Do you know how to properly upgrade from OJS 3.2.1-2 to OJS 3.3.0-7?

Software Support
1

Description of issue or problem I’m having:

I would like to upgrade our old version(3.2.1-2) to the latest version.

Errors occurred during installation:

A database error has occurred: SQLSTATE[42S02]: Base table or view not found: 1146 Table ‘pairpublication2021.email_templates_data’ doesn’t exist (SQL: UPDATE email_templates_data SET body=REPLACE(body, ‘{$submissionLayoutUrl}’, ‘{$submissionUrl}’))

Steps I took leading up to the issue:
-First, I installed the most recent version to a local file and created a new one.

-Second, once the installation is complete, I delete the new version’s database and revert to the previous version, which was 3.2.1-2.

-Third, Change installed config in the config.inc.php file

From On to Off

-Final, then process it into the local site and result is:

Errors occurred during installation:

A database error has occurred: SQLSTATE[42S02]: Base table or view not found: 1146 Table ‘pairpublication2021.email_templates_data’ doesn’t exist (SQL: UPDATE email_templates_data SET body=REPLACE(body, ‘{$submissionLayoutUrl}’, ‘{$submissionUrl}’))

What I tried to resolve the issue:

-I would like to resolve the problem on upgrade.

Application Version - e.g., OJS 3.1.2:

  • my ojs version is 3.2.1-2

Additional information, such as screenshots and error log messages if applicable:

-Here is a timeline of my upgrading procedure.

Screenshot_2

Please help me in resolving this.

thanks

Darryl

2

Hi @asmecher ; Could you help me with this issue?

3

While waiting for a response, I decided to try a manual way of transferring and entity of the database one by one by its table structure because the upgrade CLI and other methods did not proceed due to a database error. See below for the error from converting the database script.

UNKNOWN COLUMN Problem:
1. INSERT INTO authors (author_id, submission_id, seq, email, user_group_id, include_in_browse, publication_id) VALUES(1, 1, 1, ‘genarojapos@gmail.com’, 14, 1, 1);

MySQL said:
ERROR: #1054 - Unknown column ‘submission_id’ in ‘field list’

2. INSERT INTO author_settings (author_id, locale, setting_name, setting_value, setting_type) VALUES(1, ‘en_US’, ‘biography’, ‘’, ‘string’);

MySQL said:
ERROR: #1054 - Unknown column ‘setting_type’ in ‘field list’

3. INSERT INTO navigation_menu_items (navigation_menu_item_id, context_id, url, path, type) VALUES
(1, 16, NULL, NULL, ‘NMI_TYPE_USER_REGISTER’);

MySQL said:
ERROR: #1054 - Unknown column ‘url’ in ‘field list’

4. INSERT INTO publication_galleys (galley_id, locale, publication_id, label, file_id, seq, remote_url, is_approved, url_path) VALUES
(791, ‘en_US’, 20, ‘PDF’, 1258, 0, NULL, 1, NULL);

MySQL said:
ERRO: #1054 - Unknown column ‘file_id’ in ‘field list’

5. INSERT INTO review_round_files (submission_id, review_round_id, stage_id, file_id, revision) VALUES
(1, 1, 3, 2, 1);
MySQL said:
ERRO: #1054 - Unknown column ‘file_id’ in ‘field list’

6. INSERT INTO submissions (submission_id, locale, context_id, section_id, date_submitted, last_modified, status, submission_progress, stage_id, current_publication_id, date_last_activity, work_type) VALUES
(1, ‘en_US’, 9, 20, ‘2012-09-04 03:20:07’, ‘2014-09-27 06:55:44’, 3, 0, 4, 1, NULL, 0);

MySQL said:
ERRO: #1054 - Unknown column ‘section_id’ in ‘field list’

7. INSERT INTO submission_file_settings (file_id, locale, setting_name, setting_value, setting_type) VALUES
(2140, ‘en_US’, ‘name’, ‘FUNDAMENTAL SKILLS AND READINESS FOR COLLEGE ALGEBRA OF FIRST YEAR COLLEGE STUDENTS OF CAPIZ STATE UNIVERSITY, PONTEVEDRA CAMPUS, SY 2008-2009’, ‘string’),
(2140, ‘en_US’, ‘creator’, ‘Alex Buenafe’, ‘string’);

MySQL said:
ERRO: #1054 - Unknown column ‘file_id’ in ‘field list’

