b4289777c2878">Methotrexate</td>
              <td id="adecb2d44fa6767adf8c529e1b4eafe4">55/75</td>
            </tr>
            <tr id="table-row-27d3d844c33c73508f4ce2729d2f4bb6">
              <td id="d8f3c1fd0cbfd5bcc452d546eb65ec49">Plaquenil</td>
              <td id="9fe44619252664d897623f9638345494">12/75</td>
            </tr>
            <tr id="table-row-de8a2bd0c4f1ee51cd955cd8be2747d8">
              <td id="7c38b36f5877833f2cebb03b774dbe44">Sulfasalazine</td>
              <td id="cb14b09b3563eb25ff4e993817565f16">6/75</td>
            </tr>
            <tr id="table-row-f424b0471e0480708b0aecc949adfa90">
              <td id="670a98366bf404731d6f7a2d3320fe59">Azathioprine</td>
              <td id="2ff1d175b9395c18c1a7d403dee7ee82">2/75</td>
            </tr>
            <tr id="table-row-506c7455b1181ee99309063aec7689a7">
              <td id="b648dce0a93023f030710f126165ba5d" colspan="2">Immunobiology (n=23)</td>
            </tr>
            <tr id="table-row-99611b3dbdc9bdd34bccc3a130750a24">
              <td id="1a431982e77bdcbd46f414e85ee2f671">Anti-TNF (ETA / ADA))</td>
              <td id="20e3a86f0734becebcb91ae359276d12">19/23 (16/3)</td>
            </tr>
            <tr id="table-row-165a9a268bd6c1a06fbdba157c525410">
              <td id="5a36b5fe4d85ec123a80277592273535">Tocilizumab</td>
              <td id="be92e4075177c5de5b2353d2447e33ce">2/23</td>
            </tr>
            <tr id="table-row-38e70e844efb815e760e9ea6fc765c09">
              <td id="7e7cd572ede284a9ad8e7c4e5cddc6d6">Rituximab</td>
              <td id="970490335ad00c1d312a9a399a942455">2/23</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
      <table-wrap id="_table-figure-3">
        <label>Table 3</label>
        <caption>
          <title>Quality of life in young patients with JIA and control group</title>
          <p id="_paragraph-19">* Notes: PF - physical functioning; RP - role functioning due to physical condition, BP- pain intensity, GH - general health status, VT - vital activity, SF - social functioning, RE - role function, conditioned by emotional state, MH - mental health, PCS - Physical well-being, PCS - psychological well-being.</p>
        </caption>
        <table id="_table-3">
          <tbody>
            <tr id="table-row-4ff13db1e94358517676404a286df816">
              <td id="2114301e5f7607039433888f55f1d0e6">Indexes</td>
              <td id="f53bfd77155eeccad0a6adb5f4545c08">Patients with JIA (n=89)</td>
              <td id="090c667df28ebb511511e9aa8425503a">Control group (n=25)</td>
              <td id="4777aed7a7b0eb293c708a0c9657cdbe">p</td>
            </tr>
            <tr id="table-row-896eff1e6b580ad36c95b8743ad5b852">
              <td id="2ff82de3981c24eaca7fbf2ec40207d2">HAQ</td>
              <td id="31ac12b0f515710c1658f5f12bbc4a79">0.3±0.4</td>
              <td id="5dabb575a97bbc6289b32f68467fcac7"/>
              <td id="1c7aa66ca586e83c1c1e970623ddc656"/>
            </tr>
            <tr id="table-row-dec3e3b674f798814f305b19fd446c45">
              <td id="f3dac0c47d23f5e4142aabb07b3ada63">VAS patient</td>
              <td id="a11b3876d44a7cb87654779ddb0222b2">34.6±23.3</td>
              <td id="9a0abbd7b0a2259cd26f010bc27e6241"/>
              <td id="0aca23a0947212c3aac1f54a07d7d5a8"/>
            </tr>
            <tr id="table-row-27929177dce09e744dffb99e342fb1be">
              <td id="de22a016eed70a8f38e79d0841136f57">VAS doctor</td>
              <td id="4dadf6c25e998538cad317e5004903ca">27.9±24.3</td>
              <td id="b0e712aa06381984df80b8b7a68d2201"/>
              <td id="c40b6ecfcff92bdbaf34aecec9ee7a48"/>
            </tr>
            <tr id="table-row-51104164013b1c1cfb35224f351ee68f">
              <td id="e461a40ace1cb752977e5d0e7a476037" colspan="4">SF- 36</td>
            </tr>
            <tr id="table-row-1830ddfb2278b7b2e0978700ec5e94da">
              <td id="1e352d51715f5ee842754efea9593ca4" colspan="4">SF-36 physical indexes</td>
            </tr>
            <tr id="table-row-ce30060d7e63f4300b10a8a2741c899e">
              <td id="eedb9a7ff13ab2b15aaf2d2ed5cb479b">
                <bold id="_bold-9">PF</bold>
              </td>
              <td id="c9bf10495212a3fe0bfd826e088bb3e1">
                <bold id="_bold-10">74.3± 20.9</bold>
              </td>
              <td id="1ede3d44cb3170b1091ab76f22861b1c" colspan="2">
                <bold id="_bold-11">94.7±8.7</bold>
                <bold id="_bold-12">0.0002</bold>
              </td>
            </tr>
            <tr id="table-row-50e68545ef5004bee06931dcbbc7393a">
              <td id="52870d343bde54dc4461974f543e7eef">
                <bold id="_bold-13">RF</bold>
              </td>
              <td id="db85d0d9980d7c12b45a1a4d7c776478">
                <bold id="_bold-14">64.6±29.9</bold>
              </td>
              <td id="84b913d4c6f6b4738e7132331cc437f3" colspan="2">
                <bold id="_bold-15">83.8±19.5 0.02</bold>
              </td>
            </tr>
            <tr id="table-row-996c68d6fd59d9210feea68709a44f52">
              <td id="1de4915da3c15b1a42235ae7e972a025">
                <bold id="_bold-16">BP</bold>
              </td>
              <td id="4dbfb31f1ede5207e55fe25e15f5511e">
                <bold id="_bold-17">59.0±24.2</bold>
              </td>
              <td id="88cd78b9afa60c5d1e07b5050db2f3d5">
                <bold id="_bold-18">84.5±21.6</bold>
