Manual export of a journal

DeMiro5001 · March 8, 2025, 7:20pm

Manual export of one journal
I had some issues in the latest migration to 3.4.0.8. The journal is consultable but it’s not possible to add a submission, add a plugin, some placeholders are not populated correctly.

Steps I took leading up to the issue

I tried installing GitHub - lepidus/fullJournalTransfer: OJS plugin for importing/exporting a journal with all its private information (e.g. submitted articles, reviews, editorial decisions, etc.) but as stated above, I get an error on the browser console :

jquery.js?v=3.4.0.8:9940 
        
        
       POST https://domain.com/index.php/myjournal/$$$call$$$/grid/settings/plugins/settings-plugin-grid/save-upload-plugin?function=upload&category=&plugin= 500 (Internal Server Error)
send @ jquery.js?v=3.4.0.8:9940
ajax @ jquery.js?v=3.4.0.8:9521
jQuery.<computed> @ jquery.js?v=3.4.0.8:9677
$.pkp.controllers.form.AjaxFormHandler.submitForm @ AjaxFormHandler.js?v=3.4.0.8:81
(anonymous) @ Handler.js?v=3.4.0.8:304
$.pkp.controllers.form.FormHandler.submitHandler_ @ FormHandler.js?v=3.4.0.8:450
(anonymous) @ Handler.js?v=3.4.0.8:304
d @ jquery.validate.min.js?v=3.4.0.8:4
(anonymous) @ jquery.validate.min.js?v=3.4.0.8:4
dispatch @ jquery.js?v=3.4.0.8:5145
elemData.handle @ jquery.js?v=3.4.0.8:4949

Checked files and folders ownership
Restarted nginx and php8.3

What application are you using?
OJS 3.4.0-8

Information sur le serveur

Fixation du nom	Fixation de la valeur
Système d’exploitation	Linux
Version PHP	8.3.17
Version Apache	nginx/1.22.1
Pilote de base de données	mysql
Version du serveur de bases de données	10.11.6-MariaDB-0+deb12u1

I would like to start from a clean install but we need to keep the journal, issues, articles, users. What’s the right way to manually move them from the old install to the new one.

Edit : I also tried installing the plugin directly on plugins folder. And here is an nginx log :

