vitaliy-1 / jatsparser

JATSParser is aimed to be integrated with Open Journal Systems 3.0+ for transforming JATS XML to various formats

JATSParser

JATSParser is aimed to be integrated with Open Journal Systems 3.0+ for transforming JATS XML to various formats

Usage

• Install composer dependencies
• See example.php
• Doesn't deal with JATS XML metadata as it by design it should be transfered from OJS
• Transforms JATS to HTML and PDF, uses TCPDF for the latter conversion
• Has dependency from citeproc-php for support for different citation style formats

jatsparser's Issues

Rename classes to be compliant with PSR-4

Create handler for PDF Converter page

How to adjust logo size?

Hello, I want to know how to adjust logo size.

Best,
Seongho

CiteProc throws a fatal error if year isn't valid

If an article isn't assigned to a journal issue, the year tag inside may be used to indicate that the article is in press, which causes a fatal error from the CiteProc:

PHP Fatal error:  Uncaught Seboettg\CiteProc\Exception\InvalidDateTimeException: Could not create valid date with year=in press, month=1, day=1. in /home/doc/OJS/development/e-med/ojs/plugins/generic/jatsParser/JATSParser/vendor/seboettg/citeproc-php/src/Rendering/Date/DateTime.php:45

little mistake between publisherLoc and publisherName

little mistake between publisherLoc and publisherName at src/JATSParser/Back/Book.php. The problem is also at oldGregg

Text nodes shouldn't be trimmed when converted to HTML

Sometimes writers/editors will accidentally make the space after an italicized word also italic.
When it's displayed on the page, those words will run together.

For example, with a JATS XML file like this:

<italic id="italic-9">Diplomacy </italic>reimagined ...

The space between the two words is included in the <italic>, but the html generated looks like this:

<i>Diplomacy</i>
reimagined

Resulting in:

I think it's because of the trim on this line https://github.com/Vitaliy-1/JATSParser/blob/master/src/JATSParser/HTML/Text.php#L71

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.

Figures inside a <p> aren't recognized correctly.

It seems that <fig> tags are not correctly recognized if present inside a <p>.

Actually, according to the documentation this is possible (https://jats.nlm.nih.gov/publishing/tag-library/1.1/element/fig.html).

I've been trying to replace ./fig with .//fig here, but it doesn't seem to be going right...

JATSParser/src/JATSParser/Body/Document.php

Line 118 in 2e2a8ae

foreach (self::$xpath->evaluate(".//sec|./p|./list|./table-wrap|./fig|./media|./disp-quote|./verse-group", $body) as $content) {

Anchor tags

Hi Vitaly,
I think you forgot the anchor tags to jump to the figures.
In "./JATSParser/src/JATSParser/HTML/Figure.php", this works for me:

...        
	public function setContent(JATSFigure $jatsFigure) {

+               // anchor tags
+               $aNode = $this->ownerDocument->createElement("a");
+               $aNode->setAttribute("name", $jatsFigure->getId());
+               $this->appendChild($aNode);

...

Regards
Olaf

Footnotes not working

Hello @Vitaliy-1 as you suggested this is more a JATSParser than an OldGregg issue I am posting here.
We are having difficulties showing JATS generated footnotes. I am attaching one XML sample article.
4213-Texto del artículo-1643-3-10-20190829 (1).xml.zip
which renders this way on our site http://www.evidencia.org.ar/index.php/Evidencia/article/view/4213#f-a1b17f14073b
Do you think it is possible to add or fix this functionality?
Best regards

Table attributes does not render

Hi, @Vitaliy-1 we are also seeing that although our XML tables are formatted with some attributes (e.g. align), these are not considered once the XML is rendered.
Attached you will find an XML sample which renders this way http://www.evidencia.org.ar/index.php/Evidencia/article/view/4232
4232-Texto del artículo-1709-3-10-20191030 (1).xml.zip
Is it possible to add/correct this functionality?

We are using OJS 3.1.2.0 and OldGregg theme.

Best regards

Allow nullable return types for tabel label and table id

To avoid fatal error

Line breaks

Line breaks such as <br> or (in XML) <break> in the XML body text are stripped off.
Can you please add such tags?

Best regards

Edvin

Add support for disp-quote

Hi, we're testing the plugin for one of our journals. We have cites with 'disp-quote' tag in our Jats XML that is not working.

Example:

...la pobreza afecta a adolescentes y jóvenes de una manera desproporcionada: en 2008, se estimaba que 35 millones de adolescentes de la región, de edades comprendidas entre los 13 y los 19 años, vivían por debajo del umbral de la pobreza. Casi 15 millones de adolescentes, de entre 10 y 18 años, vivían con menos de 1 dólar al día.