              </td>
              <td id="3148894ccb3222bff8f89f0df39ca6b6">
                <bold id="_bold-19">0.0002</bold>
              </td>
            </tr>
            <tr id="table-row-f391598f2dd1b221b6e55783e87f05bd">
              <td id="d02fd26e47fcff5097e26ecf8cdc7016" colspan="2">GH56.5±22.6</td>
              <td id="e64ea26a684065a2391ad11933b829d8">60.1±17.1</td>
              <td id="20c9b557b723f085c06265bc7069c2b6">0.54</td>
            </tr>
            <tr id="table-row-a7b44d4ae98e59eda417b657cf52761b">
              <td id="aef4ba4f47f736ebb25796886140918c">VT</td>
              <td id="a4be2b097d0610d32d7c49d149a092d6">58.2±19.1</td>
              <td id="4e5f27adcc52e5dee543af470b4bfc4b">59.8±20.0</td>
              <td id="c3b037cbec1e93df39b422377b3e217e">0.77</td>
            </tr>
            <tr id="table-row-ac7fb5bc9fcd664816c37515393deeca">
              <td id="57cf4f41181c2ab2ee003b56ea7cc217" colspan="4">SF-36 psychological indexes</td>
            </tr>
            <tr id="table-row-9dfd2e65e7099aec72108e71419e638b">
              <td id="06c96243503332382cfbfb39268eff1a">SF</td>
              <td id="1e69ca1c407ca8886e46790bca4181c4" rowspan="4">75.8±21.269.2±33.869.3±18.6<bold id="_bold-20">46.3±8.7</bold></td>
              <td id="18525ad498855a0458ba8711a0931d69">80.5±18.2</td>
              <td id="24ba1c9e156614713aa3ed8ef9c32286" rowspan="2">0.410.52</td>
            </tr>
            <tr id="table-row-fd4eefc055bfd8f9237980509abdf9a1">
              <td id="2db651f2a808d7d2fdd6c7b94916360d">RE</td>
              <td id="745954d5d5c090be557237b748be919b">75.0±26.7</td>
            </tr>
            <tr id="table-row-a778acc1bf0550c95320489e97db5bcf">
              <td id="ef3b43fbe14e41cc8dc4a0c6d63eae85">MH</td>
              <td id="2dae15b6a945079552ae767966c98f0a">68.4±18.9</td>
              <td id="eee79ea66b741950031107c637c74c9d">0.86</td>
            </tr>
            <tr id="table-row-4540aba43fac5017b4a8c617ee8f84a2">
              <td id="3746f90011f3377fe8771cc200730152">
                <bold id="_bold-21">PCS</bold>
              </td>
              <td id="b502a4aa76f020d04ce35d724980d7c4">
                <bold id="_bold-22">55.7±6.9</bold>
              </td>
              <td id="3a856ee8e4c4642e9313d32eedbbd3fb">
                <bold id="_bold-23">0.0001</bold>
              </td>
            </tr>
            <tr id="table-row-8a14b9a96dc53b6cf22c5de1bf422cd3">
              <td id="5346bb841fb7257d4e049f76b6674008">MCS</td>
              <td id="b1502deb8bdddda369871f2dfbbe3458">47.0±10.5</td>
              <td id="1144a2aee9a767c6c0c40e52d2c690c2">45.1±11.7</td>
              <td id="e13bc50c80c1fe7880a0c6015dde16bd">0.52</td>
            </tr>
            <tr id="table-row-0ef3ef33a1ec1da2307244502ded8d7a">
              <td id="42fbb9fcf4291a3630f3ced2322044c4">PHQ-9</td>
              <td id="fd55795677e1c072cc6597933b09643b">5.8 ±5.5</td>
              <td id="eb46889f57c4f4fbaa111739a67fa98c">4.3 ±3.1</td>
              <td id="a0306b173606ce3487a331c6cb46b7e6">0.12</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
      <table-wrap id="_table-figure-4">
        <label>Table 4</label>
        <caption>
          <p id="_paragraph-21"/>
        </caption>
        <table id="_table-4">
          <tbody>
            <tr id="table-row-92191b0160702c7f679e3cde8fdfe9c5">
              <td id="7ddba55862cdbb20cf12763dd0dea6d6">HAQ</td>
              <td id="5bd0fc0a84bde2e6361fc6a9dc9db49a">0.3±0.4</td>
              <td id="2bf5201b61ae9e549692f3c0edd80d58">80.99±18.2975.99±26.79</td>
              <td id="ea24ec00323ffcca0bbcead18fd79556">34.55</td>
            </tr>
            <tr id="table-row-6e84378b04645c49fe39071866d38076">
              <td id="54f451206e3877c0c52f4d8af4bc3fc2" colspan="2">VAS patient - 34.6±23.3</td>
              <td id="7bb728d7a260f6124390edf52db2f998">32.33</td>
            </tr>
            <tr id="table-row-f458ed4e1f4d9fcb63d5136d2fdcf1eb">
              <td id="d396fb0f7ece2a0612740b035d638cbd">VAS doctor</td>
              <td id="b6239e67021d09ea8d6128a9bb81ca82">27.9±24.3</td>
              <td id="c8735fb8dde4b9df8588ab162a50b608">68.99±18.99</td>
              <td id="8e6824a844ee4c34acc06cf41380cc6e">26.55</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
      <p id="_paragraph-22">As can be seen from Table 2, patients with JIA had a worse (p&lt;0.001) physical well-being (46.3±8.7) compared with the control group (55.7±6.9). In them, there was a decrease in the indices corresponding to the physical condition (p&lt;0.001), role functioning due to the physical condition (p=0.02), and the intensity of pain (p&lt;0.001), compared with the control group. However, the indicators responsible for psychological well-being in patients with JIA did not differ from the control group.</p>
      <p id="_paragraph-23">In the analysis of functional activity communication for HAQ (Table 3), there was found a strong negative effect on physical functioning (r = -0.56, p&lt;0.001), a role-based functioning due to physical condition (r = -0.33, p &lt;0.001), pain intensity (r = -0.60, p&lt;0.001), general health (r = -0.40, p = 0.01), vital activity (r = -0.46, p &lt;0.001), social functioning (r = -0.48, p&lt;0.001), and mental health (r = -0.42, p&lt;0.001), as well as in the total score for the physical (p&lt;0.001) and psychological (p&lt;0.05) well-being.</p>
