Submissions and Transitions Between Stages Freeze

Software Support
1

Hello,

I am currently using OJS 3.1.1.4 and the spinner keeps spinning during submissions and transitions between stages, and they are therefore not processing. Below is what I found in my error log:

[26-Mar-2019 03:55:48 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:48 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:49 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:50 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:50 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:59 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:55:59 UTC] PHP Strict Standards: Declaration of SubmissionSubmitForm::fetch() should be compatible with Form::fetch($request, $template = NULL, $display = false) in /home/agoor/public_html/ojs/lib/pkp/classes/submission/form/SubmissionSubmitForm.inc.php on line 21
[26-Mar-2019 03:55:59 UTC] PHP Strict Standards: Declaration of PKPSubmissionSubmitStep1Form::validate() should be compatible with Form::validate($callHooks = true) in /home/agoor/public_html/ojs/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php on line 18
[26-Mar-2019 03:55:59 UTC] PHP Strict Standards: Declaration of PKPSubmissionSubmitStep1Form::execute() should be compatible with Form::execute() in /home/agoor/public_html/ojs/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php on line 18
[26-Mar-2019 03:55:59 UTC] PHP Strict Standards: Declaration of SubmissionSubmitStep1Form::initData() should be compatible with PKPSubmissionSubmitStep1Form::initData($data = Array) in /home/agoor/public_html/ojs/classes/submission/form/SubmissionSubmitStep1Form.inc.php on line 18
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/Form.inc.php on line 388
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 592
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::isPost() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/form/validation/FormValidatorPost.inc.php on line 38
[26-Mar-2019 03:55:59 UTC] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically, assuming $this from incompatible context in /home/agoor/public_html/ojs/lib/pkp/classes/core/PKPRequest.inc.php on line 396
[26-Mar-2019 03:55:59 UTC] PHP Warning: require_once(/home/agoor/public_html/ojs/lib/pkp/plugins/metadata/nlm30/filter/Nlm30CitationSchemaCitationAdapter.inc.php): failed to open stream: No such file or directory in /home/agoor/public_html/ojs/lib/pkp/includes/functions.inc.php on line 25
[26-Mar-2019 03:55:59 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/agoor/public_html/ojs/lib/pkp/plugins/metadata/nlm30/filter/Nlm30CitationSchemaCitationAdapter.inc.php’ (include_path=’.:/home/agoor/public_html/ojs/classes:/home/agoor/public_html/ojs/pages:/home/agoor/public_html/ojs/lib/pkp:/home/agoor/public_html/ojs/lib/pkp/classes:/home/agoor/public_html/ojs/lib/pkp/pages:/home/agoor/public_html/ojs/lib/pkp/lib/adodb:/home/agoor/public_html/ojs/lib/pkp/lib/phputf8:/home/agoor/public_html/ojs/lib/pkp/lib/pqp/classes:/home/agoor/public_html/ojs/lib/pkp/lib/smarty:.:/opt/alt/php56/usr/share/pear:/opt/alt/php56/usr/share/php’) in /home/agoor/public_html/ojs/lib/pkp/includes/functions.inc.php on line 25
[26-Mar-2019 03:56:23 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:23 UTC] PHP Strict Standards: Declaration of SubmissionFileDAO::fromRow() should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /home/agoor/public_html/ojs/classes/article/SubmissionFileDAO.inc.php on line 23
[26-Mar-2019 03:56:25 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:26 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:26 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:26 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:26 UTC] PHP Strict Standards: Declaration of SubmissionFileDAO::fromRow() should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /home/agoor/public_html/ojs/classes/article/SubmissionFileDAO.inc.php on line 23
[26-Mar-2019 03:56:26 UTC] PHP Strict Standards: Declaration of SubmissionFileDAO::fromRow() should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /home/agoor/public_html/ojs/classes/article/SubmissionFileDAO.inc.php on line 23
[26-Mar-2019 03:56:27 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[26-Mar-2019 03:56:27 UTC] PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /home/agoor/public_html/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386

Regards,
Mohamed Agoor

2

Hi @asmecher,

Could you please help me out with this?

3

Hi @Mohamed_Agoor,

The relevant error message is:

 [26-Mar-2019 03:55:59 UTC] PHP Fatal error: require_once(): Failed opening required ‘/home/agoor/public_html/ojs/lib/pkp/plugins/metadata/nlm30/filter/Nlm30CitationSchemaCitationAdapter.inc.php’ (include_path=’.:/home/agoor/public_html/ojs/classes:/home/agoor/public_html/ojs/pages:/home/agoor/public_html/ojs/lib/pkp:/home/agoor/public_html/ojs/lib/pkp/classes:/home/agoor/public_html/ojs/lib/pkp/pages:/home/agoor/public_html/ojs/lib/pkp/lib/adodb:/home/agoor/public_html/ojs/lib/pkp/lib/phputf8:/home/agoor/public_html/ojs/lib/pkp/lib/pqp/classes:/home/agoor/public_html/ojs/lib/pkp/lib/smarty:.:/opt/alt/php56/usr/share/pear:/opt/alt/php56/usr/share/php’) in /home/agoor/public_html/ojs/lib/pkp/includes/functions.inc.php on line 25

When you last upgraded, are you sure that the upgrade script completed successfully?

Regards,
Alec Smecher
Public Knowledge Project Team

4

Hi @asmecher,

Yes, I received a message notifying me of a successful upgrade.

