Error Upgrade 2.4.8.2 to 3.1.0

Hi @bozana, I get this:

[code: Installer Installer::convertSupplementaryFiles]
previousFilePath = /var/www/files/journals/4//articles/753/attachment/753-121-71 3-1-13-20110209.pdf and targetFilePath = /var/www/files/journals/4//articles/753 /submission/753-132-713-1-2-20110209.pdf previousFilePath = and targetFilePath = PHP Warning: assert(): Assertion failed in /var/www/ojs-3.1.0/lib/pkp/classe s/submission/PKPSubmissionFileDAO.inc.php on line 373
ojs2: There are no readable files in this directory tree. Are safe mode or open_basedir active?

It looks like it finds a null value and then it can not do the assert.
could you tell me which database table I can see these records in?

Yes, I start with a clean install.

I found the same situation on this topic.
I’ll try to follow his advice to see if I can fix this.

Regards,
Adriano Moreno

Hmmmm… @Adriano_Jose, I do not understand what is the problem :-\ The paths are different so I am wondering why that assertion fails. Does the target document exist?

Hmmm… @Adriano_Jose, could you check if your supplementary files are in your files folder in OJS 2.4.x (in journals//articles//supp/)? The supp files are in the DB table article_supplementary_files.
Also, when the upgrade stops/fails, are those supp files in the attachment folder (journals//articles//attachment/)?

Hi @bozana,
I did what Asmecher suggested in the post I quoted above, putting a section for all articles that did not already have a section and manually deleting, through the web interface, all records of supplemental files that did not have the files.

Now I’m encountering the following errors:

[version: 3.1.0.0]
[code: Installer Installer::syncSeriesAssocType]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics2.xml (skipped)]
[code: Installer Installer::removeReviewEntries]
[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptTimedViews.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_adaptReferrals.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptBooksForReview.xml]
[data: dbscripts/xml/upgrade/remove_timed_views_bots.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_preupdate_commentsToEditor.xml]
[code: Installer Installer::concatenateIntoAbout]
[code: Installer Installer::concatenateIntoMasthead]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_review_assignments.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_notes.xml]
[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::migrateCounterPluginUsageStatistics (skipped)]
[code: Installer Installer::migrateTimedViewsUsageStatistics (skipped)]
[code: Installer Installer::migrateDefaultUsageStatistics (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration2.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postCounterMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postTimedViewsMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type.xml]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_settings.xml]
[code: Installer Installer::installDefaultGenres]
[code: Installer Installer::migrateArticleMetadata]
[data: dbscripts/xml/upgrade/3.0.0_update.xml]
[code: Installer Installer::clearDataCache]
[code: Installer Installer::migrateUserRoles]
[code: Installer Installer::fixReviewForms]
[code: Installer Installer::htmlifyEmailTemplates]
[note: docs/release-notes/README-BEACON]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]
[code: Installer Installer::localizeCustomBlockSettings]
[code: Installer Installer::convertEditorDecisionNotes]
[code: Installer Installer::convertQueries]
[code: Installer Installer::migrateFiles]
[code: Installer Installer::convertSupplementaryFiles]
[code: Installer Installer::setFileUploader]
[code: Installer Installer::setFileName]
[data: dbscripts/xml/upgrade/3.0.0_postupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_pubId_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_galley_files.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_issue_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_submission_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_review_method.xml]
[data: dbscripts/xml/upgrade/3.0.0_edit_decisions.xml]
[code: Installer Installer::convertCommentsToEditor]
PHP Warning:  Element '<ahref|target><em><strong><cite>&                                                                        lt;code><ul><ol><li><dl><dt><dd><b>                                                                        <i><u><imgsrc|alt><sup><sub><br><p>' i                                                                        s not supported (for information on implementing this, see the support forums)                                                                          in /var/www/ojs-3.1.0/lib/pkp/lib/vendor/ezyang/htmlpurifier/library/HTMLPurifie                                                                        r/HTMLDefinition.php on line 311
[note: docs/release-notes/README-3.0]
[note: docs/release-notes/README-3.0.1]
[data: dbscripts/xml/upgrade/3.0.2_update.xml]
[note: docs/release-notes/README-3.0.2]
[code: Installer Installer::moveReviewerFiles]
ERROR: Reviewer files with ID 5871 from review assignment 696 could not be found                                                                         in the database table submission_files
ERROR: Reviewer files with ID 6899 from review assignment 872 could not be found                                                                         in the database table submission_files
ERROR: Reviewer files with ID 6694 from review assignment 884 could not be found                                                                         in the database table submission_files
ERROR: Reviewer files with ID 9692 from review assignment 1457 could not be foun                                                                        d in the database table submission_files
ERROR: Reviewer files with ID 16668 from review assignment 3323 could not be fou                                                                        nd in the database table submission_files
ERROR: Reviewer files with ID 19075 from review assignment 4319 could not be fou                                                                        nd in the database table submission_files
ERROR: Reviewer files with ID 28613 from review assignment 6584 could not be fou                                                                        nd in the database table submission_files
ERROR: Reviewer files with ID 28125 from review assignment 6585 could not be fou                                                                        nd in the database table submission_files
ERROR: Reviewer files with ID 44439 from review assignment 10663 could not be fo                                                                        und in the database table submission_files
ERROR: Reviewer files with ID 48910 from review assignment 11938 could not be fo                                                                        und in the database table submission_files
ERROR: Reviewer files with ID 42013 from review assignment 10427 could not be fo                                                                        und in the database table submission_files
ERROR: Reviewer files with ID 47250 from review assignment 12106 could not be fo                                                                        und in the database table submission_files
[code: Installer Installer::fixAuthorGroup]
[data: dbscripts/xml/upgrade/3.0.0_reviewer_files.xml]
ERROR: Upgrade failed: DB: ERROR:  null value in column "review_round_id" violat                                                                        es not-null constraint
DETALHE:  Failing row contains (4024, null, 3, 7952, 1).