      <table-wrap id="_table-figure-5">
        <label>Table 5</label>
        <caption>
          <title>Communication of functional activity with quality of life.</title>
          <p id="_paragraph-25">Figure 1 shows the results of the SF-36 questionnaire for young patients with JIA and those in the control group, where the apparent lower levels of physical health (PCS) (p&lt;0.001), role-based physical functioning are evident) - RF (p&lt;0, 05), pain intensity - BP (p&lt;0.001) and physical functioning - PF (p&lt;0.001) in patients with JIA compared with healthy subjects.</p>
          <p id="_paragraph-27">Figure 1. Quality of life in young patients with JIA and healthy individuals according to the SF-36 questionnaire.</p>
          <p id="_paragraph-28">*Notes: * - statistical significance p&lt;0.001, † - statistical significance p=0.05</p>
        </caption>
        <table id="_table-5">
          <tbody>
            <tr id="table-row-183cbd8dd9de10860ab77fe20165cbc7">
              <td id="173e7a65ff084019688f90e12197cbb2"/>
              <td id="04faf14cb54a018bd1cafb18aaeee58d">PCS</td>
              <td id="b683275dc2949cd29c3b8525270d6e72">MCS</td>
              <td id="9c189844fff35e788e52f5d13132ad46">PF</td>
              <td id="5584b90a5e259e14d5a208c4101bcca4">RF</td>
              <td id="ac6f97d999e2b89ab2e00c8c2b0a2438">BP</td>
              <td id="9fbb6e81c0ffde8980583928ad091974">GH</td>
              <td id="76cd21d540a2bba9ee2ca68e4eb71b92">VT</td>
              <td id="7d8de54be4150523ed0e7d24161e3bcb">SF</td>
              <td id="6066c8181dab1f96807ee5291294a8c5">RE</td>
              <td id="253f7f7168298cb321a60c4426f87a53">MH</td>
            </tr>
            <tr id="table-row-9de61912dce466eda00360b0d7c11cf9">
              <td id="f50741e1d910cca2e1a08eafc0e976c8"> HAQ</td>
              <td id="e8395b74ac19b70eb5ea98aa1a486ec6">-0.59</td>
              <td id="9f682c43a275db1bdae8b92517235539">-0.25</td>
              <td id="01f5c975da37dfa2e2f7a9d9636751ab">-0.56</td>
              <td id="ff2ecda34896570d153da5f5eb4932e6">-0.32</td>
              <td id="b868d4ec8fb3af836ba3cf9df363d531">-0.60</td>
              <td id="4e6b789c30a82198acab1fd4d082da63">-0.40</td>
              <td id="0a18181ddfbc590300c8d1ae74415d4b">-0.46</td>
              <td id="90311717751e10b1bade253aa9b0d8b9">-0.48</td>
              <td id="8b762e003cb0114438145ffac881fde6">-0.08</td>
              <td id="d9fdd3a1dd3f40f91c454c1fafbb3ea2">-0.42</td>
            </tr>
            <tr id="table-row-31524bc491ef1e67b33b0dbaf8db92d6">
              <td id="bb84605c73fb8690549dd49e4ea5bac4"> P</td>
              <td id="3f86b7b5fc512e753f7a8363ee5afb4c">&lt;0.001</td>
              <td id="507bd694e998913b41f4de7c21118e65">0.035</td>
              <td id="934488067ff1244540216862f29b2e92">&lt;0.001</td>
              <td id="ccb200d23caab2f82637c4e03421f58b">0.006</td>
              <td id="73cdc59a2d7b669dce540a5886718c9f">&lt;0.001</td>
              <td id="645a6417ae7fc4418646879f3ec4f459">0.001</td>
              <td id="3a4b16cb5d80466688dbc89118f1f6b5">&lt;0.001</td>
              <td id="e13ec57a3821d79876480fa70a2038f0">&lt;0.001</td>
              <td id="f14ed8e21ab881a540fb6a2db81ad222">НД</td>
              <td id="56f239f715107c0da4a8d771fb5baa47">&lt;0.001</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
    </sec>
    <sec id="sec-5">
      <title>Discussion</title>
      <sec id="sec-5_1">
        <title>Heading 3</title>
        <p id="_paragraph-29">As we expected, QoL in patients with JIA was worse than in the control group. Our findings were confirmed by data published earlier that showed a worse QoL in young people with JIA than in the control group of the corresponding age and sex [9, 16, 17, 18, 19, 20, 21]. However, our results in patients with JIA and healthy individuals are different from the data from Wipff J. et al., where authors analyzed data on patients with JIA at the stage of transmission of patients from child to an adult healthcare services during biologic therapy [22]. The SF-36 score for physical and psychological health was less influenced by the JIA in our sample than in previously published studies. These results were quite unexpected because in Ukraine biological therapy is not available for many patients [16, 18, 19, 20, 22]. There are several possible explanations for these results, including:</p>
        <list list-type="bullet" id="list-b41027a9746f7a5e55ba6342eb219700">
          <list-item>
            <p>Our patients often received GCs, which reduced the activity of the disease.</p>
          </list-item>
          <list-item>
            <p>Our sample included not only patients with JIA in the active phase that needed constant observation but also those who were in complete clinical remission and did not require medical therapy.</p>
            <list list-type="bullet">
              <list-item>
                <p>Nested List item 1</p>
              </list-item>
              <list-item>
                <p>Nested List item 2</p>
              </list-item>
            </list>
          </list-item>
        </list>
        <list list-type="bullet" id="list-d5971770b6a20fa143037d8b13df8c58">
          <list-item>
