[OJS 3.0.2 --> 3.1] Some submission files cannot be moved

Hi! We are still testing the upgrade procedure. Now we have some errors related to submission files, which cannot be moved. Here is the log:

root@ojs-test:/var/www/html# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.1.0.0]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_review_assignments.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_notes.xml (skipped)]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_payments.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/notes.xml]
[schema: lib/pkp/xml/schema/views.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::installEmailTemplate]
[data: dbscripts/xml/upgrade/3.1.0_update_a.xml]

[code: Installer Installer::fixGenreIdInFileNames]
PHP Warning: rename(/var/www/files/journals/16//articles/4479//submission/4479-1-5364-2-2-20170410.docx,/var/www/files/journals/16//articles/4479//submission/4479-192-5364-2-2-20170410.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/16//articles/4479//submission/4479-1-5364-2-2-20170410.docx” to “/var/www/files/journals/16//articles/4479//submission/4479-192-5364-2-2-20170410.docx”.
PHP Warning: rename(/var/www/files/journals/9//articles/3235//submission/3235-1-3569-2-2-20170315.docx,/var/www/files/journals/9//articles/3235//submission/3235-108-3569-2-2-20170315.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/9//articles/3235//submission/3235-1-3569-2-2-20170315.docx” to “/var/www/files/journals/9//articles/3235//submission/3235-108-3569-2-2-20170315.docx”.
PHP Warning: rename(/var/www/files/journals/9//articles/6782//submission/6782-1-8351-2-2-20170616.txt,/var/www/files/journals/9//articles/6782//submission/6782-102-8351-2-2-20170616.txt): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/9//articles/6782//submission/6782-1-8351-2-2-20170616.txt” to “/var/www/files/journals/9//articles/6782//submission/6782-102-8351-2-2-20170616.txt”.
PHP Warning: rename(/var/www/files/journals/9//articles/6800//submission/6800-1-8386-2-2-20170616.docx,/var/www/files/journals/9//articles/6800//submission/6800-108-8386-2-2-20170616.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/9//articles/6800//submission/6800-1-8386-2-2-20170616.docx” to “/var/www/files/journals/9//articles/6800//submission/6800-108-8386-2-2-20170616.docx”.
PHP Warning: rename(/var/www/files/journals/9//articles/6810//submission/6810-1-8418-2-2-20170619.docx,/var/www/files/journals/9//articles/6810//submission/6810-99-8418-2-2-20170619.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/9//articles/6810//submission/6810-1-8418-2-2-20170619.docx” to “/var/www/files/journals/9//articles/6810//submission/6810-99-8418-2-2-20170619.docx”.
PHP Warning: rename(/var/www/files/journals/9//articles/6810//submission/6810-1-8419-2-2-20170619.docx,/var/www/files/journals/9//articles/6810//submission/6810-99-8419-2-2-20170619.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/9//articles/6810//submission/6810-1-8419-2-2-20170619.docx” to “/var/www/files/journals/9//articles/6810//submission/6810-99-8419-2-2-20170619.docx”.
PHP Warning: rename(/var/www/files/journals/3//articles/6815//submission/review/6815-1-8431-1-4-20170620.docx,/var/www/files/journals/3//articles/6815//submission/review/6815-25-8431-1-4-20170620.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/3//articles/6815//submission/review/6815-1-8431-1-4-20170620.docx” to “/var/www/files/journals/3//articles/6815//submission/review/6815-25-8431-1-4-20170620.docx”.
PHP Warning: rename(/var/www/files/journals/3//articles/6815//submission/review/6815-1-8432-1-4-20170620.docx,/var/www/files/journals/3//articles/6815//submission/review/6815-25-8432-1-4-20170620.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/3//articles/6815//submission/review/6815-1-8432-1-4-20170620.docx” to “/var/www/files/journals/3//articles/6815//submission/review/6815-25-8432-1-4-20170620.docx”.
PHP Warning: rename(/var/www/files/journals/3//articles/6815//submission/review/6815-1-8433-1-4-20170620.docx,/var/www/files/journals/3//articles/6815//submission/review/6815-25-8433-1-4-20170620.docx): No such file or directory in /var/www/html/classes/install/Upgrade.inc.php on line 2486
Unable to move “/var/www/files/journals/3//articles/6815//submission/review/6815-1-8433-1-4-20170620.docx” to “/var/www/files/journals/3//articles/6815//submission/review/6815-25-8433-1-4-20170620.docx”.

[code: Installer Installer::repairKeywordsAndSubjects]

[code: Installer Installer::enabledSitePlugins]

[code: Installer Installer::moveCSSFiles]

[code: Installer Installer::moveReviewerFiles]

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

[code: Installer Installer::removeCancelledReviewAssignments]
[data: dbscripts/xml/upgrade/3.1.0_notifications.xml]
[data: dbscripts/xml/upgrade/3.1.0_notes.xml (skipped)]
[data: dbscripts/xml/upgrade/3.1.0_galley_settings.xml (skipped)]
[data: dbscripts/xml/upgrade/3.1.0_update.xml]

[code: Installer Installer::repairImageAssociations]
[note: docs/release-notes/README-3.1.0]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installDefaultNavigationMenus]
[note: docs/release-notes/README-3.1.0]

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

Here is what we have in the Apache log:

[Thu Nov 02 16:09:38.902360 2017] [:error] [pid 627] [client 10.0.3.1:38530] PHP Fatal error: Call to a member function getLocalizedTitle() on null in /var/www/html/lib/pkp/controllers/grid/notifications/NotificationsGridCellProvider.inc.php on line 156, referer: http://192.168.0.243/index.php/index/admin
[Thu Nov 02 16:09:43.613637 2017] [:error] [pid 588] [client 10.0.3.1:38544] PHP Warning: assert(): Assertion failed in /var/www/html/lib/pkp/controllers/grid/notifications/NotificationsGridCellProvider.inc.php on line 154, referer: http://192.168.0.243/index.php/index/adminhttp://192.168.0.243/index.php/index/admin

Hi @Ph_We

It looks like you have a permission issue in your filesystem. A quite similar issue related to it is described, with a provided solution, in this thread:

Regards,
Israel Cefrin
Public Knowledge Project Team

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