Migration from 3 .1.2.1 to 3.3.0.8- submission cheklist lost

Description of issue or problem I’m having:
Migration from 3 .1.2.1 to 3.3.0.8 the checklist disapear
in 3.1.2.1
image

in 3.3.0.8
image

The cheklist disapear

Steps I took leading up to the issue:
look itnot the db
in 3.1.2.1
image
in 3.3.0.8
image

**Any idea of what may have cause this ? **

Thanks, best regards

Hi @tdolley,

Likely encoding issue.
Did you perform an upgrade from a command line? There should be a related message when the migration script tried to convert this setting to JSON.

OK thanks,
But i’have done the migration few days ago.
I didn’t copy from screen the message of the migration script.
Does the message of the migration script stored in some file taht i can retrieve.
Best Regards
Thomas

I recommend repeating the upgrade locally from a backup.

Hi Vitaliy,

Here is the result of the upgrade

[root@ardeche ojs]# scl enable php73 ‘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]
[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]

[code: Installer Installer::installDefaultNavigationMenus]
PHP Notice: unserialize(): Error at offset 2692 of 2721 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 193 of 2956 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 3330 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
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 1178 of 2724 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 247 of 3214 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
WARNING: The NavigationMenu (ContextId: 5, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 5, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 25, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 25, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice: unserialize(): Error at offset 222 of 1169 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 233 of 1523 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
WARNING: The NavigationMenu (ContextId: 24, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 24, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice: unserialize(): Error at offset 213 of 1511 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
WARNING: The NavigationMenu (ContextId: 15, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 15, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice: unserialize(): Error at offset 222 of 1155 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1212 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 216 of 1130 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
WARNING: The NavigationMenu (ContextId: 26, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 26, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
PHP Notice: unserialize(): Error at offset 234 of 239 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1209 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
WARNING: The NavigationMenu (ContextId: 27, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 27, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
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 2692 of 2721 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 193 of 2956 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 3330 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 1178 of 2724 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 247 of 3214 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 222 of 1169 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 233 of 1523 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 213 of 1511 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 222 of 1155 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1212 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 216 of 1130 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 234 of 239 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1209 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252

[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]
PHP Notice: unserialize(): Error at offset 2692 of 2721 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 193 of 2956 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 3330 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 213 of 1511 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 1178 of 2724 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 247 of 3214 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 222 of 1169 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 233 of 1523 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 222 of 1155 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1212 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 216 of 1130 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 234 of 239 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252
PHP Notice: unserialize(): Error at offset 230 of 1209 bytes in /usr/share/revues-travail.cirad.fr/prod/ojs-3.3.0-x/lib/pkp/classes/db/DAO.inc.php on line 252

[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]
[data: dbscripts/xml/upgrade/3.2.0_versioning_submissionCategories.xml]
[data: dbscripts/xml/upgrade/3.2.0_last_activity.xml]
[data: dbscripts/xml/upgrade/3.2.0_url_path.xml]

[code: Installer Installer::setStatsEmailSettings]

[code: Installer Installer::fixLibraryFiles]

[code: Installer Installer::installEmailTemplate]
[note: docs/release-notes/README-3.2.0]
[data: dbscripts/xml/upgrade/3.2.1_update.xml]

[code: Installer Installer::installEmailTemplate]
[migration: PKPv3_2_1SubeditorCategoriesMigration]
[note: docs/release-notes/README-3.2.1]

[migration: PKPv3_3_0UpgradeMigration]
Removing orphaned submission_files entry ID 34434 with submission_id 31742
A submission file was expected but not found at journals/5/articles/10149/submission/copyedit/10149-37-10152-1-9-20150129.pdf.
A submission file was expected but not found at journals/5/articles/10150/submission/copyedit/10150-37-10154-1-9-20150129.pdf.
A submission file was expected but not found at journals/5/articles/10151/submission/copyedit/10151-37-10156-1-9-20150129.pdf.
A submission file was expected but not found at journals/5/articles/10152/submission/copyedit/10152-37-10158-1-9-20150129.pdf.
A submission file was expected but not found at journals/5/articles/10153/submission/copyedit/10153-37-10160-1-9-20150129.pdf.
A submission file was expected but not found at journals/5/articles/10154/submission/copyedit/10154-37-10162-1-9-20150130.pdf.


[migration: OJSv3_3_0UpgradeMigration]
Removing orphaned publication_galleys entry ID 8729 with submission_file_id 8736
[note: docs/release-notes/README-3.3.0]

[code: Installer Installer::addPluginVersions]
[post-install]

As part of the upgrade, the par of data of the *_settings tables is being serialized as JSON, rather than with PHP serialized(), as it was before. During this process, the migration script tries to unserialized the data but fails. At least this happens with settings for navigation menus and side blocks (I see the error when the correspondent script is executed).

This means that the data there is corrupted. The message isn’t specific but according to the screenshot, I’d assume an encoding issue. First of all, I’ll check the forum for similar issues, e.g.: OJS 3 Special characters no longer show since upgrade from OJS2 and Problems displaying UTF-8 encoded latin characters

You were right. I correct the data and it run smoothly now