            <p>Our results confirmed that JIA's greatest impact was on "physical functioning" and "pain intensity," which are parts of the physical well-being SF-36 factor. Thus, JIA has a greater impact on physical health than on the mental health of patients, which corresponds to scientific data [16, 18, 19, 20, 23, 24].</p>
          </list-item>
        </list>
        <p id="_paragraph-30">There is evidence of a negative relationship between QoL and the duration of the disease by the results of work by Minden K. et al. [25]. Foster et al. also noted this tendency in patients with JIA [16]. However, in our study, we did not detect the effect of the duration of the disease on the QoL indicators, although we observed the negative correlation between functional activity limitation and all components of the QoL according to the SF-36 as established, and in the previous work [1] we have shown that QoL depends on the X-ray definite degree of JIA’s progression .</p>
        <p id="_paragraph-31">Since our study showed that physical activity is most strongly affected by pain intensity, treatment with JIA should not be directed solely at the fight against inflammation through the use of NSAIDs. It is advisable to use analgesics and procedures for severe pain, including physiotherapy and/or hypnosis [26].</p>
        <p id="_paragraph-32">Patients with JIA may also have a low QoL while in remission. In our study, it was found that 3 out of 33 patients in the remission stage had a low physical well-being. In 5 out of 33 patients - a low level of mental well-being. These data coincide with the results of the study [22], in which 8/38 patients with JIA in the remission stage had a low physical well-being.</p>
        <p id="_paragraph-33">Our study has some limitations. First, our study had cross-sectional design study that limited the assessment of the natural course and QoL prognostic factors of the JIA. Second, data on the educational and socio-economic status of patients with JIA and their parents have not been collected. These factors may influence SF-36 results. Previous studies have shown that psychological factors, therapies, geographical origin, and socioeconomic differences can have an effect on pain in the JIA [27, 28]. Third, we did not evaluate the effect of treatment on QoL, especially on biological therapy, although a number of studies have shown that QoL with JIA is improved against the background of biological therapy [29, 30].</p>
        <p id="_paragraph-34">Our research also has the strengths:</p>
        <list list-type="order" id="list-02db2de90429a864edf25047f53306ab">
          <list-item>
            <p>The experimental group consisted of patients with JIA that met the criteria for ILAR in the transition period.</p>
          </list-item>
          <list-item>
            <p>The results of evaluation were compared with the control groups comprised of healthy individuals.</p>
          </list-item>
          <list-item>
            <p>This is the first study in Ukraine that included biologic therapy as a potential factor affecting QoL in the transition period.</p>
          </list-item>
        </list>
      </sec>
    </sec>
    <sec id="sec-6">
      <title>Conclusion</title>
      <p id="_paragraph-35">Juvenile idiopathic arthritis had the greatest influence during the transition from pediatric to adult rheumatological service to a physical functioning and pain intensity on SF-36 physical well-being scale. It indicates a greater effect of the disease on the physical than on the mental health in patients with JIA.</p>
    </sec>
    <sec id="sec-7">
      <title>Another conclusion</title>
      <p id="_paragraph-36">Звичаний текст тут.</p>
    </sec>
    <sec id="sec-8">
      <title>Zotero</title>
    </sec>
  </body><back>
    <ref-list>
      <ref id="1">
        <element-citation publication-type="journal">
          <day>1</day>
          <month>1</month>
          <page-range>144-150</page-range>
          <volume>154</volume>
          <year>2018</year>
          <pub-id pub-id-type="doi">10.1016/j.puhe.2017.10.016</pub-id>
          <person-group person-group-type="author">
            <name>
              <surname>Chandler</surname>
              <given-names>V.</given-names>
            </name>
          </person-group>
          <source>Public Health</source>
          <article-title>Google and suicides: what can we learn about the use of internet to prevent suicides?</article-title>
        </element-citation>
      </ref>
      <ref id="2">
        <mixed-citation publication-type="journal">References</mixed-citation>
      </ref>
      <ref id="3">
        <mixed-citation publication-type="journal">Dzhus MB. Psycho-emotional condition of young adults with juvenile idiopathic arthritis. Acta Medica Leopoliensia. 2017; 23 (1-2): 44-51.</mixed-citation>
      </ref>
      <ref id="4">
        <mixed-citation publication-type="journal">Hersh A, Scheven E, Yelin E. Adult outcome of childhood-onset rheumatic diseases. Nat Rev Rheumatol. 2011;7(5):290-295. DOI: https://doi.org/10.1038/nrrheum.2011.38 PMID: https://www.ncbi.nlm.nih.gov/pubmed/21487383 </mixed-citation>
      </ref>
      <ref id="5">
        <mixed-citation publication-type="journal">Scal P, Horvath K, Garwick A. Preparing for adulthood: health care transition counseling for youth with arthritis. Arthritis Rheum. 2009;61(1):52-57. DOI: https://doi.org/10.1002/art.24088 PMID: https://www.ncbi.nlm.nih.gov/pubmed/19116976 </mixed-citation>
      </ref>
      <ref id="6">