8. INSERT INTO submission_files (file_id, revision, source_file_id, source_revision, submission_id, file_type, file_size, original_file_name, file_stage, viewable, date_uploaded, date_modified, assoc_id, genre_id, direct_sales_price, sales_type, uploader_user_id, assoc_type) VALUES
(1, 1, NULL, NULL, 1, ‘application/pdf’, 502578, ‘321_342.pdf’, 2, 1, ‘2012-09-04 03:14:13’, ‘2012-09-04 03:14:13’, NULL, 1, NULL, NULL, 1, NULL);

MySQL said:
ERRO: #1054 - Unknown column ‘revision’ in ‘field list’

9. INSERT INTO submissions (submission_id, locale, context_id, section_id, date_submitted, last_modified, status, submission_progress, stage_id, current_publication_id, date_last_activity, work_type) VALUES
(1, ‘en_US’, 9, 20, ‘2012-09-04 03:20:07’, ‘2014-09-27 06:55:44’, 3, 0, 4, 1, NULL, 0);

MySQL said:
ERRO: #1054 - Unknown column ‘section_id’ in ‘field list’

on this error, I will double-check the \dbscripts\xml\upgrade. I will post again for any updates.

If everyone who knows this error problem kindly helps me to fix this error and share your knowledge.

Regards,

Darryl

4

I attempted to work on the database of my old OJS and the new version to see if I could fix it.

I successfully transferred the data from problems 1, 2, 3, 4, 6, and 7 to the database table structure. I attempted to delete the unknown column to see if I could handle it this way.

for the ‘submission files’ table Even though I deleted the unknown column, I received this error.

Problem Number 8:

#1452 - Cannot add or update a child row: a foreign key constraint fails (databasename.submission_files, CONSTRAINT submission_files_file_id_foreign FOREIGN KEY (file_id) REFERENCES files (file_id))

Problem Number 5:

#1452 - Cannot add or update a child row: a foreign key constraint fails (databasename.review_round_files, CONSTRAINT review_round_files_submission_file_id_foreign FOREIGN KEY (submission_file_id) REFERENCES submission_files (submission_file_id))

I haven’t checked the \dbscripts\xml\upgrade, looking for other solutions.

I will post again for any updates.

If everyone who knows this error problem kindly helps me to fix this error and share your knowledge.

Regards,

Darryl

1 Like
5

Hi Everyone,

Here I am again, hoping that someone will notice this problem! But, in any case, I conduct my own research and comprehend.

Here is Step by Step:

  1. In my response above, I did a manual import of entities in each table assigned, but the result was failed, and the errors are still coming. but, I will not stop.

  2. I returned to the original errors, email templates and email templates data. I tried all versions of xammp on my local server, from the oldest to the most recent, in order to trace the databases of all ojs versions. I noticed that the upgrade on our ojs from the previous version to the current version is incomplete.

  3. Because many xampp installations of mysql fail with access denied, I installed MySqlWorkbench to support all 5 ports for sql.

  4. I exported email templates and email templates data and imported them into our current ojs database (version 3.1.2-2). and ran the upgrade through the browser, but it did not go through, but it did show that the page was not functional. I tried again in the xampp shell, and the error was as follows:

