DB Error: Table 'xxx_ojs3.articles' doesn't exist

Thank you very much i’ll try this way

Hi @Vitaliy, I tried this way but it does not working

Code version: 3.1.2.0
Database version: 2.4.8.4
Latest version: 3.1.2.0
Database version is older than code version
Run “tools/upgrade.php upgrade” to update

php tools/upgrade.php upgrade

ERROR: Upgrade failed: DB: Table ‘articles_migration’ already exists

Hi @alejopachons

Hmm, most probably this error means that the update process was already performed before and it wasn’t successful as the database version is still 2.4.8.
Can you restore the database from a backup and perform the update process once again?
The best way is to try first on the local OJS instance.

I struggled with this error for some time.

In my case the solution was, prior to any attempt to upgrade, look at the 2.4.8 dbase articles table:

click on section.id to see if there are any NULL entries. Assign all null entries with a valid section.id number

run the upgrade through cli

Hi there @abbas_ilab!

I’m also experiencing the same problem upgrading from 2.4.2 to 3.1.2-1 . Had you succeed upgrading from 2.4.8 to to 3.x?

I am experiencing the same problem. Upgrading from 2.4.8.5 to the latest release 3.1.3.1. The error code is as under;

DB Error: Table 'escijour_ojs.articles' doesn't exist

Stack Trace:
File: /home2/escijour/public_html/classes/install/Upgrade.inc.php line 78
Function: DAO->retrieve(“SELECT article_id, journal_id, review_file_id FROM articles WHER…”)

File: /home2/escijour/public_html/lib/pkp/classes/install/Installer.inc.php line 421
Function: Upgrade->removeReviewEntries(Object(Upgrade), Array(1))

File: /home2/escijour/public_html/lib/pkp/classes/install/Installer.inc.php line 265
Function: Installer->executeAction(Array(3))

File: /home2/escijour/public_html/lib/pkp/classes/install/Installer.inc.php line 186
Function: Installer->executeInstaller()

File: /home2/escijour/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php line 40
Function: Installer->execute()

File: /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php line 104
Function: UpgradeForm->execute()

File: /home2/escijour/public_html/lib/pkp/classes/core/PKPRouter.inc.php line 390
Function: InstallHandler->installUpgrade(Array(0), Object(Request))

File: /home2/escijour/public_html/lib/pkp/classes/core/PKPPageRouter.inc.php line 231
Function: PKPRouter->_authorizeInitializeAndCallRequest(Array(2), Object(Request), Array(0), False)

File: /home2/escijour/public_html/lib/pkp/classes/core/Dispatcher.inc.php line 134
Function: PKPPageRouter->route(Object(Request))

File: /home2/escijour/public_html/lib/pkp/classes/core/PKPApplication.inc.php line 252
Function: Dispatcher->dispatch(Object(Request))

File: /home2/escijour/public_html/index.php line 68
Function: PKPApplication->execute()

I have restored the website to the previous version and tried up-gradation using cpanel softaculous again but the following message is received.

Request Timeout

This request takes too long to process, it is timed out by the server. If it should not be timed out, please contact administrator of this web site to increase ‘Connection Timeout’.

Changed to

installed = On

and visited the web. It changes the whole layout and keeps the text-only without any theme as shown here;

@asmecher sorry bothering you. Can you please assist me on this?

Hi @esciencepress,

The Table 'escijour_ojs.articles' doesn't exist error is probably caused by attempting to run an upgrade on a database that has already partially been upgraded. Make you restore from backup after a failed upgrade before trying again.

The Request Timeout problem is caused by a time limit set in your server configuration. The upgrade process can potentially take a long time, but when the server has a time limit configured, it’ll stop the upgrade and prevent it from completing. You could configure your server for a longer request time limit (this would involve both your PHP and Apache [or equivalent] configurations), but a better solution is to use the command-line upgrade tool. Again, you’ll have to restore from backup before trying again.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher

I thank you very much for this help. I have successfully been able to upgrade using command line but My System Information shows Current version: 2.4.8.5

I few errors. I am unable to work on Custom Block Manager as it shows an error message; Add Block. When I upload KeyWord cloud, and open journal website 505 error message is received and web open when the plugin is disabled. The plugin gallery section is empty. I have switched on allow_url_fopen.