        <mixed-citation publication-type="journal">Ammerlaan JW, Scholtus LW, Bijlsma HJ, Prakken BJ, Kruize AA. An urge for change: transitional care for young adults with juvenile idiopathic arthritis. Patient Educ Couns. 2013;92(1):127–129. DOI: https://doi.org/10.1016/j.pec.2013.02.006 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23490174 </mixed-citation>
      </ref>
      <ref id="7">
        <mixed-citation publication-type="journal">Wells CK, McMorris BJ, Horvath KJ, Garwick AW, Scal PB. Youth report of healthcare transition counseling and autonomy support from their rheumatologist. Pediatr Rheumatol Online J. 2012;10:36. DOI: https://doi.org/10.1186/1546-0096-10-36 </mixed-citation>
      </ref>
      <ref id="8">
        <mixed-citation publication-type="journal">Shaw KL, Southwood TR, McDonagh JE. User perspectives of transitional care for adolescents with juvenile idiopathic arthritis. Rheumatology. 2004;43(6):770–778. https://doi.org/10.1093/rheumatology/keh175 PMID: https://www.ncbi.nlm.nih.gov/pubmed/15039498 </mixed-citation>
      </ref>
      <ref id="9">
        <mixed-citation publication-type="journal">Eyckmans L, Hilderson D, Westhovens R, Wouters C, Moons P. What does it mean to grow up with juvenile idiopathic arthritis? A qualitative study on the perspectives of patients. Clin Rheumatol. 2011;30(4):459–465. DOI: https://doi.org/10.1007/s10067-010-1444-0 PMID: https://www.ncbi.nlm.nih.gov/pubmed/20383546 </mixed-citation>
      </ref>
      <ref id="10">
        <mixed-citation publication-type="journal">Tong A, Jones J, Craig JC, Singh-Grewal D. Children’s experiences of living with juvenile idiopathic arthritis: a thematic synthesis of qualitative studies. Arthritis Care Res (Hoboken). 2012;64(9):1392–1404. DOI: https://doi.org/10.1002/acr.21695   PMID: https://www.ncbi.nlm.nih.gov/pubmed/22504867  </mixed-citation>
      </ref>
      <ref id="11">
        <mixed-citation publication-type="journal"> Packham JC, Hall MA. Long-term follow-up of 246 adults with juvenile idiopathic arthritis: functional outcome. Rheumatology (Oxford). 2002;41(12):1428–1435. DOI: https://doi.org/10.1093/rheumatology/41.12.1436 PMID: https://www.ncbi.nlm.nih.gov/pubmed/12468825 </mixed-citation>
      </ref>
      <ref id="12">
        <mixed-citation publication-type="journal"> Magni-Manzoni S, Ruperto N, Pistorio A, Sala E, Solari N, Palmisani E, Cugno C, Bozzola E, Martini A, Ravelli A. Development and validation of a preliminary definition of minimal disease activity in juvenile idiopathic arthritis. Arthritis Rheum. 2008;59(8):1120–1127. DOI: https://doi.org/10.1002/art.23916 PMID: https://www.ncbi.nlm.nih.gov/pubmed/18668599 </mixed-citation>
      </ref>
      <ref id="13">
        <mixed-citation publication-type="journal"> Haverman L, Grootenhuis MA, Berg JM, Veenendaal M, Dolman KM, Swart JF, Kuijpers TW, Rossum MA. Predictors of health- related quality of life in children and adolescents with juvenile idiopathic arthritis: results from a Web-based survey. Arthritis Care Res (Hoboken). 2012;64(5):694–703. DOI: https://doi.org/10.1002/acr.21609 PMID: https://www.ncbi.nlm.nih.gov/pubmed/22238240 </mixed-citation>
      </ref>
      <ref id="14">
        <mixed-citation publication-type="journal">Kalyoncu U, Dougados M, Daurès JP, Gossec L. Reporting of patient-reported out- comes in recent trials in rheumatoid arthritis: a systematic literature review. Ann Rheum Dis. 2009;68(2):183–190. DOI: https://doi.org/10.1136/ard.2007.084848 PMID: https://www.ncbi.nlm.nih.gov/pubmed/18375533 </mixed-citation>
      </ref>
      <ref id="15">
        <mixed-citation publication-type="journal"> Bruce B, Fries JF. The Health Assessment Questionnaire (HAQ). Clin Exp Rheumatol. 2005;23(5):14–18. PMID: https://www.ncbi.nlm.nih.gov/pubmed/16273780 </mixed-citation>
      </ref>
      <ref id="16">
        <mixed-citation publication-type="journal"> Petty RE, Southwood TR, Manners P, Baum J, Glass DN, Goldenberg J, He X, Maldonado-Cocco J, Orozco-Alcala J, Prieur AM, Suarez-Almazor ME, Woo P. International League of Associations for Rheumatology classification of juvenile idiopathic arthritis: second revision, Edmonton, 2001. J Rheumatol. 2004;31(2):390–392. PMID: https://www.ncbi.nlm.nih.gov/pubmed/14760812 </mixed-citation>
      </ref>
      <ref id="17">
        <mixed-citation publication-type="journal"> Beukelman T, Patkar NM, Saag KG, Tolleson-Rinehart S, Cron RQ, DeWitt EM, Ilowite NT, Kimura Y, Laxer RM, Lovell DJ, Martini A, Rabinovich CE, Ruperto N. 2011 American College of Rheumatology recommendations for the treatment of juvenile idiopathic arthritis: initiation and safety monitoring of therapeutic agents for the treatment of arthritis and systemic features. Arthritis Care Res. 2011;63(4):465–482. DOI: https://doi.org/10.1002/acr.20460  PMID: https://www.ncbi.nlm.nih.gov/pubmed/21452260 </mixed-citation>
      </ref>
      <ref id="18">
        <mixed-citation publication-type="journal"> Foster HE, Marshall N, Myers A, Dunkley P, Griffiths ID. Outcome in adults with juvenile idiopathic arthritis: a quality of life study. Arthritis Rheum. 2003;48(3):767–775. DOI: https://doi.org/10.1002/art.10863 PMID: https://www.ncbi.nlm.nih.gov/pubmed/12632431 </mixed-citation>
      </ref>
      <ref id="19">