Can you help me, please?!

I researched and saw a case like this:

SELECT article_id, file_id, revision, source_file_id, file_name, original_file_name FROM public.article_files
where article_id = 5871
ORDER BY file_id ASC

article_id | file_id | revision| source_file_id| file_name | original_file_name
5871 | 12665 | 1 | 12664 | 5871-12665-1-CE.pdf |5871-12664-1-SM.pdf
5871 | 12668 | 1 | ‘null’ | 5871-12668-1-PB.pdf |Texto Eustáquio.pdf

Could I set source_file_id = file_id for all records?

Hi @Adriano_Jose

Those should be the files that a reviewer uploaded for a review. It seems that those files are not in the DB article_files. There are entries in the DB table review_assignments, but the files are not in the DB table article_files. Could you take a look in the DB table article_files and see if there are those files, with ids = 5871, 6899, 6694, etc. – you should not look after the article_id but file_id there? Could you also see if they are in the files folder – they should be in journals//articles//submission/review/?
And again, see what is the correct solution for your journals – are those files needed or not…

Best,
Bozana

hi @bozana, thank you too much.
Finally I understood. The reviewer_file_id that is in the review_assignments table does not exist in the article_files table. So I deleted those records from the review_assignments table.

Now I’m encountering the following errors:

[root@devojs2 ojs-3.1.0]# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.1.0.0]

[code: Installer Installer::syncSeriesAssocType]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics2.xml (skipped)]

[code: Installer Installer::removeReviewEntries]
[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptTimedViews.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_adaptReferrals.xml]
[data: dbscripts/xml/upgrade/3.0.0_adaptBooksForReview.xml]
[data: dbscripts/xml/upgrade/remove_timed_views_bots.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_preupdate_commentsToEditor.xml]

[code: Installer Installer::concatenateIntoAbout]

[code: Installer Installer::concatenateIntoMasthead]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_review_assignments.xml]
[data: dbscripts/xml/upgrade/3.1.0_preupdate_notes.xml]
[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::migrateCounterPluginUsageStatistics (skipped)]

[code: Installer Installer::migrateTimedViewsUsageStatistics (skipped)]

[code: Installer Installer::migrateDefaultUsageStatistics (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration2.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postCounterMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/2.4.0_postTimedViewsMigration.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type.xml]
[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_settings.xml]

[code: Installer Installer::installDefaultGenres]

[code: Installer Installer::migrateArticleMetadata]
[data: dbscripts/xml/upgrade/3.0.0_update.xml]

[code: Installer Installer::clearDataCache]

[code: Installer Installer::migrateUserRoles]

[code: Installer Installer::fixReviewForms]

[code: Installer Installer::htmlifyEmailTemplates]
[note: docs/release-notes/README-BEACON]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]
[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]

[code: Installer Installer::localizeCustomBlockSettings]

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]

[code: Installer Installer::migrateFiles]

[code: Installer Installer::convertSupplementaryFiles]

[code: Installer Installer::setFileUploader]