I am copying herewith error log for your help please;

[29-Nov-2019 19:44:44 UTC] PHP Deprecated: The each() function is deprecated. This message will be suppressed on further calls in /home2/escijour/public_html/lib/pkp/lib/adodb/adodb.inc.php on line 1003
[29-Nov-2019 19:44:44 UTC] Mixed localization for Journal, setting “metaCitations”
[29-Nov-2019 19:44:44 UTC] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 134
[29-Nov-2019 19:44:44 UTC] Mixed localization for Journal, setting “metaCitations”
[29-Nov-2019 19:44:44 UTC] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 134
[29-Nov-2019 19:44:44 UTC] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /home2/escijour/public_html/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0
[29-Nov-2019 19:44:44 UTC] PHP Warning: Declaration of OpenAIREDAO::setOAI(&$oai) should be compatible with PKPOAIDAO::setOAI($oai) in /home2/escijour/public_html/plugins/generic/openAIRE/OpenAIREDAO.inc.php on line 19
[29-Nov-2019 19:44:48 UTC] PHP Deprecated: The each() function is deprecated. This message will be suppressed on further calls in /home2/escijour/public_html/lib/pkp/lib/adodb/adodb.inc.php on line 1003
[29-Nov-2019 19:44:48 UTC] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /home2/escijour/public_html/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0
[29-Nov-2019 19:44:49 UTC] PHP Deprecated: The each() function is deprecated. This message will be suppressed on further calls in /home2/escijour/public_html/lib/pkp/lib/adodb/adodb.inc.php on line 1003
[29-Nov-2019 19:44:49 UTC] Mixed localization for Journal, setting “metaCitations”
[29-Nov-2019 19:44:49 UTC] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 134
[29-Nov-2019 19:44:49 UTC] Mixed localization for Journal, setting “metaCitations”
[29-Nov-2019 19:44:49 UTC] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 134
[29-Nov-2019 19:44:49 UTC] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /home2/escijour/public_html/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0
[29-Nov-2019 19:44:49 UTC] PHP Warning: Declaration of OpenAIREDAO::setOAI(&$oai) should be compatible with PKPOAIDAO::setOAI($oai) in /home2/escijour/public_html/plugins/generic/openAIRE/OpenAIREDAO.inc.php on line 19
[29-Nov-2019 19:44:49 UTC] PHP Deprecated: Non-static method PKPApplication::getCCLicenseBadge() should not be called statically in /home2/escijour/public_html/pages/article/ArticleHandler.inc.php on line 162
[29-Nov-2019 19:44:49 UTC] PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home2/escijour/public_html/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20
[29-Nov-2019 19:44:55 UTC] PHP Deprecated: The each() function is deprecated. This message will be suppressed on further calls in /home2/escijour/public_html/lib/pkp/lib/adodb/adodb.inc.php on line 1003
[29-Nov-2019 19:44:55 UTC] Mixed localization for Journal, setting “metaCitations”
[29-Nov-2019 19:44:55 UTC] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 134
[29-Nov-2019 19:44:55 UTC] Mixed localization for Journal, setting “metaCitations”

Hi @esciencepress,

If OJS still reports version 2.x, then the upgrade didn’t complete fully. Are you sure you got a confirmation message when the upgrade finished?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher

I restored to an earlier version and run the upgrade again, copying herewith log:

[escijour@srv36 public_html]$ php tools/upgrade.php check
Code version: 3.1.2.1
Database version: 2.4.8.5
Latest version: 3.1.2.2
Database version is older than code version
Run “tools/upgrade.php upgrade” to update
[escijour@srv36 public_html]$ php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.1.2.1]

[code: Installer Installer::checkPhpVersion]