        <mixed-citation publication-type="journal"> Ruperto N, Levinson JE, Ravelli A, Shear ES, Link Tague B, Murray K, Martini A, Giannini EH. Long-term health outcomes and quality of life in American and Italian inception cohorts of patients with juvenile rheumatoid arthritis; I; Outcome status. J Rheumatol. 1997;24(5):945–951. PMID: https://www.ncbi.nlm.nih.gov/pubmed/9150087 </mixed-citation>
      </ref>
      <ref id="20">
        <mixed-citation publication-type="journal"> Flatø B, Aasland A, Vinje O, Førre O. Outcome and predictive factors in juvenile rheumatoid arthritis and juvenile spondyloarthropathy. J Rheumatol. 1998;25(2):366–375. PMID: https://www.ncbi.nlm.nih.gov/pubmed/9489836 </mixed-citation>
      </ref>
      <ref id="21">
        <mixed-citation publication-type="journal"> Peterson LS, Mason T, Nelson AM, O'Fallon WM, Gabriel SE. Psychosocial outcomes and health status of adults who have had juvenile rheumatoid arthritis: a controlled, population-based study. Arthritis Rheum. 1997;40(12):2235–2240.  PMID:  https://www.ncbi.nlm.nih.gov/pubmed/9416862   </mixed-citation>
      </ref>
      <ref id="22">
        <mixed-citation publication-type="journal"> Arkela-Kautiainen M, Haapasaari J, Kautiainen H, Vikkumaa I, Malkia E, Leirisalo-Repo M. Favourable social functioning and health related quality of life of patients with JIA in early adulthood. Ann Rheum Dis. 2005;64(6):875–880. DOI: https://doi.org/10.1136/ard.2004.026591 </mixed-citation>
      </ref>
      <ref id="23">
        <mixed-citation publication-type="journal"> Oen K, Malleson PN, Cabral DA, Rosenberg AM, Petty RE, Reed M, Schroeder ML, Cheang M. Early predictors of longterm outcome in patients with juvenile rheumatoid arthritis: subset-specific correlations. J Rheumatol. 2003;30(3):585–593. URL: http://www.jrheum.org/content/30/3/585.long PMID: https://www.ncbi.nlm.nih.gov/pubmed/12610821 </mixed-citation>
      </ref>
      <ref id="24">
        <mixed-citation publication-type="journal"> Wipff J, Sparsa L, Lohse A, Quartier P, Kahan A, Deslandre CJ. Impact of juvenile idiopathic arthritis on quality of life during transition period at the era of biotherapies. Joint Bone Spine. 2015 https://doi.org/10.1016/j.jbspin.2015.03.005 PMID: https://www.ncbi.nlm.nih.gov/pubmed/26231098  </mixed-citation>
      </ref>
      <ref id="25">
        <mixed-citation publication-type="journal"> Ding T, Hall A, Jacobs K, David J. Psychological functioning of children and adolescents with juvenile idiopathic arthritis is related to physical disability but not to disease status. Rheumatology (Oxford). 2008;47(5): 660–664. DOI: https://doi.org/10.1093/rheumatology/ken095 PMID: https://www.ncbi.nlm.nih.gov/pubmed/18356173 </mixed-citation>
      </ref>
      <ref id="26">
        <mixed-citation publication-type="journal"> LeBovidge JS, Lavigne JV, Donenberg GR, Miller ML. Psychological adjustment of children and adolescents with chronic arthritis: a meta-analytic review. J Pediatr Psychol. 2003;28(1):29–39. DOI: https://doi.org/10.1093/jpepsy/28.1.29 PMID: https://www.ncbi.nlm.nih.gov/pubmed/12490628 </mixed-citation>
      </ref>
      <ref id="27">
        <mixed-citation publication-type="journal"> Minden K, Niewerth M, Listing J, Biedermann T, Bollow M, Schöntube M, Zink A. Long-term outcome in patients with juvenile idiopathic arthritis. Arthritis Rheum. 2002;46(9):2392–2401. DOI: https://doi.org/10.1002/art.10444 PMID: https://www.ncbi.nlm.nih.gov/pubmed/12355487 </mixed-citation>
      </ref>
      <ref id="28">
        <mixed-citation publication-type="journal"> Stinson JN, Luca N, Jibb LA. Assessment and management of pain in juvenile idiopathic arthritis. Pain Res Manag. 2012;17(6):91–396. DOI: https://doi.org/10.1155/2012/237258 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23248812 </mixed-citation>
      </ref>
      <ref id="29">
        <mixed-citation publication-type="journal"> Jordan JM. Effect of race and ethnicity on outcomes in arthritis and rheumatic conditions. Curr Opin Rheumatol. 1999; 11(2):98–103. DOI: https://doi.org/10.1097/00002281-199903000-00003 PMID: https://www.ncbi.nlm.nih.gov/pubmed/10319211 </mixed-citation>
      </ref>
      <ref id="30">
        <mixed-citation publication-type="journal"> Baker TA, Green CR. Intrarace differences among black and white Americans presenting for chronic pain management: the influence of age, physical health, and psychosocial factors. Pain Med. 2005;6(1):29–38. DOI: https://doi.org/10.1111/j.1526-4637.2005.05014.x PMID: https://www.ncbi.nlm.nih.gov/pubmed/15669948 </mixed-citation>
      </ref>
      <ref id="31">
        <mixed-citation publication-type="journal"> Klotsche J, Minden K, Thon A, Ganser G, Urban A, Horneff G. Improvement in Health-related Quality of Life for children with juvenile idiopathic arthritis after start of treatment with etanercept. Arthritis Care Res (Hoboken). 2014;66(2):253–262. DOI: https://doi.org/10.1002/acr.22112 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23983081 </mixed-citation>
      </ref>
      <ref id="32">
        <mixed-citation publication-type="journal"> Prince FH, Geerdink LM, Borsboom GJ, Twilt M, Rossum MA, Hoppenreijs EP, Cate RT, Koopman-Keemink Y, Santen-Hoeufft M, Raat H, Suijlekom-Smit LW. Major improvement in health-related quality of life during the use of etanercept in patients with previously refractory juvenile idiopathic arthritis. Ann Rheum Dis. 2010; 69(1):138–142. DOI: https://doi.org/10.1136/ard.2009.111260 PMID: https://www.ncbi.nlm.nih.gov/pubmed/19581280 </mixed-citation>
      </ref>
    </ref-list>
  </back></article>