DESKTOP-PC E-COM@PC C:\xampp809\htdocs\www\domain\publication
# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.3.0.8]
[code: Installer Installer::checkPhpVersion]
[code: Installer Installer::migrateSubmissionCoverImages]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_email_templates.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning_articleGalleySettings.xml (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning.xml]
PHP Fatal error:  Uncaught Doctrine\DBAL\Schema\SchemaException: There is no column with name 'submission_id' on table 'citations'. in C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\doctrine\dbal\lib\Doctrine\DBAL\Schema\SchemaException.php:86
Stack trace:
#0 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\doctrine\dbal\lib\Doctrine\DBAL\Schema\Table.php(711): Doctrine\DBAL\Schema\SchemaException::columnDoesNotExist('submission_id', 'citations')
#1 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Connection.php(884): Doctrine\DBAL\Schema\Table->getColumn('submission_id')
#2 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Grammars\RenameColumn.php(30): Illuminate\Database\Connection->getDoctrineColumn('citations', 'submission_id')
#3 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Grammars\Grammar.php(40): Illuminate\Database\Schema\Grammars\RenameColumn::compile(Object(Illuminate\Database\Schema\Grammars\MySqlGrammar), Object(Illuminate\Database\Schema\Blueprint), Object(Illuminate\Support\Fluent), Object(Illuminate\Database\MySqlConnection))
#4 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Blueprint.php(128): Illuminate\Database\Schema\Grammars\Grammar->compileRenameColumn(Object(Illuminate\Database\Schema\Blueprint), Object(Illuminate\Support\Fluent), Object(Illuminate\Database\MySqlConnection))
#5 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Blueprint.php(101): Illuminate\Database\Schema\Blueprint->toSql(Object(Illuminate\Database\MySqlConnection), Object(Illuminate\Database\Schema\Grammars\MySqlGrammar))
#6 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Builder.php(290): Illuminate\Database\Schema\Blueprint->build(Object(Illuminate\Database\MySqlConnection), Object(Illuminate\Database\Schema\Grammars\MySqlGrammar))
#7 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Schema\Builder.php(151): Illuminate\Database\Schema\Builder->build(Object(Illuminate\Database\Schema\Blueprint))
#8 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\db\DBDataXMLParser.inc.php(104): Illuminate\Database\Schema\Builder->table('citations', Object(Closure))
#9 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Connection.php(534): DBDataXMLParser->{closure}(Object(Illuminate\Database\MySqlConnection))
#10 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Connection.php(562): Illuminate\Database\Connection->Illuminate\Database\{closure}()
#11 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Connection.php(539): Illuminate\Database\Connection->withFreshQueryLog(Object(Closure))
#12 C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\laravel\framework\src\Illuminate\Database\Capsule\Manager.php(200): Illuminate\Database\Connection->pretend(Object(Closure))
#13 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\db\DBDataXMLParser.inc.php(105): Illuminate\Database\Capsule\Manager::__callStatic('pretend', Array)
#14 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(390): DBDataXMLParser->parseData('dbscripts/xml/u...')
#15 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(251): Installer->executeAction(Array)
#16 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(174): Installer->executeInstaller()
#17 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\cliTool\UpgradeTool.inc.php(89): Installer->execute()
#18 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\cliTool\UpgradeTool.inc.php(65): UpgradeTool->upgrade()
#19 C:\xampp809\htdocs\www\domain\publication\tools\upgrade.php(22): UpgradeTool->execute()
#20 {main}
  thrown in C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\doctrine\dbal\lib\Doctrine\DBAL\Schema\SchemaException.php on line 86

Now I’m going to concentrate on this error!

PHP Fatal error:  Uncaught Doctrine\DBAL\Schema\SchemaException: There is no column with name 'submission_id' on table 'citations'.

\dbscripts\xml\upgrade This folder has been thoroughly examined.

I will post again for any updates.

If everyone who knows this error problem kindly helps me to fix this error and share your knowledge.

Regards,

Darryl

6

I verified the \dbscripts\xml\upgrade now, and I’m going to do this:

1.I remove the tables citation, email templates, and email templates data from the database and import the old version of the table into the database, then perform the following query in the XAMPP shell: php tools/upgrade.php upgrade

DESKTOP E-COM@PC C:\xampp809\htdocs\www\domain\publication
# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.3.0.8]
[code: Installer Installer::checkPhpVersion]
[code: Installer Installer::migrateSubmissionCoverImages]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_email_templates.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning_articleGalleySettings.xml (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_last_activity.xml]
[schema: lib/pkp/xml/schema/common.xml]
PHP Fatal error:  Uncaught Error: Call to undefined function get_magic_quotes_runtime() in C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\adodb\adodb-php\adodb-xmlschema.inc.php:1307
Stack trace:
#0 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(364): adoSchema->__construct(Object(ADODB_mysqli))
#1 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(251): Installer->executeAction(Array)
#2 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\install\Installer.inc.php(174): Installer->executeInstaller()
#3 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\cliTool\UpgradeTool.inc.php(89): Installer->execute()
#4 C:\xampp809\htdocs\www\domain\publication\lib\pkp\classes\cliTool\UpgradeTool.inc.php(65): UpgradeTool->upgrade()
#5 C:\xampp809\htdocs\www\domain\publication\tools\upgrade.php(22): UpgradeTool->execute()
#6 {main}
  thrown in C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\adodb\adodb-php\adodb-xmlschema.inc.php on line 1307

This the error: C:\xampp809\htdocs\www\domain\publication\lib\pkp\lib\vendor\adodb\adodb-php\adodb-xmlschema.inc.php on line 1307.I tried searching for and checking the same error on this ojs community, but I couldn’t find an answer that fit the error I was having. If the same error occurs but the problem remains unsolved, the query was not completed by the author.