[code: Installer Installer::syncSeriesAssocType]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics2.xml (skipped)]

[code: Installer Installer::removeReviewEntries]
[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptTimedViews.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptReferrals.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptBooksForReview.xml]
[data: dbscripts/xml/upgrade/remove_timed_views_bots.xml]
[data: dbscripts/xml/upgrade/3.0.0_preupdate_commentsToEditor.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_review_assignments.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_notes.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_payments.xml]
[data: dbscripts/xml/upgrade/3.1.1_preupdate_citations.xml]
[data: dbscripts/xml/upgrade/3.1.2_preupdate_user_author_names.xml]
[schema: lib/pkp/xml/schema/common.xml]
[schema: lib/pkp/xml/schema/log.xml]
[schema: lib/pkp/xml/schema/announcements.xml]
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
[schema: lib/pkp/xml/schema/metadata.xml]
[schema: lib/pkp/xml/schema/reviews.xml]
[schema: lib/pkp/xml/schema/reviewForms.xml]
[schema: lib/pkp/xml/schema/controlledVocab.xml]
[schema: lib/pkp/xml/schema/submissions.xml]
[schema: lib/pkp/xml/schema/submissionFiles.xml]
[schema: lib/pkp/xml/schema/categories.xml]
[schema: lib/pkp/xml/schema/notes.xml]
[schema: lib/pkp/xml/schema/genres.xml]
[schema: lib/pkp/xml/schema/tombstone.xml]
[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]
[schema: lib/pkp/xml/schema/metrics.xml]
[schema: lib/pkp/xml/schema/views.xml]
[schema: lib/pkp/xml/schema/libraryFiles.xml]
[schema: lib/pkp/xml/schema/navigationMenus.xml]
[schema: dbscripts/xml/ojs_schema.xml]
[data: dbscripts/xml/indexes.xml]

[code: Installer Installer::installDefaultNavigationMenus]

[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]

[code: Installer Installer::migrateSRLocale]

[code: Installer Installer::migrateUserAndAuthorNames]

[code: Installer Installer::concatenateIntoAbout]

[code: Installer Installer::concatenateIntoMasthead]

[code: Installer Installer::migrateCounterPluginUsageStatistics]

[code: Installer Installer::migrateTimedViewsUsageStatistics]

[code: Installer Installer::migrateDefaultUsageStatistics (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration2.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postCounterMigration.xml]
[data: dbscripts/xml/upgrade/2.4.0_postTimedViewsMigration.xml]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type.xml]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_settings.xml]

[code: Installer Installer::installDefaultGenres]

[code: Installer Installer::migrateArticleMetadata]
[data: dbscripts/xml/upgrade/3.0.0_update.xml]

[code: Installer Installer::clearDataCache]

[code: Installer Installer::migrateUserRoles]

[code: Installer Installer::fixReviewForms]

[code: Installer Installer::htmlifyEmailTemplates]
[note: docs/release-notes/README-BEACON]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]
[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]

[code: Installer Installer::localizeCustomBlockSettings]

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]

[code: Installer Installer::migrateFiles]

[code: Installer Installer::convertSupplementaryFiles]

[code: Installer Installer::provideSupplementaryFilesForReview]

[code: Installer Installer::setFileUploader]

[code: Installer Installer::setFileName]
[data: dbscripts/xml/upgrade/3.0.0_postupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_pubId_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_galley_files.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_issue_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_submission_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_review_method.xml]
[data: dbscripts/xml/upgrade/3.0.0_edit_decisions.xml]
[data: dbscripts/xml/upgrade/3.0.1_update.xml]

[code: Installer Installer::convertCommentsToEditor]
[note: docs/release-notes/README-3.0]
[note: docs/release-notes/README-3.0.1]
[data: dbscripts/xml/upgrade/3.0.2_update.xml]
[note: docs/release-notes/README-3.0.2]

[code: Installer Installer::moveReviewerFiles]

[code: Installer Installer::fixAuthorGroup]
[data: dbscripts/xml/upgrade/3.0.0_reviewer_files.xml]

[code: Installer Installer::removeCancelledReviewAssignments]
[escijour@srv36 public_html]$

Its still showing the same; Current version: 2.4.8.5 (July 4, 2019 - 10:48 AM)

Hi @esciencepress,

I don’t see a confirmation message at the end, which means that the upgrade didn’t complete fully. Can you check your PHP error log to see if anything was recorded there?