Compatibility with OJS 3.2

fatal error on retrieving ArticleDAO
adapt plugin for article versioning
undefined method CitationDAO::getBySubmissionId
adapt plugin to a new publication schema

Rely on OJS's preview feature rather than custom preview

The existing code for the preview will quickly fall out of sync with the default theme (and won't be appropriate for other themes). Let's rely on OJS's own preview feature that you've got into 3.3. So let's plan for 3.4 to support a single fullText value in the core themes. Then you can remove the preview code here and just let the conversion save to the full text.

readme : example : url redirect to a login page from OJS

HTML example: http://ojsdemo.e-medjournal.com/index.php/jatsparser/article/view/8/8

Can you please change URL to a public webpage ?

Avoid displaying HTML escaped sequences on the front-end

See: https://forum.pkp.sfu.ca/t/new-ojs-3-theme-on-bootstrap-4/36892/265

Fatal error if submission file deleted

If a submission file has been selected under Publication > Full Text, and that file is then deleted, this plugin will throw a fatal error on line 991 (https://github.com/Vitaliy-1/JATSParserPlugin/blob/master/JatsParserPlugin.inc.php#L991) because a $submissionFile is empty. I'd suggest checking for a valid return here (https://github.com/Vitaliy-1/JATSParserPlugin/blob/master/JatsParserPlugin.inc.php#L983) before adding to the $submissionFiles array.

Language changes to full text tab

Tab: "Full-text upload" --> "Full Text"
"Generate article's fulltext from submission file in JATS XML format" --> "Create full text"
Description: "Select a production ready file in JATS XML format to create the full text. View preview" When viewing the preview without making a selection, show a warning on the preview page that says "You must select an option". Or have "default" selected already.

Reference sources not rendering

Hello
For some reason the sources in the references are not rendering.

Fatal error when installing OJS

If the JATSParserPlugin files are there in the plugins/generic folder when OJS is installed it will cause a fatal error. This is because it tries to access the database before the database exists. The following code is causing the problem:

https://github.com/Vitaliy-1/JATSParserPlugin/blob/master/JatsParserPlugin.inc.php#L33-L37

Either move it out of the register method put it behind a check for SESSION_DISABLE_INIT:

if (!defined('SESSION_DISABLE_INIT')) {
 ...
}

Compatibility with OJS 3.3.0

[ ] - adapt JATS XML galleys import as a full-text to be compatible with submission files refactoring
[ ] - adapt PDF galley creation to be compatible with submission files refactoring
[ ] - make sure that jatsParser::fullTextFileId property of the publication points to the right submission file
[ ] - fix references to supplementary files (images) inside full-text

Accessing galleys causes fatal error

PHP Fatal error:  Uncaught Error: Call to undefined method ArticleGalley::getSubmissionId() in /var/www/ojs-3.2.0/plugins/generic/jatsParser/JatsParserPlugin.inc.php:327

Scroll screen to in-text citation after the click on a correspondent reference inside reference list

PDF conversion fails on empty tags

Tested on empty td elements inside tables. This fails silently, PDF is produced with the data converted before the error. Looks like TCPDF issue. Solution: remove empty tags before passing the document to the TCPDF

In-line citations hyperlink is not working

As the plugin parses XML to HTML or PDF, it recognizes in-line citations as hyperlink, but links are broken.
That is not the case with figures as I've tested.

Additionally, reference numbers (<label>) is not recognized. All ref numbers are '1'. I think it might be the reason of In-line citation links not working.

Regards,
Sina

Wrong submission's genre id if multiple contexts

Keywords styling isn't supported well by Firefox browser

Set default citation style language format

If own isn't set, use primaryCitationStyle setting from CSL Plugin. Otherwise use one of the supported styles.

Convert JATS to PDF statically

Historically, JATS to PDF conversion is done on the fly, when a user accesses the page, TCPDF renders data and sends generated PDF to the browser, see inline (I) parameter:

JATSParserPlugin/JatsParserPlugin.inc.php

Line 343 in e861fc5

$pdfDocument->Output('article.pdf', 'I');

In 2.2 the behavior of how JATS XML is rendered has changed, which will lead to the removal of a deprecated code related to the rendering of the XML galley page.

PDF conversion should also be done statically. Add the option to create a PDF galley based on the full-text under the Publication -> Full-Text tab.

Fatal error when user locale doesn't match JATS galley locale

PHP Fatal error:  Uncaught Error: Call to a member function getFile() on null in /var/www/ojs-3.1.2-1/plugins/generic/jatsParser/JatsParserPlugin.inc.php:278

Article not assigned to the issue produces a fatal error

Trying to create PDF galley from an article that isn't assigned to an issue produces a fatal error:

Slim Application Error:
Type: Error
Message: Call to a member function getIssueIdentification() on null
File: .../ojs/plugins/generic/jatsParser/JatsParserPlugin.inc.php
Line: 151
Trace: #0 .../ojs/plugins/generic/jatsParser/JatsParserPlugin.inc.php(479): JatsParserPlugin->pdfCreation('\n<h2 class="art...', Object(Publication), Object(Request), 'uk_UA')
#1 .../ojs/lib/pkp/classes/plugins/HookRegistry.inc.php(107): JatsParserPlugin->createPdfGalley('Publication::ed...', Array)

Display converted JATS XML on article landing page

Count views for JATS XML Galleys

URL variable doesn't apply to CSL templates

Reported by a user for american-medical-association.csl. Check if this is the plugin issue or arises from citeproc-php or CSL template. See: https://forum.pkp.sfu.ca/t/jatsparserplugin-not-installing-in-3-2-1/65054/17

Style full-text on article landing page

Most of the styling should go from themes. It requires revise of all supported themes.

Example of adding Bootstrap4 in the README has drifted

The link in the README:

it must be added alongside with jQuery from the plugin main class (it is quite straightforward)

should be permalinked to:

JATSParserPlugin/JatsParserPlugin.inc.php

Lines 145 to 148 in 0bfbe3a

 $templateMgr->addStyleSheet('styles', $baseUrl . '/app/app.min.css'); 

 $templateMgr->addStyleSheet('googleFonts', 'https://fonts.googleapis.com/css?family=PT+Serif:400,700&amp;subset=cyrillic'); 

 $templateMgr->addJavaScript('fontawesome', 'https://use.fontawesome.com/releases/v5.2.0/js/all.js'); 

 $templateMgr->addJavaScript('javascript', $baseUrl . '/app/app.min.js');

Remove Bootstrap and jQuery dependencies

Currently, the plugin is supported only by themes, which use Bootstrap and associated libraries. As there isn't a reliable way to check if those are downloaded, to be supported by other themes plugin shouldn't expect them to be downloaded by themes.

Adjustments to settings form

Here are some suggested improvements to the settings form:

Change "JATSParser plugin settings menu" to "References".
Drop "force to" in the sentences. So it's just "Display references from X".
What does the default do?
Remove the "denotes required field" thing.
For the convert to PDF setting, give it a heading that says "Create PDF".
The checkbox label should say something about when the PDF is created. Is this during the XML conversion or later? Something like "Create a PDF galley when ...".