Stack trace:
#0 /var/www/ojs/lib/pkp/includes/functions.php(50): require_once()
#1 /var/www/ojs/plugins/importexport/fullJournalTransfer/FullJournalImportExportPlugin.inc.php(9): import()
#2 /var/www/ojs/plugins/importexport/fullJournalTransfer/index.php(10): require_once('...')
#3 /var/www/ojs/lib/pkp/classes/plugins/PluginRegistry.php(259): include('...')
#4 /var/www/ojs/lib/pkp/classes/plugins/PluginRegistry.php(193): PKP\plugins\PluginRegistry::_deprecatedInstantiatePlugin()
#5 /var/www/ojs/lib/pkp/classes/plugins/PluginRegistry.php(241): PKP\plugins\PluginRegistry::_instantiatePlugin()
#6 /var/www/ojs/lib/pkp/classes/plugins/PluginRegistry.php(113): PKP\plugins\PluginRegistry::_loadFromDisk()
#7 /var/www/ojs/lib/pkp/classes/plugins/PluginRegistry.php(177): PKP\plugins\PluginRegistry::loadCategory()
#" while reading response header from upstream, client: 197.14.235.118, server: domain.com, request: "POST /index.php/myjournal/$$$call$$$/grid/settings/plugins/settings-plugin-grid/save-upload-plugin?function=upload&category=&plugin= HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/myjournal/management/settings/website"
2025/03/08 19:17:47 [error] 1257949#1257949: *594785 FastCGI sent in stderr: "PHP message: PHP Deprecated:  Using php-function "in_array" as a modifier is deprecated and will be removed in a future release. Use Smarty::registerPlugin to explicitly register a custom modifier. in /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_compile_private_modifier.php on line 112; PHP message: PHP Deprecated:  Using php-function "in_array" as a modifier is deprecated and will be removed in a future release. Use Smarty::registerPlugin to explicitly register a custom modifier. in /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_compile_private_modifier.php on line 112" while reading response header from upstream, client: 197.14.235.118, server: domain.com, request: "GET /index.php/myjournal/$$$call$$$/tab/user/profile-tab/notification-settings?_=1741461448670 HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/myjournal/user/profile"
2025/03/08 19:18:00 [error] 1257949#1257949: *594785 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getDisplayName() on null in /var/www/ojs/lib/pkp/classes/i18n/Locale.php:279
Stack trace:
#0 [internal function]: PKP\i18n\Locale->PKP\i18n\{closure}()
#1 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(279): array_map()
#2 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(271): PKP\i18n\Locale->getSupportedLocales()
#3 /var/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Support/Facades/Facade.php(338): PKP\i18n\Locale->getSupportedFormLocales()
#4 /var/www/ojs/lib/pkp/classes/controllers/grid/GridCellProvider.php(68): Illuminate\Support\Facades\Facade::__callStatic()
#5 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1262): PKP\controllers\grid\GridCellProvider->render()
#6 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1163): PKP\controllers\grid\GridHandler->_renderCellInternally()
#7 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1138): PKP\controllers\grid\GridHandler->ren" while reading response header from upstream, client: 197.14.235.118, server: domain.com, request: "GET /index.php/index/$$$call$$$/grid/admin/languages/admin-language-grid/fetch-grid?_=1741461479872 HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/index/admin/settings"
2025/03/08 19:18:07 [error] 1257949#1257949: *594785 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getDisplayName() on null in /var/www/ojs/lib/pkp/classes/i18n/Locale.php:279
Stack trace:
#0 [internal function]: PKP\i18n\Locale->PKP\i18n\{closure}()
#1 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(279): array_map()
#2 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(271): PKP\i18n\Locale->getSupportedLocales()
#3 /var/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Support/Facades/Facade.php(338): PKP\i18n\Locale->getSupportedFormLocales()
#4 /var/www/ojs/lib/pkp/classes/controllers/grid/GridCellProvider.php(68): Illuminate\Support\Facades\Facade::__callStatic()
#5 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1262): PKP\controllers\grid\GridCellProvider->render()
#6 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1163): PKP\controllers\grid\GridHandler->_renderCellInternally()
#7 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1138): PKP\controllers\grid\GridHandler->ren" while reading response header from upstream, client: 197.14.235.118, server: domain.com, request: "GET /index.php/index/$$$call$$$/grid/admin/context/context-grid/fetch-grid?_=1741461486744 HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/index/admin/contexts"

Thanks for the help

DeMiro5001 · March 14, 2025, 3:01pm

I am receiving 2 or 3 emails daily of users complaining about various things broken. Apparently since the last update.
Any help would be appreciated. We have only 100 articles so far, I can move them manually if needed, but without breaking ownership of the articles.

asmecher · March 14, 2025, 6:07pm

Hi @DeMiro5001,

There’s quite a bit going on here… Can you start by describing the issues you hit during upgrade? I suspect the least complicated path would be to address those, if possible, rather than trying to migrate content elsewhere when we’re not sure of the state of that content.

Regards,
Alec Smecher
Public Knowledge Project Team

DeMiro5001 · March 14, 2025, 6:25pm

Thanks for taking time to help me.
I recieved for some users that they were unable to login. Some placeholders aren’t correcly displaying, I can’t update plugins though an update is available (when I clic update, I get a message saying that the plugin already exists).
I tried to force reupgrade to the same version, now I get a 500 error and in the nginx log :

Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67d47162e975b2_16074164()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5 /var/www/ojs/lib/pkp/classes/te" while reading response header from upstream, client: 102.159.183.227, server: domain.com, request: "GET /index.php/tjem HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com"

I already have a backup before the last action, but I can’t find the backup before the last upgrade since at that time the site seemed to behave correctly and I didn’t check that everything was ok.
If you need any further information, let me know.
By the way, the server is a KS1 from ovh running yunohost 12 (and I am the maintainer of ojs package in the yunohost catalog).

Edit :
I checked the folder structure and some files were missing, the most strange part is that I had three themes installed. So I reinstalled the theme and the site became accessible again using :
~/plugins/themes$ git clone https://github.com/madi-nuralin/material

Edit2 : I remember there was an issue with locales fixed here

asmecher · March 14, 2025, 7:34pm

Hi @DeMiro5001,

What do you get when you run php tools/upgrade.php check?

