Upgrade ojs from 3.1.2.4 to 3.3.0.4

@jnugent

Yes Health Sciences theme.
You have upgraded theme and all plugins

I suggest you try a different theme, then. If the problem is resolved, head over here:

And file an issue. You still haven’t looked at your logs or told us what the error is.

Best
Jason

@jnugent
Where are i find this logs or told in my dashbord ???

They won’t be in the OJS dashboard. You’ll need to look in your Apache server side error logs for PHP “Fatal Errors”.

Best,
Jason

@jnugent in phpmyadmin ???

No, not in phpymyadmin. They’ll be in your Apache server log. You may need to talk to your systems administrator. I suggest you read Alec’s very helpful post here:

Jason

Hi,

I’m following this thread in doing a trial upgrade from OJS 3.2.12 to 3.3.0-5.
I successfully changed all the MyISAM tables into InnoDB before the upgrade (through web), and got this error message:

A database error has occurred: SQLSTATE[HY000]: General error: 1005 Can’t create table XXXX-db.submission_files (errno: 150 “Foreign key constraint is incorrectly formed”) (SQL: alter table submission_files add constraint submission_files_file_id_foreign foreign key (file_id) references files (file_id))

This is the error log.

[16-Apr-2021 12:33:25 ***] WARNING: The NavigationMenu (ContextId: 2, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[16-Apr-2021 12:33:25 ***] WARNING: The NavigationMenu (ContextId: 2, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
[16-Apr-2021 12:33:25 ***] WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/21/submission/copyedit/21-1-61-1-9-20151124.pdf.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/22/submission/copyedit/22-1-63-1-9-20151124.pdf.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/23/submission/copyedit/23-1-65-1-9-20151126.pdf.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/24/submission/copyedit/24-1-67-1-9-20151126.pdf.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/25/submission/copyedit/25-1-69-1-9-20151126.pdf.
[16-Apr-2021 12:33:28 ***] A submission file was expected but not found at journals/2/articles/26/submission/copyedit/26-1-71-1-9-20151126.pdf.
[16-Apr-2021 12:33:29 ***] A submission file was expected but not found at journals/2/articles/71/submission/copyedit/71-1-159-1-9-20160330.pdf.
[16-Apr-2021 12:33:31 ***] A submission file was expected but not found at journals/2/articles/126/submission/review/126-1-277-1-4-20160725.doc.
[16-Apr-2021 12:33:35 ***] A submission file was expected but not found at journals/2/articles/335/submission/335-1-684-1-2-20160824.doc.
[16-Apr-2021 12:33:50 ***] A submission file was expected but not found at journals/2/articles/965/submission/965-1-2006-1-2-20161018.rar.
[16-Apr-2021 12:33:50 ***] A submission file was expected but not found at journals/2/articles/965/submission/review/965-1-2008-1-4-20161018.rar.
[16-Apr-2021 12:33:51 ***] A submission file was expected but not found at journals/2/articles/987/submission/query/987-1-2078-1-18-20161025.doc.
[16-Apr-2021 12:33:51 ***] A submission file was expected but not found at journals/2/articles/995/submission/995-1-2104-1-2-20161031.pdf.
[16-Apr-2021 12:34:20 ***] A submission file was expected but not found at journals/2/articles/1751/submission/query/1751-13-4956-2-18-20180417.jpg.
[16-Apr-2021 12:34:20 ***] A submission file was expected but not found at journals/2/articles/1751/submission/query/1751-13-4956-3-18-20180417.jpg.
[16-Apr-2021 12:34:20 ***] A submission file was expected but not found at journals/2/articles/1751/submission/1751-13-4974-2-2-20180419.jpg.
[16-Apr-2021 12:34:20 ***] A submission file was expected but not found at journals/2/articles/1750/submission/1750-13-4976-2-2-20180419.jpg.
[16-Apr-2021 12:34:57 ***] SQLSTATE[HY000]: General error: 1005 Can’t create table XXXX-db.submission_files (errno: 150 “Foreign key constraint is incorrectly formed”) (SQL: alter table submission_files add constraint submission_files_file_id_foreign foreign key (file_id) references files (file_id))

I did random check on path that reportedly missing file above e.g. journals/2/articles/21/submission/copyedit/21-1-61-1-9-20151124.pdf. and found no such path in the data folder, only journals/2/articles/21/submission NO copyedit subfolder. Same thing with this path: journals/2/articles/22/submission/copyedit/22-1-63-1-9-20151124.pdf.

Any ideas on what’s causing this and how to fix it?

Thanks.

Hello rebas_saber,

As you already able to install the upgrade, can you please share the process of how you had done this?

We are also in same problems that you mentioned in this message trail and not able to upgrade.

We are also trying to upgrade from 3.1.2.4 to 3.3.0.5. Please help with your process.

please help.

hi @jnugent

This file error log : https://we.tl/t-Da6FQ4NKwa

Hi @rebas_saber

So, we’ve explained this before earlier in this thread, but if you look at your error log:

PHP Fatal error:  Uncaught PDOException: SQLSTATE[HY000]: General error: 1267 Illegal mix of collations (utf8_general_ci,IMPLICIT) and (utf8_unicode_ci,IMPLICIT) for operation '=' in /home1/boutiorg/public_html/testBOUTIorg/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php:78

You have a mix of table encodings here. In Addition to all of your tables needing to be InnoDB, they must also be the same encoding type. You’ll need to correct these, probably in PHPMyAdmin, and make them all either utf8_general_ci or (better) utf8_unicode_ci, and then make sure your config.inc.php file specifies the one you’ve picked.

OJS 3.3 is now very strict about its database schema.

Best,
Jason

hi @jnugent

Actually all the tables are “InnoDB”, but some are “utf8_unicode_ci”, some are “utf8_general_ci”, and now everyone is “utf8_unicode_ci”

But still the same problem, the links don’t work.

Best Regard.

Hi @rebas_saber

The next step will always be in the Apache error log. If there are more fatal errors, please take those errors and search for them on the forum here. It’s unlikely that others have not encountered them.

Please make sure that you’ve correctly edited your config.inc.php file and set the default collation setting to utf8_unicode.ci, then, and uncommented it (remove the semi colon), because by default it is not

Jason

I searched for it in “config.inc.php” but did not find it.

Do I add it to this form:

Database collation
collation = utf8_general_ci

Capture1

So that the file becomes the following :

; port = 3306
; unix_socket = /var/run/mysqld/mysqld.sock

Database collation
collation = utf8_general_ci

; Enable persistent connections
persistent = Off

; Enable database debug output (very verbose!)
debug = Off

hi @jnugent

this is new file for error log : https://we.tl/t-JEoghDqIXy

Thanks u :pray:.

If you don’t have it in your config.inc.php file, then yes, you’ll need to add it. You should always compare the new TEMPLATE with your existing file and add new directives. And it shouldn’t be utf8_general_ci in your case because you’re using utf8_unicode_ci.

I’m taking the rest of the weekend off, so good luck.

Hi,

Links is working. :pray:

Thank you very much Jason,

Have a good weekend.

Hi @jnugent ,

Hope you are in good health.

I have a small problem, the “Static Pages” links are not appearing in my dashboard.

But on site they appear and work well.

test

Example: “Static Pages” : For Authors

That probably was all migrated to the navigation menu system now. You no longer need the static pages plugin to create stage pages, OJS 3.3 (and 3.2) supports it natively.

hi @jnugent

But where do I find it in the dashboard for me to modify.

I told you in my previous reply - it will be in the navigation section now. Probably Website Settings → Navigation.