Error after upgrade

  • Application Version - Upgrade from 2.4 to 3.2.0.2
  • Description of issue
    After upgrade have errors

Notice: Undefined index: gossip in /home/mydomain/public_html/lib/pkp/classes/user/UserDAO.inc.php on line 308

Notice: Undefined index: permit_metadata_edit in /home/mydomain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58

Notice: Undefined index: permit_metadata_edit in /home/mydomain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58

Notice: Undefined index: permit_metadata_edit in /home/mydomain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58

Notice: Undefined index: permit_metadata_edit in /home/mydomain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58

Notice: Undefined index: url_path in /home/mydomain/public_html/classes/issue/IssueDAO.inc.php on line 318
ADOConnection._Execute(select s., po.seq from submissions as s left join publications as po on s.current_publication_id = po.publ...) % line 1222, file: adodb.inc.php ADOConnection.Execute(select s.*, po.seqfromsubmissionsassleft joinpublicationsaspoons.current_publication_id=po.publ…, Array[1]) % line 100, file: DAO.inc.php
DAO.retrieve(select s.
, po.seq from submissions as s left join publications as po on s.current_publication_id = po.publ..., Array[4], false) % line 201, file: DAO.inc.php DAO.retrieveRange(select s.*, po.seqfromsubmissionsassleft joinpublicationsaspoons.current_publication_id=po.publ…, Array[4], null) % line 103, file: PKPSubmissionService.inc.php
PKP\Services\PKPSubmissionService.getMany(Array[5]) % line 313, file: IssueHandler.inc.php

Fatal error: Uncaught Exception: DB Error: Table ‘aida_2_ojs.publications’ doesn’t exist Query: select s., po.seq from submissions as s left join publications as po on s.current_publication_id = po.publication_id left join publications as issue_p on issue_p.submission_id = s.submission_id left join publication_settings as issue_ps on issue_p.publication_id = issue_ps.publication_id where s.context_id = ? and s.status in (?) and (issue_ps.setting_name = ? and issue_ps.setting_value in (?)) group by s.submission_id, po.seq order by po.seq asc in /home/mydomain/public_html/lib/pkp/classes/db/DAO.inc.php:703 Stack trace: #0 /home/mydomain/public_html/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_mysqli), 'select s., ...') #1 /home/mydomain/public_html/lib/pkp/classes/db/DAO.inc.php(201): DAO->retrieve('select s.*, …’, Array, false) #2 /home/mydomain/public_html/lib/pkp/classes/services/PKPSubmissionService.inc.php(103): DAO->retr in /home/mydomain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703

  • Steps you took leading up to the issue
    Follow upgrade instructions
  • Error log messages if applicable

You can post in any language, but please note there is a Spanish OJS forum and a German category on this forum.

Here error_log - Google Drive is log file

I try to update again and now have blank page error 500
This is log file:

#0 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(326): PDO->prepare(‘select * from ...') #1 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(657): Illuminate\Database\Connection->Illuminate\Database\{closure}('select * from …’, Array)
#2 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(624): Illuminate\Database\Connection->runQueryCallback(‘select * from ...', Array, Object(Closure)) #3 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(333): Illuminate\Database\Connection->run('select * from …’, Array, Object(Closure))
#4 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Query/Builder.php(2130): Illuminate\Database\Connection->select(‘select * from . in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php on line 664 [06-May-2020 17:53:07 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:53:07 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:53:07 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:53:07 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:53:07 UTC] PHP Notice: Undefined index: url_path in /home/my_domain/public_html/classes/issue/IssueDAO.inc.php on line 318 [06-May-2020 17:53:50 UTC] PHP Notice: Undefined index: url_path in /home/my_domain/public_html/classes/issue/IssueDAO.inc.php on line 318 [06-May-2020 17:53:50 UTC] PHP Fatal error: Uncaught Exception: DB Error: Table 'aida_ojs.publications' doesn't exist Query: select s.*, po.seqfromsubmissionsassleft joinpublicationsaspoons.current_publication_id=po.publication_idleft joinpublicationsasissue_ponissue_p.submission_id=s.submission_idleft joinpublication_settingsasissue_psonissue_p.publication_id=issue_ps.publication_idwheres.context_id= ? ands.status in (?, ?) and (issue_ps.setting_name= ? andissue_ps.setting_valuein (?)) group bys.submission_id, po.seqorder bypo.seqasc in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703 Stack trace: #0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_mysqli), 'selects.*, …’)
#1 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(201): DAO->retrieve(‘select s., ...', Array, false) #2 /home/my_domain/public_html/lib/pkp/classes/services/PKPSubmissionService.inc.php(103): DAO->r in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703 [06-May-2020 17:53:50 UTC] PHP Notice: Undefined index: url_path in /home/my_domain/public_html/classes/issue/IssueDAO.inc.php on line 318 [06-May-2020 17:53:50 UTC] PHP Fatal error: Uncaught Exception: DB Error: Table 'aida_ojs.publications' doesn't exist Query: select s.*, po.seqfromsubmissionsassleft joinpublicationsaspoons.current_publication_id=po.publication_idleft joinpublicationsasissue_ponissue_p.submission_id=s.submission_idleft joinpublication_settingsasissue_psonissue_p.publication_id=issue_ps.publication_idwheres.context_id= ? ands.status in (?, ?) and (issue_ps.setting_name= ? andissue_ps.setting_valuein (?)) group bys.submission_id, po.seqorder bypo.seqasc in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703 Stack trace: #0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_mysqli), 'selects.*, …’)
#1 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(201): DAO->retrieve('select s.
, ...', Array, false) #2 /home/my_domain/public_html/lib/pkp/classes/services/PKPSubmissionService.inc.php(103): DAO->r in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703 [06-May-2020 17:54:33 UTC] PHP Fatal error: Uncaught PDOException: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'aida_ojs.publications' doesn't exist in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php:326 Stack trace: #0 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(326): PDO->prepare('select * from …’)
#1 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(657): Illuminate\Database\Connection->Illuminate\Database{closure}(‘select * from ...', Array) #2 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(624): Illuminate\Database\Connection->runQueryCallback('select * from …’, Array, Object(Closure))
#3 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(333): Illuminate\Database\Connection->run('select * from ...', Array, Object(Closure)) #4 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Query/Builder.php(2130): Illuminate\Database\Connection->select('select * from . in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php on line 664
[06-May-2020 17:55:12 UTC] PHP Fatal error: Uncaught PDOException: SQLSTATE[42S02]: Base table or view not found: 1146 Table ‘aida_ojs.publications’ doesn’t exist in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php:326
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(326): PDO->prepare(‘select * from ...') #1 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(657): Illuminate\Database\Connection->Illuminate\Database\{closure}('select * from …’, Array)
#2 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(624): Illuminate\Database\Connection->runQueryCallback(‘select * from ...', Array, Object(Closure)) #3 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(333): Illuminate\Database\Connection->run('select * from …’, Array, Object(Closure))
#4 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Query/Builder.php(2130): Illuminate\Database\Connection->select(‘select * from . in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php on line 664 [06-May-2020 17:56:26 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:56:26 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:56:26 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:56:26 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58 [06-May-2020 17:56:26 UTC] PHP Notice: Undefined index: url_path in /home/my_domain/public_html/classes/issue/IssueDAO.inc.php on line 318 [06-May-2020 17:56:38 UTC] PHP Fatal error: Uncaught PDOException: SQLSTATE[42S02]: Base table or view not found: 1146 Table 'aida_ojs.publications' doesn't exist in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php:326 Stack trace: #0 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(326): PDO->prepare('select * from …’)