Regards,
Alec Smecher
Public Knowledge Project Team

DeMiro5001 · March 14, 2025, 7:55pm

php tools/upgrade.php check
Code version:      3.4.0.8
Database version:  3.4.0.8
Latest version:    3.4.0.8
Your system is up-to-date

 php -v
PHP 8.3.17 (cli) (built: Mar 10 2025 15:24:50) (NTS)
Copyright (c) The PHP Group
Zend Engine v4.3.17, Copyright (c) Zend Technologies
    with Zend OPcache v8.3.17, Copyright (c), by Zend Technologies

cat /etc/*release
ID=generic
VERSION="20250115-1993"
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
NAME="Debian GNU/Linux"
VERSION_ID="12"
VERSION="12 (bookworm)"
VERSION_CODENAME=bookworm
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"

asmecher · March 14, 2025, 8:11pm

Hi @DeMiro5001,

OK, it looks like the upgrade to 3.4.0-8 was successful – unless you manually updated your versions table to reflect the new version (please let me know if that’s the case). Please make sure you have a complete backup. I would suggest working through issues one at a time from here, rather than trying too many things at once. Otherwise it’ll be too hard to follow what’s happening.

The message you’re quoting that starts with Stack trace: is the first line below the actual error message; check above that line in the log to see the PHP error message.

Regards,
Alec Smecher
Public Knowledge Project Team

DeMiro5001 · March 14, 2025, 9:11pm

I never do that on any app unless the dev tells me to do it.

The yunohost server uses logrotate, I checked the last log and found a lot of errors (apart from the bots trying to get a Wordpress login), I copied some of them since there are a lot of duplicates :

2025/03/14 00:23:38 [error] 1485844#1485844: *804369 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getLocalizedName() on null in /var/www/ojs/cache/t_compile/02676000b417cf3b3012ae73b152010f11ccb1f3^6484802fd4fe3b9bbdd46e72bdda35bccf36a18f_0.plugins-1-plugins-generic-webFeed-generic-webFeed.atom.tpl.php:32
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_677368caefaf08_17828851()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5" while reading response header from upstream, client: 171.25.193.80, server: domain.com, request: "GET /index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/atom HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/atom"
2025/03/14 00:23:39 [error] 1485845#1485845: *804371 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getPath() on null in /var/www/ojs/cache/t_compile/54e8d4a0c6fa86b24c289bae6d81035d88bb6d69^c940d5f8376e6af774deb7e0a5efe41e5bfff906_0.plugins-1-plugins-generic-webFeed-generic-webFeed.rss.tpl.php:36
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67737c6ab2c798_44171332()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5 /var/www/" while reading response header from upstream, client: 171.25.193.80, server: domain.com, request: "GET /index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/rss HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/rss"
2025/03/14 00:23:40 [error] 1485845#1485845: *804373 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getLocalizedName() on null in /var/www/ojs/cache/t_compile/225f815d25fec5f5aeb5c3f3fc646a360faff377^c5a64687d825cbd410323f081b8e13fb7be00543_0.plugins-1-plugins-generic-webFeed-generic-webFeed.rss2.tpl.php:31
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67736cc6d92f40_64337550()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5" while reading response header from upstream, client: 171.25.193.80, server: domain.com, request: "GET /index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/rss2 HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/rss2"


2025/03/14 16:00:00 [error] 1485846#1485846: *819003 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getDisplayName() on null in /var/www/ojs/lib/pkp/classes/i18n/Locale.php:279
Stack trace:
#0 [internal function]: PKP\i18n\Locale->PKP\i18n\{closure}()
#1 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(279): array_map()
#2 /var/www/ojs/lib/pkp/classes/i18n/Locale.php(271): PKP\i18n\Locale->getSupportedLocales()
#3 /var/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Support/Facades/Facade.php(338): PKP\i18n\Locale->getSupportedFormLocales()
#4 /var/www/ojs/lib/pkp/classes/controllers/grid/GridCellProvider.php(68): Illuminate\Support\Facades\Facade::__callStatic()
#5 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1262): PKP\controllers\grid\GridCellProvider->render()
#6 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1163): PKP\controllers\grid\GridHandler->_renderCellInternally()
#7 /var/www/ojs/lib/pkp/classes/controllers/grid/GridHandler.php(1138): PKP\controllers\grid\GridHandler->ren" while reading response header from upstream, client: 102.159.183.227, server: domain.com, request: "GET /index.php/index/$$$call$$$/grid/admin/context/context-grid/fetch-grid?_=1741967999032 HTTP/2.0", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com", referrer: "https://domain.com/index.php/index/admin/contexts"