Thank you in advance
Diego

Use citeproc-php for rendering references conversion to the HTML

HTML: IDs for figures and tables are missing

Related to: https://forum.pkp.sfu.ca/t/jats-parser-v2-0-jats-xml-to-html-and-pdf-conversion/47704/58

Refactor getContent method of JATS Document and Section

[ ] - unify method for both of the classes
[ ] - map JATS Document classes with XML DOM elements

Appendix not extracted from JATS XML

The parser does not extract appendix from the XML.
Appendix are tagged with tag withing the
Here is an example of XML for appendix

.......... <title>APPENDIX</title>

With respect to our sample, the time spent to clear the 3 consistencies tested ranges from 4 up to 44 seconds. Stratifying linearly this time on 9 levels of 5 seconds, a factor of correction (FOC) is obtained to adjust the p-score in the following way: 0-5 secs =+ 1, 6-10 secs = +2, 11-15 secs = +3, 16-20 secs = +4, 21-25 secs = +5, 26-30 secs = +6, 31-35 secs = +7, 36-40 secs = +8, > 40 secs = +9 (Table V). The sum of the p-score total + FOC represents the timed p-score (tp-score). In this new role, the tp-score ranges from 5 up to 20, expressing itself as a continuum of severity ²⁶. The possibility of a clinical subdivision of the tp-score in further levels is under consideration.

Issue with inline-graphic, display-formula and fig tags

Hi,

We have the following tags in our jats xmls:
<inline-graphic xlink:href="ES12366-34-1-001-00" id="ID_8b8883f5-3d03-4d61-adf9-bbae1bb3d9ef"></inline-graphic> <disp-formula><alternatives> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bpasch-38c-2-001-ueqn001"/> </alternatives></disp-formula>
And also following tags is not working inside the table or p tag
<fig><label>Figure 1:</label><caption><p>Plots of <italic>&#x03C1;</italic> v/s c of copper surfactants (derived from fried and unfried oils) solution in benzene.</p></caption> <graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bpasch-38c-2-001-f001.jpg"/> </fig>

Please help me out from this issue.

After parsing through Vitaliy-1/JATSParser, All data is not coming in html and pdf.

Add class to p-element in poetry

Is it possible to add a class to the content in the poetry (i.e. the p-element in HTML), when it has been converted from XML into HTML. In this way the visualization of it can be changed with CSS (for example with an indent and/or italics).
You have classes like this already for e.g. headings and figures.

Display inline-formula

Hi @Vitaliy-1 , do you think it is possible that JATSParser would render math formulas as this?
We are using OldGregg Theme.

<td id="tc-314904a80e79" align="left">
			<inline-formula id="if-42f432a5f18c"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi><mml:mi>O</mml:mi><mml:mi>C</mml:mi><mml:mo>=</mml:mo><mml:mfrac><mml:munderover><mml:mrow><mml:mo>∑</mml:mo><mml:msubsup><mml:mi>n</mml:mi><mml:mi>i</mml:mi><mml:mn>2</mml:mn></mml:msubsup><mml:mo>-</mml:mo><mml:mi>N</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi><mml:mo>=</mml:mo><mml:mn>1</mml:mn></mml:mrow><mml:mi>k</mml:mi></mml:munderover><mml:mrow><mml:mi>N</mml:mi><mml:mo>(</mml:mo><mml:mi>N</mml:mi><mml:mo>-</mml:mo><mml:mn>1</mml:mn><mml:mo>)</mml:mo></mml:mrow></mml:mfrac></mml:math></inline-formula>
</td>

Best regards!

Hyperlinks to external uri inside JATS XML <p> tag

Hi @Vitaliy-1 , I need to reference a supplementary file inside a JATS XML formatted article, which has also been published as a pdf galley. The only way I thought about doing so is by adding a hyperlink inside the corresponding

tag using an <ext-link> tag as shown below…

<p id="p-8fe1d0c07051">La estructura factorial de tres factores se mantuvo en la versión final del instrumento, con las siguientes características (ver <xref id="x-98099e9a5fef" rid="tw-6e408fb0f00d" ref-type="table">Table 2</xref> y <ext-link ext-link-type="uri" xlink:href="http://www.evidencia.org.ar/index.php/Evidencia/article/view/4253/1789">material complementario</ext-link>.</p>

…but this is not actually working, actually showing nothing (I mean the “material complementario” uri) when the XML renders.

If could add this feature, it would be great! Thanks