Regards,
Mohamed Agoor

5

Hi @Mohamed_Agoor,

The upgrade process should have run the SQL statements described at ojs/3.1.1_update.xml at ojs-stable-3_1_1 · pkp/ojs · GitHub. I’m not sure why they wouldn’t have run during the upgrade, but if you’re sure the upgrade was successful, you can run them manually to resolve this. (As always, back up your database before running SQL statements.)

Regards,
Alec Smecher
Public Knowledge Project Team

6

Hi @asmecher,

So just to be clear, what I am required to do is run the SQL query that is highlighted in yellow in phpMyAdmin in order to resolve this issue? Sorry I am not as tech savvy as most people in here.

Regards,
Mohamed Agoor

7

Hi @Mohamed_Agoor,

Yes – since you have phpMyAdmin, that means you’re running OJS with MySQL, so you’d run the following queries:

DELETE FROM fs USING filter_settings fs INNER JOIN filters f ON (fs.filter_id = f.filter_id) INNER JOIN filter_groups fg ON (f.filter_group_id = fg.filter_group_id AND fg.symbolic IN ('citation=>nlm30', 'isbn=>nlm30-element-citation', 'nlm30-article-xml=>nlm23-article-xml', 'nlm30-element-citation=>isbn', 'nlm30-element-citation=>nlm30-element-citation', 'nlm30-element-citation=>nlm30-xml', 'nlm30-element-citation=>plaintext', 'nlm30=>citation', 'plaintext=>nlm30-element-citation', 'submission=>nlm23-article-xml', 'submission=>nlm30-article-xml', 'submission=>reference-list'));
DELETE FROM f USING filters f INNER JOIN filter_groups fg ON (f.filter_group_id = fg.filter_group_id AND fg.symbolic IN ('citation=>nlm30', 'isbn=>nlm30-element-citation', 'nlm30-article-xml=>nlm23-article-xml', 'nlm30-element-citation=>isbn', 'nlm30-element-citation=>nlm30-element-citation', 'nlm30-element-citation=>nlm30-xml', 'nlm30-element-citation=>plaintext', 'nlm30=>citation', 'plaintext=>nlm30-element-citation', 'submission=>nlm23-article-xml', 'submission=>nlm30-article-xml', 'submission=>reference-list'));
DELETE FROM filter_groups WHERE symbolic IN ('citation=>nlm30', 'isbn=>nlm30-element-citation', 'nlm30-article-xml=>nlm23-article-xml', 'nlm30-element-citation=>isbn', 'nlm30-element-citation=>nlm30-element-citation', 'nlm30-element-citation=>nlm30-xml', 'nlm30-element-citation=>plaintext', 'nlm30=>citation', 'plaintext=>nlm30-element-citation', 'submission=>nlm23-article-xml', 'submission=>nlm30-article-xml', 'submission=>reference-list');

Regards,
Alec Smecher
Public Knowledge Project Team

8

Hi @asmecher,

I ran the queries and the issue has been resolved. Thank you very much for your assistance. I really appreciate it.

Regards,
Mohamed Agoor

9

I have issue with saving the submission. Below i give the php log.

[28-Mar-2019 03:28:36 UTC] PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/ijiernet/public_html/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20 [28-Mar-2019 03:28:36 UTC] PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/ijiernet/public_html/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 0 [28-Mar-2019 03:28:36 UTC] PHP Warning: Declaration of SubmissionDisciplineEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/ijiernet/public_html/lib/pkp/classes/submission/SubmissionDisciplineEntryDAO.inc.php on line 0 [28-Mar-2019 03:28:36 UTC] PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/ijiernet/public_html/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 0 [28-Mar-2019 03:28:36 UTC] PHP Warning: Declaration of SubmissionSubjectEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/ijiernet/public_html/lib/pkp/classes/submission/SubmissionSubjectEntryDAO.inc.php on line 0 [28-Mar-2019 03:28:36 UTC] PHP Fatal error: Uncaught Error: Call to undefined method Application::get() in /home/ijiernet/public_html/plugins/generic/orcidProfile/OrcidProfilePlugin.inc.php:406 Stack trace: #0 /home/ijiernet/public_html/lib/pkp/classes/plugins/HookRegistry.inc.php(107): OrcidProfilePlugin->handleSubmissionSubmitStep3FormExecute(‘submissionsubmi…’, Array) #1 /home/ijiernet/public_html/lib/pkp/classes/form/Form.inc.php(314): HookRegistry::call(‘submissionsubmi…’, Array) #2 /home/ijiernet/public_html/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep3Form.inc.php(99): Form->execute() #3 /home/ijiernet/public_html/lib/pkp/pages/submission/PKPSubmissionHandler.inc.php(171): PKPSubmissionSubmitStep3Form->execute() #4 /home/ijiernet/public_html/lib/pkp/classes/core/PKPRouter.inc.php(390): PKPSubmissionHandler->saveStep(Array, Object(Request)) #5 /home/ijiernet/public_html/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false) #6 /home/ijiernet/public_html/l in /home/ijiernet/public_html/plugins/generic/orcidProfile/OrcidProfilePlugin.inc.php on line 406

image

10

Hi @Editor_IJIER,

I don’t think yours is the same issue as this thread discusses. Can you post this as a new topic?

Thanks,
Alec Smecher
Public Knowledge Project Team