Error with OJS 3.2.1-4

Hi Vitaliy,

My name is Loïc and I currently work as an intern in Opscidia, with Mr Charles Letaillieur, whom you have met at Barcelona in November of 2019.

I am contacting you today because my work involves the implementation of two of your OJS plugins (docxConverter and JATSParser) on an OJS system.

I am getting a fatal error and, after days of researches on the internet, I did not find any fix.

The aim of the workflow that I’m working on is to convert a docx document into a JATS document, then convert that JATS document into two galleys : HTML & PDF.

I am currently running OJS 3.2.1-4.

Steps to reproduce the error :

Go to Settings > Website > Plugins and make sure that JATSParser, DocxConverter & Texture Editor are enabled, and Lens galley is disabled.
Head to Submissions (make one if the queue is empty)
Click on « view submission »
Error 500

The error log :

[Mon Apr 19 11:28:52.554694 2021] [php7:notice] [pid 2524] [client 192.168.1.25:55088] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:52.563770 2021] [php7:notice] [pid 2521] [client 192.168.1.25:55096] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:52.572981 2021] [php7:notice] [pid 2528] [client 192.168.1.25:55097] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:52.608663 2021] [php7:notice] [pid 2515] [client 192.168.1.25:55098] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:52.757179 2021] [php7:notice] [pid 2521] [client 192.168.1.25:55096] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:52.911368 2021] [php7:notice] [pid 2521] [client 192.168.1.25:55096] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:57.859221 2021] [php7:notice] [pid 2515] [client 192.168.1.25:55098] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:57.938505 2021] [php7:notice] [pid 2515] [client 192.168.1.25:55098] PHP Notice: Constant CREATE_PDF_QUERY already defined in /var/www/html/ojs2/plugins/themes/opscidia-custom-theme/OpscidiaCustomThemePlugin.inc.php on line 22, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:58.053598 2021] [php7:warn] [pid 2515] [client 192.168.1.25:55098] PHP Warning: array_unique() expects parameter 1 to be array, null given in /var/www/html/ojs2/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 1001, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions [Mon Apr 19 11:28:58.075433 2021] [php7:error] [pid 2515] [client 192.168.1.25:55098] PHP Fatal error: Uncaught Pimple\\Exception\\UnknownIdentifierException: Identifier "submissionFile" is not defined. in /var/www/html/ojs2/lib/pkp/lib/vendor/pimple/pimple/src/Pimple/Container.php:101\nStack trace:\n#0 /var/www/html/ojs2/lib/pkp/classes/core/PKPServices.inc.php(69): Pimple\\Container->offsetGet()
#1 /var/www/html/ojs2/lib/pkp/classes/core/PKPServices.inc.php(50): PKPServices->_getFromContainer()
#2 /var/www/html/ojs2/plugins/generic/jatsParser/JatsParserPlugin.inc.php(341): PKPServices::get()
#3 /var/www/html/ojs2/lib/pkp/classes/plugins/HookRegistry.inc.php(107): JatsParserPlugin->publicationTemplateData()
#4 /var/www/html/ojs2/lib/pkp/classes/template/PKPTemplateManager.inc.php(1256): HookRegistry::call()
#5 /var/www/html/ojs2/cache/t_compile/ee131ee78aae66ec621d8f4e466e22416bf8d89c^5b2b400be3d78bc0ae391c12ce66fa93bd43d118_0.app.workflowworkflow.tpl.php(262): PKPTemplateManager->smartyCallHook()
#6 /var/www/html/ojs2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content in /var/www/html/ojs2/lib/pkp/lib/vendor/pimple/pimple/src/Pimple/Container.php on line 101, referer: http://192.168.1.11/ojs2/index.php/myjournal/submissions

Things I’ve done :

Disable Lens Galley Plugin
chown www-data recursively on the jatsParser directory
chmod 777 recursively on the jatsParser directory
Restart apache
Restart my Ubuntu20Server machine

I am sending you a video with this issue, of the error that I’m getting ! It shows precisely the error 500 and where it occurs.

Link → https://drive.google.com/file/d/10SPBEX8U_jG_MNma9KIHJT_CbRVMntkZ/view?usp=sharing

Do you have any ideas about this error ?

Any help would be greatly appreciated !

Thanks by advance :)

Loïc

Some article causing fatal error.

PHP Fatal error: Uncaught Error: Call to a member function getCategory() on null in /var/www/html/gas/plugins/generic/jatsParser/JatsParserPlugin.inc.php:778

Full stack trace : PHP Fatal error: Uncaught Error: Call to a member function getCategory() on null in /var/www/html/gas/plugins/generic/jatsParser/JatsParserPlugin.inc.php:778\nStack trace:\n#0 /var/www/html/gas/plugins/generic/jatsParser/JatsParserPlugin.inc.php(745): JatsParserPlugin->_setSupplImgPath()\n#1 /var/www/html/gas/lib/pkp/classes/plugins/HookRegistry.inc.php(107): JatsParserPlugin->displayFullText()\n#2 /var/www/html/gas/lib/pkp/classes/template/PKPTemplateManager.inc.php(1518): HookRegistry::call()\n#3 /var/www/html/gas/cache/t_compile/20ced12b90181983811d6a2d3549ed558a082564^336dc0f1b5d798bf1eac48afc5cf61399e302932_0.app.frontendobjectsarticledet.php(197): PKPTemplateManager->smartyCallHook()\n#4 /var/www/html/gas/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_60f92c1ca7da66_11928898()\n#5 /var/www/html/gas/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()\n#6 /var/www/html/gas/lib/pkp/lib/vendor/s in /var/www/html/gas/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 778

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	$templateMgr->addStyleSheet('styles', $baseUrl . '/app/app.min.css');
	$templateMgr->addStyleSheet('googleFonts', 'https://fonts.googleapis.com/css?family=PT+Serif:400,700&subset=cyrillic');
	$templateMgr->addJavaScript('fontawesome', 'https://use.fontawesome.com/releases/v5.2.0/js/all.js');
	$templateMgr->addJavaScript('javascript', $baseUrl . '/app/app.min.js');