#1 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(657): Illuminate\Database\Connection->Illuminate\Database{closure}(‘select * from ...', Array) #2 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(624): Illuminate\Database\Connection->runQueryCallback('select * from …’, Array, Object(Closure))
#3 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php(333): Illuminate\Database\Connection->run(‘select * from ...', Array, Object(Closure)) #4 /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Query/Builder.php(2130): Illuminate\Database\Connection->select('select * from . in /home/my_domain/public_html/lib/pkp/lib/vendor/illuminate/database/Connection.php on line 664
[06-May-2020 17:59:15 UTC] PHP Fatal error: Uncaught Exception: DB Error: Unknown column ‘assoc_type’ in ‘where clause’ Query: UPDATE email_templates SET assoc_type = 530 WHERE assoc_type = ‘526’ in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_mysqli), ‘UPDATE email_te…’)
#1 /home/my_domain/public_html/classes/install/Upgrade.inc.php(731): DAO->update(‘UPDATE email_te…’)
#2 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(417): Upgrade->syncSeriesAssocType(Object(Upgrade), Array)
#3 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(263): Installer->executeAction(Array)
#4 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#5 /home/my_domain/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php(42): Installer->execute()
#6 /home/my_domain/public_html/lib/pkp/pages/install/InstallHandler.inc.php(106): UpgradeForm->execute()
#7 /home/my_domain/public in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703
[06-May-2020 17:59:23 UTC] PHP Fatal error: Uncaught Exception: DB Error: Unknown column ‘assoc_type’ in ‘where clause’ Query: UPDATE email_templates SET assoc_type = 530 WHERE assoc_type = ‘526’ in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_mysqli), ‘UPDATE email_te…’)
#1 /home/my_domain/public_html/classes/install/Upgrade.inc.php(731): DAO->update(‘UPDATE email_te…’)
#2 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(417): Upgrade->syncSeriesAssocType(Object(Upgrade), Array)
#3 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(263): Installer->executeAction(Array)
#4 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#5 /home/my_domain/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php(42): Installer->execute()
#6 /home/my_domain/public_html/lib/pkp/pages/install/InstallHandler.inc.php(106): UpgradeForm->execute()
#7 /home/my_domain/public in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703
[06-May-2020 18:06:36 UTC] PHP Fatal error: Uncaught Exception: DB Error: Unknown column ‘assoc_type’ in ‘where clause’ Query: UPDATE email_templates SET assoc_type = 530 WHERE assoc_type = ‘526’ in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_mysqli), ‘UPDATE email_te…’)
#1 /home/my_domain/public_html/classes/install/Upgrade.inc.php(731): DAO->update(‘UPDATE email_te…’)
#2 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(417): Upgrade->syncSeriesAssocType(Object(Upgrade), Array)
#3 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(263): Installer->executeAction(Array)
#4 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#5 /home/my_domain/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php(42): Installer->execute()
#6 /home/my_domain/public_html/lib/pkp/pages/install/InstallHandler.inc.php(106): UpgradeForm->execute()
#7 /home/my_domain/public in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703
[06-May-2020 18:07:34 UTC] PHP Fatal error: Uncaught Exception: DB Error: Unknown column ‘assoc_type’ in ‘where clause’ Query: UPDATE email_templates SET assoc_type = 530 WHERE assoc_type = ‘526’ in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_mysqli), ‘UPDATE email_te…’)
#1 /home/my_domain/public_html/classes/install/Upgrade.inc.php(731): DAO->update(‘UPDATE email_te…’)
#2 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(417): Upgrade->syncSeriesAssocType(Object(Upgrade), Array)
#3 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(263): Installer->executeAction(Array)
#4 /home/my_domain/public_html/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#5 /home/my_domain/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php(42): Installer->execute()
#6 /home/my_domain/public_html/lib/pkp/pages/install/InstallHandler.inc.php(106): UpgradeForm->execute()
#7 /home/my_domain/public in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: gossip in /home/my_domain/public_html/lib/pkp/classes/user/UserDAO.inc.php on line 308
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: gossip in /home/my_domain/public_html/lib/pkp/classes/user/UserDAO.inc.php on line 308
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: gossip in /home/my_domain/public_html/lib/pkp/classes/user/UserDAO.inc.php on line 308
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: permit_metadata_edit in /home/my_domain/public_html/lib/pkp/classes/security/UserGroupDAO.inc.php on line 58
[06-May-2020 18:08:05 UTC] PHP Notice: Undefined index: url_path in /home/my_domain/public_html/classes/issue/IssueDAO.inc.php on line 318
[06-May-2020 18:08:05 UTC] PHP Fatal error: Uncaught Exception: DB Error: Table ‘aida_ojs.publications’ doesn’t exist Query: select s., po.seq from submissions as s left join publications as po on s.current_publication_id = po.publication_id left join publications as issue_p on issue_p.submission_id = s.submission_id left join publication_settings as issue_ps on issue_p.publication_id = issue_ps.publication_id where s.context_id = ? and s.status in (?) and (issue_ps.setting_name = ? and issue_ps.setting_value in (?)) group by s.submission_id, po.seq order by po.seq asc in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_mysqli), 'select s.
, ...') #1 /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php(201): DAO->retrieve('select s.*, …’, Array, false)
#2 /home/my_domain/public_html/lib/pkp/classes/services/PKPSubmissionService.inc.php(103): DAO->retr in /home/my_domain/public_html/lib/pkp/classes/db/DAO.inc.php on line 703