I will post again for any updates.

If everyone who knows this error problem kindly helps me to fix this error and share your knowledge.

Regards,

Darryl

7

Hi @OJS_Darryl,

No need to take these steps for an upgrade. Here’s an instruction: https://github.com/pkp/ojs/blob/stable-3_3_1/docs/UPGRADE.md

Performing a test upgrade locally is a good idea. Can you perform it on an intact database (from a backup) and check if there are any errors?

9

@Vitaliy, Thanks for the response;

No need to take these steps for an upgrade. Here’s an instruction: ojs/UPGRADE.md at stable-3_3_1 · pkp/ojs · GitHub

*I did already on this procedure, but I got this error.:

Regards,

Darryl

10

Sorry, didn’t notice.

According to description, this function is removed starting from PHP 8.0. Can you specify what PHP version you were using in this upgrade? I don’t think that OJS 3.3.0 supports PHP above 7.4

1 Like
11

@Vitaliy ,

Thanks for your response; I’m currently working on the 3.1.2-2 version because my database was corrupted and I didn’t back it up; I’m tracing the databases. I’m currently running PHP 7.0.8. Because my database is broken, I need to trace the issue in the database first.

regards,

Darryl

12

Now I’m attempting to revert to version 3.1.2.1. I saw similar problem, but I was able to upgrade to version 3.1.2.1.

# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.1.2.1]
[code: Installer Installer::checkPhpVersion]
[schema: lib/pkp/xml/schema/common.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/log.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/announcements.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/metadata.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/reviews.xml]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
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[schema: lib/pkp/xml/schema/reviewForms.xml]
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[schema: lib/pkp/xml/schema/controlledVocab.xml]
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[schema: lib/pkp/xml/schema/submissions.xml]
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[schema: lib/pkp/xml/schema/submissionFiles.xml]
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[schema: lib/pkp/xml/schema/categories.xml]
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[schema: lib/pkp/xml/schema/notes.xml]
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[schema: lib/pkp/xml/schema/genres.xml]
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[schema: lib/pkp/xml/schema/tombstone.xml]
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[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]
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[schema: lib/pkp/xml/schema/metrics.xml]
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[schema: lib/pkp/xml/schema/views.xml]
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[schema: lib/pkp/xml/schema/libraryFiles.xml]
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[schema: lib/pkp/xml/schema/navigationMenus.xml]
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[schema: dbscripts/xml/ojs_schema.xml]
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[data: dbscripts/xml/indexes.xml]
[code: Installer Installer::installDefaultNavigationMenus]
WARNING: The NavigationMenu (ContextId: 16, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 16, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice:  unserialize(): Error at offset 159 of 254 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 159 of 254 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
WARNING: The NavigationMenu (ContextId: 9, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 9, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice:  unserialize(): Error at offset 159 of 254 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 157 of 252 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 157 of 252 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
WARNING: The NavigationMenu (ContextId: 13, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 13, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice:  unserialize(): Error at offset 157 of 252 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 158 of 208 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 158 of 208 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
WARNING: The NavigationMenu (ContextId: 14, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 14, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice:  unserialize(): Error at offset 158 of 208 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
PHP Notice:  unserialize(): Error at offset 159 of 254 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 157 of 252 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
PHP Notice:  unserialize(): Error at offset 158 of 208 bytes in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\db\DAO.inc.php on line 352
[code: Installer Installer::migrateUserAndAuthorNames (skipped)]
[code: Installer Installer::addPluginVersions]
[post-install]
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
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PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be passed by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267
PHP Notice:  Only variables should be assigned by reference in C:\xampp\htdocs\www\philair.ph\publication\lib\pkp\classes\cliTool\UpgradeTool.inc.php on line 97

Successfully upgraded to version 3.1.2.1

The screenshot of the result of the revert upgrade article is missing.

Screenshot_6

in the journal submission section:
Screenshot_12

I’ll try my luck with the 3.2.0-3 version.

