JATS Parser v2.0: JATS XML to HTML and PDF conversion

jats

#21

The last error message is below:


#22

I think that this problem is due to the differences between old and new OldGreggThemePlugin.inc files.

Old plugin seems like this:

New plugin seems like this:

How can I solve this problem?

Now my journal website is off. May you help me about this urgently?

Thanks in advance


#23

Hi @ikram

I don’t see any syntax related errors in the code. Can you confirm that you are using PHP 7.1+?


#24

Yes, my php version is PHP 7.2


#25

This error says that there is a syntax error in pointed part of code. And I know that this code is valid for PHP7.1+
How did you check you PHP version?


#26

I use return type declarations that was introduced in PHP7.1 and those errors are quite the same for cases, when PHP interpreter doesn’t support them.


#27

I am so sorry. First I looked here before.

But then when I look at phpinfo version 5.6 I saw :frowning:

I wonder how to upgrade php version


#28

Whenever you unzip the file to the installation directory / plugins / generic / the plugins activation screen inside the OJS does not load. I can access the screen but keep searching the plugins and never open the relationship. When I exclude the folder it normalizes the loading.


#29

Hi @Walter_Luiz_Oliveira

Do you have an access to the PHP error log? Do you see there any errors or fatal errors while trying to access plugins activation screen with unpacked JATS Parser?


#30

Hi Vitaly.
I have already installed this plugin, I am trying to use it and I can not find the way to do it in the production stage of the article.
You could attach some images of how it works, to see where I should use it.
In the galley I upload a doc to generate the XML JATS and then the HTML and PDF?
Thank you…


#31

It works just like Lens Viewer. Once JATS XML is published, the plugin starts to handle request for that page and displays it as HTML. The only thing that you can control from the settings - is what citations to show, from OJS or XML file.
The plugin that converts DOCX to JATS is not ready yet.


#32

Vitaliy, thanks for your quick response! I thought that the OJS generated an XML JATS and from this it could generate an HTML and a PDF.
According to what you tell me, is it necessary to upload the JATS XML file in the galleys to generate HTML and PDF?


#33

Yes. You need to upload JATS XML, moreover it should be compliant to what the plugin expects.
Conversion of DOCX to JATS XML is a different case. There are several free tools available, but all of them are not perfect and require manual editing.
Basically, right now I’m trying to create such a plugin that will parse DOCX mostly ideally, but it is far from being ready: https://github.com/Vitaliy-1/docxConverter


#34

Thank you so much for your answer and resolve my doubts.
ElianaG


#35

Hi @Vitaliy, I am trying to install your jatsParserPlugin to render HTML and PDFs from XML published galleys (using DOCX2JATS). However once installed, the Installed Plugins tab gets never ending loading.

I’ve previously and successfully installed and activated OldGregg plugin theme and deactivated eLife Lens Article Viewer plugin.

To minimize posible conflicts and errors I’ve also tested it on a fresh OJS 3.1.0.1 installed version, and have also uploaded your xml example file on galley. Have also tried to install jatsParserPlugin on a fresh copy of OJS on local XAMPP server with no success…

Where may I be failing with?

Best regards!


This is my Server Information

OS platform Linux
PHP version 7.2.15-0ubuntu0.18.04.1
Apache version nginx/1.15.6
Database driver mysqli
Database server version 5.7.25-0ubuntu0.18.04.2

To install jatsParserPlugin I’ve done:

cd plugins/generic

git clone https://github.com/Vitaliy-1/JATSParserPlugin.git jatsParser

cd jatsParser

git submodule update --init --recursive

This are the final lines of my website error log:

> 1976 PHP message: PHP Warning:  Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible w     ith ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/forge/evidencia.ml/lib/pkp/classes/su     bmission/SubmissionKeywordEntryDAO.inc.php on line 20" while reading response header from upstream, client: 209.13.86.23, server: evidencia.ml, request:      "GET /index.php/evidencia/article/view/3 HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evi     dencia.ml/index.php/evidencia/index"
> 1977 2019/02/14 17:27:03 [error] 6896#6896: *1988 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/management/settings/website HTTP/1.1", upstream: "fastcgi://unix:/var/run/php     /php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/submissions"
> 1978 2019/02/14 17:27:04 [error] 6896#6896: *1988 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/page/page/user-nav-backend?_=1550165224621 HTTP/1.1", upstream: "f     astcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/management/settings/website"
> 1979 2019/02/14 17:27:04 [error] 6896#6896: *1991 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003
> 1980 PHP message: PHP Warning:  Declaration of ContextSettingsForm::fetch($request, $params = NULL) should be compatible with Form::fetch($request, $template      = NULL, $display = false) in /home/forge/evidencia.ml/lib/pkp/classes/controllers/tab/settings/form/ContextSettingsForm.inc.php on line 20
> 1981 PHP message: PHP Warning:  Declaration of ContextSettingsForm::initData($request) should be compatible with Form::initData() in /home/forge/evidencia.ml/     lib/pkp/classes/controllers/tab/settings/form/ContextSettingsForm.inc.php on line 20
> 1982 PHP message: PHP Warning:  Declaration of ContextSettingsForm::readInputData($request) should be compatible with Form::readInputData() in /home/forge/evi     dencia.ml/lib/pkp/classes/controllers/tab/settings/form/ContextSettingsForm.inc.php on line 20
> 1983 PHP message: PHP Warning:  Declaration of ContextSettingsForm::execute($request) should be compatible with Form::execute() in /home/forge/evidencia.ml/li     b/pkp/classes/controllers/tab/settings/form/ContextSettingsForm.inc.php on line 20
> 1984 PHP message: PHP Warning:  Declaration of PKPAppearanceForm::fetch($request) should be compatible with ContextSettingsForm::fetch($request, $params = NUL     L) in /home/forge/evidencia.ml/lib/pkp/controllers/tab/settings/appearance/form/PKPAppearanceForm.inc.php on line 18
> 1985 PHP message: PHP Deprecated:  Non-static method PKPRequest::getUserVar() should not be called statically in /home/forge/evidencia.ml/lib/pkp/classes/form     /Form.inc.php on line 369
> 1986 PHP message: PHP Deprecated:  Non-static method PKPRequest::_checkThis() should not be called statically in /home/forge/evidencia.ml/lib/pkp/classes/core     /PKPRequest.inc.php on line 592" while reading response header from upstream, client: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/eviden     cia/$$$call$$$/tab/se
> 1987 2019/02/14 17:27:04 [error] 6896#6896: *1988 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/page/page/tasks?_=1550165224623 HTTP/1.1", upstream: "fastcgi://un     ix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/management/settings/website"
> 1988 2019/02/14 17:27:04 [error] 6896#6896: *1988 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/grid/notifications/task-notifications-grid/fetch-grid?_=1550165224     624 HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/managem     ent/settings/website"
> 1989 2019/02/14 17:27:05 [error] 6896#6896: *1996 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "POST /index.php/evidencia/notification/fetchNotification HTTP/1.1", upstream: "fastcgi://unix:/var/run     /php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/management/settings/website"
> 1990 2019/02/14 17:27:05 [error] 6896#6896: *1996 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003
> 1991 PHP message: PHP Warning:  Declaration of BlockPluginsListbuilderHandler::initialize($request) should be compatible with MultipleListsListbuilderHandler:     :initialize($request, $args = NULL) in /home/forge/evidencia.ml/lib/pkp/controllers/listbuilder/settings/BlockPluginsListbuilderHandler.inc.php on line 1     7" while reading response header from upstream, client: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/listbuilder/set     tings/block-plugins-listbuilder/fetch?_=1550165224625 HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer     : "http://evidencia.ml/index.php/evidencia/management/settings/website"
> 1992 2019/02/14 17:27:14 [error] 6896#6896: *1996 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/tab/settings/website-settings-tab/show-tab?tab=plugins&_=155016522     4626 HTTP/1.1", upstream: "fastcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/manage     ment/settings/website"
> 1993 2019/02/14 17:27:14 [error] 6896#6896: *1996 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003
> 1994 PHP message: PHP Warning:  Declaration of CategoryGridHandler::doSpecificFetchGridActions($args, $request, &$templateMgr) should be compatible with GridH     andler::doSpecificFetchGridActions($args, $request, $templateMgr) in /home/forge/evidencia.ml/lib/pkp/classes/controllers/grid/CategoryGridHandler.inc.ph     p on line 0
> 1995 PHP message: PHP Warning:  Declaration of UploadPluginForm::fetch($request) should be compatible with Form::fetch($request, $template = NULL, $display =      false) in /home/forge/evidencia.ml/lib/pkp/controllers/grid/plugins/form/UploadPluginForm.inc.php on line 22
> 1996 PHP message: PHP Warning:  Declaration of UploadPluginForm::execute($request) should be compatible with Form::execute() in /home/forge/evidencia.ml/lib/p     kp/controllers/grid/plugins/form/UploadPluginForm.inc.php on line 22
> 1997 PHP message: PHP Warning:  Declaration of PluginGridHandler::initialize($request) should be compatible with CategoryGridHandler::initialize($request, $ar     gs = NULL) in /home/forge/evidencia.ml/lib/pkp/classes/controllers/grid/plugins/PluginGridHandler.inc.php on line 20
> 1998 PHP message: PHP Warning:  Declaration of PluginGridHandler::loadCategoryData($request, &$categoryDataElement, $filter) should be compatible with Categor     yGridHandler::loadCategoryData($request, &$categoryDataElement, $filter = NULL) in /home/forge/evidencia.ml/lib/pkp/classes/controllers/grid/plugins/Plug     inGridHandler.inc.php on line 20
> 1999 PHP message: PHP Warning:  Declaration of SettingsPluginGridHandler::loadCategoryData($request, $categoryDataElement, $filter) should be compatible with      PluginGridHandler::loadCategoryData($request, &$categoryDataElement, $filter) in /home/forge/evidencia.ml/controllers/grid/settings/plugins/SettingsPlugi     nGridHandler.inc.php on line 18
> 2000 PHP message: PHP Fatal error:  Cannot dec
> 2001 2019/02/14 17:27:14 [error] 6896#6896: *1988 FastCGI sent in stderr: "PHP message: PHP Deprecated:  The each() function is deprecated. This message will      be suppressed on further calls in /home/forge/evidencia.ml/lib/pkp/lib/adodb/adodb.inc.php on line 1003" while reading response header from upstream, cli     ent: 209.13.86.23, server: evidencia.ml, request: "GET /index.php/evidencia/$$$call$$$/grid/plugins/plugin-gallery-grid/fetch-grid?_=1550165224628 HTTP/1     .1", upstream: "fastcgi://unix:/var/run/php/php7.2-fpm.sock:", host: "evidencia.ml", referrer: "http://evidencia.ml/index.php/evidencia/management/settin     gs/website"

#36

Hi @GabeLon,

This error seems to be truncated. Most probable reason is a conflict between identical classes from Old Gregg theme and JATS Parser plugin.
Can you completely delete Old Gregg theme from the OJS instance?
Can you show the whole error message?