[code: Installer Installer::setFileName]
[data: dbscripts/xml/upgrade/3.0.0_postupdate.xml]
[data: dbscripts/xml/upgrade/3.0.0_pubId_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_galley_files.xml]
[data: dbscripts/xml/upgrade/3.0.0_postupgrade_metrics.xml]
[data: dbscripts/xml/upgrade/3.0.0_issue_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_submission_settings.xml]
[data: dbscripts/xml/upgrade/3.0.0_review_method.xml]
[data: dbscripts/xml/upgrade/3.0.0_edit_decisions.xml]

[code: Installer Installer::convertCommentsToEditor]
PHP Warning: Element ‘<ahref|target><em><strong><cite><code><ul><ol><li><dl><dt><dd><b><i><u><imgsrc|alt><sup><sub><br><p>’ is not supported (for information on implementing this, see the support forums) in /var/www/ojs-3.1.0/lib/pkp/lib/vendor/ezyang/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php on line 311
[note: docs/release-notes/README-3.0]
[note: docs/release-notes/README-3.0.1]
[data: dbscripts/xml/upgrade/3.0.2_update.xml]
[note: docs/release-notes/README-3.0.2]

[code: Installer Installer::moveReviewerFiles]
ERROR: Reviewer files with ID 5871 from review assignment 696 could not be found in the database table submission_files
ERROR: Reviewer files with ID 6899 from review assignment 872 could not be found in the database table submission_files
ERROR: Reviewer files with ID 6694 from review assignment 884 could not be found in the database table submission_files
ERROR: Reviewer files with ID 9692 from review assignment 1457 could not be found in the database table submission_files
ERROR: Reviewer files with ID 16668 from review assignment 3323 could not be found in the database table submission_files
ERROR: Reviewer files with ID 19075 from review assignment 4319 could not be found in the database table submission_files
ERROR: Reviewer files with ID 28125 from review assignment 6585 could not be found in the database table submission_files
ERROR: Reviewer files with ID 28613 from review assignment 6584 could not be found in the database table submission_files
ERROR: Reviewer files with ID 42013 from review assignment 10427 could not be found in the database table submission_files
ERROR: Reviewer files with ID 44439 from review assignment 10663 could not be found in the database table submission_files
ERROR: Reviewer files with ID 48910 from review assignment 11938 could not be found in the database table submission_files
ERROR: Reviewer files with ID 47250 from review assignment 12106 could not be found in the database table submission_files

[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]
[data: dbscripts/xml/upgrade/3.1.0_galley_settings.xml]
[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]
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
PHP Warning: Invalid argument supplied for foreach() in /var/www/ojs-3.1.0/lib/pkp/classes/navigationMenu/NavigationMenuItemDAO.inc.php on line 343
[note: docs/release-notes/README-3.1.0]

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

Setup completes, but several menus appear with ##
Any tips?

Regards,
Adriano moreno

Hi @Adriano_Jose

Hmmm… you have the same error messages again. Maybe you did not removed the correct rows?
Either you should delete those entries from your DB table review_assignments where review_file_id is in (5871, 6899, 6694, 9692, 16668, 19075, 28125, 28613, 42013, 44439, 48910, 47250)
Or
where review_id is in (696, 872, 884, 1457, 3323, 4319, 6585, 6584, 10427, 10663, 11938, 12106).

(Also, did you check if the files are in the files folder?)

How many comments to editor (column name comments_to_ed) do you have in your DB table articles? It seems that one of them contains HTML elements that are not supported :open_mouth:

And concerning the installDefaultNavigationMenus errors: What do you have in your DB table site, in the column supported_locales?

Best,
Bozana

Hi @bozana,
thank you.

I’m fixing the bugs according to your tips.
About installDefaultNavigationMenus errors, in the DB table site its has just: 'en_US:es_ES:pt_BR:fr_FR' in the column supported_locales. Is there something wrong?

Hi @Adriano_Jose,
Hmmm… no that looks good…
Hmmm… :thinking:

Hi
I’m upgrading OJS 2.4.6 to OJS 3.1.0-1 and when I run “php tools/upgrade.php upgrade” always return such error

PHP Fatal error: Uncaught Error: Call to a member function getId() on null in /ojs_v3.1.0_1/classes/install/Upgrade.inc.php:1103
Stack trace:
#0 /ojs_v3.1.0_1/lib/pkp/classes/install/Installer.inc.php(415): Upgrade->convertSupplementaryFiles(Object(Upgrade), Array)
#1 /ojs_v3.1.0_1/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)
#2 /ojs_v3.1.0_1/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#3 /ojs_v3.1.0_1/lib/pkp/classes/cliTool/UpgradeTool.inc.php(88): Installer->execute()
#4 /ojs_v3.1.0_1/lib/pkp/classes/cliTool/UpgradeTool.inc.php(64): UpgradeTool->upgrade()
#5 /ojs_v3.1.0_1/tools/upgrade.php(34): UpgradeTool->execute()
#6 {main}
thrown in /ojs_v3.1.0_1/classes/install/Upgrade.inc.php on line 1103

My system consists of the following:

PHP 7.0
MySQL 5.7.21
Apache 2.4.18

I don’t know how could i solve that?

