Embed Galley Plugin not working in OJS 3.3.0

Hello,
I would like to display the full article in the abstract page. I already installed the Embed Galley Plugin but it is not working. The Jats Parser plugin doesn’t work either.
Any help would be appreciated

This is my error log:

[20-Sep-2022 23:23:00 UTC] PHP Deprecated: Non-static method PKPApplication::getRequest() should not be called statically in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php on line 123
[20-Sep-2022 23:23:00 UTC] PHP Fatal error: Uncaught Error: Call to undefined method SubmissionFile::getFilePath() in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php:146
Stack trace:
#0 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php(126): EmbedGalleyPlugin->_parseXml(Object(SubmissionFile))
#1 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/classes/plugins/HookRegistry.inc.php(107): EmbedGalleyPlugin->embedHtml(‘Templates::Arti…’, Array)
#2 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/classes/template/PKPTemplateManager.inc.php(1518): HookRegistry::call(‘Templates::Arti…’, Array)
#3 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/cache/t_compile/93b4f13326abf2c920de729fdcdace1580d9bcb7^addd65021fadf964339ab08cd1aa93ba59b14e9c_0.app.frontendobjectsarticledet.php(602): PKPTemplateManager->smartyCallHook(Array, Object(Smar in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php on line 146
[20-Sep-2022 23:23:05 UTC] PHP Deprecated: Non-static method PKPApplication::getRequest() should not be called statically in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php on line 123
[20-Sep-2022 23:23:05 UTC] PHP Fatal error: Uncaught Error: Call to undefined method SubmissionFile::getFilePath() in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php:146
Stack trace:
#0 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php(126): EmbedGalleyPlugin->_parseXml(Object(SubmissionFile))
#1 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/classes/plugins/HookRegistry.inc.php(107): EmbedGalleyPlugin->embedHtml(‘Templates::Arti…’, Array)
#2 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/classes/template/PKPTemplateManager.inc.php(1518): HookRegistry::call(‘Templates::Arti…’, Array)
#3 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/cache/t_compile/93b4f13326abf2c920de729fdcdace1580d9bcb7^addd65021fadf964339ab08cd1aa93ba59b14e9c_0.app.frontendobjectsarticledet.php(602): PKPTemplateManager->smartyCallHook(Array, Object(Smar in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/embedGalley/EmbedGalleyPlugin.inc.php on line 146
[20-Sep-2022 23:31:29 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/JATSParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/JATSParser/JatsParserPlugin.inc.php on line 13

Hi @Ana,

Are you able to also indicate which version of the plugin you’re using and the method that you used to install it (e.g. plugin gallery, or other means).

-Roger
PKP Team

Hi, thank you for answering.
Both are the newest versions available, I uploaded them via ftp to the “generic” folder. I tried with older versions too, but they are not working. The Jats Parser plugin seems to crash the OJS because when I upload it, the “Installed Plugins” section doesn’t load.

Hi @Ana,

Typically, installing from the plugin gallery is the best best bet as the plugin updates available there have been tested with your OJS version. Installing plugins outside of this method sometimes creates this issue - are you unable to uninstall the JATS plugin to see if that is causing the issue with your plugin gallery?

-Roger
PKP Team

Hi,
I’m unable to install both plugins from the plugin gallery because they don’t exist there. I already searched for them, and there are no results.

Hi @Ana,

If the plugin is not in the plugin gallery that’s an indication that the plugin has not been tested with your given version of OJS. Installing plugins that are not in the gallery can be risky and lead to even breaking your OJS instance in some instances, which is why we advise that users proceed with caution when installing plugins outside of the gallery: https://docs.pkp.sfu.ca/plugin-inventory/en/#plugin-gallery-vs-external-plugins

-Roger
PKP Team

Hi,
If that is the situation, then how can I display the HTML of an article’s XML in the same page where the abstract is? I tried with different plugins and none is working.

Hi @Ana,

So the JATS plugin within your plugin gallery is not installing? It should work, but there might be something going on with your plugin gallery - perhaps as a next step you should look at your PHP Error logs and see if anything is happening there with your plugin gallery that is preventing this plugin from working.

-Roger
PKP Team

Hi,
I can’t install the Jats Parser plugin form the gallery. There are no more lines in the error log besides the ones I already posted. Here is a screen shot of the search results when I type “JATS”. As you can see I installed the three of them, and none is displaying the XML in the abstract section.

Screen Shot 2022-09-28 at 11.47.49

Hi @Ana,

Thanks for clarifying. I’m not entirely sure what to do at this stage, but I’ll see if some of my colleagues are able to assist when they are available.

-Roger
PKP Team

Hi @Ana,

This error means that JATS Parser Plugin wasn’t installed correctly. Likely you copied the source code without installation.