Regards,
Alec Smecher
Public Knowledge Project Team

I have access to the cPanel. Can you please guide me how to check the PHP error log.

Hi @esciencepress,

See How do I find my PHP error log?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher

Following are the errors recorded in my cpanel.

2019-11-29 18:39:57.532903 [NOTICE] [1015039] [46.229.168.135:53450] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:52.494644 [INFO] [1015039] [54.36.148.16:36318:HTTP2-1] File not found [/home2/escijour/public_html/search/404.shtml]
2019-11-29 18:39:52.494628 [INFO] [1015039] [54.36.148.16:36318:HTTP2-1] File not found [/home2/escijour/public_html/search/index.php/record/view/424]
2019-11-29 18:39:37.288187 [NOTICE] [1015039] [46.229.168.161:2084] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/db/SettingsDAO.inc.php on line 35
2019-11-29 18:39:37.285191 [NOTICE] [1015039] [46.229.168.161:2084] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:37.282840 [NOTICE] [1015039] [46.229.168.161:2084] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:37.281026 [NOTICE] [1015039] [46.229.168.161:2084] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:36.115505 [NOTICE] [1015039] [46.229.168.150:32922] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:36.113553 [NOTICE] [1015039] [46.229.168.150:32922] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:32.195278 [NOTICE] [1015039] [5.188.211.26:50625] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:32.194417 [NOTICE] [1015039] [5.188.211.26:50625] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:32.190903 [NOTICE] [1015039] [5.188.211.26:50625] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:31.785493 [NOTICE] [1015039] [5.188.211.26:55125] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:31.782740 [NOTICE] [1015039] [5.188.211.26:55125] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:31.778923 [NOTICE] [1015039] [5.188.211.26:55125] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.794485 [NOTICE] [1015039] [54.36.150.72:33090:HTTP2-1] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.792980 [NOTICE] [1015039] [54.36.150.72:33090:HTTP2-1] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.706637 [NOTICE] [1015039] [5.188.211.26:51085] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:30.704988 [NOTICE] [1015039] [5.188.211.26:51085] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.703427 [NOTICE] [1015039] [5.188.211.26:51085] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.306209 [NOTICE] [1015039] [5.188.211.26:59730] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:30.303838 [NOTICE] [1015039] [5.188.211.26:59730] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:29.600822 [NOTICE] [1015039] [5.188.211.26:35759] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:29.598525 [NOTICE] [1015039] [5.188.211.26:35759] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:29.596901 [NOTICE] [1015039] [5.188.211.26:35759] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:29.354744 [NOTICE] [1015039] [5.188.211.26:46280] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:29.352066 [NOTICE] [1015039] [5.188.211.26:46280] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:28.245228 [NOTICE] [1015039] [5.188.211.26:34690] [STDERR] PHP Warning: Declaration of InstallHandler::validate($request) should be compatible with PKPHandler::validate($requiredContexts = NULL, $request = NULL) in /home2/escijour/public_html/lib/pkp/pages/install/InstallHandler.inc.php on line 0
2019-11-29 18:39:28.242669 [NOTICE] [1015039] [5.188.211.26:34690] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:28.238456 [NOTICE] [1015039] [5.188.211.26:34690] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:27.986634 [NOTICE] [1015039] [5.188.211.26:38177] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:27.985005 [NOTICE] [1015039] [5.188.211.26:38177] [STDERR] PHP Warning: Cannot use a scalar value as an array in /home2/escijour/public_html/lib/pkp/classes/core/DataObject.inc.php on line 133
2019-11-29 18:39:27.520357 [NOTICE] [1015039] [5.188.211.26:47810] [STDERR] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically in /home2/escijour/public_html/lib/pkp/classes/core/PKPRequest.inc.php on line 396
2019-11-29 18:39:27.520353 [NOTICE] [1015039] [5.188.211.26:47810] [STDERR] PHP Deprecated: Non-static method PKPRequest::isPost() should not be called statically in /home2/escijour/public_html/lib/pkp/classes/form/validation/FormValidatorPost.inc.php on line 38
2019-11-29 18:39:27.520349 [NOTICE] [1015039] [5.188.211.26:47810] [STDERR] PHP Deprecated: Non-static method PKPRequest::_checkThis() should not be called statically in /home2/escijour/public_html/lib/pkp/classes/core/PKPRequest.inc.php on line 594
2019-11-29 18:39:27.520345 [NOTICE] [1015039] [5.188.211.26:47810] [STDERR] PHP Deprecated: Non-static method PKPRequest::getUserVar() should not be called statically in /home2/escijour/public_html/lib/pkp/classes/form/Form.inc.php on line 377