2025/03/14 18:38:34 [error] 1596769#1596769: *821378 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getOption() on null in /var/www/ojs/cache/t_compile/e4e805c14686dcba7d240e68e365443ce59de811^e64e579388e5615e11e939b12134d6ae8679eba6_0.app.frontendpagesindexJournal.tpl.php:36
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67d47162e975b2_16074164()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5 /var/www/ojs/lib/pkp/classes/te" while reading response header from upstream, client: 2001:41d0:401:3000::1676, server: domain.com, request: "GET /index.php/tjem HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com"
2025/03/14 19:13:19 [error] 1596772#1596772: *821927 open() "/usr/share/nginx/htmlindex.php" failed (2: No such file or directory), client: 82.145.215.206, server: domain.com, request: "GET /apple-touch-icon.png HTTP/1.1", host: "domain.com"
2025/03/14 19:38:13 [error] 1596758#1596758: *822660 open() "/usr/share/nginx/htmlindex.php" failed (2: No such file or directory), client: 102.129.223.92, server: domain.com, request: "GET /en/contact%09%092024-06-19+22:49%09Ready+contact+form+successfully+found+/+Requires+captcha+input%09http://domain.com%09%09%09%09%09 HTTP/1.1", host: "domain.com"
2025/03/14 20:34:48 [error] 1596765#1596765: *823475 FastCGI sent in stderr: "PHP message: PHP Deprecated:  Using php-function "date" as a modifier is deprecated and will be removed in a future release. Use Smarty::registerPlugin to explicitly register a custom modifier. in /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_compile_private_modifier.php on line 112; PHP message: PHP Deprecated:  Using php-function "date" as a modifier is deprecated and will be removed in a future release. Use Smarty::registerPlugin to explicitly register a custom modifier. in /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_compile_private_modifier.php on line 112; PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getLocalizedName() on null in /var/www/ojs/cache/t_compile/225f815d25fec5f5aeb5c3f3fc646a360faff377^c5a64687d825cbd410323f081b8e13fb7be00543_0.plugins-1-plugins-generic-webFeed-generic-webFeed.rss2.tpl.php:31
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67d492e88ba048_36918865()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5" while reading response header from upstream, client: 66.249.64.6, server: domain.com, request: "GET /index.php/tjem/gateway/plugin/WebFeedGatewayPlugin/rss2 HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php8.3-fpm-ojs.sock:", host: "domain.com"

asmecher · March 14, 2025, 9:47pm

Hi @DeMiro5001,

I see several fixable issues:

1. Call to a member function getOption() on null

2025/03/14 18:38:34 [error] 1596769#1596769: *821378 FastCGI sent in stderr: "PHP message: PHP Fatal error:  Uncaught Error: Call to a member function getOption() on null in /var/www/ojs/cache/t_compile/e4e805c14686dcba7d240e68e365443ce59de811^e64e579388e5615e11e939b12134d6ae8679eba6_0.app.frontendpagesindexJournal.tpl.php:36
Stack trace:
#0 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_67d47162e975b2_16074164()
#1 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode()
#2 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(217): Smarty_Template_Compiled->render()
#3 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(238): Smarty_Internal_Template->render()
#4 /var/www/ojs/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_templatebase.php(134): Smarty_Internal_TemplateBase->_execute()
#5 /var/www/ojs/lib/pkp/classes/te...

To solve this, see: Upgrading from 3.4.0.4 to 3.4.0.7 - #2 by asmecher

2. Call to a member function getDisplayName() on null

This appears to be due to OJS trying to operate in a locale that your server doesn’t support.

First, what is the locale setting in the [i18n] section of your config.inc.php?