Regards,

Darryl

13

Hello Everyone;

Because the database is broken, I am tracing the problem until I get this error while running on XAMPP Shell Command for Upgrade: OJS 3.2.0.3. Even though the upgrade is failing, I’ve noticed that 6 tables have been added to the database ( temp_tables).

ERROR: Upgrade failed: DB: Subquery returns more than 1 row

# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.2.0.3]
[code: Installer Installer::checkPhpVersion]
[code: Installer Installer::migrateSubmissionCoverImages]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_email_templates.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning_articleGalleySettings.xml (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_last_activity.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]
WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
[code: Installer Installer::migrateUserAndAuthorNames (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_stylesheet.xml]
[data: dbscripts/xml/upgrade/3.2.0_archiving_settings.xml]
[data: dbscripts/xml/upgrade/3.2.0_update.xml]
[data: dbscripts/xml/upgrade/3.2.0_navigation_menu_items_locale_change.xml]
[code: Installer Installer::migrateSiteLocales]
[code: Installer Installer::migrateSidebarBlocks]
[code: Installer Installer::migrateSiteStylesheet]
[code: Installer Installer::migrateMetadataSettings]
[code: Installer Installer::createLicenseTerms]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::changeUserRolesAndStageAssignmentsForStagePermitSubmissionEdit]
[data: dbscripts/xml/upgrade/3.2.0_versioning.xml]
ERROR: Upgrade failed: DB: Subquery returns more than 1 row

Debug: On;

ERROR: Upgrade failed: DB: Unknown column 'a.primary_contact' in 'where clause'
PKP-Database-Logger 1630683389.2696: -----
(mysqli): UPDATE sessions
                                SET
                                        user_id = NULL,
                                        ip_address = '',
                                        user_agent = '',
                                        created = 1630683389,
                                        last_used = 1630683389,
                                        remember = 0,
                                        data = '',
                                        domain = ''
                                WHERE session_id = 'emb7hbt4j39vfvhksijs94kj7j'

Browser Label: http://localhost:8080/www/domain/publication/index.php/journal/submissions

ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                               ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                            DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                         ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                      ControlledVocabDAO._build(submissionKeyword, 1048588, 770) % line   31, file: SubmissionKeywordDAO.inc.php
                                                                  ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                               ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                            DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                         ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                      ControlledVocabDAO._build(submissionSubject, 1048588, 770) % line   31, file: SubmissionSubjectDAO.inc.php
                                                                  ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                               ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                            DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                         ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                      ControlledVocabDAO._build(submissionDiscipline, 1048588, 770) % line   31, file: SubmissionDisciplineDAO.inc.php
                                                                  ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                               ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                            DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                         ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                      ControlledVocabDAO._build(submissionLanguage, 1048588, 770) % line   31, file: SubmissionLanguageDAO.inc.php
                                                                  ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                               ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                            DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                         ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                      ControlledVocabDAO._build(submissionAgency, 1048588, 770) % line   30, file: SubmissionAgencyDAO.inc.php
                                                                                    ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                                                 ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                                              DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                           ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO._build(submissionKeyword, 1048588, 770) % line   31, file: SubmissionKeywordDAO.inc.php
                                                                                    ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                                                 ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                                              DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                           ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO._build(submissionSubject, 1048588, 770) % line   31, file: SubmissionSubjectDAO.inc.php
                                                                                    ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                                                 ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                                              DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                           ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO._build(submissionDiscipline, 1048588, 770) % line   31, file: SubmissionDisciplineDAO.inc.php
                                                                                    ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                                                 ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                                              DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                           ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO._build(submissionLanguage, 1048588, 770) % line   31, file: SubmissionLanguageDAO.inc.php
                                                                                    ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 770)) % line 1222, file: adodb.inc.php
                                                                                 ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 770), Array[1]) % line  229, file: DAO.inc.php
                                                                              DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                           ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO._build(submissionAgency, 1048588, 770) % line   30, file: SubmissionAgencyDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 1522)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 1522), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionKeyword, 1048588, 1522) % line   31, file: SubmissionKeywordDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 1522)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 1522), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionSubject, 1048588, 1522) % line   31, file: SubmissionSubjectDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 1522)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 1522), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionDiscipline, 1048588, 1522) % line   31, file: SubmissionDisciplineDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 1522)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 1522), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionLanguage, 1048588, 1522) % line   31, file: SubmissionLanguageDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 1522)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 1522), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionAgency, 1048588, 1522) % line   30, file: SubmissionAgencyDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 2545)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionKeyword', 1048588, 2545), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionKeyword, 1048588, 2545) % line   31, file: SubmissionKeywordDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 2545)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionSubject', 1048588, 2545), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionSubject, 1048588, 2545) % line   31, file: SubmissionSubjectDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 2545)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionDiscipline', 1048588, 2545), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionDiscipline, 1048588, 2545) % line   31, file: SubmissionDisciplineDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 2545)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionLanguage', 1048588, 2545), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionLanguage, 1048588, 2545) % line   31, file: SubmissionLanguageDAO.inc.php
                                                                                 ADOConnection._Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 2545)) % line 1222, file: adodb.inc.php
                                                                              ADOConnection.Execute(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				('submissionAgency', 1048588, 2545), Array[1]) % line  229, file: DAO.inc.php
                                                                           DAO.update(INSERT INTO controlled_vocabs 				(symbolic, assoc_type, assoc_id) 				VALUES 				(?, ?, ?), Array[3], true, false) % line  109, file: ControlledVocabDAO.inc.php
                                                                        ControlledVocabDAO.insertObject(Object:ControlledVocab, false) % line   60, file: ControlledVocabDAO.inc.php
                                                                     ControlledVocabDAO._build(submissionAgency, 1048588, 2545) % line   30, file: SubmissionAgencyDAO.inc.php