Hi @komir,

It looks to me like the upgrade did not complete fully. When you ran it, did you get an error message? Did you receive a confirmation that the upgrade had completed?

Regards,
Alec Smecher
Public Knowledge Project Team

No, I didn’t get any notification. After press Upgrade get a white page with error 500
I see in the log:

17:53:50 UTC] PHP Fatal error: Uncaught Exception: DB Error: Table 'aida_ojs.publications' doesn't exist Query: select s .*,

and when look in DB cant find ojs.publications ? Is there any way to create it manually or solve the problem in some other way?
Thank you

Hi @komir,

I’d suggest…

  • Restore your database and files directory from your 2.4.x backup
  • Run the upgrade again, using the PHP command line if possible
  • Immediately after the upgrade completes, check the PHP error log (and the output of the PHP command line if you’re using that to run the upgrade)

That should get you more information on what went wrong during upgrade.

Incidentally, OJS 3.2.0-3 has been released, and I’d suggest upgrading directly from 2.4.x to 3.2.0-3 if possible. There are some upgrade fixes included in 3.2.0-3 that might help.

Regards,
Alec Smecher
Public Knowledge Project Team

Thank you for you help.
Please, I have filling that something is wrong with my DB v2.4. Where can I check if something is wrong with it?

Hi @komir,

The output from the upgrade script will help identify problems with the OJS 2.4 database. We don’t have a database checking tool for OJS, however. Is there something specific that seems wrong with your database?

Regards,
Alec Smecher
Public Knowledge Project Team

Think yes, on update now get a error
A database error has occurred: Duplicate entry ‘3-2-7-1’ for key ‘review_round_files_pkey’

Hi @komir,

Have a look at this thread: Upgrade Failed: DB: Duplicate entry '759-606-2984-1' for key 'review_round_files_pkey'

Regards,
Alec Smecher
Public Knowledge Project Team

Hi, I follow they suggested Upgrade to 3.0.0: pkey violation on review_rounds · Issue #1921 · pkp/pkp-lib · GitHub
but don’t know did I make it wright.

  1. Restore from backup v2.4
  2. I opened phpMyAdmin
  3. Opened my database
  4. In Query add

CREATE TABLE review_rounds_old SELECT * FROM review_rounds;
DELETE FROM review_rounds WHERE review_round_id NOT IN (SELECT MIN(review_round_id) >>FROM review_rounds_old GROUP BY submission_id, round);
DROP TABLE review_rounds_old;
like this here https://nimb.ws/KxWnjY

  1. and run it like this here https://nimb.ws/KxWnjY
  2. After that run upgrade but still have an error

Hi @komir,

I suspect the upgrade still didn’t finish, but it may have gotten further this time. Can you check to see whether the upgrade caused an error message?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi I have repeat procedure but still stuck with error
A database error has occurred: Duplicate entry ‘3-2-7-1’ for key ‘review_round_files_pkey’

Do you have any idea?

This is I have in error log

[07-May-2020 21:33:09 UTC] WARNING: Unable to find a match for “141-596-1-RV.docx” in “files/journals/1//articles/141/”. Skipping this file.
[07-May-2020 21:33:09 UTC] WARNING: Unable to find a match for “144-603-1-RV.docx” in “files/journals/1//articles/144/”. Skipping this file.
[07-May-2020 21:33:20 UTC] WARNING: The NavigationMenu (ContextId: 1, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[07-May-2020 21:33:20 UTC] WARNING: The NavigationMenu (ContextId: 1, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
[07-May-2020 21:33:20 UTC] WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[07-May-2020 21:33:29 UTC] Duplicate entry ‘3-2-7-1’ for key ‘review_round_files_pkey’
[07-May-2020 21:35:28 UTC] PHP Fatal error: Uncaught Exception: DB Error: Unknown column ‘assoc_type’ in ‘where clause’ Query: UPDATE email_templates SET assoc_type = 530 WHERE assoc_type = ‘526’ in /home/my_name/public_html/lib/pkp/classes/db/DAO.inc.php:703
Stack trace:
#0 /home/my_name/public_html/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_mysqli), ‘UPDATE email_te…’)
#1 /home/my_name/public_html/classes/install/Upgrade.inc.php(742): DAO->update(‘UPDATE email_te…’)
#2 /home/my_name/public_html/lib/pkp/classes/install/Installer.inc.php(417): Upgrade->syncSeriesAssocType(Object(Upgrade), Array)
#3 /home/my_name/public_html/lib/pkp/classes/install/Installer.inc.php(263): Installer->executeAction(Array)
#4 /home/my_name/public_html/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#5 /home/my_name/public_html/lib/pkp/classes/install/form/UpgradeForm.inc.php(42): Installer->execute()
#6 /home/my_name/public_html/lib/pkp/pages/install/InstallHandler.inc.php(106): UpgradeForm->execute()
#7 /home/my_name/public in /home/my_name*/public_html/lib/pkp/classes/db/DAO.inc.php on line 703

Hi @komir,

Can you confirm whether your OJS 2.4.x database dump has an assoc_type column in the email_templates and email_templates_data tables? It should; if it doesn’t, then is it possible that it’s already been through a failed upgrade attempt to OJS 3.x?

Regards,
Alec Smecher
Public Knowledge Project Team