Second, what do you get for the following database queries?

SELECT installed_locales, supported_locales FROM site;
SELECT DISTINCT primary_locale FROM journals;
SELECT DISTINCT setting_name, setting_value FROM journal_settings WHERE setting_name IN ('supportedFormLocales', 'supportedLocales', 'supportedSubmissionLocales');

Regards,
Alec Smecher
Public Knowledge Project Team

DeMiro5001 · March 14, 2025, 11:50pm

This probably happened when the material theme got deleted during the update, but I don’t understand why it got deleted as well as all the other themes and some plugins. I found only the default theme in the theme folder.

;;;;;;;;;;;;;;;;;;;;;;;;;
; Localization Settings ;
;;;;;;;;;;;;;;;;;;;;;;;;;

[i18n]

; Default locale
locale = fr_FR

; Database connection character set
connection_charset = utf8

MariaDB [ojs]> SELECT installed_locales, supported_locales FROM site;
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| installed_locales                                                                                                                                                                                                                                      | supported_locales                                            
                              |
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ["bs","ca","cs","da","de","el","es","eu","fi","fr_CA","fr_FR","gd","he","hi","hr","hu","hy","id","is","it","ja","ko","mk","nb","nl","pl","pt_BR","pt_PT","ro","ru","sk","sl","sr@cyrillic","sr@latin","sv","tr","uk","vi","zh_CN","ar","fa","ku","en"] | ["bs","ca","cs","da","de","el","es","eu","fi","fr_CA","fr_FR","gd","he","hi","hr","hu","hy","id","is","it","ja","ko","mk","nb","nl","pl","pt_BR","pt_PT","ro","ru","sk","sl","sr@cyrillic","sr@latin","sv","tr","uk","vi","zh_CN","ar","fa","ku","en"] |
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

MariaDB [ojs]> SELECT DISTINCT primary_locale FROM journals;
+----------------+
| primary_locale |
+----------------+
| fr_FR          |
+----------------+

MariaDB [ojs]> SELECT DISTINCT setting_name, setting_value FROM journal_settings WHERE setting_name IN ('supportedFormLocales', 'supportedLocales', 'supportedSubmissionLocales');
+----------------------------+---------------+
| setting_name               | setting_value |
+----------------------------+---------------+
| supportedFormLocales       | ["en"]        |
| supportedLocales           | ["en"]        |
| supportedSubmissionLocales | ["en"]        |
+----------------------------+---------------+

asmecher · March 14, 2025, 11:52pm

Hi @DeMiro5001,

What is the language of your journal/site? It looks like the site is configured for French, but submissions etc. are English-only.

Regards,
Alec Smecher
Public Knowledge Project Team

DeMiro5001 · March 14, 2025, 11:58pm

The backend and the frontend are in French indeed. I thought that it was possible to switch languages, because i usually use English and my collaborators use French.
The journal is French/English

DeMiro5001 · March 15, 2025, 9:47am

Should I change it in the config file ?

DeMiro5001 · March 15, 2025, 12:58pm

So I changed the “locale = en” in the config file.
The placeholders are fixed. The submission (file upload) is functioning again. I asked my collaborator to test the rest of the workflow.
What is still broken, plugin updates.
When I check the plugin gallery, I see a lot of plugins with available updates

When I launch the update, I get an error stating that the plugin is already installed, and is newer than the version available in the plugin gallery.

When I check the plugin folder :

:/var/www/ojs/plugins# tree -L 2
.
├── blocks
│   ├── browse
│   ├── developedBy
│   ├── information
│   ├── languageToggle
│   ├── makeSubmission
│   └── subscription
├── gateways
│   └── resolver
├── generic
│   ├── acron
│   ├── announcementFeed
│   ├── citationStyleLanguage
│   ├── crossref
│   ├── customBlockManager
│   ├── datacite
│   ├── driver
│   ├── dublinCoreMeta
│   ├── googleAnalytics
│   ├── googleScholar
│   ├── htmlArticleGalley
│   ├── lensGalley
│   ├── orcidProfile
│   ├── pdfJsViewer
│   ├── recommendByAuthor
│   ├── recommendBySimilarity
│   ├── staticPages
│   ├── tinymce
│   ├── usageEvent
│   └── webFeed
├── importexport
│   ├── doaj
│   ├── native
│   ├── pubmed
│   └── users
├── metadata
│   └── dc11
├── oaiMetadataFormats
│   ├── dc
│   ├── marc
│   ├── marcxml
│   └── rfc1807
├── paymethod
│   ├── manual
│   └── paypal
├── pubIds
│   └── urn
├── reports
│   ├── articles
│   ├── counter
│   ├── reviewReport
│   └── subscriptions
└── themes
    ├── default
    ├── material
    └── material-v3_0_4-0.tar.gz