Regards,

Darryl

14

I know my information may be not connected directly with the original question in this thread, but I had some database related problems while upgrading to the latest release and I solved them successfully, so I think I can share my experience here, so it may help some people (or maybe give some useful information for code-makers).

The first problem was connected with NULL-values in ‘review_assignments’ table. I had such error message:
SQLSTATE[22004]: Null value not allowed: 1138 Invalid use of NULL value (SQL: ALTER TABLE review_assignments CHANGE review_round_id review_round_id BIGINT NOT NULL)
The following SQL request (before starting the upgrade procedure) solved the problem:
update review_assignments SET review_round_id = 0 WHERE review_round_id IS NULL;

Need to mention that in a week before upgrading we moved to a new hosting provider, so MAYBE some problems I describe appeared while exporting and importing the base. Really, maybe some export/import options were not set properly but everything worked fine (on the new server already) before this upgrading attempt.

The second problem was more serious and I spent hours to find the reason (and a good solution) of it. The error message was the following:
MySQL Error Code 1215: “Cannot add foreign key constraint” (SQL: alter table submission_files add constraint submission_files_file_id_foreign foreign key (file_id) references files (file_id))
This error was already mentioned earlier here, but let me tell what was the reason in my case.
As other people explained earlier the problem is connected with different Database Engine type for those tables (“MyISAM” vs “InnoDB”), and yes I could see it in my MySQL database - they were different. But … I couldn’t just change the engine for one of the tables (‘files’) manually, because it was created (or recreated) by upgrade script every time I tried to start it! So the problem was connected with hosting server settings (MySQL settings) - the default database engine for newly created tables on this server was set to “MyISAM” so Upgrade script couldn’t pass that line with creating “foreign key constraint”.
You may say - change your sever settings and forget about this problem, but … with affordable shared hosting service we use, such settings are not available for us, so I had to find another solution.
I won’t describe it all in details now (my post is too long even without it already) but in two words - I had to modify file /lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Schema/Grammars/MySqlGrammar.php - it has “datbase-engine name” related function (“compileCreateEngine”) but it seems it was not used (not involved in forming final sql-request string) - the engine name wasn’t appended. I changed the code there a bit to force this function be used (with ‘InnoDB’ as database engine name) in every table creation request and my problems was solved.

One important suggestion to those who have problems with database during upgrade procedure: export your database BEFORE trying to upgrade for the first time and restore it EVERY time before trying to upgrade again (after fixing something in your settings or anything else). I had to try many times (because of my “default database engine” problem) and every time I restored the database and applied that “fix” about NULL-values before trying to start upgrade script again.