For OJS 3.3.0, the latest version is 2.1.9-4, package is available here: Release 2.1.9-4 · Vitaliy-1/JATSParserPlugin · GitHub (file with .tar.gz extension). This can be uploaded through the dashboard interface or manually. Note the directory name, it’s jatsParser rather than JATSParser.

I can also give instructions on how to install from the source code but that requires also Git and Composer to be installed.

1 Like

Thank you.
Now I’m getting the following errors in my php log:

[06-Oct-2022 21:38:22 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/JATSParserPlugin-2.1.9.4/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/JATSParserPlugin-2.1.9.4/JatsParserPlugin.inc.php on line 13
[06-Oct-2022 21:40:30 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[06-Oct-2022 21:42:05 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[06-Oct-2022 21:50:56 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[06-Oct-2022 21:52:05 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[06-Oct-2022 21:52:13 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php73/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13

The error looks the same, PHP cannot find the path to the autoload file, which suggests that the plugin isn’t installed. Did you use jatsParser-2.1.9-4.tar.gz archive or copy the source code?

I installed it using the jatsParser-2.1.9-4.tar.gz archive through the dashboard interface. By the way, when I click on “save”, it gets stucked on loading and does nothing for hours. If I click “cancel” installed plugins gets stucked.
Screen Shot 2022-10-11 at 18.14.16
Screen Shot 2022-10-11 at 18.14.16

I suspect there should be an associated error in the PHP log, can you check it, just after the plugin installation fails?
E.g., something like insufficient PHP upload filesize limit (it should be more than a package): https://stackoverflow.com/questions/1122418/changing-upload-max-filesize-on-php
Nevertheless, the log should tell more.

The PHP log is still the same, it has the same errors. I checked the upload filesize limit and it is 256M.

#0 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_6345f7759b3f43_59747850(Object(Smarty_Internal_Template))
#1 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode(Object(Smarty_Internal_Template))
#2 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(216): Smarty_Template_Compiled->render(Object(Smarty_Internal_Template))
#3 /home/customer/www/revistalatinoamericanad in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/cache/t_compile/480451dc2b75b35c64354d7c4cad1157538fd42d^e64e579388e5615e11e939b12134d6ae8679eba6_0.app.frontendpagesindexJournal.php on line 37
[11-Oct-2022 23:14:08 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php74/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[11-Oct-2022 23:17:48 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php74/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[12-Oct-2022 00:05:18 UTC] ojs2: 404 Not Found
[12-Oct-2022 05:52:15 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:13:27 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:18:43 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:46:07 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:46:38 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:47:08 UTC] ojs2: 404 Not Found
[12-Oct-2022 13:54:52 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:05:24 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:16:36 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:16:58 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:24:55 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:28:43 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:39:48 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:52:08 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:55:53 UTC] ojs2: 404 Not Found
[12-Oct-2022 14:57:31 UTC] ojs2: 404 Not Found
[12-Oct-2022 15:05:33 UTC] ojs2: 404 Not Found
[12-Oct-2022 15:10:52 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php74/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13

Can you check if the file referenced in the error message exists? If not, likely the release didn’t get fully unpacked and in this case I’d expect a message describing the reason.

If you have access to the server, you can just manually unpack the archive to the plugin directory (and don’t forget to set directory/files permissions appropriately)

Maybe that’s the problem, because there are no files or folders inside JATSParser folder. I downloaded the source code and uncompressed it, lookd into JATSParser folder and is empty too.
Screen Shot 2022-10-13 at 12.21.39

Yes, if downloading the source code, it won’t include submodules, e.g. JATSParser. That’s why you need to install the package with the release, it’s named jatsParser-2.1.9-4.tar.gz (not the Source code tar.gz). Here’s the direct link: github.com/Vitaliy-1/JATSParserPlugin/releases/download/2.1.9.4/jatsParser-2.1.9-4.tar.gz

Thank you. I was able to install it correctly with that file, however it is still not working. Now I have new errors in the log.

[19-Oct-2022 15:09:26 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/vendor/autoload.php’ (include_path=‘.:/usr/local/php74/pear’) in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JatsParserPlugin.inc.php on line 13
[19-Oct-2022 15:16:57 UTC] PHP Fatal error: Uncaught Error: Call to a member function removeChild() on null in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Par.php:63
Stack trace:
#0 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Par.php(16): JATSParser\Body\Par->findExtractRemoveBlockElements(Object(DOMElement), Object(DOMXPath))
#1 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Section.php(88): JATSParser\Body\Par->__construct(Object(DOMElement))
#2 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Section.php(34): JATSParser\Body\Section->extractContent(Object(DOMElement))
#3 /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Document.php(121): JATSParser\Body\S in /home/customer/www/revistalatinoamericanadepoblacion.org/public_html/plugins/generic/jatsParser/JATSParser/src/JATSParser/Body/Par.php on line 63