It seems there is a mismatch between the plugin folder and the plugins in the web interface.
I will try to digg more as soon as I get home.

DeMiro5001 · March 15, 2025, 9:20pm

It seems that I didn’t preserve “locale” and “plugins” during the upgrade.
In the pre-upgrade version, there was a language selector on the frontend, now there isn’t. And some plugins folders do not exist.
I have set ojs to use English.

Is there a way to redownload the “locale” folder without breaking it.

 ls locale/
ar           bg  ckb  da   el  es     fa     fr_FR  he  hsb  id  ja  ko  lv  mr  nl     pt_PT  se   sk  sr@cyrillic  th  und          uz@latin  zh_Hant
az           bs  cnr  de   en  es_MX  fi     gd     hi  hu   is  ka  ky  mk  ms  pl     ro     si   sl  sr@latin     tr  ur           vi
be@cyrillic  ca  cs   dsb  eo  eu     fr_CA  gl     hr  hy   it  kk  lt  mn  nb  pt_BR  ru     sid  sq  sv           uk  uz@cyrillic  zh_CN

And is there a way to download the missing plugins or list all the installed plugins? Or a better suggestion?

tree -L 2 plugins
plugins
├── blocks
│   ├── browse
│   ├── developedBy
│   ├── information
│   ├── languageToggle
│   ├── makeSubmission
│   └── subscription
├── gateways
│   └── resolver
├── generic
│   ├── acron
│   ├── announcementFeed
│   ├── citationStyleLanguage
│   ├── crossref
│   ├── customBlockManager
│   ├── datacite
│   ├── driver
│   ├── dublinCoreMeta
│   ├── googleAnalytics
│   ├── googleScholar
│   ├── htmlArticleGalley
│   ├── lensGalley
│   ├── orcidProfile
│   ├── pdfJsViewer
│   ├── recommendByAuthor
│   ├── recommendBySimilarity
│   ├── staticPages
│   ├── tinymce
│   ├── usageEvent
│   └── webFeed
├── importexport
│   ├── doaj
│   ├── native
│   ├── pubmed
│   └── users
├── metadata
│   └── dc11
├── oaiMetadataFormats
│   ├── dc
│   ├── marc
│   ├── marcxml
│   └── rfc1807
├── paymethod
│   ├── manual
│   └── paypal
├── pubIds
│   └── urn
├── reports
│   ├── articles
│   ├── counter
│   ├── reviewReport
│   └── subscriptions
└── themes
    ├── default
    ├── material
    └── material-v3_0_4-0.tar.gz

56 directories, 1 file

I prefer not to roll backup to the latest backup because these are a lot of changes in the journal that I prefer not to loose.

DeMiro5001 · March 16, 2025, 12:20pm

I have copied the plugin folder from the backup over the plugin folder of the current install. This fixed some of the issues. Some plugins required manual update using the github release from the admin interface.
I will have to check them one by one.

Is back in the admin area after I enabled a second language in the language section.

I will continue examining if all the issues are resolved

DeMiro5001 · March 21, 2025, 11:28pm

The journal works fine so far.
Thank you so much @asmecher for your precious help.
It would have been helpful if the upgrade check warned about inconsistencies between the plugins list in the database and the plugins folder.

asmecher · March 22, 2025, 2:33pm

Hi @DeMiro5001,

Glad to hear you’re back on the road! We’re aware that the upgrade process needs improvements, including around plugins; we hope to be able to get to it soon.

Thanks,
Alec Smecher
Public Knowledge Project Team

asmecher · March 24, 2025, 3:00pm

This topic was automatically closed after 9 days. New replies are no longer allowed.