Hi @Adriano_Jose and @bozana
Do you know how I can find all the files with the same problem where you comment that?

Every week I starting a new process upgrade with new id error:
ERROR: Upgrade failed: DB: ERROR: null value in column "review_round_id

I have more than 200 journals.

Regards,
xavi

Hi @xavi

Could you maybe explain a little bit more what is exactly happening in your upgrade? – Could you post the steps that are done and where it stops (i.e. the output you get when you start the upgrade via CLI with “php tools/upgarede.php upgrade”)?
Also, what were the earlier steps, for earlier upgrade attempts, that you did?

Best,
Bozana

Oh, OK, now I see the other post: Upgrade to OJS 3.0 from 2.4.8.0 - Error while converting supplementary files - #72 by xavi

I am not sure if I am thinking right, but could you execute this SQL on your 2.4.x DB:
SELECT ra.review_id, ra.submission_id, ra.reviewer_file_id FROM review_assignments ra WHERE ra.reviewer_file_id IS NOT NULL AND ra.reviewer_file_id NOT IN (SELECT file_id FROM article_files)
to see if a reviewer file is missing in the article_files table.

EDIT: maybe also this SQL:
SELECT DISTINCT ra.submission_id, ra.round, af.revision FROM review_assignments ra, article_files af, articles a WHERE (ra.submission_id, ra.round) NOT IN (SELECT rr.submission_id, rr.round FROM review_rounds rr) AND a.article_id = ra.submission_id AND af.article_id = a.article_id AND af.file_id = a.review_file_id AND af.round = ra.round
to see if eventually a review round entry is missing in the DB.

Best,
Bozana

HI @bozana,
I executed this query:
SELECT DISTINCT ra.submission_id, ra.round, af.revision FROM review_assignments ra, article_files af, articles a WHERE (ra.submission_id, ra.round) NOT IN (SELECT rr.submission_id, rr.round FROM review_rounds rr) AND a.article_id = ra.submission_id AND af.article_id = a.article_id AND af.file_id = a.review_file_id AND af.round = ra.round;

I look this:

| submission_id| round | revision |
|261823| 1| 1|
|267199| 1| 1|


With the first query:

SELECT ra.review_id, ra.submission_id, ra.reviewer_file_id FROM review_assignments ra WHERE ra.reviewer_file_id IS NOT NULL AND ra.reviewer_file_id NOT IN (SELECT file_id FROM article_files)

I can see this:

|review_id|submission_id|reviewer_file_id|
|568 | 305936 | 435326 |

I will wait to next week to checked if my upgrade process is fail about some submission_id appear from this query.

Regards,
xavi.

Hi @xavi

Hmmm… If I understand it correctly, there are a few problems in your 2.4.x DB:

  1. Two entries in the DB table review_rounds are missing for two articles that are/were already assigned to a reviewer. These are articles 261823 and 267199. Could you double check those articles as editor via GUI, to see their review workflow step – are/were they assigned to a reviewer and what is their current status?
    Eventually you would then need to insert an entry in the DB manually, but lets first see what you see via GUI and if there is anything suspicious with those two articles…
  2. The reviewer file with the id 435326 from the article 305936 seems not to exist in the DB table article_files. Could you please double check that? Also, could you see if there is a file with the name something like “305936-435326-…-RV…” in your files folder, for that article 305936?

Best,
Bozana

Hi @bozana,

The file 305936-435326-…-RV is not exists.

  • I checked the history from GUI and I can see:
  • The round 3 review by XXXX for submission 305936 has been cleared.
  • The submission 305936 has been archived.
    It’s not result with this query

    SELECT * FROM article_files WHERE article_id=305936 AND file_id=435326


Article: 261823:
The article was publicated with QuickSubmit and this article has 3 reviewers:

  • First reviewer not recomendations
  • Second reviewer Not accepted
  • Third reviewer was deleted
  • This article was archived

Article: 267199:

  • Added a new PDF and assigned a reviewer but it didn’t something.
  • Archived article.
  • It could be a testing process in OJS

I'm not sure about this problems, I can delete the last Article (267199)

Regards,
xavi,