2 Likes
15

Hello @Dip ;

Thank you for sharing your Database experience. I’d like to know how to tell if your database is set to MYISAM or InnoDB. Which version of OJS is using these settings?

regards,

Darryl

16

Everything I described in my post took place during upgrade to OJS 3.3.0.8.
As for “InnoDB vs MyISAM” server-settings (I mean, which database-engine is set as “default” on the MySQL-Server) - you can see it by starting phpMyAdmin: On the main (“Home”) screen of phpMyAdmin find “Engines” in the top menu, go there and you’ll see a list of all database-engines available on this server. Then click “InnoDB” (for example) and you’ll see full information about it, including “InnoDB is the default storage engine on this MySQL server” (IF IT IS REALLY SET AS DEFAULT). In my case I had no such line for “InnoDB”, but had it for MyISAM (“MyISAM is the default storage engine on this MySQL server”), so all new tables created or re-created by Upgrade script got this type of database engine “automatically”.
If it is important - my MySQL server here is 5.6.51 and phpMyAdmin is 4.9.7, PHP version: 7.3.28

Maybe I just missed some “secret” OJS option in config-file that sets the database-engine to be used by OJS while creating tables (not to rely on server defaults) - there should be some option to explicitly define it but I didn’t find it, so had to change the library code a lil (as I mentioned earlier) to get tables be always created with InnoDB engine.

1 Like
17

@Dip ;

MYISAM and INNODB are giving me a nightmare.

When I double-checked my old backup database from two years ago, I discovered it had 147 tables created in MyISAM and InnoDB. The InnoDB Engine is number 28, and the MYISAM Engine is number 119. Before I proceed with the latest update, I just want to fix the database.

Screenshot_1

18

Yes, I upgraded from 3.1.2-1 to 3.2.1-4! I checked our 2019 back up database and verified manually and On the Debug setting in config.php.

Screenshot_4
Screenshot_4959×464 21.4 KB

I’m not finished yet; I’ll try to fix the other database that’s giving me trouble.

regards,

Darryl

19

Hello;

I pursue to upgrade the 3.2.1.4 version directly to the latest version which is the ojs 3.3.0-8, but I am confused I got this error:

Database query
alter table `review_files` add constraint `review_files_submission_file_id_foreign` foreign key (`submission_file_id`) references `submission_files` (`submission_file_id`)
[]
ERROR: Upgrade failed: DB: SQLSTATE[HY000]: General error: 1005 Can't create table `pairojs2007_ojs-3.3.0-3`.`#sql-ac4_3d3` (errno: 150 "Foreign key constraint is incorrectly formed") (SQL: alter table `submission_file_revisions` add constraint `submission_file_revisions_submission_file_id_foreign` foreign key (`submission_file_id`) references `submission_files` (`submission_file_id`))

regards,

Darryl

20

I think this error is connected with the same problem as I described earlier - “InnoDB vs MyISAM” (not the same table in your case than it was for me, but similar error message).
It seems, that (as I said earlier) the only way to upgrade OJS without getting such errors is to have all tables set to “InnoDB" database-engine. Where possible it can be changed manually in phpMyAdmin for each table with "MyISAM” engine or (if "MyISAM” is a default database-engine on your mySQL-server, like it was in my case, and you can’t change server-settings) only fixing PKP/OJS libraries can force tables to be always created by OJS scripts with “InnoDB” database-engine.

1 Like
21

@Dip ;

Thank you for your response; now that I understand what you’re saying, I manually changed the Engine from MyISAM to InnoDB and ran the update, but I received this ERROR.

Database query
ALTER TABLE temp_published_submissions MODIFY COLUMN date_published DATE NULL
[]
Database query

                        INSERT INTO publications (access_status, date_published, last_modified, locale, section_id, seq, submission_id, status, version)
                                SELECT COALESCE(ps.access_status, 0), COALESCE(ps.date_published, NULL), s.last_modified, s.locale, s.section_id, COALESCE(ps.seq, 0), s.submission_id, s.status, 1
                                FROM temp_submissions as s
                                LEFT JOIN temp_published_submissions as ps
                                        ON (s.submission_id = ps.submission_id)
                                GROUP BY s.submission_id, ps.access_status, ps.date_published, s.last_modified, s.section_id, ps.seq, s.locale, s.status;

[]
ERROR: Upgrade failed: DB: SQLSTATE[42S22]: Column not found: 1054 Unknown column 'a.primary_contact' in 'where clause' (SQL:
                        UPDATE publications as p
                        SET primary_contact_id = (
                                SELECT a.author_id
                                FROM temp_authors as a
                                WHERE a.submission_id = p.submission_id
                                        AND a.primary_contact = 1
                                LIMIT 1
                        )
                )

regards,

Darryl