Hi @esciencepress,

I don’t see anything relevant there; look for something containing “Fatal error”.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher

I appreciate your help. My website was down for this upgrade related issues so I have restored the web to an earlier version, duplicated the website and the database to a test folder, and run the upgrade process using command line. The same happened, upgrade process stopped at the following lines in command line screen;

[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]

[code: Installer Installer::localizeCustomBlockSettings]

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]

[code: Installer Installer::migrateFiles]

[code: Installer Installer::convertSupplementaryFiles]

[code: Installer Installer::provideSupplementaryFilesForReview]
[escijour@srv36 test]$

In the error_log found in the test folder, I found the following errors at the end;

[30-Nov-2019 17:29:10 UTC] PHP Fatal error:  Uncaught Error: Call to a member function getFileId() on null in /home2/escijour/public_html/test/lib/pkp/classes/file/SubmissionFileManager.inc.php:184
Stack trace:
#0 /home2/escijour/public_html/test/classes/install/Upgrade.inc.php(1473): SubmissionFileManager->copyFileToFileStage('718', 2, 4, NULL, true)
#1 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(421): Upgrade->provideSupplementaryFilesForReview(Object(Upgrade), Array)
#2 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)
#3 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#4 /home2/escijour/public_html/test/lib/pkp/classes/cliTool/UpgradeTool.inc.php(88): Installer->execute()
#5 /home2/escijour/public_html/test/lib/pkp/classes/cliTool/UpgradeTool.inc.php(64): UpgradeTool->upgrade()
#6 /home2/escijour/public_html/test/tools/upgrade.php(34): UpgradeTool->execute()
#7 {main}
  thrown in /home2/escijour/public_html/test/lib/pkp/classes/file/SubmissionFileManager.inc.php on line 184

Hi @esciencepress,

I suspect your OJS 2.x database has an inconsistency. Take a look at Call to a member function getFileId() on null upgrading to 3.1.2 (and replies).

Regards,
Alec Smecher
Public Knowledge Project Team

After fixing this, started from scratch and now facing this error log.

[30-Nov-2019 19:08:05 UTC] PHP Fatal error: Uncaught Error: Call to a member function getFullName() on null in /home2/escijour/public_html/test/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php:480
Stack trace:
#0 /home2/escijour/public_html/test/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php(135): ReviewAssignmentDAO->_fromRow(Array)
#1 /home2/escijour/public_html/test/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php(531): ReviewAssignmentDAO->getById(‘3575’)
#2 /home2/escijour/public_html/test/classes/install/Upgrade.inc.php(2019): ReviewAssignmentDAO->deleteById(‘3575’)
#3 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(421): Upgrade->removeCancelledReviewAssignments(Object(Upgrade), Array)
#4 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)
#5 /home2/escijour/public_html/test/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#6 /home2/escijour/public_html/test/li in /home2/escijour/public_html/test/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php on line 480